From 7c28c71c7870f63aa196d292de87ea63af620e92 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 10 Jan 2022 10:38:53 -0800 Subject: [PATCH 001/155] Squashed 'modules/pmi/' changes from 5ebc345aeb..fa61820fad fa61820fad Update copyright year d127e19fc0 Squashed 'tools/dev_tools/' changes from e5d19974..b7538367 403971a59b Remove broken link to Codacy dd1c0e1f99 Update to Python 3.10 git-subtree-dir: modules/pmi git-subtree-split: fa61820fadfefa5abbad5f528d0fd55fc63497d4 --- modules/pmi/.github/workflows/build.yml | 2 +- modules/pmi/README.md | 1 - modules/pmi/include/CompositeRestraint.h | 2 +- modules/pmi/include/MembraneRestraint.h | 2 +- modules/pmi/include/Resolution.h | 2 +- modules/pmi/include/Symmetric.h | 2 +- modules/pmi/include/TransformMover.h | 2 +- modules/pmi/include/Uncertainty.h | 2 +- modules/pmi/include/utilities.h | 2 +- modules/pmi/src/CompositeRestraint.cpp | 2 +- modules/pmi/src/Resolution.cpp | 2 +- modules/pmi/src/Symmetric.cpp | 2 +- modules/pmi/src/TransformMover.cpp | 2 +- modules/pmi/src/Uncertainty.cpp | 2 +- modules/pmi/tools/dev_tools/.github/workflows/build.yml | 2 +- modules/pmi/tools/dev_tools/cleanup_code.py | 9 ++++++--- modules/pmi/tools/dev_tools/make_all_header.py | 2 +- modules/pmi/tools/dev_tools/test/test_header.py | 2 +- 18 files changed, 22 insertions(+), 20 deletions(-) diff --git a/modules/pmi/.github/workflows/build.yml b/modules/pmi/.github/workflows/build.yml index 9785fb9384..fb507bb1de 100644 --- a/modules/pmi/.github/workflows/build.yml +++ b/modules/pmi/.github/workflows/build.yml @@ -13,7 +13,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: [2.7, 3.9] + python-version: ["2.7", "3.10"] runs-on: ${{ matrix.os }} steps: diff --git a/modules/pmi/README.md b/modules/pmi/README.md index b4427c9057..e821018a77 100644 --- a/modules/pmi/README.md +++ b/modules/pmi/README.md @@ -2,7 +2,6 @@ [![Build Status](https://github.com/salilab/pmi/workflows/build/badge.svg?branch=develop)](https://github.com/salilab/pmi/actions?query=workflow%3Abuild) [![codecov](https://codecov.io/gh/salilab/pmi/branch/develop/graph/badge.svg)](https://codecov.io/gh/salilab/pmi) -[![Codacy Badge](https://api.codacy.com/project/badge/Grade/bcced071b3f541449d723a774ea09026)](https://www.codacy.com/app/salilab/pmi?utm_source=github.com&utm_medium=referral&utm_content=salilab/pmi&utm_campaign=Badge_Grade) This module contains a variety of high-level Python classes to simplify the construction of a modeling protocol in IMP. One recent diff --git a/modules/pmi/include/CompositeRestraint.h b/modules/pmi/include/CompositeRestraint.h index 3fc5e8985f..fa077cd38b 100644 --- a/modules/pmi/include/CompositeRestraint.h +++ b/modules/pmi/include/CompositeRestraint.h @@ -3,7 +3,7 @@ * \brief A restraint for ambiguous cross-linking MS data and multiple * state approach. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/pmi/include/MembraneRestraint.h b/modules/pmi/include/MembraneRestraint.h index 165b19669e..853f54a3aa 100644 --- a/modules/pmi/include/MembraneRestraint.h +++ b/modules/pmi/include/MembraneRestraint.h @@ -2,7 +2,7 @@ * \file IMP/pmi/MembraneRestraint.h * \brief Favor configurations where target is in the membrane. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/pmi/include/Resolution.h b/modules/pmi/include/Resolution.h index 3bca47fedd..9434429d99 100644 --- a/modules/pmi/include/Resolution.h +++ b/modules/pmi/include/Resolution.h @@ -2,7 +2,7 @@ * \file IMP/pmi/Resolution.h * \brief A decorator for particles with resolution * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPPMI_RESOLUTION_H diff --git a/modules/pmi/include/Symmetric.h b/modules/pmi/include/Symmetric.h index 5c00781ce1..fe74dce11d 100644 --- a/modules/pmi/include/Symmetric.h +++ b/modules/pmi/include/Symmetric.h @@ -2,7 +2,7 @@ * \file IMP/pmi/Symmetric.h * \brief A decorator for symmetric particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPPMI_SYMMETRIC_H diff --git a/modules/pmi/include/TransformMover.h b/modules/pmi/include/TransformMover.h index 777afff22c..bdfaf1981d 100644 --- a/modules/pmi/include/TransformMover.h +++ b/modules/pmi/include/TransformMover.h @@ -2,7 +2,7 @@ * \file IMP/pmi/TransformMover.h * \brief A mover that transforms a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/pmi/include/Uncertainty.h b/modules/pmi/include/Uncertainty.h index b821af1498..89e9f7e5ae 100644 --- a/modules/pmi/include/Uncertainty.h +++ b/modules/pmi/include/Uncertainty.h @@ -2,7 +2,7 @@ * \file IMP/pmi/Uncertainty.h * \brief A decorator for particles with Uncertainty * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPPMI_UNCERTAINTY_H diff --git a/modules/pmi/include/utilities.h b/modules/pmi/include/utilities.h index 75907405ba..97e9215cdc 100644 --- a/modules/pmi/include/utilities.h +++ b/modules/pmi/include/utilities.h @@ -2,7 +2,7 @@ * \file IMP/pmi/utilities.h * \brief Useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPPMI_UTILITIES_H diff --git a/modules/pmi/src/CompositeRestraint.cpp b/modules/pmi/src/CompositeRestraint.cpp index a6b99a1b75..11d84123d3 100644 --- a/modules/pmi/src/CompositeRestraint.cpp +++ b/modules/pmi/src/CompositeRestraint.cpp @@ -5,7 +5,7 @@ * and ambiguous assignment. To be used with * cross-linking mass-spectrometry data. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/pmi/src/Resolution.cpp b/modules/pmi/src/Resolution.cpp index 068df4d90e..bcbd6849f9 100644 --- a/modules/pmi/src/Resolution.cpp +++ b/modules/pmi/src/Resolution.cpp @@ -2,7 +2,7 @@ * \file Resolution.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/pmi/src/Symmetric.cpp b/modules/pmi/src/Symmetric.cpp index 2e9061db46..3fee681c12 100644 --- a/modules/pmi/src/Symmetric.cpp +++ b/modules/pmi/src/Symmetric.cpp @@ -2,7 +2,7 @@ * \file Symmetric.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/pmi/src/TransformMover.cpp b/modules/pmi/src/TransformMover.cpp index 0ed4dd028c..1d9e25232e 100644 --- a/modules/pmi/src/TransformMover.cpp +++ b/modules/pmi/src/TransformMover.cpp @@ -2,7 +2,7 @@ * \file TransformMover.cpp * \brief A mover that transforms a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/pmi/src/Uncertainty.cpp b/modules/pmi/src/Uncertainty.cpp index ceca8fff46..cbe45312e0 100644 --- a/modules/pmi/src/Uncertainty.cpp +++ b/modules/pmi/src/Uncertainty.cpp @@ -2,7 +2,7 @@ * \file Uncertainty.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/pmi/tools/dev_tools/.github/workflows/build.yml b/modules/pmi/tools/dev_tools/.github/workflows/build.yml index a489620443..8a286104cf 100644 --- a/modules/pmi/tools/dev_tools/.github/workflows/build.yml +++ b/modules/pmi/tools/dev_tools/.github/workflows/build.yml @@ -9,7 +9,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: [2.7, 3.7, 3.8, 3.9] + python-version: [2.7, 3.7, 3.8, 3.9, "3.10"] runs-on: ${{ matrix.os }} steps: diff --git a/modules/pmi/tools/dev_tools/cleanup_code.py b/modules/pmi/tools/dev_tools/cleanup_code.py index 4d506b538e..dd664d47c7 100755 --- a/modules/pmi/tools/dev_tools/cleanup_code.py +++ b/modules/pmi/tools/dev_tools/cleanup_code.py @@ -14,7 +14,10 @@ except ImportError: from Queue import Queue # python2 from threading import Thread -import distutils.spawn +try: + from shutil import which # python3.3 or later +except ImportError: + from distutils.spawn import find_executable as which sys.path.append(os.path.split(sys.argv[0])) import python_tools @@ -60,13 +63,13 @@ if options.clang_format == "auto": options.clang_format = None for name in ["clang-format-3.4", "clang-format"]: - if distutils.spawn.find_executable(name): + if which(name): options.clang_format = name break if options.autopep8 == "auto": options.autopep8 = None for name in ["autopep8"]: - if distutils.spawn.find_executable(name): + if which(name): options.autopep8 = name break diff --git a/modules/pmi/tools/dev_tools/make_all_header.py b/modules/pmi/tools/dev_tools/make_all_header.py index b194691df2..288c9e1ac0 100755 --- a/modules/pmi/tools/dev_tools/make_all_header.py +++ b/modules/pmi/tools/dev_tools/make_all_header.py @@ -31,7 +31,7 @@ def _add_includes(headers, output): * \\file %s * \\brief Include all non-deprecated headers in %s. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ """ % (includepath, includepath[:-2].replace('/', '.'))] guard = includepath.replace( diff --git a/modules/pmi/tools/dev_tools/test/test_header.py b/modules/pmi/tools/dev_tools/test/test_header.py index 56a710697f..a00c32bd4a 100644 --- a/modules/pmi/tools/dev_tools/test/test_header.py +++ b/modules/pmi/tools/dev_tools/test/test_header.py @@ -32,7 +32,7 @@ def test_header(self): * \\file test.h * \\brief Include all non-deprecated headers in test. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef TEST_H From 8fa8422af16073ad183b654a81b7d1b6d93d34a6 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 10 Jan 2022 10:39:29 -0800 Subject: [PATCH 002/155] Squashed 'modules/rmf/dependency/RMF/' changes from 1f9442a766..468586c638 468586c638 Update copyright year 110d43922b Squashed 'tools/dev_tools/' changes from 8e5ec80a..b7538367 git-subtree-dir: modules/rmf/dependency/RMF git-subtree-split: 468586c638d793eb3fd71cec66a70d4c1c21d2d0 --- modules/rmf/dependency/RMF/README.md | 2 +- modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp | 2 +- modules/rmf/dependency/RMF/bin/common.h | 2 +- modules/rmf/dependency/RMF/bin/rmf3_dump.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_cat.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_frames.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_info.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_interpolate.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_pdb.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_show.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_signature.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_slice.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_transform.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_update.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_validate.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_xml.cpp | 2 +- modules/rmf/dependency/RMF/config.h.in | 2 +- modules/rmf/dependency/RMF/doc/Main.md | 2 +- modules/rmf/dependency/RMF/include/RMF/BufferConstHandle.h | 2 +- modules/rmf/dependency/RMF/include/RMF/BufferHandle.h | 2 +- modules/rmf/dependency/RMF/include/RMF/CoordinateTransformer.h | 2 +- modules/rmf/dependency/RMF/include/RMF/Decorator.h | 2 +- modules/rmf/dependency/RMF/include/RMF/Enum.h | 2 +- modules/rmf/dependency/RMF/include/RMF/FileConstHandle.h | 2 +- modules/rmf/dependency/RMF/include/RMF/FileHandle.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/ConstAttributes.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/ConstFile.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/ConstGroup.h | 2 +- .../dependency/RMF/include/RMF/HDF5/DataSetAccessPropertiesD.h | 2 +- .../RMF/include/RMF/HDF5/DataSetCreationPropertiesD.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetIndexD.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/File.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/Group.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/MutableAttributes.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/Object.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h | 2 +- .../rmf/dependency/RMF/include/RMF/HDF5/infrastructure_macros.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/internal/types.h | 2 +- modules/rmf/dependency/RMF/include/RMF/HDF5/types.h | 2 +- modules/rmf/dependency/RMF/include/RMF/ID.h | 2 +- modules/rmf/dependency/RMF/include/RMF/Label.h | 2 +- modules/rmf/dependency/RMF/include/RMF/NodeConstHandle.h | 2 +- modules/rmf/dependency/RMF/include/RMF/NodeHandle.h | 2 +- modules/rmf/dependency/RMF/include/RMF/Nullable.h | 2 +- modules/rmf/dependency/RMF/include/RMF/RestoreCurrentFrame.h | 2 +- modules/rmf/dependency/RMF/include/RMF/SetCurrentFrame.h | 2 +- modules/rmf/dependency/RMF/include/RMF/TraverseHelper.h | 2 +- modules/rmf/dependency/RMF/include/RMF/Vector.h | 2 +- modules/rmf/dependency/RMF/include/RMF/compiler_macros.h | 2 +- modules/rmf/dependency/RMF/include/RMF/constants.h | 2 +- modules/rmf/dependency/RMF/include/RMF/decorator/alternatives.h | 2 +- modules/rmf/dependency/RMF/include/RMF/decorator/bond.h | 2 +- modules/rmf/dependency/RMF/include/RMF/decorator/labels.h | 2 +- modules/rmf/dependency/RMF/include/RMF/decorator/reference.h | 2 +- .../rmf/dependency/RMF/include/RMF/decorator/representation.h | 2 +- modules/rmf/dependency/RMF/include/RMF/decorators.h | 2 +- modules/rmf/dependency/RMF/include/RMF/enums.h | 2 +- modules/rmf/dependency/RMF/include/RMF/exceptions.h | 2 +- modules/rmf/dependency/RMF/include/RMF/info.h | 2 +- modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/SharedData.h | 2 +- .../dependency/RMF/include/RMF/internal/SharedDataCategory.h | 2 +- .../rmf/dependency/RMF/include/RMF/internal/SharedDataData.h | 2 +- .../dependency/RMF/include/RMF/internal/SharedDataData_impl.h | 2 +- .../rmf/dependency/RMF/include/RMF/internal/SharedDataFile.h | 2 +- .../rmf/dependency/RMF/include/RMF/internal/SharedDataFrames.h | 2 +- .../dependency/RMF/include/RMF/internal/SharedDataHierarchy.h | 2 +- .../rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h | 2 +- .../dependency/RMF/include/RMF/internal/SharedDataUserData.h | 2 +- .../rmf/dependency/RMF/include/RMF/internal/SharedData_impl.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/Transform.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/errors.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/hash.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/large_set_map.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/paths.h | 2 +- .../dependency/RMF/include/RMF/internal/shared_data_factories.h | 2 +- .../dependency/RMF/include/RMF/internal/shared_data_ranges.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/small_set_map.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h | 2 +- modules/rmf/dependency/RMF/include/RMF/internal/use.h | 2 +- modules/rmf/dependency/RMF/include/RMF/keys.h | 2 +- modules/rmf/dependency/RMF/include/RMF/log.h | 2 +- modules/rmf/dependency/RMF/include/RMF/names.h | 2 +- modules/rmf/dependency/RMF/include/RMF/show_hierarchy.h | 2 +- modules/rmf/dependency/RMF/include/RMF/signature.h | 2 +- modules/rmf/dependency/RMF/include/RMF/traits.h | 2 +- modules/rmf/dependency/RMF/include/RMF/types.h | 2 +- modules/rmf/dependency/RMF/include/RMF/utility.h | 2 +- modules/rmf/dependency/RMF/include/RMF/validate.h | 2 +- modules/rmf/dependency/RMF/plugins/vmd/Data.cpp | 2 +- modules/rmf/dependency/RMF/plugins/vmd/Data.h | 2 +- modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp | 2 +- modules/rmf/dependency/RMF/plugins/vmd/init.cpp | 2 +- modules/rmf/dependency/RMF/src/BufferConstHandle.cpp | 2 +- modules/rmf/dependency/RMF/src/CoordinateTransformer.cpp | 2 +- modules/rmf/dependency/RMF/src/Enum.cpp | 2 +- modules/rmf/dependency/RMF/src/FileConstHandle.cpp | 2 +- modules/rmf/dependency/RMF/src/FileHandle.cpp | 2 +- modules/rmf/dependency/RMF/src/NodeConstHandle.cpp | 2 +- modules/rmf/dependency/RMF/src/NodeHandle.cpp | 2 +- modules/rmf/dependency/RMF/src/RestoreCurrentFrame.cpp | 2 +- modules/rmf/dependency/RMF/src/SetCurrentFrame.cpp | 2 +- modules/rmf/dependency/RMF/src/TraverseHelper.cpp | 2 +- modules/rmf/dependency/RMF/src/backend/BackwardsIO.h | 2 +- modules/rmf/dependency/RMF/src/backend/BackwardsIOBase.h | 2 +- modules/rmf/dependency/RMF/src/backend/IO.cpp | 2 +- modules/rmf/dependency/RMF/src/backend/IO.h | 2 +- modules/rmf/dependency/RMF/src/backend/IOFactory.h | 2 +- modules/rmf/dependency/RMF/src/backend/KeyFilter.h | 2 +- modules/rmf/dependency/RMF/src/backend/SharedDataAdaptor.h | 2 +- modules/rmf/dependency/RMF/src/backend/avro/data_file.cpp | 2 +- modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h | 2 +- .../rmf/dependency/RMF/src/backend/avro/encode_decode_util.h | 2 +- modules/rmf/dependency/RMF/src/backend/avro/factory.cpp | 2 +- modules/rmf/dependency/RMF/src/backend/avro/io.h | 2 +- modules/rmf/dependency/RMF/src/backend/avro/traits.h | 2 +- modules/rmf/dependency/RMF/src/backend/backward_types.h | 2 +- .../RMF/src/backend/deprecated_avro/AvroKeysAndCategories.h | 2 +- .../dependency/RMF/src/backend/deprecated_avro/AvroSharedData.h | 2 +- .../RMF/src/backend/deprecated_avro/AvroSharedData.impl.h | 2 +- .../RMF/src/backend/deprecated_avro/AvroSharedData.types.h | 2 +- .../RMF/src/backend/deprecated_avro/MultipleAvroFileBase.cpp | 2 +- .../RMF/src/backend/deprecated_avro/MultipleAvroFileBase.h | 2 +- .../RMF/src/backend/deprecated_avro/MultipleAvroFileReader.cpp | 2 +- .../RMF/src/backend/deprecated_avro/MultipleAvroFileReader.h | 2 +- .../RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.cpp | 2 +- .../RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.h | 2 +- .../RMF/src/backend/deprecated_avro/SingleAvroFile.cpp | 2 +- .../dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.h | 2 +- .../RMF/src/backend/deprecated_avro/avro_schema_io.cpp | 2 +- .../dependency/RMF/src/backend/deprecated_avro/avro_schema_io.h | 2 +- .../rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp | 2 +- .../RMF/src/backend/deprecated_hdf5/HDF5DataSetCache1D.h | 2 +- .../RMF/src/backend/deprecated_hdf5/HDF5DataSetCache2D.h | 2 +- .../RMF/src/backend/deprecated_hdf5/HDF5DataSetCache3D.h | 2 +- .../RMF/src/backend/deprecated_hdf5/HDF5DataSetCacheD.h | 2 +- .../RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp | 2 +- .../dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h | 2 +- .../rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp | 2 +- modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/names.h | 2 +- modules/rmf/dependency/RMF/src/decorator/alternatives.cpp | 2 +- modules/rmf/dependency/RMF/src/decorators.cpp | 2 +- modules/rmf/dependency/RMF/src/enums.cpp | 2 +- modules/rmf/dependency/RMF/src/exceptions.cpp | 2 +- modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp | 2 +- modules/rmf/dependency/RMF/src/info.cpp | 2 +- modules/rmf/dependency/RMF/src/internal/SharedData.cpp | 2 +- modules/rmf/dependency/RMF/src/internal/Transform.cpp | 2 +- modules/rmf/dependency/RMF/src/internal/clone_shared_data.h | 2 +- modules/rmf/dependency/RMF/src/internal/paths.cpp | 2 +- modules/rmf/dependency/RMF/src/internal/shared_data_equality.h | 2 +- .../rmf/dependency/RMF/src/internal/shared_data_factories.cpp | 2 +- modules/rmf/dependency/RMF/src/internal/shared_data_maps.h | 2 +- modules/rmf/dependency/RMF/src/log.cpp | 2 +- modules/rmf/dependency/RMF/src/names.cpp | 2 +- modules/rmf/dependency/RMF/src/show_hierarchy.cpp | 2 +- modules/rmf/dependency/RMF/src/signature.cpp | 2 +- modules/rmf/dependency/RMF/src/utility.cpp | 2 +- modules/rmf/dependency/RMF/src/validate.cpp | 2 +- modules/rmf/dependency/RMF/test/test_associations.cpp | 2 +- modules/rmf/dependency/RMF/test/test_avro2_validate.cpp | 2 +- modules/rmf/dependency/RMF/test/test_buffer.cpp | 2 +- modules/rmf/dependency/RMF/test/test_fill.cpp | 2 +- modules/rmf/dependency/RMF/tools/build/_decorators.py | 2 +- .../dependency/RMF/tools/dev_tools/.github/workflows/build.yml | 2 +- modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py | 2 +- modules/rmf/dependency/RMF/tools/dev_tools/test/test_header.py | 2 +- 169 files changed, 169 insertions(+), 169 deletions(-) diff --git a/modules/rmf/dependency/RMF/README.md b/modules/rmf/dependency/RMF/README.md index 4afbaa7924..61ab395a1e 100644 --- a/modules/rmf/dependency/RMF/README.md +++ b/modules/rmf/dependency/RMF/README.md @@ -14,7 +14,7 @@ and score data. The main documentation is found on the [web site](http://integrativemodeling.org/rmf/nightly/doc/). -Copyright 2007-2021 IMP Inventors. +Copyright 2007-2022 IMP Inventors. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp b/modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp index d95408e9f6..afe2b7af5b 100644 --- a/modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp +++ b/modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp @@ -2,7 +2,7 @@ * \brief Benchmark typical creation, traversal and loading with different RMF * backends. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/common.h b/modules/rmf/dependency/RMF/bin/common.h index 9f6ed95722..e8037dcd1f 100644 --- a/modules/rmf/dependency/RMF/bin/common.h +++ b/modules/rmf/dependency/RMF/bin/common.h @@ -1,6 +1,6 @@ /** * \file common.h - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef RMF_COMMON_H diff --git a/modules/rmf/dependency/RMF/bin/rmf3_dump.cpp b/modules/rmf/dependency/RMF/bin/rmf3_dump.cpp index 5f526453c6..06f6e84925 100644 --- a/modules/rmf/dependency/RMF/bin/rmf3_dump.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf3_dump.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_cat.cpp b/modules/rmf/dependency/RMF/bin/rmf_cat.cpp index 9d73a7b9c8..cc89df7675 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_cat.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_cat.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_frames.cpp b/modules/rmf/dependency/RMF/bin/rmf_frames.cpp index 6c796930eb..82dd48f6a2 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_frames.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_frames.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_info.cpp b/modules/rmf/dependency/RMF/bin/rmf_info.cpp index bd5c275647..eba41a7ba3 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_info.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_info.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_interpolate.cpp b/modules/rmf/dependency/RMF/bin/rmf_interpolate.cpp index cd161f32ec..983c5e0add 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_interpolate.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_interpolate.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_pdb.cpp b/modules/rmf/dependency/RMF/bin/rmf_pdb.cpp index 0369709d5c..aba7505254 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_pdb.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_pdb.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include // IWYU pragma: keep diff --git a/modules/rmf/dependency/RMF/bin/rmf_show.cpp b/modules/rmf/dependency/RMF/bin/rmf_show.cpp index adf699f730..ee3b38b33e 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_show.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_show.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_signature.cpp b/modules/rmf/dependency/RMF/bin/rmf_signature.cpp index 5a273cc070..e06be3e041 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_signature.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_signature.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_slice.cpp b/modules/rmf/dependency/RMF/bin/rmf_slice.cpp index a81d20f5b0..893a6f906f 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_slice.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_slice.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_transform.cpp b/modules/rmf/dependency/RMF/bin/rmf_transform.cpp index 91d017332e..c2b6654cdc 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_transform.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_transform.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_update.cpp b/modules/rmf/dependency/RMF/bin/rmf_update.cpp index 0064d7e477..b81d8f726a 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_update.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_update.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_validate.cpp b/modules/rmf/dependency/RMF/bin/rmf_validate.cpp index f13351e333..317ef542f8 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_validate.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_validate.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/bin/rmf_xml.cpp b/modules/rmf/dependency/RMF/bin/rmf_xml.cpp index 542d60de22..40c3a338c6 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_xml.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_xml.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/dependency/RMF/config.h.in b/modules/rmf/dependency/RMF/config.h.in index 8f2f12a735..dda2d498cd 100644 --- a/modules/rmf/dependency/RMF/config.h.in +++ b/modules/rmf/dependency/RMF/config.h.in @@ -4,7 +4,7 @@ * Provide version information, plus macros to mark functions and * classes as exported from a DLL/.so and to set up namespaces. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/doc/Main.md b/modules/rmf/dependency/RMF/doc/Main.md index ebdf721ef5..7de426e7c0 100644 --- a/modules/rmf/dependency/RMF/doc/Main.md +++ b/modules/rmf/dependency/RMF/doc/Main.md @@ -19,7 +19,7 @@ See Also see the [rmf examples](https://github.com/salilab/rmf_examples) repository for examples of interesting or problematic RMF files. -Copyright 2007-2021 IMP Inventors. +Copyright 2007-2022 IMP Inventors. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/modules/rmf/dependency/RMF/include/RMF/BufferConstHandle.h b/modules/rmf/dependency/RMF/include/RMF/BufferConstHandle.h index 814377bae3..4aa71609a9 100644 --- a/modules/rmf/dependency/RMF/include/RMF/BufferConstHandle.h +++ b/modules/rmf/dependency/RMF/include/RMF/BufferConstHandle.h @@ -2,7 +2,7 @@ * \file RMF/BufferConstHandle.h * \brief Declare RMF::BufferConstHandle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/BufferHandle.h b/modules/rmf/dependency/RMF/include/RMF/BufferHandle.h index 1b93b90708..7392f40b63 100644 --- a/modules/rmf/dependency/RMF/include/RMF/BufferHandle.h +++ b/modules/rmf/dependency/RMF/include/RMF/BufferHandle.h @@ -2,7 +2,7 @@ * \file RMF/BufferHandle.h * \brief Declare RMF::BufferHandle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/CoordinateTransformer.h b/modules/rmf/dependency/RMF/include/RMF/CoordinateTransformer.h index d356357041..ed58817a8d 100644 --- a/modules/rmf/dependency/RMF/include/RMF/CoordinateTransformer.h +++ b/modules/rmf/dependency/RMF/include/RMF/CoordinateTransformer.h @@ -2,7 +2,7 @@ * \file RMF/CoordinateTransformer.h * \brief Declare the RMF::CoordinateTransformer class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/Decorator.h b/modules/rmf/dependency/RMF/include/RMF/Decorator.h index 17cd0f2a12..7fa6c984e7 100644 --- a/modules/rmf/dependency/RMF/include/RMF/Decorator.h +++ b/modules/rmf/dependency/RMF/include/RMF/Decorator.h @@ -2,7 +2,7 @@ * \file RMF/Decorator.h * \brief Mostly empty base classes for decorators and factories. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/Enum.h b/modules/rmf/dependency/RMF/include/RMF/Enum.h index a9085fa52a..5269f4fcb3 100644 --- a/modules/rmf/dependency/RMF/include/RMF/Enum.h +++ b/modules/rmf/dependency/RMF/include/RMF/Enum.h @@ -2,7 +2,7 @@ * \file RMF/Enum.h * \brief Declaration of RMF::Enum. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/FileConstHandle.h b/modules/rmf/dependency/RMF/include/RMF/FileConstHandle.h index 629d432d2f..518fea48bb 100644 --- a/modules/rmf/dependency/RMF/include/RMF/FileConstHandle.h +++ b/modules/rmf/dependency/RMF/include/RMF/FileConstHandle.h @@ -2,7 +2,7 @@ * \file RMF/FileConstHandle.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/FileHandle.h b/modules/rmf/dependency/RMF/include/RMF/FileHandle.h index dc332dadb5..d77abb8ee9 100644 --- a/modules/rmf/dependency/RMF/include/RMF/FileHandle.h +++ b/modules/rmf/dependency/RMF/include/RMF/FileHandle.h @@ -2,7 +2,7 @@ * \file RMF/FileHandle.h * \brief Declaration for RMF::FileHandle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstAttributes.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstAttributes.h index 8b4e6ac95d..fbfdcf9b25 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstAttributes.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstAttributes.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/ConstAttributes.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h index 0fc91efffa..273f08bcad 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/ConstDataSetD.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstFile.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstFile.h index d9d7487206..efc3f6b2c7 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstFile.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstFile.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/ConstFile.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstGroup.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstGroup.h index db3de114f3..4b3afa0c2d 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstGroup.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstGroup.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/ConstGroup.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetAccessPropertiesD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetAccessPropertiesD.h index fcadeb776d..c2c0a508c6 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetAccessPropertiesD.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetAccessPropertiesD.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/DataSetAccessPropertiesD.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetCreationPropertiesD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetCreationPropertiesD.h index a895336ca5..9e3bcda6ab 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetCreationPropertiesD.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetCreationPropertiesD.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/DataSetCreationPropertiesD.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h index 05d39872a9..c6eac2435f 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/DataSetD.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetIndexD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetIndexD.h index 5c6ff4b8bc..0a6169fb77 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetIndexD.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetIndexD.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/DataSetIndexD.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/File.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/File.h index 26d806f92e..edf081f49b 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/File.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/File.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/File.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/Group.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/Group.h index 42d8fe1e88..6583a936ab 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/Group.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/Group.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/Group.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/MutableAttributes.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/MutableAttributes.h index 4f35b1b502..6079322075 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/MutableAttributes.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/MutableAttributes.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/MutableAttributes.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/Object.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/Object.h index 81d2a00598..05316bfaa4 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/Object.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/Object.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/Object.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h index ee7722d7a0..75b11e8256 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/handle.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/infrastructure_macros.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/infrastructure_macros.h index afae11e516..f05ec25dee 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/infrastructure_macros.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/infrastructure_macros.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/infrastructure_macros.h * \brief Various general useful macros for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/internal/types.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/internal/types.h index a690133873..e397f378c4 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/internal/types.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/internal/types.h @@ -2,7 +2,7 @@ * \file RMF/types.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/types.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/types.h index e4b04e2ccd..f22e102a8e 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/types.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/types.h @@ -2,7 +2,7 @@ * \file RMF/HDF5/types.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/ID.h b/modules/rmf/dependency/RMF/include/RMF/ID.h index 80a6ef1dfb..674f4ebf44 100644 --- a/modules/rmf/dependency/RMF/include/RMF/ID.h +++ b/modules/rmf/dependency/RMF/include/RMF/ID.h @@ -2,7 +2,7 @@ * \file RMF/ID.h * \brief Declaration of RMF::ID. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/Label.h b/modules/rmf/dependency/RMF/include/RMF/Label.h index 0c72fc900c..452690994c 100644 --- a/modules/rmf/dependency/RMF/include/RMF/Label.h +++ b/modules/rmf/dependency/RMF/include/RMF/Label.h @@ -2,7 +2,7 @@ * \file RMF/Label.h * \brief Declaration of RMF::Label. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/NodeConstHandle.h b/modules/rmf/dependency/RMF/include/RMF/NodeConstHandle.h index 0eafb21a43..860963c1a9 100644 --- a/modules/rmf/dependency/RMF/include/RMF/NodeConstHandle.h +++ b/modules/rmf/dependency/RMF/include/RMF/NodeConstHandle.h @@ -2,7 +2,7 @@ * \file RMF/NodeConstHandle.h * \brief Declaration of NodeConstHandlke. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/NodeHandle.h b/modules/rmf/dependency/RMF/include/RMF/NodeHandle.h index 2b5138e19f..36e27ca90d 100644 --- a/modules/rmf/dependency/RMF/include/RMF/NodeHandle.h +++ b/modules/rmf/dependency/RMF/include/RMF/NodeHandle.h @@ -2,7 +2,7 @@ * \file RMF/NodeHandle.h * \brief Declaration of NodeHandle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/Nullable.h b/modules/rmf/dependency/RMF/include/RMF/Nullable.h index bd9debde6c..dd36c7434f 100644 --- a/modules/rmf/dependency/RMF/include/RMF/Nullable.h +++ b/modules/rmf/dependency/RMF/include/RMF/Nullable.h @@ -2,7 +2,7 @@ * \file RMF/Nullable.h * \brief A helper class for allowing nice return of possibly null values. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/RestoreCurrentFrame.h b/modules/rmf/dependency/RMF/include/RMF/RestoreCurrentFrame.h index eadf4cc529..daa51cddc9 100644 --- a/modules/rmf/dependency/RMF/include/RMF/RestoreCurrentFrame.h +++ b/modules/rmf/dependency/RMF/include/RMF/RestoreCurrentFrame.h @@ -2,7 +2,7 @@ * \file RMF/RestoreCurrentFrame.h * \brief Restore the current frame when exiting a scope. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/SetCurrentFrame.h b/modules/rmf/dependency/RMF/include/RMF/SetCurrentFrame.h index 0528f7b86e..e3d669131e 100644 --- a/modules/rmf/dependency/RMF/include/RMF/SetCurrentFrame.h +++ b/modules/rmf/dependency/RMF/include/RMF/SetCurrentFrame.h @@ -2,7 +2,7 @@ * \file RMF/SetCurrentFrame.h * \brief Temporarily change the current frame. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/TraverseHelper.h b/modules/rmf/dependency/RMF/include/RMF/TraverseHelper.h index b9c3eb31c0..afd32e9515 100644 --- a/modules/rmf/dependency/RMF/include/RMF/TraverseHelper.h +++ b/modules/rmf/dependency/RMF/include/RMF/TraverseHelper.h @@ -2,7 +2,7 @@ * \file RMF/TraverseHelper.h * \brief A helper class for managing data when traversing an RMF. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/Vector.h b/modules/rmf/dependency/RMF/include/RMF/Vector.h index 2655ca2fb3..0d6108ceec 100644 --- a/modules/rmf/dependency/RMF/include/RMF/Vector.h +++ b/modules/rmf/dependency/RMF/include/RMF/Vector.h @@ -2,7 +2,7 @@ * \file RMF/Vector.h * \brief Represent coordinates. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/compiler_macros.h b/modules/rmf/dependency/RMF/include/RMF/compiler_macros.h index 64ba32ad70..ec16614de8 100644 --- a/modules/rmf/dependency/RMF/include/RMF/compiler_macros.h +++ b/modules/rmf/dependency/RMF/include/RMF/compiler_macros.h @@ -2,7 +2,7 @@ * \file RMF/compiler_macros.h * \brief Various compiler workarounds * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef RMF_INTERNAL_COMPILER_MACROS_H diff --git a/modules/rmf/dependency/RMF/include/RMF/constants.h b/modules/rmf/dependency/RMF/include/RMF/constants.h index c34dc798d0..d48cad8bb1 100644 --- a/modules/rmf/dependency/RMF/include/RMF/constants.h +++ b/modules/rmf/dependency/RMF/include/RMF/constants.h @@ -2,7 +2,7 @@ * \file RMF/constants.h * \brief Various constants. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/decorator/alternatives.h b/modules/rmf/dependency/RMF/include/RMF/decorator/alternatives.h index 889ba2293d..dd2316f9af 100644 --- a/modules/rmf/dependency/RMF/include/RMF/decorator/alternatives.h +++ b/modules/rmf/dependency/RMF/include/RMF/decorator/alternatives.h @@ -2,7 +2,7 @@ * \file RMF/decorator/alternatives.h * \brief Helper functions for manipulating RMF files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/decorator/bond.h b/modules/rmf/dependency/RMF/include/RMF/decorator/bond.h index bbc13a75ea..ab93d6cb5a 100644 --- a/modules/rmf/dependency/RMF/include/RMF/decorator/bond.h +++ b/modules/rmf/dependency/RMF/include/RMF/decorator/bond.h @@ -2,7 +2,7 @@ * \file RMF/decorator/bond.h * \brief Helper functions for manipulating RMF files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/decorator/labels.h b/modules/rmf/dependency/RMF/include/RMF/decorator/labels.h index 4ecf8e986b..3202e6ff62 100644 --- a/modules/rmf/dependency/RMF/include/RMF/decorator/labels.h +++ b/modules/rmf/dependency/RMF/include/RMF/decorator/labels.h @@ -2,7 +2,7 @@ * \file RMF/decorator/labels.h * \brief Helper functions for manipulating RMF files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/decorator/reference.h b/modules/rmf/dependency/RMF/include/RMF/decorator/reference.h index fe23846f41..21e6c0889a 100644 --- a/modules/rmf/dependency/RMF/include/RMF/decorator/reference.h +++ b/modules/rmf/dependency/RMF/include/RMF/decorator/reference.h @@ -2,7 +2,7 @@ * \file RMF/decorator/reference.h * \brief Add a pointer from a node to another reference node. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/decorator/representation.h b/modules/rmf/dependency/RMF/include/RMF/decorator/representation.h index b0a3247c04..58db831460 100644 --- a/modules/rmf/dependency/RMF/include/RMF/decorator/representation.h +++ b/modules/rmf/dependency/RMF/include/RMF/decorator/representation.h @@ -2,7 +2,7 @@ * \file RMF/decorator/representation.h * \brief Helper functions for manipulating RMF files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/decorators.h b/modules/rmf/dependency/RMF/include/RMF/decorators.h index 1034964026..390c5fa9cb 100644 --- a/modules/rmf/dependency/RMF/include/RMF/decorators.h +++ b/modules/rmf/dependency/RMF/include/RMF/decorators.h @@ -2,7 +2,7 @@ * \file RMF/decorators.h * \brief Import all the decorators headers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/enums.h b/modules/rmf/dependency/RMF/include/RMF/enums.h index 6badbfadc9..87963a2f2b 100644 --- a/modules/rmf/dependency/RMF/include/RMF/enums.h +++ b/modules/rmf/dependency/RMF/include/RMF/enums.h @@ -2,7 +2,7 @@ * \file RMF/enums.h * \brief The various enums used in RMF. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/exceptions.h b/modules/rmf/dependency/RMF/include/RMF/exceptions.h index 62231460ad..16aef81af6 100644 --- a/modules/rmf/dependency/RMF/include/RMF/exceptions.h +++ b/modules/rmf/dependency/RMF/include/RMF/exceptions.h @@ -2,7 +2,7 @@ * \file RMF/exceptions.h * \brief Declarations of the various exception types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/info.h b/modules/rmf/dependency/RMF/include/RMF/info.h index 454d7a704f..0874be918b 100644 --- a/modules/rmf/dependency/RMF/include/RMF/info.h +++ b/modules/rmf/dependency/RMF/include/RMF/info.h @@ -2,7 +2,7 @@ * \file RMF/info.h * \brief Show info about the file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h b/modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h index 60cdd9d249..03402303db 100644 --- a/modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h +++ b/modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h @@ -2,7 +2,7 @@ * \file RMF/infrastructure_macros.h * \brief Various general useful macros for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedData.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedData.h index f181f7e38e..55817a73f6 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedData.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedData.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataCategory.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataCategory.h index a094c15468..492c12d57e 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataCategory.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataCategory.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData.h index 456e2b624d..989e044606 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData_impl.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData_impl.h index b93093df48..70cdbb952e 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData_impl.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData_impl.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataFile.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataFile.h index 0d453b1d68..7048ec52f1 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataFile.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataFile.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataFrames.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataFrames.h index 77d02fa447..eefea4da3d 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataFrames.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataFrames.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataHierarchy.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataHierarchy.h index e9f0cbddd6..6414867702 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataHierarchy.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataHierarchy.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h index 5cf0b3d812..05d776b5ba 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataUserData.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataUserData.h index 0cee12ae64..88af574903 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataUserData.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataUserData.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedData_impl.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedData_impl.h index e3cf82336a..a04234747a 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedData_impl.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedData_impl.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/Transform.h b/modules/rmf/dependency/RMF/include/RMF/internal/Transform.h index 79b0348684..c2683a055b 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/Transform.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/Transform.h @@ -2,7 +2,7 @@ * \file RMF/internal/Transform.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/errors.h b/modules/rmf/dependency/RMF/include/RMF/internal/errors.h index f85879e2c9..a2f7c6c494 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/errors.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/errors.h @@ -2,7 +2,7 @@ * \file RMF/operations.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/hash.h b/modules/rmf/dependency/RMF/include/RMF/internal/hash.h index 6eeb10bf99..f24e874b7e 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/hash.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/hash.h @@ -2,7 +2,7 @@ * \file compatibility/hash.h * \brief Make sure that we avoid errors in specialization of boost hash * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef RMF_INTERNAL_HASH_H diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/large_set_map.h b/modules/rmf/dependency/RMF/include/RMF/internal/large_set_map.h index 19e56e31d2..46356cb210 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/large_set_map.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/large_set_map.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/paths.h b/modules/rmf/dependency/RMF/include/RMF/internal/paths.h index eff52530e4..d1f465b59b 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/paths.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/paths.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/shared_data_factories.h b/modules/rmf/dependency/RMF/include/RMF/internal/shared_data_factories.h index 543c970708..f6b3a2d6ad 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/shared_data_factories.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/shared_data_factories.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/shared_data_ranges.h b/modules/rmf/dependency/RMF/include/RMF/internal/shared_data_ranges.h index 967ff95f68..a3598da8a9 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/shared_data_ranges.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/shared_data_ranges.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/small_set_map.h b/modules/rmf/dependency/RMF/include/RMF/internal/small_set_map.h index f7f16e356d..5722d7ed35 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/small_set_map.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/small_set_map.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h b/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h index 0dff5ba941..85dc2f6a71 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h @@ -2,7 +2,7 @@ * \file internal/swig_helpers.h * \brief Functions for use in swig wrappers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef RMF_INTERNAL_SWIG_HELPERS_H diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/use.h b/modules/rmf/dependency/RMF/include/RMF/internal/use.h index 06efe512f9..8c5387c180 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/use.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/use.h @@ -2,7 +2,7 @@ * \file RMF/operations.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/keys.h b/modules/rmf/dependency/RMF/include/RMF/keys.h index d707db2677..3a39b10f27 100644 --- a/modules/rmf/dependency/RMF/include/RMF/keys.h +++ b/modules/rmf/dependency/RMF/include/RMF/keys.h @@ -2,7 +2,7 @@ * \file RMF/keys.h * \brief Declarations of the various key types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/log.h b/modules/rmf/dependency/RMF/include/RMF/log.h index 0ed4308c78..ec995468b7 100644 --- a/modules/rmf/dependency/RMF/include/RMF/log.h +++ b/modules/rmf/dependency/RMF/include/RMF/log.h @@ -2,7 +2,7 @@ * \file RMF/log.h * \brief Functions and macros for logging. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/names.h b/modules/rmf/dependency/RMF/include/RMF/names.h index cb79cc323a..77056dd647 100644 --- a/modules/rmf/dependency/RMF/include/RMF/names.h +++ b/modules/rmf/dependency/RMF/include/RMF/names.h @@ -2,7 +2,7 @@ * \file RMF/names.h * \brief Functions to check if names are valid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/show_hierarchy.h b/modules/rmf/dependency/RMF/include/RMF/show_hierarchy.h index 56b3979540..a5fe3e34e4 100644 --- a/modules/rmf/dependency/RMF/include/RMF/show_hierarchy.h +++ b/modules/rmf/dependency/RMF/include/RMF/show_hierarchy.h @@ -2,7 +2,7 @@ * \file RMF/show_hierarchy.h * \brief Functions to show the hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/signature.h b/modules/rmf/dependency/RMF/include/RMF/signature.h index 2232470e7e..fdbc7631bf 100644 --- a/modules/rmf/dependency/RMF/include/RMF/signature.h +++ b/modules/rmf/dependency/RMF/include/RMF/signature.h @@ -2,7 +2,7 @@ * \file RMF/signature.h * \brief Return a (long) string describing a file that can be compared. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/traits.h b/modules/rmf/dependency/RMF/include/RMF/traits.h index 529815b56c..0cb997e46d 100644 --- a/modules/rmf/dependency/RMF/include/RMF/traits.h +++ b/modules/rmf/dependency/RMF/include/RMF/traits.h @@ -2,7 +2,7 @@ * \file RMF/traits.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/types.h b/modules/rmf/dependency/RMF/include/RMF/types.h index dd3e160baf..2688bbfe8d 100644 --- a/modules/rmf/dependency/RMF/include/RMF/types.h +++ b/modules/rmf/dependency/RMF/include/RMF/types.h @@ -4,7 +4,7 @@ * Use RMF_TYPES_HEADER to replace it with another header. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/utility.h b/modules/rmf/dependency/RMF/include/RMF/utility.h index bb46da5198..deb84469ca 100644 --- a/modules/rmf/dependency/RMF/include/RMF/utility.h +++ b/modules/rmf/dependency/RMF/include/RMF/utility.h @@ -2,7 +2,7 @@ * \file RMF/utility.h * \brief Helper functions for manipulating RMF files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/include/RMF/validate.h b/modules/rmf/dependency/RMF/include/RMF/validate.h index c0299e4146..724dfd8910 100644 --- a/modules/rmf/dependency/RMF/include/RMF/validate.h +++ b/modules/rmf/dependency/RMF/include/RMF/validate.h @@ -2,7 +2,7 @@ * \file RMF/validate.h * \brief Support for validating the data in a file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/plugins/vmd/Data.cpp b/modules/rmf/dependency/RMF/plugins/vmd/Data.cpp index 7749c9a887..56d6269a0e 100644 --- a/modules/rmf/dependency/RMF/plugins/vmd/Data.cpp +++ b/modules/rmf/dependency/RMF/plugins/vmd/Data.cpp @@ -2,7 +2,7 @@ * \file rmfplugin.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/plugins/vmd/Data.h b/modules/rmf/dependency/RMF/plugins/vmd/Data.h index b7121044a5..f275129008 100644 --- a/modules/rmf/dependency/RMF/plugins/vmd/Data.h +++ b/modules/rmf/dependency/RMF/plugins/vmd/Data.h @@ -2,7 +2,7 @@ * \file rmfplugin.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp b/modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp index 692d91972b..64e91a5278 100644 --- a/modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp +++ b/modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp @@ -2,7 +2,7 @@ * \file rmfplugin.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/plugins/vmd/init.cpp b/modules/rmf/dependency/RMF/plugins/vmd/init.cpp index 440eb7baf0..09a8e44f33 100644 --- a/modules/rmf/dependency/RMF/plugins/vmd/init.cpp +++ b/modules/rmf/dependency/RMF/plugins/vmd/init.cpp @@ -1,6 +1,6 @@ /** * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include "Data.h" diff --git a/modules/rmf/dependency/RMF/src/BufferConstHandle.cpp b/modules/rmf/dependency/RMF/src/BufferConstHandle.cpp index 80d5ca09b3..9f33a3e232 100644 --- a/modules/rmf/dependency/RMF/src/BufferConstHandle.cpp +++ b/modules/rmf/dependency/RMF/src/BufferConstHandle.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/CoordinateTransformer.cpp b/modules/rmf/dependency/RMF/src/CoordinateTransformer.cpp index 33a0a4c6b4..c32136f497 100644 --- a/modules/rmf/dependency/RMF/src/CoordinateTransformer.cpp +++ b/modules/rmf/dependency/RMF/src/CoordinateTransformer.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/Enum.cpp b/modules/rmf/dependency/RMF/src/Enum.cpp index b1f5ad4404..c336c7c76e 100644 --- a/modules/rmf/dependency/RMF/src/Enum.cpp +++ b/modules/rmf/dependency/RMF/src/Enum.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/FileConstHandle.cpp b/modules/rmf/dependency/RMF/src/FileConstHandle.cpp index 7e2110734c..8e50148c36 100644 --- a/modules/rmf/dependency/RMF/src/FileConstHandle.cpp +++ b/modules/rmf/dependency/RMF/src/FileConstHandle.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/FileHandle.cpp b/modules/rmf/dependency/RMF/src/FileHandle.cpp index dac1f0368f..5d569c6b91 100644 --- a/modules/rmf/dependency/RMF/src/FileHandle.cpp +++ b/modules/rmf/dependency/RMF/src/FileHandle.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/NodeConstHandle.cpp b/modules/rmf/dependency/RMF/src/NodeConstHandle.cpp index 42d0c2781d..983018dbf7 100644 --- a/modules/rmf/dependency/RMF/src/NodeConstHandle.cpp +++ b/modules/rmf/dependency/RMF/src/NodeConstHandle.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/NodeHandle.cpp b/modules/rmf/dependency/RMF/src/NodeHandle.cpp index 8ebe5d1ce2..bde17c484c 100644 --- a/modules/rmf/dependency/RMF/src/NodeHandle.cpp +++ b/modules/rmf/dependency/RMF/src/NodeHandle.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/RestoreCurrentFrame.cpp b/modules/rmf/dependency/RMF/src/RestoreCurrentFrame.cpp index b463c10b53..32f4a1d79b 100644 --- a/modules/rmf/dependency/RMF/src/RestoreCurrentFrame.cpp +++ b/modules/rmf/dependency/RMF/src/RestoreCurrentFrame.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/SetCurrentFrame.cpp b/modules/rmf/dependency/RMF/src/SetCurrentFrame.cpp index c7e320aca6..e6ae307f1c 100644 --- a/modules/rmf/dependency/RMF/src/SetCurrentFrame.cpp +++ b/modules/rmf/dependency/RMF/src/SetCurrentFrame.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/TraverseHelper.cpp b/modules/rmf/dependency/RMF/src/TraverseHelper.cpp index 7e38f86145..54c3cab2fe 100644 --- a/modules/rmf/dependency/RMF/src/TraverseHelper.cpp +++ b/modules/rmf/dependency/RMF/src/TraverseHelper.cpp @@ -2,7 +2,7 @@ * \file RMF/TraverseHelper.cpp * \brief A helper class for managing data when traversing an RMF. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/BackwardsIO.h b/modules/rmf/dependency/RMF/src/backend/BackwardsIO.h index cdc4ee151d..43acb4c9ab 100644 --- a/modules/rmf/dependency/RMF/src/backend/BackwardsIO.h +++ b/modules/rmf/dependency/RMF/src/backend/BackwardsIO.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/BackwardsIOBase.h b/modules/rmf/dependency/RMF/src/backend/BackwardsIOBase.h index 0647289813..d203c6c7db 100644 --- a/modules/rmf/dependency/RMF/src/backend/BackwardsIOBase.h +++ b/modules/rmf/dependency/RMF/src/backend/BackwardsIOBase.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/IO.cpp b/modules/rmf/dependency/RMF/src/backend/IO.cpp index 4b7c95b659..49e79a7d01 100644 --- a/modules/rmf/dependency/RMF/src/backend/IO.cpp +++ b/modules/rmf/dependency/RMF/src/backend/IO.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/IO.h b/modules/rmf/dependency/RMF/src/backend/IO.h index 7516da0c35..5ffbf287ec 100644 --- a/modules/rmf/dependency/RMF/src/backend/IO.h +++ b/modules/rmf/dependency/RMF/src/backend/IO.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/IOFactory.h b/modules/rmf/dependency/RMF/src/backend/IOFactory.h index dbbaee063b..12af15065d 100644 --- a/modules/rmf/dependency/RMF/src/backend/IOFactory.h +++ b/modules/rmf/dependency/RMF/src/backend/IOFactory.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/KeyFilter.h b/modules/rmf/dependency/RMF/src/backend/KeyFilter.h index 64e12b25a1..0359ac74dc 100644 --- a/modules/rmf/dependency/RMF/src/backend/KeyFilter.h +++ b/modules/rmf/dependency/RMF/src/backend/KeyFilter.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/SharedDataAdaptor.h b/modules/rmf/dependency/RMF/src/backend/SharedDataAdaptor.h index c5dc70586c..68460c13fd 100644 --- a/modules/rmf/dependency/RMF/src/backend/SharedDataAdaptor.h +++ b/modules/rmf/dependency/RMF/src/backend/SharedDataAdaptor.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/avro/data_file.cpp b/modules/rmf/dependency/RMF/src/backend/avro/data_file.cpp index 3d20aa0252..86ff0b4862 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/data_file.cpp +++ b/modules/rmf/dependency/RMF/src/backend/avro/data_file.cpp @@ -1,6 +1,6 @@ /** * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h b/modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h index dd3c2c6f3f..9e2afb6338 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h +++ b/modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h @@ -1,6 +1,6 @@ /** * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/avro/encode_decode_util.h b/modules/rmf/dependency/RMF/src/backend/avro/encode_decode_util.h index c8927b9ffe..93ab7b4b4a 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/encode_decode_util.h +++ b/modules/rmf/dependency/RMF/src/backend/avro/encode_decode_util.h @@ -1,6 +1,6 @@ /** * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/avro/factory.cpp b/modules/rmf/dependency/RMF/src/backend/avro/factory.cpp index 71fd4e22b8..cff2127c12 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/factory.cpp +++ b/modules/rmf/dependency/RMF/src/backend/avro/factory.cpp @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/avro/io.h b/modules/rmf/dependency/RMF/src/backend/avro/io.h index 221aff7504..e28c228722 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/io.h +++ b/modules/rmf/dependency/RMF/src/backend/avro/io.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/avro/traits.h b/modules/rmf/dependency/RMF/src/backend/avro/traits.h index 9f3d46d6c5..45ee69b343 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/traits.h +++ b/modules/rmf/dependency/RMF/src/backend/avro/traits.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/backward_types.h b/modules/rmf/dependency/RMF/src/backend/backward_types.h index d17bc53aa9..2ee3fdff8f 100644 --- a/modules/rmf/dependency/RMF/src/backend/backward_types.h +++ b/modules/rmf/dependency/RMF/src/backend/backward_types.h @@ -2,7 +2,7 @@ * \file RMF/types.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroKeysAndCategories.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroKeysAndCategories.h index 89a88db416..25802375da 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroKeysAndCategories.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroKeysAndCategories.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.h index 4a7d8b66d9..1f2c29ea83 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.impl.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.impl.h index 49a6203af4..bc6a8d4e68 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.impl.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.impl.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.types.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.types.h index 68ae228255..dca9fe8d3c 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.types.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/AvroSharedData.types.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileBase.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileBase.cpp index 7e02a727a3..824f423cb4 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileBase.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileBase.cpp @@ -2,7 +2,7 @@ * \file RMF/paths.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileBase.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileBase.h index 74420321c0..bb558a7b0f 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileBase.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileBase.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileReader.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileReader.cpp index 00fadda077..e6155cb452 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileReader.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileReader.cpp @@ -2,7 +2,7 @@ * \file RMF/paths.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileReader.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileReader.h index d4f69a0d7a..b9615538f5 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileReader.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileReader.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.cpp index 0870be0cdf..7cb37afad9 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.cpp @@ -2,7 +2,7 @@ * \file RMF/paths.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.h index a6fd86926f..c0fac20b51 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/MultipleAvroFileWriter.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.cpp index 6e47be65a1..8c3a727a46 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.cpp @@ -2,7 +2,7 @@ * \file RMF/paths.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.h index 4bb601fd5f..a8c8a3efc4 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/SingleAvroFile.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/avro_schema_io.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/avro_schema_io.cpp index 44685e211c..d5bea82ab6 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/avro_schema_io.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/avro_schema_io.cpp @@ -2,7 +2,7 @@ * \file RMF/paths.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/avro_schema_io.h b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/avro_schema_io.h index a808c8ef0e..776badd483 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/avro_schema_io.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/avro_schema_io.h @@ -2,7 +2,7 @@ * \file compatibility/hash.h * \brief Make sure that we avoid errors in specialization of boost hash * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef RMF_INTERNAL_AVRO_SCHEMA_IO_H diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp index 7a8895e2a8..d8c4c3780f 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp @@ -2,7 +2,7 @@ * \file RMF/paths.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache1D.h b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache1D.h index a2ecd18e62..4dbed2ca24 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache1D.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache1D.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache2D.h b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache2D.h index 07e938ec0d..5c27ce3cd3 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache2D.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache2D.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache3D.h b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache3D.h index 3a6427c52c..2b4b583a89 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache3D.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCache3D.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCacheD.h b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCacheD.h index 990f65fa60..bfdbdeae6a 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCacheD.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5DataSetCacheD.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp index 90260c3a12..42eacf4fbc 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h index 9f3bbcf8a7..3d89bc92a0 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp index 5b4f99a10b..15b5dac967 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp @@ -2,7 +2,7 @@ * \file RMF/paths.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/names.h b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/names.h index 6443171492..2fed52ca91 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/names.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/names.h @@ -2,7 +2,7 @@ * \file RMF/names.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/decorator/alternatives.cpp b/modules/rmf/dependency/RMF/src/decorator/alternatives.cpp index 4867259d8c..7efda60130 100644 --- a/modules/rmf/dependency/RMF/src/decorator/alternatives.cpp +++ b/modules/rmf/dependency/RMF/src/decorator/alternatives.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/decorators.cpp b/modules/rmf/dependency/RMF/src/decorators.cpp index a4f248011b..62d6866842 100644 --- a/modules/rmf/dependency/RMF/src/decorators.cpp +++ b/modules/rmf/dependency/RMF/src/decorators.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/enums.cpp b/modules/rmf/dependency/RMF/src/enums.cpp index 0341bcb3c0..7319c25919 100644 --- a/modules/rmf/dependency/RMF/src/enums.cpp +++ b/modules/rmf/dependency/RMF/src/enums.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/exceptions.cpp b/modules/rmf/dependency/RMF/src/exceptions.cpp index 90b8a57374..a1bf374afa 100644 --- a/modules/rmf/dependency/RMF/src/exceptions.cpp +++ b/modules/rmf/dependency/RMF/src/exceptions.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp b/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp index 2e1a139e7c..908277191c 100644 --- a/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp +++ b/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/info.cpp b/modules/rmf/dependency/RMF/src/info.cpp index 5b2460ef02..ac804b9736 100644 --- a/modules/rmf/dependency/RMF/src/info.cpp +++ b/modules/rmf/dependency/RMF/src/info.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/internal/SharedData.cpp b/modules/rmf/dependency/RMF/src/internal/SharedData.cpp index 321d0fbbad..0672d4143b 100644 --- a/modules/rmf/dependency/RMF/src/internal/SharedData.cpp +++ b/modules/rmf/dependency/RMF/src/internal/SharedData.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/internal/Transform.cpp b/modules/rmf/dependency/RMF/src/internal/Transform.cpp index 53cf3b55ce..d310bda38c 100644 --- a/modules/rmf/dependency/RMF/src/internal/Transform.cpp +++ b/modules/rmf/dependency/RMF/src/internal/Transform.cpp @@ -2,7 +2,7 @@ * \file RMF/Transform.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/internal/clone_shared_data.h b/modules/rmf/dependency/RMF/src/internal/clone_shared_data.h index 5ad5593c05..e17906341a 100644 --- a/modules/rmf/dependency/RMF/src/internal/clone_shared_data.h +++ b/modules/rmf/dependency/RMF/src/internal/clone_shared_data.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/internal/paths.cpp b/modules/rmf/dependency/RMF/src/internal/paths.cpp index 9c8f33df38..e0013fb235 100644 --- a/modules/rmf/dependency/RMF/src/internal/paths.cpp +++ b/modules/rmf/dependency/RMF/src/internal/paths.cpp @@ -2,7 +2,7 @@ * \file RMF/paths.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/internal/shared_data_equality.h b/modules/rmf/dependency/RMF/src/internal/shared_data_equality.h index 604db0c4b6..e79faae13b 100644 --- a/modules/rmf/dependency/RMF/src/internal/shared_data_equality.h +++ b/modules/rmf/dependency/RMF/src/internal/shared_data_equality.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/internal/shared_data_factories.cpp b/modules/rmf/dependency/RMF/src/internal/shared_data_factories.cpp index 7fa4bceec6..7ca77527f0 100644 --- a/modules/rmf/dependency/RMF/src/internal/shared_data_factories.cpp +++ b/modules/rmf/dependency/RMF/src/internal/shared_data_factories.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/internal/shared_data_maps.h b/modules/rmf/dependency/RMF/src/internal/shared_data_maps.h index ccf0ef3daf..db86b0ed3a 100644 --- a/modules/rmf/dependency/RMF/src/internal/shared_data_maps.h +++ b/modules/rmf/dependency/RMF/src/internal/shared_data_maps.h @@ -2,7 +2,7 @@ * \file RMF/internal/SharedData.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/log.cpp b/modules/rmf/dependency/RMF/src/log.cpp index dfd221bde9..e284d4970f 100644 --- a/modules/rmf/dependency/RMF/src/log.cpp +++ b/modules/rmf/dependency/RMF/src/log.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ // IWYU pragma: no_include diff --git a/modules/rmf/dependency/RMF/src/names.cpp b/modules/rmf/dependency/RMF/src/names.cpp index 07813ffefb..46c0277d60 100644 --- a/modules/rmf/dependency/RMF/src/names.cpp +++ b/modules/rmf/dependency/RMF/src/names.cpp @@ -2,7 +2,7 @@ * \file RMF/names.cpp * \brief Functions to check if names are valid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/show_hierarchy.cpp b/modules/rmf/dependency/RMF/src/show_hierarchy.cpp index efbc4ef116..3b31816fbc 100644 --- a/modules/rmf/dependency/RMF/src/show_hierarchy.cpp +++ b/modules/rmf/dependency/RMF/src/show_hierarchy.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/signature.cpp b/modules/rmf/dependency/RMF/src/signature.cpp index 0976dfd1d8..5b4435cdd8 100644 --- a/modules/rmf/dependency/RMF/src/signature.cpp +++ b/modules/rmf/dependency/RMF/src/signature.cpp @@ -2,7 +2,7 @@ * \file RMF/signature.cpp * \brief Return a (long) string describing a file that can be compared. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/utility.cpp b/modules/rmf/dependency/RMF/src/utility.cpp index 5ab066ca09..97af6de835 100644 --- a/modules/rmf/dependency/RMF/src/utility.cpp +++ b/modules/rmf/dependency/RMF/src/utility.cpp @@ -2,7 +2,7 @@ * \file RMF/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/src/validate.cpp b/modules/rmf/dependency/RMF/src/validate.cpp index 8cf8a0d093..4c273e45bb 100644 --- a/modules/rmf/dependency/RMF/src/validate.cpp +++ b/modules/rmf/dependency/RMF/src/validate.cpp @@ -2,7 +2,7 @@ * \file RMF/validate.h * \brief Support for validating the data in a file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/test/test_associations.cpp b/modules/rmf/dependency/RMF/test/test_associations.cpp index d8930da00f..f662864879 100644 --- a/modules/rmf/dependency/RMF/test/test_associations.cpp +++ b/modules/rmf/dependency/RMF/test/test_associations.cpp @@ -2,7 +2,7 @@ * \file test_associations.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/rmf/dependency/RMF/test/test_avro2_validate.cpp b/modules/rmf/dependency/RMF/test/test_avro2_validate.cpp index 0718d4c26b..22147648a5 100644 --- a/modules/rmf/dependency/RMF/test/test_avro2_validate.cpp +++ b/modules/rmf/dependency/RMF/test/test_avro2_validate.cpp @@ -1,6 +1,6 @@ /** * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/test/test_buffer.cpp b/modules/rmf/dependency/RMF/test/test_buffer.cpp index 53e13e7f28..ab639865d5 100644 --- a/modules/rmf/dependency/RMF/test/test_buffer.cpp +++ b/modules/rmf/dependency/RMF/test/test_buffer.cpp @@ -2,7 +2,7 @@ * \file test_associations.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/rmf/dependency/RMF/test/test_fill.cpp b/modules/rmf/dependency/RMF/test/test_fill.cpp index 9754a5a56b..c6a301a1dc 100644 --- a/modules/rmf/dependency/RMF/test/test_fill.cpp +++ b/modules/rmf/dependency/RMF/test/test_fill.cpp @@ -2,7 +2,7 @@ * \file test_fill.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/tools/build/_decorators.py b/modules/rmf/dependency/RMF/tools/build/_decorators.py index 28dd6b1145..bc9293add7 100755 --- a/modules/rmf/dependency/RMF/tools/build/_decorators.py +++ b/modules/rmf/dependency/RMF/tools/build/_decorators.py @@ -541,7 +541,7 @@ def make_header(name, infos, deps): * \\file RMF/decorator/%(name)s.h * \\brief Helper functions for manipulating RMF files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/.github/workflows/build.yml b/modules/rmf/dependency/RMF/tools/dev_tools/.github/workflows/build.yml index a489620443..8a286104cf 100644 --- a/modules/rmf/dependency/RMF/tools/dev_tools/.github/workflows/build.yml +++ b/modules/rmf/dependency/RMF/tools/dev_tools/.github/workflows/build.yml @@ -9,7 +9,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: [2.7, 3.7, 3.8, 3.9] + python-version: [2.7, 3.7, 3.8, 3.9, "3.10"] runs-on: ${{ matrix.os }} steps: diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py b/modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py index b194691df2..288c9e1ac0 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py @@ -31,7 +31,7 @@ def _add_includes(headers, output): * \\file %s * \\brief Include all non-deprecated headers in %s. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ """ % (includepath, includepath[:-2].replace('/', '.'))] guard = includepath.replace( diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/test/test_header.py b/modules/rmf/dependency/RMF/tools/dev_tools/test/test_header.py index 56a710697f..a00c32bd4a 100644 --- a/modules/rmf/dependency/RMF/tools/dev_tools/test/test_header.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/test/test_header.py @@ -32,7 +32,7 @@ def test_header(self): * \\file test.h * \\brief Include all non-deprecated headers in test. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef TEST_H From cf9f97d2c3bd545a6bda0ed66f75cc9715b43cec Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 10 Jan 2022 10:46:22 -0800 Subject: [PATCH 003/155] Get latest npctransport --- modules/npctransport | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/npctransport b/modules/npctransport index 43f9923d97..ca1afb458e 160000 --- a/modules/npctransport +++ b/modules/npctransport @@ -1 +1 @@ -Subproject commit 43f9923d97c6ac873b057ce251b65fa0aa3561a8 +Subproject commit ca1afb458ee96f3976a1a294ef0a021cb2c6fa6f From 2a78709d99c5e2aa8c81fe27664f4f0fb77ab048 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 10 Jan 2022 10:56:55 -0800 Subject: [PATCH 004/155] Update copyright year --- README.md | 2 +- doc/manual/licenses.md | 2 +- modules/algebra/benchmark/benchmark_grid_traversal.cpp | 2 +- modules/algebra/benchmark/benchmark_knn.cpp | 2 +- modules/algebra/benchmark/benchmark_rotate.cpp | 2 +- modules/algebra/benchmark/benchmark_surface.cpp | 2 +- modules/algebra/examples/grid.cpp | 2 +- modules/algebra/include/BoundingBoxD.h | 2 +- modules/algebra/include/Cone3D.h | 2 +- modules/algebra/include/Cylinder3D.h | 2 +- modules/algebra/include/Ellipsoid3D.h | 2 +- modules/algebra/include/Gaussian3D.h | 2 +- modules/algebra/include/GeometricPrimitiveD.h | 2 +- modules/algebra/include/GridD.h | 2 +- modules/algebra/include/Line3D.h | 2 +- modules/algebra/include/LinearFit.h | 2 +- modules/algebra/include/ParabolicFit.h | 2 +- modules/algebra/include/Plane3D.h | 2 +- modules/algebra/include/ReferenceFrame3D.h | 2 +- modules/algebra/include/Reflection3D.h | 2 +- modules/algebra/include/Rotation2D.h | 2 +- modules/algebra/include/Rotation3D.h | 2 +- modules/algebra/include/Segment3D.h | 2 +- modules/algebra/include/Sphere3D.h | 2 +- modules/algebra/include/SphereD.h | 2 +- modules/algebra/include/SpherePatch3D.h | 2 +- modules/algebra/include/SphericalVector3D.h | 2 +- modules/algebra/include/Torus3D.h | 2 +- modules/algebra/include/Transformation2D.h | 2 +- modules/algebra/include/Transformation3D.h | 2 +- modules/algebra/include/Triangle3D.h | 2 +- modules/algebra/include/UnitSimplexD.h | 2 +- modules/algebra/include/Vector2D.h | 2 +- modules/algebra/include/Vector3D.h | 2 +- modules/algebra/include/VectorBaseD.h | 2 +- modules/algebra/include/VectorD.h | 2 +- modules/algebra/include/algebra_macros.h | 2 +- modules/algebra/include/connolly_surface.h | 2 +- modules/algebra/include/constants.h | 2 +- modules/algebra/include/distance.h | 2 +- modules/algebra/include/eigen_analysis.h | 2 +- modules/algebra/include/endian.h | 2 +- modules/algebra/include/geometric_alignment.h | 2 +- modules/algebra/include/geometric_primitive_macros.h | 2 +- modules/algebra/include/grid_embeddings.h | 2 +- modules/algebra/include/grid_indexes.h | 2 +- modules/algebra/include/grid_ranges.h | 2 +- modules/algebra/include/grid_storages.h | 2 +- modules/algebra/include/grid_utility.h | 2 +- modules/algebra/include/internal/MinimalSet.h | 2 +- modules/algebra/include/internal/ann.h | 2 +- modules/algebra/include/internal/grid_3d_impl.h | 2 +- modules/algebra/include/internal/grid_apply.h | 2 +- modules/algebra/include/internal/grid_internal.h | 2 +- modules/algebra/include/internal/grid_interpolation.h | 2 +- modules/algebra/include/internal/grid_range_d.h | 2 +- modules/algebra/include/internal/internal_vector_generators.h | 2 +- modules/algebra/include/internal/linear_knn.h | 2 +- modules/algebra/include/internal/multi_array_helpers.h | 2 +- modules/algebra/include/internal/quaternion_derivatives.h | 2 +- modules/algebra/include/internal/swig.h | 2 +- modules/algebra/include/internal/utility.h | 2 +- modules/algebra/include/internal/vector.h | 2 +- modules/algebra/include/io.h | 2 +- modules/algebra/include/python_only.h | 2 +- modules/algebra/include/shortest_segment.h | 2 +- modules/algebra/include/standard_grids.h | 2 +- modules/algebra/include/utility.h | 2 +- modules/algebra/include/vector_generators.h | 2 +- modules/algebra/include/vector_metrics.h | 2 +- modules/algebra/include/vector_search.h | 2 +- modules/algebra/src/Cone3D.cpp | 2 +- modules/algebra/src/Cylinder3D.cpp | 2 +- modules/algebra/src/Ellipsoid3D.cpp | 2 +- modules/algebra/src/Gaussian3D.cpp | 2 +- modules/algebra/src/Line3D.cpp | 2 +- modules/algebra/src/LinearFit.cpp | 2 +- modules/algebra/src/ParabolicFit.cpp | 2 +- modules/algebra/src/ReferenceFrame3D.cpp | 2 +- modules/algebra/src/Rotation3D.cpp | 2 +- modules/algebra/src/Segment3D.cpp | 2 +- modules/algebra/src/Sphere3D.cpp | 2 +- modules/algebra/src/Sphere3DPatch.cpp | 2 +- modules/algebra/src/SphericalVector3D.cpp | 2 +- modules/algebra/src/Transformation2D.cpp | 2 +- modules/algebra/src/Transformation3D.cpp | 2 +- modules/algebra/src/Triangle3D.cpp | 2 +- modules/algebra/src/connolly_surface.cpp | 2 +- modules/algebra/src/eigen_analysis.cpp | 2 +- modules/algebra/src/endian.cpp | 2 +- modules/algebra/src/geometric_alignment.cpp | 2 +- modules/algebra/src/internal/utility.cpp | 2 +- modules/algebra/src/io.cpp | 2 +- modules/algebra/src/shortest_segment.cpp | 2 +- modules/algebra/src/vector_generators.cpp | 2 +- modules/algebra/src/vector_metrics.cpp | 2 +- modules/algebra/src/vector_search.cpp | 2 +- modules/algebra/test/test_grid.cpp | 2 +- modules/algebra/test/test_grid_apply.cpp | 2 +- modules/algebra/test/test_grid_storage.cpp | 2 +- modules/atom/benchmark/benchmark_incremental_mc.cpp | 2 +- modules/atom/benchmark/benchmark_md_charmm.cpp | 2 +- modules/atom/benchmark/benchmark_pdb.cpp | 2 +- modules/atom/benchmark/benchmark_refiners.cpp | 2 +- modules/atom/bin/ligand_score.cpp | 2 +- modules/atom/bin/ligand_score_multiple.cpp | 2 +- modules/atom/bin/pdb_check.cpp | 2 +- modules/atom/include/AngleSingletonScore.h | 2 +- modules/atom/include/Atom.h | 2 +- modules/atom/include/BerendsenThermostatOptimizerState.h | 2 +- modules/atom/include/BondEndpointsRefiner.h | 2 +- modules/atom/include/BondPairContainer.h | 2 +- modules/atom/include/BondSingletonScore.h | 2 +- modules/atom/include/BondedPairFilter.h | 2 +- modules/atom/include/BrownianDynamics.h | 2 +- modules/atom/include/BrownianDynamicsTAMD.h | 2 +- modules/atom/include/CAAngleRestraint.h | 2 +- modules/atom/include/CADihedralRestraint.h | 2 +- modules/atom/include/CHARMMAtom.h | 2 +- modules/atom/include/CHARMMParameters.h | 2 +- modules/atom/include/CHARMMStereochemistryRestraint.h | 2 +- modules/atom/include/CenterOfMass.h | 2 +- modules/atom/include/Chain.h | 2 +- modules/atom/include/Charged.h | 2 +- modules/atom/include/Copy.h | 2 +- modules/atom/include/CoulombPairScore.h | 2 +- modules/atom/include/CoverBond.h | 2 +- modules/atom/include/Diffusion.h | 2 +- modules/atom/include/DihedralSingletonScore.h | 2 +- modules/atom/include/Domain.h | 2 +- modules/atom/include/DopePairScore.h | 2 +- modules/atom/include/EzRestraint.h | 2 +- modules/atom/include/ForceFieldParameters.h | 2 +- modules/atom/include/Fragment.h | 2 +- modules/atom/include/HelixRestraint.h | 2 +- modules/atom/include/Hierarchy.h | 2 +- modules/atom/include/ImproperSingletonScore.h | 2 +- modules/atom/include/LangevinThermostatOptimizerState.h | 2 +- modules/atom/include/LennardJones.h | 2 +- modules/atom/include/LennardJonesPairScore.h | 2 +- modules/atom/include/LoopStatisticalPairScore.h | 2 +- modules/atom/include/Mass.h | 2 +- modules/atom/include/MolecularDynamics.h | 2 +- modules/atom/include/Molecule.h | 2 +- modules/atom/include/OrientedSoapPairScore.h | 2 +- modules/atom/include/RemoveRigidMotionOptimizerState.h | 2 +- modules/atom/include/RemoveTranslationOptimizerState.h | 2 +- modules/atom/include/Representation.h | 2 +- modules/atom/include/Residue.h | 2 +- modules/atom/include/SameResiduePairFilter.h | 2 +- modules/atom/include/SecondaryStructureResidue.h | 2 +- modules/atom/include/Selection.h | 2 +- modules/atom/include/Simulator.h | 2 +- modules/atom/include/SoapPairFilter.h | 2 +- modules/atom/include/State.h | 2 +- modules/atom/include/StereochemistryPairFilter.h | 2 +- modules/atom/include/StructureSource.h | 2 +- modules/atom/include/TAMDCentroid.h | 2 +- modules/atom/include/TAMDParticle.h | 2 +- modules/atom/include/VelocityScalingOptimizerState.h | 2 +- modules/atom/include/alignment.h | 2 +- modules/atom/include/angle_decorators.h | 2 +- modules/atom/include/atom_macros.h | 2 +- modules/atom/include/bond_decorators.h | 2 +- modules/atom/include/bond_graph.h | 2 +- modules/atom/include/charmm_segment_topology.h | 2 +- modules/atom/include/charmm_topology.h | 2 +- modules/atom/include/constants.h | 2 +- modules/atom/include/dihedrals.h | 2 +- modules/atom/include/distance.h | 2 +- modules/atom/include/element.h | 2 +- modules/atom/include/estimates.h | 2 +- modules/atom/include/force_fields.h | 2 +- modules/atom/include/hierarchy_tools.h | 2 +- modules/atom/include/internal/ExcludedPair.h | 2 +- modules/atom/include/internal/Gaussian.h | 2 +- modules/atom/include/internal/SelectionPredicate.h | 2 +- modules/atom/include/internal/Sigmoid.h | 2 +- modules/atom/include/internal/bond_graph_boost_functions.h | 2 +- modules/atom/include/internal/bond_graph_functors.h | 2 +- modules/atom/include/internal/bond_helpers.h | 2 +- modules/atom/include/internal/charmm_helpers.h | 2 +- modules/atom/include/internal/mol2.h | 2 +- modules/atom/include/internal/pdb.h | 2 +- modules/atom/include/internal/soap_bond_separation.h | 2 +- modules/atom/include/internal/soap_chain_separation.h | 2 +- modules/atom/include/mmcif.h | 2 +- modules/atom/include/mol2.h | 2 +- modules/atom/include/pdb.h | 2 +- modules/atom/include/protein_ligand_score.h | 2 +- modules/atom/include/python_only.h | 2 +- modules/atom/include/secondary_structure_reader.h | 2 +- modules/atom/include/smoothing_functions.h | 2 +- modules/atom/src/AngleSingletonScore.cpp | 2 +- modules/atom/src/Atom.cpp | 2 +- modules/atom/src/BerendsenThermostatOptimizerState.cpp | 2 +- modules/atom/src/BondEndpointsRefiner.cpp | 2 +- modules/atom/src/BondPairContainer.cpp | 2 +- modules/atom/src/BondSingletonScore.cpp | 2 +- modules/atom/src/BondedPairFilter.cpp | 2 +- modules/atom/src/BrownianDynamics.cpp | 2 +- modules/atom/src/BrownianDynamicsTAMD.cpp | 2 +- modules/atom/src/CAAngleRestraint.cpp | 2 +- modules/atom/src/CADihedralRestraint.cpp | 2 +- modules/atom/src/CHARMMAtom.cpp | 2 +- modules/atom/src/CHARMMParameters.cpp | 2 +- modules/atom/src/CHARMMStereochemistryRestraint.cpp | 2 +- modules/atom/src/CenterOfMass.cpp | 2 +- modules/atom/src/Chain.cpp | 2 +- modules/atom/src/Charged.cpp | 2 +- modules/atom/src/Copy.cpp | 2 +- modules/atom/src/CoulombPairScore.cpp | 2 +- modules/atom/src/CoverBond.cpp | 2 +- modules/atom/src/Diffusion.cpp | 2 +- modules/atom/src/DihedralSingletonScore.cpp | 2 +- modules/atom/src/Domain.cpp | 2 +- modules/atom/src/DopePairScore.cpp | 2 +- modules/atom/src/EzRestraint.cpp | 2 +- modules/atom/src/ForceFieldParameters.cpp | 2 +- modules/atom/src/Fragment.cpp | 2 +- modules/atom/src/HelixRestraint.cpp | 2 +- modules/atom/src/Hierarchy.cpp | 2 +- modules/atom/src/ImproperSingletonScore.cpp | 2 +- modules/atom/src/LangevinThermostatOptimizerState.cpp | 2 +- modules/atom/src/LennardJones.cpp | 2 +- modules/atom/src/LennardJonesPairScore.cpp | 2 +- modules/atom/src/LoopStatisticalPairScore.cpp | 2 +- modules/atom/src/Mass.cpp | 2 +- modules/atom/src/MolecularDynamics.cpp | 2 +- modules/atom/src/Molecule.cpp | 2 +- modules/atom/src/RemoveRigidMotionOptimizerState.cpp | 2 +- modules/atom/src/RemoveTranslationOptimizerState.cpp | 2 +- modules/atom/src/Representation.cpp | 2 +- modules/atom/src/Residue.cpp | 2 +- modules/atom/src/SameResiduePairFilter.cpp | 2 +- modules/atom/src/SecondaryStructureResidue.cpp | 2 +- modules/atom/src/Selection.cpp | 2 +- modules/atom/src/Simulator.cpp | 2 +- modules/atom/src/State.cpp | 2 +- modules/atom/src/StereochemistryPairFilter.cpp | 2 +- modules/atom/src/StructureSource.cpp | 2 +- modules/atom/src/TAMDCentroid.cpp | 2 +- modules/atom/src/TAMDParticle.cpp | 2 +- modules/atom/src/VelocityScalingOptimizerState.cpp | 2 +- modules/atom/src/alignment.cpp | 2 +- modules/atom/src/angle_decorators.cpp | 2 +- modules/atom/src/bond_decorators.cpp | 2 +- modules/atom/src/bond_graph.cpp | 2 +- modules/atom/src/charmm_topology.cpp | 2 +- modules/atom/src/dihedrals.cpp | 2 +- modules/atom/src/distance.cpp | 2 +- modules/atom/src/element.cpp | 2 +- modules/atom/src/estimates.cpp | 2 +- modules/atom/src/force_fields.cpp | 2 +- modules/atom/src/hierarchy_tools.cpp | 2 +- modules/atom/src/internal/charmm_helpers.cpp | 2 +- modules/atom/src/internal/mol2.cpp | 2 +- modules/atom/src/internal/pdb.cpp | 2 +- modules/atom/src/mmcif.cpp | 2 +- modules/atom/src/mol2.cpp | 2 +- modules/atom/src/pdb.cpp | 2 +- modules/atom/src/protein_ligand_score.cpp | 2 +- modules/atom/src/secondary_structure_reader.cpp | 2 +- modules/atom/src/smoothing_functions.cpp | 2 +- modules/benchmark/benchmark/benchmark_nothing.cpp | 2 +- modules/benchmark/include/Profiler.h | 2 +- modules/benchmark/include/benchmark_macros.h | 2 +- modules/benchmark/include/internal/control.h | 2 +- modules/benchmark/include/internal/flags.h | 2 +- modules/benchmark/include/internal/utility.h | 2 +- modules/benchmark/include/utility.h | 2 +- modules/benchmark/src/Profiler.cpp | 2 +- modules/benchmark/src/internal/control.cpp | 2 +- modules/benchmark/src/internal/flags.cpp | 2 +- modules/benchmark/src/internal/utility.cpp | 2 +- modules/benchmark/src/utility.cpp | 2 +- modules/cgal/include/internal/bounding_sphere.h | 2 +- modules/cgal/include/internal/knn.h | 2 +- modules/cgal/include/internal/polygons.h | 2 +- modules/cgal/include/internal/polyhedrons.h | 2 +- modules/cgal/include/internal/sphere_cover.h | 2 +- modules/cgal/include/internal/union_of_balls.h | 2 +- modules/cgal/src/internal/bounding_sphere.cpp | 2 +- modules/cgal/src/internal/errors.cpp | 2 +- modules/cgal/src/internal/knn.cpp | 2 +- modules/cgal/src/internal/polygons.cpp | 2 +- modules/cgal/src/internal/polyhedrons.cpp | 2 +- modules/cgal/src/internal/sphere_cover.cpp | 2 +- modules/cgal/src/internal/union_of_balls.cpp | 2 +- modules/cnmultifit/include/AlignSymmetric.h | 2 +- modules/cnmultifit/include/CnSymmAxisDetector.h | 2 +- modules/cnmultifit/include/MolCnSymmAxisDetector.h | 2 +- modules/cnmultifit/include/cn_rmsd.h | 2 +- modules/cnmultifit/include/internal/Parameters.h | 2 +- modules/cnmultifit/include/symmetric_multifit.h | 2 +- modules/cnmultifit/include/symmetry_utils.h | 2 +- modules/cnmultifit/src/AlignSymmetric.cpp | 2 +- modules/cnmultifit/src/CnSymmAxisDetector.cpp | 2 +- modules/cnmultifit/src/MolCnSymmAxisDetector.cpp | 2 +- modules/cnmultifit/src/cn_rmsd.cpp | 2 +- modules/cnmultifit/src/internal/Parameters.cpp | 2 +- modules/cnmultifit/src/symmetric_multifit.cpp | 2 +- modules/cnmultifit/src/symmetry_utils.cpp | 2 +- modules/container/benchmark/benchmark_close_pairs_finders.cpp | 2 +- modules/container/benchmark/benchmark_connectivity.cpp | 2 +- modules/container/benchmark/benchmark_evaluate.cpp | 2 +- modules/container/benchmark/benchmark_random_collisions.cpp | 2 +- modules/container/benchmark/benchmark_rigid_collisions.cpp | 2 +- modules/container/include/AllBipartitePairContainer.h | 2 +- modules/container/include/AllPairContainer.h | 2 +- modules/container/include/CloseBipartitePairContainer.h | 2 +- modules/container/include/ClosePairContainer.h | 2 +- modules/container/include/ConnectingPairContainer.h | 2 +- modules/container/include/ConsecutivePairContainer.h | 2 +- modules/container/include/generic.h | 2 +- .../container/include/internal/CloseBipartitePairContainer.h | 2 +- modules/container/include/internal/ClosePairContainer.h | 2 +- modules/container/src/AllBipartitePairContainer.cpp | 2 +- modules/container/src/AllPairContainer.cpp | 2 +- modules/container/src/CloseBipartitePairContainer.cpp | 2 +- modules/container/src/ClosePairContainer.cpp | 2 +- modules/container/src/ConnectingPairContainer.cpp | 2 +- modules/container/src/ConsecutivePairContainer.cpp | 2 +- .../container/src/internal/CloseBipartitePairContainer.cpp | 2 +- modules/container/src/internal/ClosePairContainer.cpp | 2 +- modules/container/test/test_consecutive_pair_container.cpp | 2 +- modules/core/benchmark/benchmark_omp_evaluate.cpp | 2 +- modules/core/benchmark/benchmark_xyz_access.cpp | 2 +- modules/core/include/AngleRestraint.h | 2 +- modules/core/include/AngleTripletScore.h | 2 +- modules/core/include/BallMover.h | 2 +- modules/core/include/BoundingBox3DSingletonScore.h | 2 +- modules/core/include/BoundingSphere3DSingletonScore.h | 2 +- modules/core/include/BoxSweepClosePairsFinder.h | 2 +- modules/core/include/CentroidOfRefined.h | 2 +- modules/core/include/ChecksScoreState.h | 2 +- modules/core/include/ChildrenRefiner.h | 2 +- modules/core/include/ClosePairsFinder.h | 2 +- modules/core/include/ClosePairsPairScore.h | 2 +- modules/core/include/ClosedCubicSpline.h | 2 +- modules/core/include/ConjugateGradients.h | 2 +- modules/core/include/ConnectivityRestraint.h | 2 +- modules/core/include/ConstantRestraint.h | 2 +- modules/core/include/Cosine.h | 2 +- modules/core/include/CoverRefined.h | 2 +- modules/core/include/DataObject.h | 2 +- modules/core/include/DerivativesFromRefined.h | 2 +- modules/core/include/DerivativesToRefined.h | 2 +- modules/core/include/DiameterRestraint.h | 2 +- modules/core/include/DihedralRestraint.h | 2 +- modules/core/include/DirectionMover.h | 2 +- modules/core/include/DistancePairScore.h | 2 +- modules/core/include/DistanceRestraint.h | 2 +- modules/core/include/DistanceToSingletonScore.h | 2 +- modules/core/include/ExcludedVolumeRestraint.h | 2 +- modules/core/include/FixedRefiner.h | 2 +- modules/core/include/Gaussian.h | 2 +- modules/core/include/GenericAttributeSingletonScore.h | 2 +- modules/core/include/GridClosePairsFinder.h | 2 +- modules/core/include/Harmonic.h | 2 +- modules/core/include/HarmonicLowerBound.h | 2 +- modules/core/include/HarmonicUpperBound.h | 2 +- modules/core/include/HarmonicWell.h | 2 +- modules/core/include/Hierarchy.h | 2 +- modules/core/include/IncrementalScoringFunction.h | 2 +- modules/core/include/LeavesRefiner.h | 2 +- modules/core/include/Linear.h | 2 +- modules/core/include/LogNormalMover.h | 2 +- modules/core/include/MCCGSampler.h | 2 +- modules/core/include/MSConnectivityRestraint.h | 2 +- modules/core/include/MinimumRestraint.h | 2 +- modules/core/include/MonteCarlo.h | 2 +- modules/core/include/MonteCarloMover.h | 2 +- modules/core/include/MoveStatisticsScoreState.h | 2 +- modules/core/include/MultipleBinormalRestraint.h | 2 +- modules/core/include/NearestNeighborsClosePairsFinder.h | 2 +- modules/core/include/NeighborsTable.h | 2 +- modules/core/include/NormalMover.h | 2 +- modules/core/include/OpenCubicSpline.h | 2 +- modules/core/include/PeriodicOptimizerState.h | 2 +- modules/core/include/QuadraticClosePairsFinder.h | 2 +- modules/core/include/RefinedPairsPairScore.h | 2 +- modules/core/include/RestraintsScoringFunction.h | 2 +- modules/core/include/RigidBodyAnglePairScore.h | 2 +- modules/core/include/RigidBodyDistancePairScore.h | 2 +- modules/core/include/RigidBodyMover.h | 2 +- modules/core/include/RigidBodyTunneler.h | 2 +- modules/core/include/RigidBodyUmbrella.h | 2 +- modules/core/include/RigidClosePairsFinder.h | 2 +- modules/core/include/SerialMover.h | 2 +- modules/core/include/SphereDistancePairScore.h | 2 +- modules/core/include/StatisticalPairScore.h | 2 +- modules/core/include/SteepestDescent.h | 2 +- modules/core/include/SubsetMover.h | 2 +- modules/core/include/Surface.h | 2 +- modules/core/include/SurfaceDistancePairScore.h | 2 +- modules/core/include/SurfaceMover.h | 2 +- modules/core/include/SurfaceSymmetryConstraint.h | 2 +- modules/core/include/SurfaceTetheredChain.h | 2 +- modules/core/include/TableRefiner.h | 2 +- modules/core/include/Transform.h | 2 +- modules/core/include/TransformedDistancePairScore.h | 2 +- modules/core/include/TruncatedHarmonic.h | 2 +- modules/core/include/Typed.h | 2 +- modules/core/include/TypedPairScore.h | 2 +- modules/core/include/VolumeRestraint.h | 2 +- modules/core/include/WeightedDerivativesToRefined.h | 2 +- modules/core/include/WeightedSum.h | 2 +- modules/core/include/WeightedSumOfExponential.h | 2 +- modules/core/include/XYZ.h | 2 +- modules/core/include/XYZR.h | 2 +- modules/core/include/blame.h | 2 +- modules/core/include/direction.h | 2 +- modules/core/include/generic.h | 2 +- modules/core/include/internal/MovedSingletonContainer.h | 2 +- modules/core/include/internal/angle_helpers.h | 2 +- modules/core/include/internal/close_pairs_helpers.h | 2 +- modules/core/include/internal/container_helpers.h | 2 +- modules/core/include/internal/dihedral_helpers.h | 2 +- modules/core/include/internal/evaluate_distance_pair_score.h | 2 +- modules/core/include/internal/graph_base.h | 2 +- modules/core/include/internal/grid_close_pairs_impl.h | 2 +- modules/core/include/internal/hierarchy_helpers.h | 2 +- modules/core/include/internal/incremental_scoring_function.h | 2 +- modules/core/include/internal/remove_pointers.h | 2 +- modules/core/include/internal/rigid_bodies.h | 2 +- modules/core/include/internal/rigid_body_tree.h | 2 +- modules/core/include/internal/sinks.h | 2 +- modules/core/include/internal/truncated_harmonic.h | 2 +- modules/core/include/internal/tunneler_helpers.h | 2 +- modules/core/include/model_statistics.h | 2 +- modules/core/include/predicates.h | 2 +- modules/core/include/provenance.h | 2 +- modules/core/include/python_only.h | 2 +- modules/core/include/rigid_bodies.h | 2 +- modules/core/include/rigid_body_geometries.h | 2 +- modules/core/include/symmetry.h | 2 +- modules/core/include/utility.h | 2 +- modules/core/src/AngleRestraint.cpp | 2 +- modules/core/src/AngleTripletScore.cpp | 2 +- modules/core/src/BallMover.cpp | 2 +- modules/core/src/BoundingBox3DSingletonScore.cpp | 2 +- modules/core/src/BoundingSphere3DSingletonScore.cpp | 2 +- modules/core/src/BoxSweepClosePairsFinder.cpp | 2 +- modules/core/src/CentroidOfRefined.cpp | 2 +- modules/core/src/ChecksScoreState.cpp | 2 +- modules/core/src/ChildrenRefiner.cpp | 2 +- modules/core/src/ClosePairsFinder.cpp | 2 +- modules/core/src/ClosePairsPairScore.cpp | 2 +- modules/core/src/ClosedCubicSpline.cpp | 2 +- modules/core/src/ConjugateGradients.cpp | 2 +- modules/core/src/ConnectivityRestraint.cpp | 2 +- modules/core/src/ConstantRestraint.cpp | 2 +- modules/core/src/Cosine.cpp | 2 +- modules/core/src/CoverRefined.cpp | 2 +- modules/core/src/DerivativesFromRefined.cpp | 2 +- modules/core/src/DerivativesToRefined.cpp | 2 +- modules/core/src/DiameterRestraint.cpp | 2 +- modules/core/src/DihedralRestraint.cpp | 2 +- modules/core/src/DirectionMover.cpp | 2 +- modules/core/src/DistanceRestraint.cpp | 2 +- modules/core/src/DistanceToSingletonScore.cpp | 2 +- modules/core/src/ExcludedVolumeRestraint.cpp | 2 +- modules/core/src/FixedRefiner.cpp | 2 +- modules/core/src/Gaussian.cpp | 2 +- modules/core/src/GenericAttributeSingletonScore.cpp | 2 +- modules/core/src/GridClosePairsFinder.cpp | 2 +- modules/core/src/Hierarchy.cpp | 2 +- modules/core/src/IncrementalScoringFunction.cpp | 2 +- modules/core/src/LeavesRefiner.cpp | 2 +- modules/core/src/LogNormalMover.cpp | 2 +- modules/core/src/MCCGSampler.cpp | 2 +- modules/core/src/MSConnectivityRestraint.cpp | 2 +- modules/core/src/MinimumRestraint.cpp | 2 +- modules/core/src/MonteCarlo.cpp | 2 +- modules/core/src/MonteCarloMover.cpp | 2 +- modules/core/src/MoveStatisticsScoreState.cpp | 2 +- modules/core/src/MultipleBinormalRestraint.cpp | 2 +- modules/core/src/NearestNeighborsClosePairsFinder.cpp | 2 +- modules/core/src/NeighborsTable.cpp | 2 +- modules/core/src/NormalMover.cpp | 2 +- modules/core/src/QuadraticClosePairsFinder.cpp | 2 +- modules/core/src/RefinedPairsPairScore.cpp | 2 +- modules/core/src/RigidBodyAnglePairScore.cpp | 2 +- modules/core/src/RigidBodyDistancePairScore.cpp | 2 +- modules/core/src/RigidBodyMover.cpp | 2 +- modules/core/src/RigidBodyTunneler.cpp | 2 +- modules/core/src/RigidBodyUmbrella.cpp | 2 +- modules/core/src/RigidClosePairsFinder.cpp | 2 +- modules/core/src/SerialMover.cpp | 2 +- modules/core/src/SphereDistancePairScore.cpp | 2 +- modules/core/src/SteepestDescent.cpp | 2 +- modules/core/src/SubsetMover.cpp | 2 +- modules/core/src/Surface.cpp | 2 +- modules/core/src/SurfaceMover.cpp | 2 +- modules/core/src/SurfaceSymmetryConstraint.cpp | 2 +- modules/core/src/TableRefiner.cpp | 2 +- modules/core/src/Transform.cpp | 2 +- modules/core/src/TransformedDistancePairScore.cpp | 2 +- modules/core/src/Typed.cpp | 2 +- modules/core/src/TypedPairScore.cpp | 2 +- modules/core/src/VolumeRestraint.cpp | 2 +- modules/core/src/WeightedDerivativesToRefined.cpp | 2 +- modules/core/src/XYZ.cpp | 2 +- modules/core/src/XYZR.cpp | 2 +- modules/core/src/blame.cpp | 2 +- modules/core/src/direction.cpp | 2 +- modules/core/src/internal/MovedSingletonContainer.cpp | 2 +- modules/core/src/internal/close_pairs_helpers.cpp | 2 +- modules/core/src/internal/graph_base.cpp | 2 +- modules/core/src/internal/incremental_scoring_function.cpp | 2 +- modules/core/src/internal/rigid_body_tree.cpp | 2 +- modules/core/src/internal/tunneler_helpers.cpp | 2 +- modules/core/src/model_statistics.cpp | 2 +- modules/core/src/provenance.cpp | 2 +- modules/core/src/rigid_bodies.cpp | 2 +- modules/core/src/rigid_body_geometries.cpp | 2 +- modules/core/src/symmetry.cpp | 2 +- modules/core/src/utility.cpp | 2 +- modules/core/test/test_generic.cpp | 2 +- modules/core/test/test_soft_sphere.cpp | 2 +- modules/display/include/Color.h | 2 +- modules/display/include/Colored.h | 2 +- modules/display/include/FilterGeometry.h | 2 +- modules/display/include/GeometryProcessor.h | 2 +- modules/display/include/GeometrySet.h | 2 +- modules/display/include/LogOptimizerState.h | 2 +- modules/display/include/PymolWriter.h | 2 +- modules/display/include/Writer.h | 2 +- modules/display/include/declare_Geometry.h | 2 +- modules/display/include/display_macros.h | 2 +- modules/display/include/geometry.h | 2 +- modules/display/include/geometry_macros.h | 2 +- modules/display/include/internal/utility.h | 2 +- modules/display/include/internal/writers.h | 2 +- modules/display/include/particle_geometry.h | 2 +- modules/display/include/primitive_geometries.h | 2 +- modules/display/include/python_only.h | 2 +- modules/display/include/restraint_geometry.h | 2 +- modules/display/include/writer_macros.h | 2 +- modules/display/src/Color.cpp | 2 +- modules/display/src/Colored.cpp | 2 +- modules/display/src/FilterGeometry.cpp | 2 +- modules/display/src/GeometryProcessor.cpp | 2 +- modules/display/src/LogOptimizerState.cpp | 2 +- modules/display/src/PymolWriter.cpp | 2 +- modules/display/src/Writer.cpp | 2 +- modules/display/src/geometry.cpp | 2 +- modules/display/src/internal/utility.cpp | 2 +- modules/display/src/internal/writers.cpp | 2 +- modules/display/src/particle_geometry.cpp | 2 +- modules/display/src/restraint_geometry.cpp | 2 +- modules/domino/benchmark/benchmark_domino2.cpp | 2 +- modules/domino/benchmark/benchmark_domino_container.cpp | 2 +- modules/domino/include/Assignment.h | 2 +- modules/domino/include/BranchAndBoundSampler.h | 2 +- modules/domino/include/DependencyScoreState.h | 2 +- modules/domino/include/DiscreteSampler.h | 2 +- modules/domino/include/DominoSampler.h | 2 +- modules/domino/include/Order.h | 2 +- modules/domino/include/Slice.h | 2 +- modules/domino/include/Subset.h | 2 +- modules/domino/include/analysis.h | 2 +- modules/domino/include/assignment_containers.h | 2 +- modules/domino/include/assignment_tables.h | 2 +- modules/domino/include/domino_macros.h | 2 +- modules/domino/include/interactive.h | 2 +- modules/domino/include/internal/inference_utility.h | 2 +- modules/domino/include/internal/tree_inference.h | 2 +- modules/domino/include/particle_states.h | 2 +- modules/domino/include/subset_filters.h | 2 +- modules/domino/include/subset_graphs.h | 2 +- modules/domino/include/subset_scores.h | 2 +- modules/domino/include/utility.h | 2 +- modules/domino/src/Assignment.cpp | 2 +- modules/domino/src/BranchAndBoundSampler.cpp | 2 +- modules/domino/src/DependencyScoreState.cpp | 2 +- modules/domino/src/DiscreteSampler.cpp | 2 +- modules/domino/src/DominoSampler.cpp | 2 +- modules/domino/src/Order.cpp | 2 +- modules/domino/src/Slice.cpp | 2 +- modules/domino/src/Subset.cpp | 2 +- modules/domino/src/analysis.cpp | 2 +- modules/domino/src/assignment_containers.cpp | 2 +- modules/domino/src/assignment_tables.cpp | 2 +- modules/domino/src/interactive.cpp | 2 +- modules/domino/src/internal/inference_utility.cpp | 2 +- modules/domino/src/internal/tree_inference.cpp | 2 +- modules/domino/src/particle_states.cpp | 2 +- modules/domino/src/subset_filters.cpp | 2 +- modules/domino/src/subset_graphs.cpp | 2 +- modules/domino/src/subset_scores.cpp | 2 +- modules/domino/src/utility.cpp | 2 +- modules/em/benchmark/benchmark_density.cpp | 2 +- modules/em/include/CoarseCC.h | 2 +- modules/em/include/CoarseCCatIntervals.h | 2 +- modules/em/include/CoarseConvolution.h | 2 +- modules/em/include/DensityFillingRestraint.h | 2 +- modules/em/include/DensityHeader.h | 2 +- modules/em/include/DensityMap.h | 2 +- modules/em/include/EMReaderWriter.h | 2 +- modules/em/include/EnvelopeFitRestraint.h | 2 +- modules/em/include/EnvelopePenetrationRestraint.h | 2 +- modules/em/include/EnvelopeScore.h | 2 +- modules/em/include/FitRestraint.h | 2 +- modules/em/include/ImageHeader.h | 2 +- modules/em/include/KernelParameters.h | 2 +- modules/em/include/MRCReaderWriter.h | 2 +- modules/em/include/MapDistanceTransform.h | 2 +- modules/em/include/MapReaderWriter.h | 2 +- modules/em/include/PCAAligner.h | 2 +- modules/em/include/PCAFitRestraint.h | 2 +- modules/em/include/SampledDensityMap.h | 2 +- modules/em/include/SpiderHeader.h | 2 +- modules/em/include/SpiderReaderWriter.h | 2 +- modules/em/include/SurfaceShellDensityMap.h | 2 +- modules/em/include/Voxel.h | 2 +- modules/em/include/XplorReaderWriter.h | 2 +- modules/em/include/converters.h | 2 +- modules/em/include/def.h | 2 +- modules/em/include/density_utilities.h | 2 +- modules/em/include/embedding.h | 2 +- modules/em/include/envelope_penetration.h | 2 +- modules/em/include/exp.h | 2 +- modules/em/include/header_converters.h | 2 +- modules/em/include/internal/EMHeader.h | 2 +- modules/em/include/internal/MRCHeader.h | 2 +- modules/em/include/internal/RadiusDependentKernelParameters.h | 2 +- modules/em/include/internal/XplorHeader.h | 2 +- modules/em/include/masking.h | 2 +- modules/em/include/rigid_fitting.h | 2 +- modules/em/src/CoarseCC.cpp | 2 +- modules/em/src/CoarseCCatIntervals.cpp | 2 +- modules/em/src/CoarseConvolution.cpp | 2 +- modules/em/src/DensityFillingRestraint.cpp | 2 +- modules/em/src/DensityHeader.cpp | 2 +- modules/em/src/DensityMap.cpp | 2 +- modules/em/src/EMReaderWriter.cpp | 2 +- modules/em/src/EnvelopeFitRestraint.cpp | 2 +- modules/em/src/EnvelopePenetrationRestraint.cpp | 2 +- modules/em/src/EnvelopeScore.cpp | 2 +- modules/em/src/FitRestraint.cpp | 2 +- modules/em/src/ImageHeader.cpp | 2 +- modules/em/src/KernelParameters.cpp | 2 +- modules/em/src/MRCReaderWriter.cpp | 2 +- modules/em/src/MapDistanceTransform.cpp | 2 +- modules/em/src/PCAAligner.cpp | 2 +- modules/em/src/PCAFitRestraint.cpp | 2 +- modules/em/src/SampledDensityMap.cpp | 2 +- modules/em/src/SpiderReaderWriter.cpp | 2 +- modules/em/src/SurfaceShellDensityMap.cpp | 2 +- modules/em/src/Voxel.cpp | 2 +- modules/em/src/XplorReaderWriter.cpp | 2 +- modules/em/src/converters.cpp | 2 +- modules/em/src/density_utilities.cpp | 2 +- modules/em/src/embedding.cpp | 2 +- modules/em/src/envelope_penetration.cpp | 2 +- modules/em/src/header_converters.cpp | 2 +- modules/em/src/internal/EMHeader.cpp | 2 +- modules/em/src/internal/MRCHeader.cpp | 2 +- modules/em/src/masking.cpp | 2 +- modules/em/src/rigid_fitting.cpp | 2 +- modules/em2d/bin/create_single_particle_images.cpp | 2 +- modules/em2d/include/CenteredMat.h | 2 +- modules/em2d/include/CollisionCrossSection.h | 2 +- modules/em2d/include/DummyRestraint.h | 2 +- modules/em2d/include/Em2DRestraint.h | 2 +- modules/em2d/include/FFToperations.h | 2 +- modules/em2d/include/Fine2DRegistrationRestraint.h | 2 +- modules/em2d/include/Image.h | 2 +- modules/em2d/include/ImageReaderWriter.h | 2 +- modules/em2d/include/JPGImageReaderWriter.h | 2 +- modules/em2d/include/PCAFitRestraint.h | 2 +- modules/em2d/include/PolarResamplingParameters.h | 2 +- modules/em2d/include/ProjectionFinder.h | 2 +- modules/em2d/include/ProjectionMask.h | 2 +- modules/em2d/include/ProjectionParameters.h | 2 +- modules/em2d/include/RegistrationResult.h | 2 +- modules/em2d/include/RelativePositionMover.h | 2 +- modules/em2d/include/RigidBodiesImageFitRestraint.h | 2 +- modules/em2d/include/SpiderImageReaderWriter.h | 2 +- modules/em2d/include/TIFFImageReaderWriter.h | 2 +- modules/em2d/include/align2D.h | 2 +- modules/em2d/include/domino_filter_tables.h | 2 +- modules/em2d/include/domino_filters.h | 2 +- modules/em2d/include/domino_particle_states.h | 2 +- modules/em2d/include/filenames_manipulation.h | 2 +- modules/em2d/include/hierarchical_clustering.h | 2 +- modules/em2d/include/image_processing.h | 2 +- modules/em2d/include/internal/Image2D.h | 2 +- modules/em2d/include/internal/ImageTransform.h | 2 +- modules/em2d/include/internal/Projection.h | 2 +- modules/em2d/include/internal/ProjectionSphere.h | 2 +- modules/em2d/include/internal/Projector.h | 2 +- modules/em2d/include/internal/clustering_helper.h | 2 +- modules/em2d/include/internal/image_processing_helper.h | 2 +- modules/em2d/include/internal/rotation_helper.h | 2 +- modules/em2d/include/model_interaction.h | 2 +- modules/em2d/include/opencv_interface.h | 2 +- modules/em2d/include/project.h | 2 +- modules/em2d/include/scores2D.h | 2 +- modules/em2d/src/CollisionCrossSection.cpp | 2 +- modules/em2d/src/DummyRestraint.cpp | 2 +- modules/em2d/src/Em2DRestraint.cpp | 2 +- modules/em2d/src/FFToperations.cpp | 2 +- modules/em2d/src/Fine2DRegistrationRestraint.cpp | 2 +- modules/em2d/src/Image.cpp | 2 +- modules/em2d/src/PCAFitRestraint.cpp | 2 +- modules/em2d/src/ProjectionFinder.cpp | 2 +- modules/em2d/src/ProjectionMask.cpp | 2 +- modules/em2d/src/ProjectionParameters.cpp | 2 +- modules/em2d/src/RegistrationResult.cpp | 2 +- modules/em2d/src/RelativePositionMover.cpp | 2 +- modules/em2d/src/RigidBodiesImageFitRestraint.cpp | 2 +- modules/em2d/src/align2D.cpp | 2 +- modules/em2d/src/domino_filter_tables.cpp | 2 +- modules/em2d/src/domino_filters.cpp | 2 +- modules/em2d/src/domino_particle_states.cpp | 2 +- modules/em2d/src/hierarchical_clustering.cpp | 2 +- modules/em2d/src/image_processing.cpp | 2 +- modules/em2d/src/internal/Image2D.cpp | 2 +- modules/em2d/src/internal/Projection.cpp | 2 +- modules/em2d/src/internal/ProjectionSphere.cpp | 2 +- modules/em2d/src/internal/Projector.cpp | 2 +- modules/em2d/src/internal/image_processing_helper.cpp | 2 +- modules/em2d/src/internal/rotation_helper.cpp | 2 +- modules/em2d/src/model_interaction.cpp | 2 +- modules/em2d/src/opencv_interface.cpp | 2 +- modules/em2d/src/project.cpp | 2 +- modules/em2d/src/scores2D.cpp | 2 +- modules/em2d/utility/process_pdb.cpp | 2 +- modules/em2d/utility/score_model.cpp | 2 +- modules/example/include/ExampleComplexRestraint.h | 2 +- modules/example/include/ExampleConstraint.h | 2 +- modules/example/include/ExampleDecorator.h | 2 +- modules/example/include/ExampleObject.h | 2 +- modules/example/include/ExamplePairScore.h | 2 +- modules/example/include/ExampleRestraint.h | 2 +- modules/example/include/ExampleSingletonModifier.h | 2 +- modules/example/include/ExampleSubsetFilterTable.h | 2 +- modules/example/include/ExampleTemplateClass.h | 2 +- modules/example/include/ExampleUnaryFunction.h | 2 +- modules/example/include/complex_assembly.h | 2 +- modules/example/include/counting.h | 2 +- modules/example/include/creating_restraints.h | 2 +- modules/example/include/optimizing.h | 2 +- modules/example/include/randomizing.h | 2 +- modules/example/src/ExampleComplexRestraint.cpp | 2 +- modules/example/src/ExampleConstraint.cpp | 2 +- modules/example/src/ExampleDecorator.cpp | 2 +- modules/example/src/ExampleObject.cpp | 2 +- modules/example/src/ExamplePairScore.cpp | 2 +- modules/example/src/ExampleRestraint.cpp | 2 +- modules/example/src/ExampleSingletonModifier.cpp | 2 +- modules/example/src/ExampleSubsetFilterTable.cpp | 2 +- modules/example/src/complex_assembly.cpp | 2 +- modules/example/src/optimize_balls.cpp | 2 +- modules/example/src/use_example_dependency.cpp | 2 +- modules/example/utility/example_program.cpp | 2 +- modules/foxs/bin/foxs.cpp | 2 +- modules/foxs/include/internal/ColorCoder.h | 2 +- modules/foxs/include/internal/Gnuplot.h | 2 +- modules/foxs/include/internal/JmolWriter.h | 2 +- modules/foxs/src/internal/ColorCoder.cpp | 2 +- modules/foxs/src/internal/Gnuplot.cpp | 2 +- modules/foxs/src/internal/JmolWriter.cpp | 2 +- modules/gsl/include/ConjugateGradients.h | 2 +- modules/gsl/include/GSLOptimizer.h | 2 +- modules/gsl/include/QuasiNewton.h | 2 +- modules/gsl/include/Simplex.h | 2 +- modules/gsl/include/internal/helpers.h | 2 +- modules/gsl/src/ConjugateGradients.cpp | 2 +- modules/gsl/src/GSLOptimizer.cpp | 2 +- modules/gsl/src/QuasiNewton.cpp | 2 +- modules/gsl/src/Simplex.cpp | 2 +- modules/gsl/src/internal/helpers.cpp | 2 +- modules/integrative_docking/bin/combine_scores.cpp | 2 +- modules/integrative_docking/bin/cross_links_score.cpp | 2 +- modules/integrative_docking/bin/cross_links_single_score.cpp | 2 +- modules/integrative_docking/bin/em2d_score.cpp | 2 +- modules/integrative_docking/bin/em2d_single_score.cpp | 2 +- modules/integrative_docking/bin/em3d_score.cpp | 2 +- modules/integrative_docking/bin/em3d_single_score.cpp | 2 +- modules/integrative_docking/bin/interface_cross_links.cpp | 2 +- modules/integrative_docking/bin/interface_rtc.cpp | 2 +- modules/integrative_docking/bin/nmr_rtc_score.cpp | 2 +- modules/integrative_docking/bin/recompute_zscore.cpp | 2 +- modules/integrative_docking/bin/saxs_score.cpp | 2 +- modules/integrative_docking/bin/soap_score.cpp | 2 +- modules/integrative_docking/include/internal/CrossLink.h | 2 +- .../integrative_docking/include/internal/CrossLinkingResult.h | 2 +- .../include/internal/DockingDistanceRestraint.h | 2 +- modules/integrative_docking/include/internal/EM2DFitResult.h | 2 +- modules/integrative_docking/include/internal/EM3DFitResult.h | 2 +- modules/integrative_docking/include/internal/EMFit.h | 2 +- modules/integrative_docking/include/internal/MapScorer.h | 2 +- modules/integrative_docking/include/internal/NMR_RTCResult.h | 2 +- modules/integrative_docking/include/internal/Normalization.h | 2 +- modules/integrative_docking/include/internal/ResidueContent.h | 2 +- modules/integrative_docking/include/internal/Result.h | 2 +- modules/integrative_docking/include/internal/SAXSResult.h | 2 +- modules/integrative_docking/include/internal/SOAPResult.h | 2 +- modules/integrative_docking/include/internal/helpers.h | 2 +- modules/integrative_docking/include/internal/soap_score.h | 2 +- modules/integrative_docking/src/internal/CrossLink.cpp | 2 +- modules/integrative_docking/src/internal/EMFit.cpp | 2 +- modules/integrative_docking/src/internal/MapScorer.cpp | 2 +- modules/integrative_docking/src/internal/Normalization.cpp | 2 +- modules/integrative_docking/src/internal/ResidueContent.cpp | 2 +- modules/integrative_docking/src/internal/Result.cpp | 2 +- modules/integrative_docking/src/internal/helpers.cpp | 2 +- modules/integrative_docking/src/internal/soap_score.cpp | 2 +- modules/isd/include/AmbiguousNOERestraint.h | 2 +- modules/isd/include/AmbiguousRestraint.h | 2 +- modules/isd/include/AtomicCrossLinkMSRestraint.h | 2 +- modules/isd/include/CrossLinkData.h | 2 +- modules/isd/include/CrossLinkMSRestraint.h | 2 +- modules/isd/include/CysteineCrossLinkData.h | 2 +- modules/isd/include/CysteineCrossLinkRestraint.h | 2 +- modules/isd/include/FNormal.h | 2 +- modules/isd/include/FStudentT.h | 2 +- modules/isd/include/FretData.h | 2 +- modules/isd/include/FretRestraint.h | 2 +- modules/isd/include/GammaPrior.h | 2 +- modules/isd/include/GaussianAnchorEMRestraint.h | 2 +- modules/isd/include/GaussianEMRestraint.h | 2 +- modules/isd/include/GaussianProcessInterpolation.h | 2 +- modules/isd/include/GaussianProcessInterpolationRestraint.h | 2 +- modules/isd/include/GaussianRestraint.h | 2 +- modules/isd/include/HybridMonteCarlo.h | 2 +- modules/isd/include/ISDRestraint.h | 2 +- modules/isd/include/JeffreysRestraint.h | 2 +- modules/isd/include/LogWrapper.h | 2 +- modules/isd/include/LognormalAmbiguousRestraint.h | 2 +- modules/isd/include/LognormalRestraint.h | 2 +- modules/isd/include/MarginalHBondRestraint.h | 2 +- modules/isd/include/MarginalNOERestraint.h | 2 +- modules/isd/include/MolecularDynamics.h | 2 +- modules/isd/include/MolecularDynamicsMover.h | 2 +- modules/isd/include/MultivariateFNormalSufficient.h | 2 +- modules/isd/include/NOERestraint.h | 2 +- modules/isd/include/NormalSigmaPCRestraint.h | 2 +- modules/isd/include/Nuisance.h | 2 +- modules/isd/include/PenalizedComplexityPrior.h | 2 +- modules/isd/include/RepulsiveDistancePairScore.h | 2 +- modules/isd/include/Scale.h | 2 +- modules/isd/include/StudentTRestraint.h | 2 +- modules/isd/include/Switching.h | 2 +- modules/isd/include/TALOSRestraint.h | 2 +- modules/isd/include/UniformPrior.h | 2 +- modules/isd/include/Weight.h | 2 +- modules/isd/include/WeightMover.h | 2 +- modules/isd/include/WeightRestraint.h | 2 +- modules/isd/include/bivariate_functions.h | 2 +- modules/isd/include/distribution.h | 2 +- modules/isd/include/em_utilities.h | 2 +- modules/isd/include/internal/cg_eigen.h | 2 +- modules/isd/include/internal/timer.h | 2 +- modules/isd/include/univariate_functions.h | 2 +- modules/isd/include/vonMises.h | 2 +- modules/isd/include/vonMisesKappaConjugateRestraint.h | 2 +- modules/isd/include/vonMisesKappaJeffreysRestraint.h | 2 +- modules/isd/include/vonMisesSufficient.h | 2 +- modules/isd/src/AmbiguousNOERestraint.cpp | 2 +- modules/isd/src/AmbiguousRestraint.cpp | 2 +- modules/isd/src/AtomicCrossLinkMSRestraint.cpp | 2 +- modules/isd/src/CrossLinkData.cpp | 2 +- modules/isd/src/CrossLinkMSRestraint.cpp | 2 +- modules/isd/src/CysteineCrossLinkData.cpp | 2 +- modules/isd/src/CysteineCrossLinkRestraint.cpp | 2 +- modules/isd/src/FStudentT.cpp | 2 +- modules/isd/src/FretData.cpp | 2 +- modules/isd/src/FretRestraint.cpp | 2 +- modules/isd/src/GammaPrior.cpp | 2 +- modules/isd/src/GaussianAnchorEMRestraint.cpp | 2 +- modules/isd/src/GaussianEMRestraint.cpp | 2 +- modules/isd/src/GaussianProcessInterpolation.cpp | 2 +- modules/isd/src/GaussianProcessInterpolationRestraint.cpp | 2 +- modules/isd/src/GaussianRestraint.cpp | 2 +- modules/isd/src/HybridMonteCarlo.cpp | 2 +- modules/isd/src/ISDRestraint.cpp | 2 +- modules/isd/src/JeffreysRestraint.cpp | 2 +- modules/isd/src/LogWrapper.cpp | 2 +- modules/isd/src/LognormalAmbiguousRestraint.cpp | 2 +- modules/isd/src/LognormalRestraint.cpp | 2 +- modules/isd/src/MarginalHBondRestraint.cpp | 2 +- modules/isd/src/MarginalNOERestraint.cpp | 2 +- modules/isd/src/MolecularDynamics.cpp | 2 +- modules/isd/src/MolecularDynamicsMover.cpp | 2 +- modules/isd/src/MultivariateFNormalSufficient.cpp | 2 +- modules/isd/src/NOERestraint.cpp | 2 +- modules/isd/src/NormalSigmaPCRestraint.cpp | 2 +- modules/isd/src/Nuisance.cpp | 2 +- modules/isd/src/PenalizedComplexityPrior.cpp | 2 +- modules/isd/src/RepulsiveDistancePairScore.cpp | 2 +- modules/isd/src/Scale.cpp | 2 +- modules/isd/src/StudentTRestraint.cpp | 2 +- modules/isd/src/Switching.cpp | 2 +- modules/isd/src/TALOSRestraint.cpp | 2 +- modules/isd/src/UniformPrior.cpp | 2 +- modules/isd/src/Weight.cpp | 2 +- modules/isd/src/WeightMover.cpp | 2 +- modules/isd/src/WeightRestraint.cpp | 2 +- modules/isd/src/distribution.cpp | 2 +- modules/isd/src/vonMisesKappaConjugateRestraint.cpp | 2 +- modules/isd/src/vonMisesKappaJeffreysRestraint.cpp | 2 +- modules/isd/test/test_MultivariateFNormalSufficient.cpp | 2 +- modules/kernel/compiler/has_auto.cpp | 2 +- modules/kernel/compiler/has_debug_vector.cpp | 2 +- modules/kernel/compiler/has_unique_ptr.cpp | 2 +- modules/kernel/include/Array.h | 2 +- modules/kernel/include/AttributeOptimizer.h | 2 +- modules/kernel/include/Configuration.h | 2 +- modules/kernel/include/ConfigurationSet.h | 2 +- modules/kernel/include/ConstVector.h | 2 +- modules/kernel/include/Constraint.h | 2 +- modules/kernel/include/CreateLogContext.h | 2 +- modules/kernel/include/Decorator.h | 2 +- modules/kernel/include/DerivativeAccumulator.h | 2 +- modules/kernel/include/Flag.h | 2 +- modules/kernel/include/FloatIndex.h | 2 +- modules/kernel/include/Index.h | 2 +- modules/kernel/include/InputAdaptor.h | 2 +- modules/kernel/include/Key.h | 2 +- modules/kernel/include/Model.h | 2 +- modules/kernel/include/ModelObject.h | 2 +- modules/kernel/include/NonCopyable.h | 2 +- modules/kernel/include/Object.h | 2 +- modules/kernel/include/Optimizer.h | 2 +- modules/kernel/include/OptimizerState.h | 2 +- modules/kernel/include/Particle.h | 2 +- modules/kernel/include/Pointer.h | 2 +- modules/kernel/include/RAII.h | 2 +- modules/kernel/include/Refiner.h | 2 +- modules/kernel/include/Restraint.h | 2 +- modules/kernel/include/RestraintInfo.h | 2 +- modules/kernel/include/RestraintSet.h | 2 +- modules/kernel/include/Sampler.h | 2 +- modules/kernel/include/ScoreAccumulator.h | 2 +- modules/kernel/include/ScoreState.h | 2 +- modules/kernel/include/ScoringFunction.h | 2 +- modules/kernel/include/SetCheckState.h | 2 +- modules/kernel/include/SetLogState.h | 2 +- modules/kernel/include/Showable.h | 2 +- modules/kernel/include/UnaryFunction.h | 2 +- modules/kernel/include/Undecorator.h | 2 +- modules/kernel/include/Value.h | 2 +- modules/kernel/include/Vector.h | 2 +- modules/kernel/include/VersionInfo.h | 2 +- modules/kernel/include/WarningContext.h | 2 +- modules/kernel/include/WeakPointer.h | 2 +- modules/kernel/include/base_macros.h | 2 +- modules/kernel/include/base_types.h | 2 +- modules/kernel/include/base_utility.h | 2 +- modules/kernel/include/bracket_macros.h | 2 +- modules/kernel/include/cache.h | 2 +- modules/kernel/include/check_macros.h | 2 +- modules/kernel/include/comparison_macros.h | 2 +- modules/kernel/include/compiler_macros.h | 2 +- modules/kernel/include/constants.h | 2 +- modules/kernel/include/container_base.h | 2 +- modules/kernel/include/container_macros.h | 2 +- modules/kernel/include/decorator_macros.h | 2 +- modules/kernel/include/dependency_graph.h | 2 +- modules/kernel/include/deprecation.h | 2 +- modules/kernel/include/deprecation_macros.h | 2 +- modules/kernel/include/doxygen_macros.h | 2 +- modules/kernel/include/enums.h | 2 +- modules/kernel/include/exception.h | 2 +- modules/kernel/include/file.h | 2 +- modules/kernel/include/flags.h | 2 +- modules/kernel/include/functor.h | 2 +- modules/kernel/include/generic.h | 2 +- modules/kernel/include/graph_macros.h | 2 +- modules/kernel/include/hash.h | 2 +- modules/kernel/include/hash_macros.h | 2 +- modules/kernel/include/input_output.h | 2 +- modules/kernel/include/internal/AccumulatorScoreModifier.h | 2 +- modules/kernel/include/internal/AttributeTable.h | 2 +- modules/kernel/include/internal/ContainerConstraint.h | 2 +- modules/kernel/include/internal/ContainerRestraint.h | 2 +- modules/kernel/include/internal/ContainerScoreState.h | 2 +- modules/kernel/include/internal/DynamicListContainer.h | 2 +- modules/kernel/include/internal/ExponentialNumber.h | 2 +- modules/kernel/include/internal/Flag.h | 2 +- modules/kernel/include/internal/IndexingIterator.h | 2 +- modules/kernel/include/internal/ListLikeContainer.h | 2 +- modules/kernel/include/internal/NestedIterator.h | 2 +- modules/kernel/include/internal/PointerBase.h | 2 +- modules/kernel/include/internal/PrefixStream.h | 2 +- modules/kernel/include/internal/RestraintsScoringFunction.h | 2 +- modules/kernel/include/internal/StaticListContainer.h | 2 +- modules/kernel/include/internal/TupleConstraint.h | 2 +- modules/kernel/include/internal/TupleRestraint.h | 2 +- modules/kernel/include/internal/Unit.h | 2 +- modules/kernel/include/internal/Vector.h | 2 +- modules/kernel/include/internal/attribute_tables.h | 2 +- modules/kernel/include/internal/base_graph_utility.h | 2 +- modules/kernel/include/internal/base_static.h | 2 +- modules/kernel/include/internal/cache.h | 2 +- modules/kernel/include/internal/constants.h | 2 +- modules/kernel/include/internal/container_helpers.h | 2 +- modules/kernel/include/internal/create_decomposition.h | 2 +- modules/kernel/include/internal/cuda_helper_functions.h | 2 +- modules/kernel/include/internal/deprecation.h | 2 +- modules/kernel/include/internal/directories.h | 2 +- modules/kernel/include/internal/eat.h | 2 +- modules/kernel/include/internal/evaluate_utility.h | 2 +- modules/kernel/include/internal/functors.h | 2 +- modules/kernel/include/internal/graph_utility.h | 2 +- modules/kernel/include/internal/ifile.h | 2 +- modules/kernel/include/internal/input_output_exception.h | 2 +- modules/kernel/include/internal/key_helpers.h | 2 +- modules/kernel/include/internal/log.h | 2 +- modules/kernel/include/internal/log_stream.h | 2 +- modules/kernel/include/internal/moved_particles_cache.h | 2 +- modules/kernel/include/internal/pdb.h | 2 +- .../kernel/include/internal/random_number_generation_boost.h | 2 +- .../kernel/include/internal/random_number_generation_cuda.h | 2 +- modules/kernel/include/internal/range.h | 2 +- modules/kernel/include/internal/restraint_evaluation.h | 2 +- modules/kernel/include/internal/scoring_functions.h | 2 +- modules/kernel/include/internal/static.h | 2 +- modules/kernel/include/internal/swig.h | 2 +- modules/kernel/include/internal/swig_base.h | 2 +- modules/kernel/include/internal/swig_helpers.h | 2 +- modules/kernel/include/internal/swig_helpers_base.h | 2 +- modules/kernel/include/internal/units.h | 2 +- modules/kernel/include/internal/utility.h | 2 +- modules/kernel/include/io.h | 2 +- modules/kernel/include/live_objects.h | 2 +- modules/kernel/include/log.h | 2 +- modules/kernel/include/log_macros.h | 2 +- modules/kernel/include/macros.h | 2 +- modules/kernel/include/math.h | 2 +- modules/kernel/include/model_object_helpers.h | 2 +- modules/kernel/include/nullptr.h | 2 +- modules/kernel/include/nullptr_macros.h | 2 +- modules/kernel/include/object_cast.h | 2 +- modules/kernel/include/object_macros.h | 2 +- modules/kernel/include/particle_index.h | 2 +- modules/kernel/include/python_only.h | 2 +- modules/kernel/include/raii_macros.h | 2 +- modules/kernel/include/random.h | 2 +- modules/kernel/include/random_utils.h | 2 +- modules/kernel/include/ref_counted_macros.h | 2 +- modules/kernel/include/scoped.h | 2 +- modules/kernel/include/set_map_macros.h | 2 +- modules/kernel/include/showable_macros.h | 2 +- modules/kernel/include/swap_macros.h | 2 +- modules/kernel/include/swig_macros.h | 2 +- modules/kernel/include/thread_macros.h | 2 +- modules/kernel/include/threads.h | 2 +- modules/kernel/include/tuple_macros.h | 2 +- modules/kernel/include/types.h | 2 +- modules/kernel/include/utility.h | 2 +- modules/kernel/include/utility_macros.h | 2 +- modules/kernel/include/value_macros.h | 2 +- modules/kernel/include/vector_property_map.h | 2 +- modules/kernel/include/warning_macros.h | 2 +- modules/kernel/pyext/IMP_kernel.dispatcher.i | 2 +- modules/kernel/src/AttributeOptimizer.cpp | 2 +- modules/kernel/src/Configuration.cpp | 2 +- modules/kernel/src/ConfigurationSet.cpp | 2 +- modules/kernel/src/Constraint.cpp | 2 +- modules/kernel/src/Container.cpp | 2 +- modules/kernel/src/Decorator.cpp | 2 +- modules/kernel/src/Model.cpp | 2 +- modules/kernel/src/ModelObject.cpp | 2 +- modules/kernel/src/Model_dependencies.cpp | 2 +- modules/kernel/src/Model_evaluate.cpp | 2 +- modules/kernel/src/Object.cpp | 2 +- modules/kernel/src/Optimizer.cpp | 2 +- modules/kernel/src/OptimizerState.cpp | 2 +- modules/kernel/src/Particle.cpp | 2 +- modules/kernel/src/Refiner.cpp | 2 +- modules/kernel/src/Restraint.cpp | 2 +- modules/kernel/src/RestraintInfo.cpp | 2 +- modules/kernel/src/RestraintSet.cpp | 2 +- modules/kernel/src/Sampler.cpp | 2 +- modules/kernel/src/ScoreAccumulator.cpp | 2 +- modules/kernel/src/ScoreState.cpp | 2 +- modules/kernel/src/ScoringFunction.cpp | 2 +- modules/kernel/src/SetCheckState.cpp | 2 +- modules/kernel/src/SetLogState.cpp | 2 +- modules/kernel/src/Showable.cpp | 2 +- modules/kernel/src/UnaryFunction.cpp | 2 +- modules/kernel/src/VersionInfo.cpp | 2 +- modules/kernel/src/WarningContext.cpp | 2 +- modules/kernel/src/base_types.cpp | 2 +- modules/kernel/src/base_utility.cpp | 2 +- modules/kernel/src/dependency_graph.cpp | 2 +- modules/kernel/src/deprecation.cpp | 2 +- modules/kernel/src/enums.cpp | 2 +- modules/kernel/src/exception.cpp | 2 +- modules/kernel/src/file.cpp | 2 +- modules/kernel/src/flags.cpp | 4 ++-- modules/kernel/src/internal/PrefixStream.cpp | 2 +- modules/kernel/src/internal/base_static.cpp | 2 +- modules/kernel/src/internal/base_static.h | 2 +- modules/kernel/src/internal/constants.cpp | 2 +- modules/kernel/src/internal/directories.cpp | 2 +- modules/kernel/src/internal/graph_utility.cpp | 2 +- modules/kernel/src/internal/input_output_exception.cpp | 2 +- modules/kernel/src/internal/key_helpers.cpp | 2 +- modules/kernel/src/internal/log_stream.cpp | 2 +- modules/kernel/src/internal/moved_particles_cache.cpp | 2 +- modules/kernel/src/internal/pdb.cpp | 2 +- modules/kernel/src/internal/random_number_generation_cuda.cu | 2 +- modules/kernel/src/internal/restraint_evaluation.cpp | 2 +- modules/kernel/src/internal/static.cpp | 2 +- modules/kernel/src/internal/swig.cpp | 2 +- modules/kernel/src/internal/swig_base.cpp | 2 +- modules/kernel/src/internal/utility.cpp | 2 +- modules/kernel/src/io.cpp | 2 +- modules/kernel/src/log.cpp | 2 +- modules/kernel/src/model_object_helpers.cpp | 2 +- modules/kernel/src/nullptr.cpp | 2 +- modules/kernel/src/particle_index.cpp | 2 +- modules/kernel/src/random.cpp | 2 +- modules/kernel/src/threads.cpp | 2 +- modules/kernel/src/utility.cpp | 2 +- modules/kernel/test/test_cache.cpp | 2 +- modules/kernel/test/test_get_has_attribute.cpp | 2 +- modules/kernel/test/test_memory.cpp | 2 +- modules/kernel/test/test_pair_memoizer.cpp | 2 +- modules/kernel/test/test_pdb.cpp | 2 +- modules/kernel/test/test_protection.cpp | 2 +- modules/kernel/test/test_set_internal_coordinates.cpp | 2 +- modules/kernel/test/test_show.cpp | 2 +- modules/kernel/test/test_stream_io.cpp | 2 +- modules/kinematics/bin/rrt_ccd.cpp | 2 +- modules/kinematics/bin/rrt_sample.cpp | 2 +- modules/kinematics/include/CCDLoopClosure.h | 2 +- modules/kinematics/include/CompositeJoint.h | 2 +- modules/kinematics/include/DOF.h | 2 +- modules/kinematics/include/DOFValues.h | 2 +- modules/kinematics/include/DOFsSampler.h | 2 +- modules/kinematics/include/Joint.h | 2 +- modules/kinematics/include/KinematicForest.h | 2 +- modules/kinematics/include/KinematicForestScoreState.h | 2 +- modules/kinematics/include/KinematicNode.h | 2 +- modules/kinematics/include/PrismaticJoint.h | 2 +- modules/kinematics/include/ProteinKinematics.h | 2 +- modules/kinematics/include/RMSDClustering.h | 2 +- modules/kinematics/include/RRT.h | 2 +- modules/kinematics/include/RevoluteJointMover.h | 2 +- modules/kinematics/include/TransformationJoint.h | 2 +- modules/kinematics/include/UniformBackboneSampler.h | 2 +- modules/kinematics/include/directional_DOFs.h | 2 +- modules/kinematics/include/helpers.h | 2 +- modules/kinematics/include/internal/graph_helpers.h | 2 +- modules/kinematics/include/local_planners.h | 2 +- modules/kinematics/include/revolute_joints.h | 2 +- modules/kinematics/src/CCDLoopClosure.cpp | 2 +- modules/kinematics/src/CompositeJoint.cpp | 2 +- modules/kinematics/src/DOF.cpp | 2 +- modules/kinematics/src/Joint.cpp | 2 +- modules/kinematics/src/KinematicForest.cpp | 2 +- modules/kinematics/src/KinematicForestScoreState.cpp | 2 +- modules/kinematics/src/KinematicNode.cpp | 2 +- modules/kinematics/src/PrismaticJoint.cpp | 2 +- modules/kinematics/src/ProteinKinematics.cpp | 2 +- modules/kinematics/src/RMSDClustering.cpp | 2 +- modules/kinematics/src/RRT.cpp | 2 +- modules/kinematics/src/RevoluteJointMover.cpp | 2 +- modules/kinematics/src/TransformationJoint.cpp | 2 +- modules/kinematics/src/UniformBackboneSampler.cpp | 2 +- modules/kinematics/src/helpers.cpp | 2 +- modules/kinematics/src/local_planners.cpp | 2 +- modules/kinematics/src/revolute_joints.cpp | 2 +- modules/kmeans/include/KMeans.h | 2 +- modules/kmeans/src/KMeans.cpp | 2 +- modules/misc/include/CommonEndpointPairFilter.h | 2 +- modules/misc/include/CustomXYZR.h | 2 +- modules/misc/include/DecayPairContainerOptimizerState.h | 2 +- modules/misc/include/FreelyJointedChain.h | 2 +- modules/misc/include/LogPairScore.h | 2 +- modules/misc/include/LowestRefinedPairScore.h | 2 +- modules/misc/include/MetricClosePairsFinder.h | 2 +- modules/misc/include/SoftCylinderPairScore.h | 2 +- modules/misc/include/StateAdaptor.h | 2 +- modules/misc/include/WormLikeChain.h | 2 +- modules/misc/src/CommonEndpointPairFilter.cpp | 2 +- modules/misc/src/CustomXYZR.cpp | 2 +- modules/misc/src/DecayPairContainerOptimizerState.cpp | 2 +- modules/misc/src/LowestRefinedPairScore.cpp | 2 +- modules/misc/src/SoftCylinderPairScore.cpp | 2 +- modules/misc/src/StateAdaptor.cpp | 2 +- modules/misc/test/test_metric_close_pairs.cpp | 2 +- modules/mpi/include/ReplicaExchange.h | 2 +- modules/mpi/include/internal/mpi_helpers.h | 2 +- modules/mpi/src/ReplicaExchange.cpp | 2 +- modules/mpi/src/internal/mpi_helpers.cpp | 2 +- modules/mpi/utility/hello_world.cpp | 2 +- modules/multi_state/bin/multi_foxs.cpp | 4 ++-- modules/multi_state/include/EnsembleGenerator.h | 2 +- modules/multi_state/include/MultiStateModel.h | 2 +- modules/multi_state/include/MultiStateModelScore.h | 2 +- modules/multi_state/include/SAXSMultiStateModelScore.h | 2 +- modules/multi_state/include/stat_helpers.h | 2 +- modules/multi_state/src/EnsembleGenerator.cpp | 2 +- modules/multi_state/src/stat_helpers.cpp | 2 +- modules/multifit/benchmark/benchmark_excluded_volume.cpp | 2 +- modules/multifit/benchmark/benchmark_excluded_volume.h | 2 +- .../benchmark/benchmark_excluded_volume_close_pair.cpp | 2 +- .../multifit/benchmark/benchmark_excluded_volume_pairs.cpp | 2 +- modules/multifit/benchmark/benchmark_excluded_volume_wev3.cpp | 2 +- .../multifit/benchmark/benchmark_geometric_complementarity.py | 2 +- modules/multifit/include/AlignmentParams.h | 2 +- modules/multifit/include/ComplementarityRestraint.h | 2 +- modules/multifit/include/DataPointsAssignment.h | 2 +- modules/multifit/include/DensityDataPoints.h | 2 +- modules/multifit/include/FittingSolutionRecord.h | 2 +- modules/multifit/include/GeometricHash.h | 2 +- modules/multifit/include/RadiusOfGyrationRestraint.h | 2 +- modules/multifit/include/RigidLeavesRefiner.h | 2 +- modules/multifit/include/SettingsData.h | 2 +- modules/multifit/include/WeightedExcludedVolumeRestraint.h | 2 +- modules/multifit/include/anchor_graph.h | 2 +- modules/multifit/include/anchor_utilities.h | 2 +- modules/multifit/include/anchors_reader.h | 2 +- modules/multifit/include/coarse_molecule.h | 2 +- modules/multifit/include/connolly_surface.h | 2 +- modules/multifit/include/density_analysis.h | 2 +- modules/multifit/include/ensemble_analysis.h | 2 +- modules/multifit/include/fft_based_rigid_fitting.h | 2 +- modules/multifit/include/fitting_solutions_reader_writer.h | 2 +- modules/multifit/include/fitting_states.h | 2 +- modules/multifit/include/fitting_tools.h | 2 +- modules/multifit/include/fitting_utils.h | 2 +- modules/multifit/include/internal/FFTWGrid.h | 2 +- modules/multifit/include/internal/FFTWPlan.h | 2 +- modules/multifit/include/internal/GeometricComplementarity.h | 2 +- modules/multifit/include/internal/SurfaceMatching.h | 2 +- modules/multifit/include/internal/fft_fitting_utils.h | 2 +- modules/multifit/include/internal/reader_writer_utility.h | 2 +- modules/multifit/include/merge_tree_utils.h | 2 +- modules/multifit/include/path_reader_writer.h | 2 +- modules/multifit/include/pca_based_rigid_fitting.h | 2 +- modules/multifit/include/protein_anchors_mapping_reader.h | 2 +- modules/multifit/include/proteomics_em_alignment_atomic.h | 2 +- modules/multifit/include/proteomics_reader.h | 2 +- modules/multifit/include/weighted_excluded_volume.h | 2 +- modules/multifit/src/AlignmentParams.cpp | 2 +- modules/multifit/src/ComplementarityRestraint.cpp | 2 +- modules/multifit/src/DataPointsAssignment.cpp | 2 +- modules/multifit/src/DensityDataPoints.cpp | 2 +- modules/multifit/src/FittingSolutionRecord.cpp | 2 +- modules/multifit/src/RadiusOfGyrationRestraint.cpp | 2 +- modules/multifit/src/RigidLeavesRefiner.cpp | 2 +- modules/multifit/src/SettingsData.cpp | 2 +- modules/multifit/src/WeightedExcludedVolumeRestraint.cpp | 2 +- modules/multifit/src/anchor_graph.cpp | 2 +- modules/multifit/src/anchor_utilities.cpp | 2 +- modules/multifit/src/anchors_reader.cpp | 2 +- modules/multifit/src/coarse_molecule.cpp | 2 +- modules/multifit/src/connolly_surface.cpp | 2 +- modules/multifit/src/density_analysis.cpp | 2 +- modules/multifit/src/ensemble_analysis.cpp | 2 +- modules/multifit/src/fft_based_rigid_fitting.cpp | 2 +- modules/multifit/src/fitting_solutions_reader_writer.cpp | 2 +- modules/multifit/src/fitting_states.cpp | 2 +- modules/multifit/src/fitting_tools.cpp | 2 +- modules/multifit/src/fitting_utils.cpp | 2 +- modules/multifit/src/internal/FFTWPlan.cpp | 2 +- modules/multifit/src/internal/GeometricComplementarity.cpp | 2 +- modules/multifit/src/internal/SurfaceMatching.cpp | 2 +- modules/multifit/src/internal/fft_fitting_utils.cpp | 2 +- modules/multifit/src/merge_tree_utils.cpp | 2 +- modules/multifit/src/path_reader_writer.cpp | 2 +- modules/multifit/src/pca_based_rigid_fitting.cpp | 2 +- modules/multifit/src/protein_anchors_mapping_reader.cpp | 2 +- modules/multifit/src/proteomics_em_alignment_atomic.cpp | 2 +- modules/multifit/src/proteomics_reader.cpp | 2 +- modules/multifit/src/weighted_excluded_volume.cpp | 2 +- modules/multifit/test/medium_test_match_transformations.cpp | 2 +- modules/multifit/test/test_geometric_complementarity.cpp | 2 +- modules/multifit/test/test_geometric_hash.cpp | 2 +- modules/multifit/utility/atoms2anchors.cpp | 2 +- modules/multifit/utility/single_prot_fft_fit.cpp | 2 +- modules/multifit/utility/single_prot_pca_fit.cpp | 2 +- modules/npc/include/CompositeRestraint.h | 2 +- modules/npc/include/MinimumSphereDistancePairScore.h | 2 +- modules/npc/include/ProteinLocalizationRestraint.h | 2 +- modules/npc/src/CompositeRestraint.cpp | 2 +- modules/npc/src/MinimumSphereDistancePairScore.cpp | 2 +- modules/npc/src/ProteinLocalizationRestraint.cpp | 2 +- modules/rmf/benchmark/benchmark_brownian.cpp | 2 +- modules/rmf/benchmark/benchmark_load.cpp | 2 +- modules/rmf/benchmark/benchmark_save.cpp | 2 +- modules/rmf/bin/pdb_rmf.cpp | 2 +- modules/rmf/bin/rmf_display.cpp | 2 +- modules/rmf/bin/rmf_simplify.cpp | 2 +- modules/rmf/include/HierarchyLoadLink.h | 2 +- modules/rmf/include/HierarchySaveLink.h | 2 +- modules/rmf/include/RMFWriter.h | 2 +- modules/rmf/include/SaveOptimizerState.h | 2 +- modules/rmf/include/associations.h | 2 +- modules/rmf/include/atom_io.h | 2 +- modules/rmf/include/atom_links.h | 2 +- modules/rmf/include/frames.h | 2 +- modules/rmf/include/geometry_io.h | 2 +- modules/rmf/include/internal/atom_links_coordinate_helpers.h | 2 +- modules/rmf/include/internal/atom_links_gaussians.h | 2 +- modules/rmf/include/internal/atom_links_rigid_bodies.h | 2 +- modules/rmf/include/internal/atom_links_static.h | 2 +- modules/rmf/include/internal/atom_links_xyzs.h | 2 +- modules/rmf/include/internal/hierarchy_links_helpers.h | 2 +- modules/rmf/include/internal/link_helpers.h | 2 +- modules/rmf/include/link_macros.h | 2 +- modules/rmf/include/links.h | 2 +- modules/rmf/include/particle_io.h | 2 +- modules/rmf/include/restraint_io.h | 2 +- modules/rmf/include/simple_links.h | 2 +- modules/rmf/src/HierarchyLoadLink.cpp | 2 +- modules/rmf/src/HierarchySaveLink.cpp | 2 +- modules/rmf/src/RMFWriter.cpp | 2 +- modules/rmf/src/SaveOptimizerState.cpp | 2 +- modules/rmf/src/associations.cpp | 2 +- modules/rmf/src/atom_io.cpp | 2 +- modules/rmf/src/frames.cpp | 2 +- modules/rmf/src/geometry_io.cpp | 2 +- modules/rmf/src/internal/atom_links_gaussians.cpp | 2 +- modules/rmf/src/internal/atom_links_rigid_bodies.cpp | 2 +- modules/rmf/src/internal/atom_links_static.cpp | 2 +- modules/rmf/src/internal/atom_links_xyzs.cpp | 2 +- modules/rmf/src/internal/hierarchy_links_helpers.cpp | 2 +- modules/rmf/src/internal/link_helpers.cpp | 2 +- modules/rmf/src/links.cpp | 2 +- modules/rmf/src/particle_io.cpp | 2 +- modules/rmf/src/restraint_io.cpp | 2 +- modules/rmf/test/test_errors.cpp | 2 +- modules/rotamer/include/RotamerCalculator.h | 2 +- modules/rotamer/include/RotamerLibrary.h | 2 +- modules/rotamer/src/RotamerCalculator.cpp | 2 +- modules/rotamer/src/RotamerLibrary.cpp | 2 +- modules/saxs/include/ChiFreeScore.h | 2 +- modules/saxs/include/ChiScore.h | 2 +- modules/saxs/include/ChiScoreLog.h | 2 +- modules/saxs/include/DerivativeCalculator.h | 2 +- modules/saxs/include/Distribution.h | 2 +- modules/saxs/include/FitParameters.h | 2 +- modules/saxs/include/FormFactorTable.h | 2 +- modules/saxs/include/Profile.h | 2 +- modules/saxs/include/ProfileClustering.h | 2 +- modules/saxs/include/ProfileFitter.h | 2 +- modules/saxs/include/RadiusOfGyrationRestraint.h | 2 +- modules/saxs/include/RatioVolatilityScore.h | 2 +- modules/saxs/include/Restraint.h | 2 +- modules/saxs/include/RigidBodiesProfileHandler.h | 2 +- modules/saxs/include/SolventAccessibleSurface.h | 2 +- modules/saxs/include/WeightedFitParameters.h | 2 +- modules/saxs/include/WeightedProfileFitter.h | 2 +- modules/saxs/include/internal/exp_function.h | 2 +- modules/saxs/include/internal/sinc_function.h | 2 +- modules/saxs/include/internal/variance_helpers.h | 2 +- modules/saxs/include/nnls.h | 2 +- modules/saxs/include/utility.h | 2 +- modules/saxs/src/ChiFreeScore.cpp | 2 +- modules/saxs/src/ChiScore.cpp | 2 +- modules/saxs/src/ChiScoreLog.cpp | 2 +- modules/saxs/src/DerivativeCalculator.cpp | 2 +- modules/saxs/src/Distribution.cpp | 2 +- modules/saxs/src/FormFactorTable.cpp | 2 +- modules/saxs/src/Profile.cpp | 2 +- modules/saxs/src/ProfileClustering.cpp | 2 +- modules/saxs/src/RadiusOfGyrationRestraint.cpp | 2 +- modules/saxs/src/RatioVolatilityScore.cpp | 2 +- modules/saxs/src/Restraint.cpp | 2 +- modules/saxs/src/RigidBodiesProfileHandler.cpp | 2 +- modules/saxs/src/SolventAccessibleSurface.cpp | 2 +- modules/saxs/src/utility.cpp | 2 +- modules/score_functor/include/AddScores.h | 2 +- modules/score_functor/include/DistancePairScore.h | 2 +- modules/score_functor/include/DistancePairScoreWithCache.h | 2 +- modules/score_functor/include/Dope.h | 2 +- modules/score_functor/include/Harmonic.h | 2 +- modules/score_functor/include/HarmonicLowerBound.h | 2 +- modules/score_functor/include/HarmonicUpperBound.h | 2 +- modules/score_functor/include/LinearLowerBound.h | 2 +- modules/score_functor/include/LoopStatistical.h | 2 +- modules/score_functor/include/OpenCubicSpline.h | 2 +- modules/score_functor/include/OrientedSoap.h | 2 +- modules/score_functor/include/PointToSphereDistance.h | 2 +- modules/score_functor/include/Score.h | 2 +- modules/score_functor/include/ScoreUnaryFunction.h | 2 +- modules/score_functor/include/ScoreWithCache.h | 2 +- modules/score_functor/include/Shift.h | 2 +- modules/score_functor/include/SingletonStatistical.h | 2 +- modules/score_functor/include/Soap.h | 2 +- modules/score_functor/include/SphereDistance.h | 2 +- modules/score_functor/include/Statistical.h | 2 +- modules/score_functor/include/SurfaceDistancePairScore.h | 2 +- modules/score_functor/include/UnaryFunctionEvaluate.h | 2 +- modules/score_functor/include/WeightScore.h | 2 +- modules/score_functor/include/distance_pair_score_macros.h | 2 +- modules/score_functor/include/internal/PMFTable.h | 2 +- modules/score_functor/include/internal/RawOpenCubicSpline.h | 2 +- modules/score_functor/include/internal/SASTable.h | 2 +- modules/score_functor/include/internal/direction_helpers.h | 2 +- modules/score_functor/include/internal/soap_hdf5.h | 2 +- modules/score_functor/include/internal/soap_helpers.h | 2 +- modules/score_functor/include/internal/surface_helpers.h | 2 +- .../include/surface_distance_pair_score_macros.h | 2 +- modules/score_functor/src/Dope.cpp | 2 +- modules/score_functor/src/LoopStatistical.cpp | 2 +- modules/score_functor/src/internal/RawOpenCubicSpline.cpp | 2 +- modules/score_functor/src/internal/direction_helpers.cpp | 2 +- modules/score_functor/src/internal/soap_hdf5.cpp | 2 +- modules/score_functor/src/internal/soap_helpers.cpp | 2 +- modules/score_functor/src/internal/surface_helpers.cpp | 2 +- .../score_functor/test/test_functor_distance_pair_scores.cpp | 2 +- modules/spb/bin/spb.cpp | 2 +- modules/spb/bin/spb_analysis.cpp | 2 +- modules/spb/bin/spb_cluster.cpp | 2 +- modules/spb/bin/spb_density_perbead.cpp | 2 +- modules/spb/include/AttributeDistancePairScore.h | 2 +- modules/spb/include/BoxedMover.h | 2 +- modules/spb/include/CellMover.h | 2 +- modules/spb/include/ChiSquareMetric.h | 2 +- modules/spb/include/ContactMapMetric.h | 2 +- modules/spb/include/DiameterRgyrRestraint.h | 2 +- modules/spb/include/DistanceRMSDMetric.h | 2 +- modules/spb/include/DistanceTerminiRestraint.h | 2 +- modules/spb/include/EM2DRestraint.h | 2 +- modules/spb/include/Gaussian.h | 2 +- modules/spb/include/HelixDecorator.h | 2 +- modules/spb/include/ISDRestraint.h | 2 +- modules/spb/include/KinkPairScore.h | 2 +- modules/spb/include/MolecularDynamicsWithWte.h | 2 +- modules/spb/include/MonteCarloWithWte.h | 2 +- modules/spb/include/NuisanceRangeModifier.h | 2 +- modules/spb/include/PbcBoxedMover.h | 2 +- modules/spb/include/PbcBoxedRigidBodyMover.h | 2 +- modules/spb/include/RMSDMetric.h | 2 +- modules/spb/include/RigidBodyNewMover.h | 2 +- modules/spb/include/RigidBodyPackingScore.h | 2 +- modules/spb/include/SameParticlePairFilter.h | 2 +- modules/spb/include/SameRigidBodyPairFilter.h | 2 +- modules/spb/include/TiltSingletonScore.h | 2 +- modules/spb/include/TransformationSymmetry.h | 2 +- modules/spb/include/TwoStateGoModelRestraint.h | 2 +- modules/spb/include/UniformBoundedRestraint.h | 2 +- modules/spb/include/pt_stuff.h | 2 +- modules/spb/include/spb_ISD_particles.h | 2 +- modules/spb/include/spb_assemble_restraints.h | 2 +- modules/spb/include/spb_main.h | 2 +- modules/spb/include/spb_parser.h | 2 +- modules/spb/include/spb_representation.h | 2 +- modules/spb/include/spb_restraint.h | 2 +- modules/spb/include/spb_sampler.h | 2 +- modules/spb/src/AttributeDistancePairScore.cpp | 2 +- modules/spb/src/BoxedMover.cpp | 2 +- modules/spb/src/CellMover.cpp | 2 +- modules/spb/src/ChiSquareMetric.cpp | 2 +- modules/spb/src/ContactMapMetric.cpp | 2 +- modules/spb/src/DiameterRgyrRestraint.cpp | 2 +- modules/spb/src/DistanceRMSDMetric.cpp | 2 +- modules/spb/src/DistanceTerminiRestraint.cpp | 2 +- modules/spb/src/EM2DRestraint.cpp | 2 +- modules/spb/src/HelixDecorator.cpp | 2 +- modules/spb/src/KinkPairScore.cpp | 2 +- modules/spb/src/MolecularDynamicsWithWte.cpp | 2 +- modules/spb/src/MonteCarloWithWte.cpp | 2 +- modules/spb/src/NuisanceRangeModifier.cpp | 2 +- modules/spb/src/PbcBoxedMover.cpp | 2 +- modules/spb/src/PbcBoxedRigidBodyMover.cpp | 2 +- modules/spb/src/RMSDMetric.cpp | 2 +- modules/spb/src/RigidBodyNewMover.cpp | 2 +- modules/spb/src/RigidBodyPackingScore.cpp | 2 +- modules/spb/src/SameParticlePairFilter.cpp | 2 +- modules/spb/src/SameRigidBodyPairFilter.cpp | 2 +- modules/spb/src/TiltSingletonScore.cpp | 2 +- modules/spb/src/TransformationSymmetry.cpp | 2 +- modules/spb/src/TwoStateGoModelRestraint.cpp | 2 +- modules/spb/src/UniformBoundedRestraint.cpp | 2 +- modules/spb/src/pt_stuff.cpp | 2 +- modules/spb/src/spb_ISD_particles.cpp | 2 +- modules/spb/src/spb_assemble_restraints.cpp | 2 +- modules/spb/src/spb_parser.cpp | 2 +- modules/spb/src/spb_representation.cpp | 2 +- modules/spb/src/spb_restraint.cpp | 2 +- modules/spb/src/spb_sampler.cpp | 2 +- modules/statistics/include/ChiSquareMetric.h | 2 +- modules/statistics/include/Embedding.h | 2 +- modules/statistics/include/HistogramD.h | 2 +- modules/statistics/include/Metric.h | 2 +- modules/statistics/include/PartitionalClustering.h | 2 +- modules/statistics/include/PartitionalClusteringWithCenter.h | 2 +- .../include/RecursivePartitionalClusteringEmbedding.h | 2 +- .../statistics/include/RecursivePartitionalClusteringMetric.h | 2 +- modules/statistics/include/embeddings.h | 2 +- modules/statistics/include/internal/ClusteringEngine.h | 2 +- modules/statistics/include/internal/DataPoints.h | 2 +- modules/statistics/include/internal/KMCenters.h | 2 +- modules/statistics/include/internal/KMCentersNode.h | 2 +- modules/statistics/include/internal/KMCentersNodeLeaf.h | 2 +- modules/statistics/include/internal/KMCentersNodeSplit.h | 2 +- modules/statistics/include/internal/KMCentersTree.h | 2 +- modules/statistics/include/internal/KMData.h | 2 +- modules/statistics/include/internal/KMFilterCenters.h | 2 +- modules/statistics/include/internal/KMLProxy.h | 2 +- modules/statistics/include/internal/KMLocalSearch.h | 2 +- modules/statistics/include/internal/KMLocalSearchLloyd.h | 2 +- modules/statistics/include/internal/KMRectangle.h | 2 +- modules/statistics/include/internal/KMTerminationCondition.h | 2 +- .../include/internal/TrivialPartitionalClustering.h | 2 +- modules/statistics/include/internal/VQClustering.h | 2 +- modules/statistics/include/internal/centrality_clustering.h | 2 +- modules/statistics/include/internal/histogram.h | 2 +- modules/statistics/include/internal/random_generator.h | 2 +- modules/statistics/include/metric_clustering.h | 2 +- modules/statistics/include/metrics.h | 2 +- modules/statistics/include/point_clustering.h | 2 +- modules/statistics/include/python_only.h | 2 +- modules/statistics/include/utility.h | 2 +- modules/statistics/src/ChiSquareMetric.cpp | 2 +- modules/statistics/src/Embedding.cpp | 2 +- modules/statistics/src/HistogramD.cpp | 2 +- modules/statistics/src/Metric.cpp | 2 +- modules/statistics/src/PartitionalClustering.cpp | 2 +- modules/statistics/src/PartitionalClusteringWithCenter.cpp | 2 +- .../src/RecursivePartitionalClusteringEmbedding.cpp | 2 +- .../statistics/src/RecursivePartitionalClusteringMetric.cpp | 2 +- modules/statistics/src/embeddings.cpp | 2 +- modules/statistics/src/internal/DataPoints.cpp | 2 +- modules/statistics/src/internal/KMCenters.cpp | 2 +- modules/statistics/src/internal/KMCentersNode.cpp | 2 +- modules/statistics/src/internal/KMCentersNodeLeaf.cpp | 2 +- modules/statistics/src/internal/KMCentersNodeSplit.cpp | 2 +- modules/statistics/src/internal/KMCentersTree.cpp | 2 +- modules/statistics/src/internal/KMData.cpp | 2 +- modules/statistics/src/internal/KMFilterCenters.cpp | 2 +- modules/statistics/src/internal/KMLProxy.cpp | 2 +- modules/statistics/src/internal/KMLocalSearch.cpp | 2 +- modules/statistics/src/internal/KMLocalSearchLloyd.cpp | 2 +- modules/statistics/src/internal/KMRectangle.cpp | 2 +- modules/statistics/src/internal/VQClustering.cpp | 2 +- modules/statistics/src/internal/centrality_clustering.cpp | 2 +- modules/statistics/src/metric_clustering.cpp | 2 +- modules/statistics/src/metrics.cpp | 2 +- modules/statistics/src/point_clustering.cpp | 2 +- modules/statistics/src/utility.cpp | 2 +- modules/statistics/test/test_histograph_1d.cpp | 2 +- modules/symmetry/include/BallMover.h | 2 +- modules/symmetry/include/RigidBodyMover.h | 2 +- modules/symmetry/src/BallMover.cpp | 2 +- modules/symmetry/src/RigidBodyMover.cpp | 2 +- modules/test/include/test_macros.h | 2 +- tools/build/config_templates/header.h | 2 +- tools/build/config_templates/src.cpp | 2 +- .../container_templates/container/ClassnameContainerSet.h | 2 +- .../container/ClassnameContainerStatistics.h | 2 +- .../container_templates/container/ClassnamesConstraint.h | 2 +- .../container_templates/container/ClassnamesOptimizerState.h | 2 +- .../build/container_templates/container/ClassnamesRestraint.h | 2 +- .../container/DistributeClassnamesScoreState.h | 2 +- .../container/DynamicListClassnameContainer.h | 2 +- .../container/EventClassnamesOptimizerState.h | 2 +- .../container/InContainerClassnameFilter.h | 2 +- .../container_templates/container/ListClassnameContainer.h | 2 +- .../container_templates/container/MinimumClassnameRestraint.h | 2 +- .../container_templates/container/MinimumClassnameScore.h | 2 +- .../container/PredicateClassnamesRestraint.h | 2 +- tools/build/container_templates/container/classnames.cpp | 2 +- .../container/internal/ClassnameContainerIndex.h | 2 +- tools/build/container_templates/core/ClassnameConstraint.h | 2 +- tools/build/container_templates/core/ClassnameRestraint.h | 2 +- tools/build/container_templates/core/classname_predicates.cpp | 2 +- tools/build/container_templates/core/classname_predicates.h | 2 +- tools/build/container_templates/kernel/ClassnameContainer.h | 2 +- .../container_templates/kernel/ClassnameDerivativeModifier.h | 2 +- tools/build/container_templates/kernel/ClassnameModifier.h | 2 +- tools/build/container_templates/kernel/ClassnamePredicate.h | 2 +- tools/build/container_templates/kernel/ClassnameScore.h | 2 +- tools/build/container_templates/kernel/classname_macros.h | 2 +- tools/build/container_templates/kernel/classnames.cpp | 2 +- tools/build/make_swig_wrapper.py | 2 +- tools/debian/copyright | 2 +- tools/nightly-tests/test-install/test.cpp | 2 +- tools/nightly-tests/test-install/test_rmf.cpp | 2 +- tools/w32/pyapp_wrapper.c | 2 +- 1583 files changed, 1585 insertions(+), 1585 deletions(-) diff --git a/README.md b/README.md index 3e06c3a28b..241c1920ca 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ new shell. Copyright and License information ================================= -IMP is Copyright 2007-2021 IMP Inventors. The IMP Inventors are +IMP is Copyright 2007-2022 IMP Inventors. The IMP Inventors are Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman, Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan, Seung Joong Kim, Yannick Spill, Riccardo Pellarin. diff --git a/doc/manual/licenses.md b/doc/manual/licenses.md index d4d39229de..07bc0d8eec 100644 --- a/doc/manual/licenses.md +++ b/doc/manual/licenses.md @@ -1,7 +1,7 @@ Copyright and licenses {#licenses} ====================== -%IMP is Copyright 2007-2021 %IMP Inventors. The %IMP Inventors are +%IMP is Copyright 2007-2022 %IMP Inventors. The %IMP Inventors are Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman, Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan, Seung Joong Kim, Yannick Spill, Riccardo Pellarin. diff --git a/modules/algebra/benchmark/benchmark_grid_traversal.cpp b/modules/algebra/benchmark/benchmark_grid_traversal.cpp index 0ca4ae4989..41afbbe1d5 100644 --- a/modules/algebra/benchmark/benchmark_grid_traversal.cpp +++ b/modules/algebra/benchmark/benchmark_grid_traversal.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/algebra/benchmark/benchmark_knn.cpp b/modules/algebra/benchmark/benchmark_knn.cpp index f45956d6cc..f713023569 100644 --- a/modules/algebra/benchmark/benchmark_knn.cpp +++ b/modules/algebra/benchmark/benchmark_knn.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/algebra/benchmark/benchmark_rotate.cpp b/modules/algebra/benchmark/benchmark_rotate.cpp index 53020e2874..722f3e37cc 100644 --- a/modules/algebra/benchmark/benchmark_rotate.cpp +++ b/modules/algebra/benchmark/benchmark_rotate.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/algebra/benchmark/benchmark_surface.cpp b/modules/algebra/benchmark/benchmark_surface.cpp index 7185b36d8e..3d7ebaec44 100644 --- a/modules/algebra/benchmark/benchmark_surface.cpp +++ b/modules/algebra/benchmark/benchmark_surface.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/algebra/examples/grid.cpp b/modules/algebra/examples/grid.cpp index 270e8294d6..65fd1b8aa2 100644 --- a/modules/algebra/examples/grid.cpp +++ b/modules/algebra/examples/grid.cpp @@ -2,7 +2,7 @@ * \example grid.cpp * \brief Show some of the basics of using a grid from C++. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/algebra/include/BoundingBoxD.h b/modules/algebra/include/BoundingBoxD.h index 54b3aad871..5d6deb055c 100644 --- a/modules/algebra/include/BoundingBoxD.h +++ b/modules/algebra/include/BoundingBoxD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/BoundingBoxD.h \brief A bounding box in D dimensions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Cone3D.h b/modules/algebra/include/Cone3D.h index 8a6f41711e..5b46a7b0e1 100644 --- a/modules/algebra/include/Cone3D.h +++ b/modules/algebra/include/Cone3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Cone3D.h * \brief Represent a cone in 3D. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_CONE_3D_H diff --git a/modules/algebra/include/Cylinder3D.h b/modules/algebra/include/Cylinder3D.h index c6d3f49ba2..ce48235a8e 100644 --- a/modules/algebra/include/Cylinder3D.h +++ b/modules/algebra/include/Cylinder3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Cylinder3D.h * \brief Represent a cylinder in 3D. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_CYLINDER_3D_H diff --git a/modules/algebra/include/Ellipsoid3D.h b/modules/algebra/include/Ellipsoid3D.h index fdecfd5056..c0d31b03d8 100644 --- a/modules/algebra/include/Ellipsoid3D.h +++ b/modules/algebra/include/Ellipsoid3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Ellipsoid3D.h \brief Simple 3D ellipsoid class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Gaussian3D.h b/modules/algebra/include/Gaussian3D.h index 460f283c88..7af197ad28 100644 --- a/modules/algebra/include/Gaussian3D.h +++ b/modules/algebra/include/Gaussian3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Gaussian3D.h * \brief Gaussian shape * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/GeometricPrimitiveD.h b/modules/algebra/include/GeometricPrimitiveD.h index 1fb9b4529c..198bd6789a 100644 --- a/modules/algebra/include/GeometricPrimitiveD.h +++ b/modules/algebra/include/GeometricPrimitiveD.h @@ -2,7 +2,7 @@ * \file IMP/algebra/GeometricPrimitiveD.h * \brief Base class for geometric types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/GridD.h b/modules/algebra/include/GridD.h index 73a605b0d5..a847671319 100644 --- a/modules/algebra/include/GridD.h +++ b/modules/algebra/include/GridD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/GridD.h \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Line3D.h b/modules/algebra/include/Line3D.h index 9719830ffd..f7acdd09b6 100644 --- a/modules/algebra/include/Line3D.h +++ b/modules/algebra/include/Line3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Line3D.h * \brief Simple implementation of lines in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_LINE_3D_H diff --git a/modules/algebra/include/LinearFit.h b/modules/algebra/include/LinearFit.h index 53d46f3b23..f81d52d09c 100644 --- a/modules/algebra/include/LinearFit.h +++ b/modules/algebra/include/LinearFit.h @@ -2,7 +2,7 @@ * \file IMP/algebra/LinearFit.h * \brief Linear fit of data points * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/ParabolicFit.h b/modules/algebra/include/ParabolicFit.h index 187cf709f4..1fb266e829 100644 --- a/modules/algebra/include/ParabolicFit.h +++ b/modules/algebra/include/ParabolicFit.h @@ -2,7 +2,7 @@ * \file IMP/algebra/ParabolicFit.h * \brief Fit data with parabola * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Plane3D.h b/modules/algebra/include/Plane3D.h index c5d1a764cc..9ad3425ece 100644 --- a/modules/algebra/include/Plane3D.h +++ b/modules/algebra/include/Plane3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Plane3D.h \brief Simple 3D plane class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/ReferenceFrame3D.h b/modules/algebra/include/ReferenceFrame3D.h index 9125b35a3a..d21088f04b 100644 --- a/modules/algebra/include/ReferenceFrame3D.h +++ b/modules/algebra/include/ReferenceFrame3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/ReferenceFrame3D.h * \brief A reference frame in 3D. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Reflection3D.h b/modules/algebra/include/Reflection3D.h index 3de3b52c53..e49f4efd75 100644 --- a/modules/algebra/include/Reflection3D.h +++ b/modules/algebra/include/Reflection3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Reflection3D.h \brief Reflect about a plane in 3D. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Rotation2D.h b/modules/algebra/include/Rotation2D.h index 010d73ef0d..91c52a1c42 100644 --- a/modules/algebra/include/Rotation2D.h +++ b/modules/algebra/include/Rotation2D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Rotation2D.h * \brief Represent a rotation in 2D space. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_ROTATION_2D_H diff --git a/modules/algebra/include/Rotation3D.h b/modules/algebra/include/Rotation3D.h index 819e62ae2d..03346ab828 100644 --- a/modules/algebra/include/Rotation3D.h +++ b/modules/algebra/include/Rotation3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Rotation3D.h \brief Simple 3D rotation class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Segment3D.h b/modules/algebra/include/Segment3D.h index 554e763200..0a55952745 100644 --- a/modules/algebra/include/Segment3D.h +++ b/modules/algebra/include/Segment3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Segment3D.h * \brief Simple implementation of segments in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_SEGMENT_3D_H diff --git a/modules/algebra/include/Sphere3D.h b/modules/algebra/include/Sphere3D.h index 2e889362d1..84eb4ba772 100644 --- a/modules/algebra/include/Sphere3D.h +++ b/modules/algebra/include/Sphere3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Sphere3D.h \brief Simple 3D sphere class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/SphereD.h b/modules/algebra/include/SphereD.h index 6581ae8b74..a1dd649d55 100644 --- a/modules/algebra/include/SphereD.h +++ b/modules/algebra/include/SphereD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/SphereD.h \brief Simple 3D sphere class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/SpherePatch3D.h b/modules/algebra/include/SpherePatch3D.h index d903c42a80..5a4bb46489 100644 --- a/modules/algebra/include/SpherePatch3D.h +++ b/modules/algebra/include/SpherePatch3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/SpherePatch3D.h \brief Simple 3D sphere patch class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/SphericalVector3D.h b/modules/algebra/include/SphericalVector3D.h index 030da0ee78..25e8983833 100644 --- a/modules/algebra/include/SphericalVector3D.h +++ b/modules/algebra/include/SphericalVector3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/SphericalVector3D.h * \brief Stores and converts spherical coordinates * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_SPHERICAL_VECTOR_3D_H diff --git a/modules/algebra/include/Torus3D.h b/modules/algebra/include/Torus3D.h index 4aa7df3099..a03e1223af 100644 --- a/modules/algebra/include/Torus3D.h +++ b/modules/algebra/include/Torus3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Torus3D.h * \brief Represent a torus in 3D. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_TORUS_3D_H diff --git a/modules/algebra/include/Transformation2D.h b/modules/algebra/include/Transformation2D.h index 37d9359eab..f8f678134b 100644 --- a/modules/algebra/include/Transformation2D.h +++ b/modules/algebra/include/Transformation2D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Transformation2D.h * \brief 2D transformations. - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Transformation3D.h b/modules/algebra/include/Transformation3D.h index 3a3c072eb0..563fc72e0d 100644 --- a/modules/algebra/include/Transformation3D.h +++ b/modules/algebra/include/Transformation3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Transformation3D.h * \brief Simple 3D transformation class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Triangle3D.h b/modules/algebra/include/Triangle3D.h index 13f134fe96..95a7572492 100644 --- a/modules/algebra/include/Triangle3D.h +++ b/modules/algebra/include/Triangle3D.h @@ -2,7 +2,7 @@ * \file IMP/algebra/Triangle3D.h * \brief Represent a triangle in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_TRIANGLE_3D_H diff --git a/modules/algebra/include/UnitSimplexD.h b/modules/algebra/include/UnitSimplexD.h index 8305af9c25..fcdf0fadb8 100644 --- a/modules/algebra/include/UnitSimplexD.h +++ b/modules/algebra/include/UnitSimplexD.h @@ -2,7 +2,7 @@ * \file IMP/algebra/UnitSimplexD.h * \brief Simple unit simplex class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Vector2D.h b/modules/algebra/include/Vector2D.h index 4b1c2d70a6..8896349837 100644 --- a/modules/algebra/include/Vector2D.h +++ b/modules/algebra/include/Vector2D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Vector2D.h \brief Simple 2D vector class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/Vector3D.h b/modules/algebra/include/Vector3D.h index e553c16227..fc2280eb90 100644 --- a/modules/algebra/include/Vector3D.h +++ b/modules/algebra/include/Vector3D.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/Vector3D.h \brief Simple 3D vector class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/VectorBaseD.h b/modules/algebra/include/VectorBaseD.h index e11fdbe138..d0a11cfd00 100644 --- a/modules/algebra/include/VectorBaseD.h +++ b/modules/algebra/include/VectorBaseD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/VectorBaseD.h \brief Simple D vector class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/VectorD.h b/modules/algebra/include/VectorD.h index d3da42b3d0..7c0c1cada7 100644 --- a/modules/algebra/include/VectorD.h +++ b/modules/algebra/include/VectorD.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/VectorD.h \brief Simple D vector class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/algebra_macros.h b/modules/algebra/include/algebra_macros.h index 45c720d718..d284e394cc 100644 --- a/modules/algebra/include/algebra_macros.h +++ b/modules/algebra/include/algebra_macros.h @@ -2,7 +2,7 @@ * \file IMP/algebra/algebra_macros.h * \brief Various helper macros. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/connolly_surface.h b/modules/algebra/include/connolly_surface.h index 6f5ec84500..c9de23ed00 100644 --- a/modules/algebra/include/connolly_surface.h +++ b/modules/algebra/include/connolly_surface.h @@ -2,7 +2,7 @@ * \file IMP/algebra/connolly_surface.h * \brief Generate surface for a set of atoms. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/constants.h b/modules/algebra/include/constants.h index dbc5f65c55..4e5a41ca3e 100644 --- a/modules/algebra/include/constants.h +++ b/modules/algebra/include/constants.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/constants.h \brief Various useful constants. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/distance.h b/modules/algebra/include/distance.h index 6a0aa13c1a..72652e9561 100644 --- a/modules/algebra/include/distance.h +++ b/modules/algebra/include/distance.h @@ -2,7 +2,7 @@ * \file IMP/algebra/distance.h * \brief Distance metrics. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/eigen_analysis.h b/modules/algebra/include/eigen_analysis.h index dfd5242cda..70ad41c362 100644 --- a/modules/algebra/include/eigen_analysis.h +++ b/modules/algebra/include/eigen_analysis.h @@ -2,7 +2,7 @@ * \file IMP/algebra/eigen_analysis.h * \brief Principal component analysis of a set of points * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_EIGEN_ANALYSIS_H diff --git a/modules/algebra/include/endian.h b/modules/algebra/include/endian.h index c89e067598..fdad3fbe39 100644 --- a/modules/algebra/include/endian.h +++ b/modules/algebra/include/endian.h @@ -2,7 +2,7 @@ * \file IMP/algebra/endian.h * \brief Functions to deal with byte order. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_ENDIAN_H diff --git a/modules/algebra/include/geometric_alignment.h b/modules/algebra/include/geometric_alignment.h index 20b2d78ce0..333e61cb40 100644 --- a/modules/algebra/include/geometric_alignment.h +++ b/modules/algebra/include/geometric_alignment.h @@ -2,7 +2,7 @@ * \file IMP/algebra/geometric_alignment.h * \brief align sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_GEOMETRIC_ALIGNMENT_H diff --git a/modules/algebra/include/geometric_primitive_macros.h b/modules/algebra/include/geometric_primitive_macros.h index 299f64c442..90a17a1d4f 100644 --- a/modules/algebra/include/geometric_primitive_macros.h +++ b/modules/algebra/include/geometric_primitive_macros.h @@ -2,7 +2,7 @@ * \file IMP/algebra/geometric_primitive_macros.h * \brief Various important macros for implementing geometry. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/grid_embeddings.h b/modules/algebra/include/grid_embeddings.h index 41fc758707..f3094300f2 100644 --- a/modules/algebra/include/grid_embeddings.h +++ b/modules/algebra/include/grid_embeddings.h @@ -2,7 +2,7 @@ * \file IMP/algebra/grid_embeddings.h * \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/grid_indexes.h b/modules/algebra/include/grid_indexes.h index 163d6bb3d2..100a70bed0 100644 --- a/modules/algebra/include/grid_indexes.h +++ b/modules/algebra/include/grid_indexes.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/grid_indexes.h \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/grid_ranges.h b/modules/algebra/include/grid_ranges.h index 1eeb585baa..6f1fe135db 100644 --- a/modules/algebra/include/grid_ranges.h +++ b/modules/algebra/include/grid_ranges.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/grid_ranges.h \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/grid_storages.h b/modules/algebra/include/grid_storages.h index b90b3b469f..0fa1ccaee3 100644 --- a/modules/algebra/include/grid_storages.h +++ b/modules/algebra/include/grid_storages.h @@ -2,7 +2,7 @@ * \file IMP/algebra/grid_storages.h * \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/grid_utility.h b/modules/algebra/include/grid_utility.h index ea93119f7e..b253d2a33b 100644 --- a/modules/algebra/include/grid_utility.h +++ b/modules/algebra/include/grid_utility.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/grid_utility.h Utility functions for working with grids. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/internal/MinimalSet.h b/modules/algebra/include/internal/MinimalSet.h index 73b1ec3842..164dee19c6 100644 --- a/modules/algebra/include/internal/MinimalSet.h +++ b/modules/algebra/include/internal/MinimalSet.h @@ -1,7 +1,7 @@ /** * \file MinimalSet.h \brief Maintain a set of low scoring elements. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/internal/ann.h b/modules/algebra/include/internal/ann.h index 88dc1d21d7..3b33fd3263 100644 --- a/modules/algebra/include/internal/ann.h +++ b/modules/algebra/include/internal/ann.h @@ -1,7 +1,7 @@ /** * \file internal/ann.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_ANN_H diff --git a/modules/algebra/include/internal/grid_3d_impl.h b/modules/algebra/include/internal/grid_3d_impl.h index afa3caa7c0..36d867c26a 100644 --- a/modules/algebra/include/internal/grid_3d_impl.h +++ b/modules/algebra/include/internal/grid_3d_impl.h @@ -1,7 +1,7 @@ /** * \file grid_3d_impl.h \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/internal/grid_apply.h b/modules/algebra/include/internal/grid_apply.h index ef198b9203..df602b706c 100644 --- a/modules/algebra/include/internal/grid_apply.h +++ b/modules/algebra/include/internal/grid_apply.h @@ -1,7 +1,7 @@ /** * \file output_helpers.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_GRID_APPLY_H diff --git a/modules/algebra/include/internal/grid_internal.h b/modules/algebra/include/internal/grid_internal.h index cc622d5dcf..9ffe96ca88 100644 --- a/modules/algebra/include/internal/grid_internal.h +++ b/modules/algebra/include/internal/grid_internal.h @@ -1,7 +1,7 @@ /** * \file output_helpers.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_GRID_INTERNAL_H diff --git a/modules/algebra/include/internal/grid_interpolation.h b/modules/algebra/include/internal/grid_interpolation.h index 4e89d8db93..483dcc38d6 100644 --- a/modules/algebra/include/internal/grid_interpolation.h +++ b/modules/algebra/include/internal/grid_interpolation.h @@ -1,7 +1,7 @@ /** * \file output_helpers.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_GRID_INTERPOLATION_H diff --git a/modules/algebra/include/internal/grid_range_d.h b/modules/algebra/include/internal/grid_range_d.h index 7d948be813..885843c9ae 100644 --- a/modules/algebra/include/internal/grid_range_d.h +++ b/modules/algebra/include/internal/grid_range_d.h @@ -1,7 +1,7 @@ /** * \file grid_range_D.h \brief Simple D vector class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/internal/internal_vector_generators.h b/modules/algebra/include/internal/internal_vector_generators.h index 1e85c62a20..fea00dafea 100644 --- a/modules/algebra/include/internal/internal_vector_generators.h +++ b/modules/algebra/include/internal/internal_vector_generators.h @@ -1,7 +1,7 @@ /** * \file cgal_predicates.h * \brief predicates implemented using CGAL - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_VECTOR_GENERATORS_H diff --git a/modules/algebra/include/internal/linear_knn.h b/modules/algebra/include/internal/linear_knn.h index 42e33958fe..e43768691d 100644 --- a/modules/algebra/include/internal/linear_knn.h +++ b/modules/algebra/include/internal/linear_knn.h @@ -1,7 +1,7 @@ /** * \file internal/linear_knn.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_LINEAR_KNN_H diff --git a/modules/algebra/include/internal/multi_array_helpers.h b/modules/algebra/include/internal/multi_array_helpers.h index 571319c83a..0055a784cb 100644 --- a/modules/algebra/include/internal/multi_array_helpers.h +++ b/modules/algebra/include/internal/multi_array_helpers.h @@ -1,7 +1,7 @@ /** * \file multi_array_helpers.h \brief helpers for multi_array. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/internal/quaternion_derivatives.h b/modules/algebra/include/internal/quaternion_derivatives.h index b6df3518da..da5183d27a 100644 --- a/modules/algebra/include/internal/quaternion_derivatives.h +++ b/modules/algebra/include/internal/quaternion_derivatives.h @@ -1,7 +1,7 @@ /** * \file quaternion_derivatives.h * \brief Derivatives of quaternions - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_QUATERNION_DERIVATIVES_H diff --git a/modules/algebra/include/internal/swig.h b/modules/algebra/include/internal/swig.h index 367fe796e3..4b1b82cf39 100644 --- a/modules/algebra/include/internal/swig.h +++ b/modules/algebra/include/internal/swig.h @@ -1,7 +1,7 @@ /** * \file internal/ann.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_SWIG_H diff --git a/modules/algebra/include/internal/utility.h b/modules/algebra/include/internal/utility.h index 55c9877607..e799c7d7d5 100644 --- a/modules/algebra/include/internal/utility.h +++ b/modules/algebra/include/internal/utility.h @@ -1,7 +1,7 @@ /** * \file algebra/internal/utility.h * \brief Functions to deal with very common math operations - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_UTILITY_H diff --git a/modules/algebra/include/internal/vector.h b/modules/algebra/include/internal/vector.h index 81f84b4b91..7c53c9cc26 100644 --- a/modules/algebra/include/internal/vector.h +++ b/modules/algebra/include/internal/vector.h @@ -1,7 +1,7 @@ /** * \file cgal_predicates.h * \brief predicates implemented using CGAL - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_INTERNAL_VECTOR_H diff --git a/modules/algebra/include/io.h b/modules/algebra/include/io.h index 1f08def5db..5e9e9a78d0 100644 --- a/modules/algebra/include/io.h +++ b/modules/algebra/include/io.h @@ -2,7 +2,7 @@ * \file IMP/algebra/io.h * \brief Classes to write entities in algebra to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/python_only.h b/modules/algebra/include/python_only.h index f019a0468b..e71e7d312b 100644 --- a/modules/algebra/include/python_only.h +++ b/modules/algebra/include/python_only.h @@ -2,7 +2,7 @@ * \file IMP/algebra/python_only.h * \brief Functionality only available in Python. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/shortest_segment.h b/modules/algebra/include/shortest_segment.h index 83f80e5ac0..90c9d9bd43 100644 --- a/modules/algebra/include/shortest_segment.h +++ b/modules/algebra/include/shortest_segment.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/shortest_segment.h * \brief Get the shortest segment connecting two geometric objects. - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_SHORTEST_SEGMENT_H diff --git a/modules/algebra/include/standard_grids.h b/modules/algebra/include/standard_grids.h index b19556d114..db6f812dbb 100644 --- a/modules/algebra/include/standard_grids.h +++ b/modules/algebra/include/standard_grids.h @@ -2,7 +2,7 @@ * \file IMP/algebra/standard_grids.h * \brief All grids that are in the Python API should be defined here. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/utility.h b/modules/algebra/include/utility.h index 6ef10a426c..0ace221901 100644 --- a/modules/algebra/include/utility.h +++ b/modules/algebra/include/utility.h @@ -2,7 +2,7 @@ * \file IMP/algebra/utility.h * \brief Functions to deal with very common math operations * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPALGEBRA_UTILITY_H diff --git a/modules/algebra/include/vector_generators.h b/modules/algebra/include/vector_generators.h index 830616011c..6d83612cea 100644 --- a/modules/algebra/include/vector_generators.h +++ b/modules/algebra/include/vector_generators.h @@ -2,7 +2,7 @@ * \file IMP/algebra/vector_generators.h * \brief Functions to generate vectors. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/vector_metrics.h b/modules/algebra/include/vector_metrics.h index 0ff3439baa..5b22853bbb 100644 --- a/modules/algebra/include/vector_metrics.h +++ b/modules/algebra/include/vector_metrics.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/vector_metrics.h \brief Functions to generate vectors. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/include/vector_search.h b/modules/algebra/include/vector_search.h index a7d005bf6c..4950094cb5 100644 --- a/modules/algebra/include/vector_search.h +++ b/modules/algebra/include/vector_search.h @@ -1,7 +1,7 @@ /** * \file IMP/algebra/vector_search.h \brief Functions to search over vectors. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/Cone3D.cpp b/modules/algebra/src/Cone3D.cpp index 764cb54348..142b9ba03a 100644 --- a/modules/algebra/src/Cone3D.cpp +++ b/modules/algebra/src/Cone3D.cpp @@ -2,7 +2,7 @@ * \file Cone3D.cpp * \brief simple implementation of cones in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include IMPALGEBRA_BEGIN_NAMESPACE diff --git a/modules/algebra/src/Cylinder3D.cpp b/modules/algebra/src/Cylinder3D.cpp index 0992402753..48f88c60d4 100644 --- a/modules/algebra/src/Cylinder3D.cpp +++ b/modules/algebra/src/Cylinder3D.cpp @@ -2,7 +2,7 @@ * \file Cylinder3D.cpp * \brief stores a cylinder * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/algebra/src/Ellipsoid3D.cpp b/modules/algebra/src/Ellipsoid3D.cpp index afa24980bf..37e340915b 100644 --- a/modules/algebra/src/Ellipsoid3D.cpp +++ b/modules/algebra/src/Ellipsoid3D.cpp @@ -2,7 +2,7 @@ * \file Ellipsoid3D.cpp * \brief simple implementation of ellipsoids in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/algebra/src/Gaussian3D.cpp b/modules/algebra/src/Gaussian3D.cpp index bd12d00a18..3f462ea9d1 100644 --- a/modules/algebra/src/Gaussian3D.cpp +++ b/modules/algebra/src/Gaussian3D.cpp @@ -2,7 +2,7 @@ * \file Gaussian3D.cpp * \brief Gaussian shape * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/algebra/Gaussian3D.h" diff --git a/modules/algebra/src/Line3D.cpp b/modules/algebra/src/Line3D.cpp index 646d14ef2c..9a9232024c 100644 --- a/modules/algebra/src/Line3D.cpp +++ b/modules/algebra/src/Line3D.cpp @@ -2,7 +2,7 @@ * \file Line3D.cpp * \brief Simple implementation of lines in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/algebra/src/LinearFit.cpp b/modules/algebra/src/LinearFit.cpp index ac1d50d55b..2f8aa83a5a 100644 --- a/modules/algebra/src/LinearFit.cpp +++ b/modules/algebra/src/LinearFit.cpp @@ -2,7 +2,7 @@ * \file LinearFit * \brief Linear fit of data points * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/ParabolicFit.cpp b/modules/algebra/src/ParabolicFit.cpp index e28b3e20f7..2313467e5a 100644 --- a/modules/algebra/src/ParabolicFit.cpp +++ b/modules/algebra/src/ParabolicFit.cpp @@ -1,7 +1,7 @@ /** * \file Parabolic \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/ReferenceFrame3D.cpp b/modules/algebra/src/ReferenceFrame3D.cpp index d7b23edbab..08742d6f47 100644 --- a/modules/algebra/src/ReferenceFrame3D.cpp +++ b/modules/algebra/src/ReferenceFrame3D.cpp @@ -1,7 +1,7 @@ /** * \file Rotation3D.cpp \brief Simple 3D rotation class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/Rotation3D.cpp b/modules/algebra/src/Rotation3D.cpp index 8e695a78bb..7efcc5f518 100644 --- a/modules/algebra/src/Rotation3D.cpp +++ b/modules/algebra/src/Rotation3D.cpp @@ -1,7 +1,7 @@ /** * \file Rotation3D.cpp \brief Simple 3D rotation class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/Segment3D.cpp b/modules/algebra/src/Segment3D.cpp index 7157f7e0b3..604857c1d3 100644 --- a/modules/algebra/src/Segment3D.cpp +++ b/modules/algebra/src/Segment3D.cpp @@ -2,7 +2,7 @@ * \file Segment3D.cpp * \brief simple implementation of segments in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include IMPALGEBRA_BEGIN_NAMESPACE diff --git a/modules/algebra/src/Sphere3D.cpp b/modules/algebra/src/Sphere3D.cpp index b47589f9de..7cf64e2fef 100644 --- a/modules/algebra/src/Sphere3D.cpp +++ b/modules/algebra/src/Sphere3D.cpp @@ -2,7 +2,7 @@ * \file Sphere3D.cpp * \brief simple implementation of spheres in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/algebra/Sphere3D.h" #include diff --git a/modules/algebra/src/Sphere3DPatch.cpp b/modules/algebra/src/Sphere3DPatch.cpp index 2f1c7dcf8a..ebf890353a 100644 --- a/modules/algebra/src/Sphere3DPatch.cpp +++ b/modules/algebra/src/Sphere3DPatch.cpp @@ -1,7 +1,7 @@ /** * \file SpherePatch3D.cpp \brief Simple 3D sphere patch class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/SphericalVector3D.cpp b/modules/algebra/src/SphericalVector3D.cpp index ea637b750e..a15157b7a7 100644 --- a/modules/algebra/src/SphericalVector3D.cpp +++ b/modules/algebra/src/SphericalVector3D.cpp @@ -1,7 +1,7 @@ /** * \file SphericalVector3D.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/algebra/SphericalVector3D.h" diff --git a/modules/algebra/src/Transformation2D.cpp b/modules/algebra/src/Transformation2D.cpp index 9fed504fe6..710639876f 100644 --- a/modules/algebra/src/Transformation2D.cpp +++ b/modules/algebra/src/Transformation2D.cpp @@ -2,7 +2,7 @@ * \file Transformation2D.cpp * \brief Simple 2D transformation class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/algebra/Transformation2D.h" #include "IMP/algebra/geometric_alignment.h" diff --git a/modules/algebra/src/Transformation3D.cpp b/modules/algebra/src/Transformation3D.cpp index 15d43f96cb..0bcdb47e83 100644 --- a/modules/algebra/src/Transformation3D.cpp +++ b/modules/algebra/src/Transformation3D.cpp @@ -2,7 +2,7 @@ * \file Transformation3D.cpp * \brief Simple 3D transformation class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/algebra/Transformation3D.h" #include "IMP/algebra/Transformation2D.h" diff --git a/modules/algebra/src/Triangle3D.cpp b/modules/algebra/src/Triangle3D.cpp index c19cfce380..ea24e2b645 100644 --- a/modules/algebra/src/Triangle3D.cpp +++ b/modules/algebra/src/Triangle3D.cpp @@ -2,7 +2,7 @@ * \file Triangle3D.cpp * \brief simple implementation of triangles in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/algebra/src/connolly_surface.cpp b/modules/algebra/src/connolly_surface.cpp index 20a9d63998..e7d56baada 100644 --- a/modules/algebra/src/connolly_surface.cpp +++ b/modules/algebra/src/connolly_surface.cpp @@ -1,7 +1,7 @@ /** * \file connolly_surface.cpp \brief Generate surface for a set of atoms * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/eigen_analysis.cpp b/modules/algebra/src/eigen_analysis.cpp index abcb5c0f72..3ab989c7c0 100644 --- a/modules/algebra/src/eigen_analysis.cpp +++ b/modules/algebra/src/eigen_analysis.cpp @@ -2,7 +2,7 @@ * \file eigen_analysis.cpp * \brief Principal component analysis of a set of points * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/algebra/eigen_analysis.h" diff --git a/modules/algebra/src/endian.cpp b/modules/algebra/src/endian.cpp index 50d89593d3..c3b2a1401a 100644 --- a/modules/algebra/src/endian.cpp +++ b/modules/algebra/src/endian.cpp @@ -1,7 +1,7 @@ /** * \file endian.cpp * \brief Functions to deal with endianess - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/algebra/src/geometric_alignment.cpp b/modules/algebra/src/geometric_alignment.cpp index 4dbccfa5ec..59e03d0ad0 100644 --- a/modules/algebra/src/geometric_alignment.cpp +++ b/modules/algebra/src/geometric_alignment.cpp @@ -2,7 +2,7 @@ * \file geometric_alignment.cpp * \brief Support for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/internal/utility.cpp b/modules/algebra/src/internal/utility.cpp index b657ba2a0b..2d4c8132e2 100644 --- a/modules/algebra/src/internal/utility.cpp +++ b/modules/algebra/src/internal/utility.cpp @@ -1,7 +1,7 @@ /** * \file output_helpers.cpp * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * Adapted with permission from Xmip 2.2 */ #include "IMP/algebra/internal/utility.h" diff --git a/modules/algebra/src/io.cpp b/modules/algebra/src/io.cpp index 3a8176b233..173c44eb3a 100644 --- a/modules/algebra/src/io.cpp +++ b/modules/algebra/src/io.cpp @@ -2,7 +2,7 @@ * \file io.cpp * \brief Support for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/shortest_segment.cpp b/modules/algebra/src/shortest_segment.cpp index 1344e26f30..b2ce931d5e 100644 --- a/modules/algebra/src/shortest_segment.cpp +++ b/modules/algebra/src/shortest_segment.cpp @@ -2,7 +2,7 @@ * \file Segment3D.cpp * \brief simple implementation of segments in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/algebra/src/vector_generators.cpp b/modules/algebra/src/vector_generators.cpp index 01dcf9c53a..0cb28c4406 100644 --- a/modules/algebra/src/vector_generators.cpp +++ b/modules/algebra/src/vector_generators.cpp @@ -2,7 +2,7 @@ * \file vector_generators.cpp * \brief Support for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/vector_metrics.cpp b/modules/algebra/src/vector_metrics.cpp index 882b91a1af..26744d11a0 100644 --- a/modules/algebra/src/vector_metrics.cpp +++ b/modules/algebra/src/vector_metrics.cpp @@ -2,7 +2,7 @@ * \file vector_generators.cpp * \brief Support for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/src/vector_search.cpp b/modules/algebra/src/vector_search.cpp index 0d641d3946..b9e042fd59 100644 --- a/modules/algebra/src/vector_search.cpp +++ b/modules/algebra/src/vector_search.cpp @@ -2,7 +2,7 @@ * \file vector_search.cpp * \brief Support for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/algebra/test/test_grid.cpp b/modules/algebra/test/test_grid.cpp index a3b221d895..43d7a3d9cb 100644 --- a/modules/algebra/test/test_grid.cpp +++ b/modules/algebra/test/test_grid.cpp @@ -1,7 +1,7 @@ /** * \file test_grid.cpp \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/algebra/test/test_grid_apply.cpp b/modules/algebra/test/test_grid_apply.cpp index 7c7476c5fb..5346a6a13a 100644 --- a/modules/algebra/test/test_grid_apply.cpp +++ b/modules/algebra/test/test_grid_apply.cpp @@ -1,7 +1,7 @@ /** * \file test_grid.cpp \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/algebra/test/test_grid_storage.cpp b/modules/algebra/test/test_grid_storage.cpp index 390b049e48..8b6806baad 100644 --- a/modules/algebra/test/test_grid_storage.cpp +++ b/modules/algebra/test/test_grid_storage.cpp @@ -1,7 +1,7 @@ /** * \file test_grid.cpp \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/atom/benchmark/benchmark_incremental_mc.cpp b/modules/atom/benchmark/benchmark_incremental_mc.cpp index 3402ca6aa1..5fa358a7b9 100644 --- a/modules/atom/benchmark/benchmark_incremental_mc.cpp +++ b/modules/atom/benchmark/benchmark_incremental_mc.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/atom/benchmark/benchmark_md_charmm.cpp b/modules/atom/benchmark/benchmark_md_charmm.cpp index 189aafc309..676c04848c 100644 --- a/modules/atom/benchmark/benchmark_md_charmm.cpp +++ b/modules/atom/benchmark/benchmark_md_charmm.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/atom/benchmark/benchmark_pdb.cpp b/modules/atom/benchmark/benchmark_pdb.cpp index 88f8110814..244ba91ec0 100644 --- a/modules/atom/benchmark/benchmark_pdb.cpp +++ b/modules/atom/benchmark/benchmark_pdb.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/atom/benchmark/benchmark_refiners.cpp b/modules/atom/benchmark/benchmark_refiners.cpp index ca08f99eb1..c712401289 100644 --- a/modules/atom/benchmark/benchmark_refiners.cpp +++ b/modules/atom/benchmark/benchmark_refiners.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/atom/bin/ligand_score.cpp b/modules/atom/bin/ligand_score.cpp index 0577c8e260..4d4c83893d 100644 --- a/modules/atom/bin/ligand_score.cpp +++ b/modules/atom/bin/ligand_score.cpp @@ -1,7 +1,7 @@ /** * \file ligand_score.cpp \brief A class for reading mol2 files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/bin/ligand_score_multiple.cpp b/modules/atom/bin/ligand_score_multiple.cpp index 2b8ab2a01e..90261a960e 100644 --- a/modules/atom/bin/ligand_score_multiple.cpp +++ b/modules/atom/bin/ligand_score_multiple.cpp @@ -1,7 +1,7 @@ /** * \file ligand_score.cpp \brief A class for reading mol2 files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/bin/pdb_check.cpp b/modules/atom/bin/pdb_check.cpp index 2fca64332e..dbeddf5054 100644 --- a/modules/atom/bin/pdb_check.cpp +++ b/modules/atom/bin/pdb_check.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/atom/include/AngleSingletonScore.h b/modules/atom/include/AngleSingletonScore.h index dba6ede78e..8bd6eaf66c 100644 --- a/modules/atom/include/AngleSingletonScore.h +++ b/modules/atom/include/AngleSingletonScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/AngleSingletonScore.h * \brief A score on the deviation of an angle from ideality. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_ANGLE_SINGLETON_SCORE_H diff --git a/modules/atom/include/Atom.h b/modules/atom/include/Atom.h index ddde1c6276..73828ef9c9 100644 --- a/modules/atom/include/Atom.h +++ b/modules/atom/include/Atom.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/Atom.h \brief Simple atom decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/BerendsenThermostatOptimizerState.h b/modules/atom/include/BerendsenThermostatOptimizerState.h index b4c036b4cb..cf72adb272 100644 --- a/modules/atom/include/BerendsenThermostatOptimizerState.h +++ b/modules/atom/include/BerendsenThermostatOptimizerState.h @@ -3,7 +3,7 @@ * \brief Maintains temperature during molecular dynamics using a * Berendsen thermostat. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/BondEndpointsRefiner.h b/modules/atom/include/BondEndpointsRefiner.h index b087fd777e..d53dd014ea 100644 --- a/modules/atom/include/BondEndpointsRefiner.h +++ b/modules/atom/include/BondEndpointsRefiner.h @@ -2,7 +2,7 @@ * \file IMP/atom/BondEndpointsRefiner.h * \brief Return the endpoints of a bond. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_BOND_ENDPOINTS_REFINER_H diff --git a/modules/atom/include/BondPairContainer.h b/modules/atom/include/BondPairContainer.h index 36a9c74078..9708b40329 100644 --- a/modules/atom/include/BondPairContainer.h +++ b/modules/atom/include/BondPairContainer.h @@ -2,7 +2,7 @@ * \file IMP/atom/BondPairContainer.h * \brief A fake container for bonds * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_BOND_PAIR_CONTAINER_H diff --git a/modules/atom/include/BondSingletonScore.h b/modules/atom/include/BondSingletonScore.h index 42845897b5..7ef5c82975 100644 --- a/modules/atom/include/BondSingletonScore.h +++ b/modules/atom/include/BondSingletonScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/BondSingletonScore.h * \brief A Score on the distance between a the two particles in a bond. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_BOND_SINGLETON_SCORE_H diff --git a/modules/atom/include/BondedPairFilter.h b/modules/atom/include/BondedPairFilter.h index 44c683f01e..56142c594c 100644 --- a/modules/atom/include/BondedPairFilter.h +++ b/modules/atom/include/BondedPairFilter.h @@ -2,7 +2,7 @@ * \file IMP/atom/BondedPairFilter.h * \brief A fake container for bonds * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_BONDED_PAIR_FILTER_H diff --git a/modules/atom/include/BrownianDynamics.h b/modules/atom/include/BrownianDynamics.h index ae73940ca4..c6d7bc2d2e 100644 --- a/modules/atom/include/BrownianDynamics.h +++ b/modules/atom/include/BrownianDynamics.h @@ -2,7 +2,7 @@ * \file IMP/atom/BrownianDynamics.h * \brief Simple Brownian dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/BrownianDynamicsTAMD.h b/modules/atom/include/BrownianDynamicsTAMD.h index 92d08c68a5..f840b440ca 100644 --- a/modules/atom/include/BrownianDynamicsTAMD.h +++ b/modules/atom/include/BrownianDynamicsTAMD.h @@ -2,7 +2,7 @@ * \file IMP/atom/BrownianDynamicsTAMD.h * \brief Simple molecular dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/CAAngleRestraint.h b/modules/atom/include/CAAngleRestraint.h index 5a0ad72e69..bd965e98f1 100644 --- a/modules/atom/include/CAAngleRestraint.h +++ b/modules/atom/include/CAAngleRestraint.h @@ -2,7 +2,7 @@ * \file IMP/atom/CAAngleRestraint.h * \brief Angle restraint between three residues in CA-only representation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/CADihedralRestraint.h b/modules/atom/include/CADihedralRestraint.h index 8988e75ce7..3b73ba6681 100644 --- a/modules/atom/include/CADihedralRestraint.h +++ b/modules/atom/include/CADihedralRestraint.h @@ -2,7 +2,7 @@ * \file IMP/atom/CADihedralRestraint.h * \brief Dihedral restraint between five residues in CA-only representation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/CHARMMAtom.h b/modules/atom/include/CHARMMAtom.h index 0440461aae..74abf6a967 100644 --- a/modules/atom/include/CHARMMAtom.h +++ b/modules/atom/include/CHARMMAtom.h @@ -2,7 +2,7 @@ * \file IMP/atom/CHARMMAtom.h * \brief A decorator for an atom that has a defined CHARMM type. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/CHARMMParameters.h b/modules/atom/include/CHARMMParameters.h index 45934ffd7e..c451849cc3 100644 --- a/modules/atom/include/CHARMMParameters.h +++ b/modules/atom/include/CHARMMParameters.h @@ -2,7 +2,7 @@ * \file IMP/atom/CHARMMParameters.h * \brief access to CHARMM force field parameters * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/CHARMMStereochemistryRestraint.h b/modules/atom/include/CHARMMStereochemistryRestraint.h index eb71a4a828..121277af17 100644 --- a/modules/atom/include/CHARMMStereochemistryRestraint.h +++ b/modules/atom/include/CHARMMStereochemistryRestraint.h @@ -2,7 +2,7 @@ * \file IMP/atom/CHARMMStereochemistryRestraint.h * \brief Class to maintain CHARMM stereochemistry. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/CenterOfMass.h b/modules/atom/include/CenterOfMass.h index 2f2d2baab7..91e6d19983 100644 --- a/modules/atom/include/CenterOfMass.h +++ b/modules/atom/include/CenterOfMass.h @@ -2,7 +2,7 @@ * \file IMP/atom/CenterOfMass.h * \brief A decorator for particles with mass * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_CENTER_OF_MASS_H diff --git a/modules/atom/include/Chain.h b/modules/atom/include/Chain.h index e9fed82d65..ff928e4407 100644 --- a/modules/atom/include/Chain.h +++ b/modules/atom/include/Chain.h @@ -2,7 +2,7 @@ * \file IMP/atom/Chain.h * \brief Store the chain ID * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_CHAIN_H diff --git a/modules/atom/include/Charged.h b/modules/atom/include/Charged.h index 05455bebd4..6327fcc0ca 100644 --- a/modules/atom/include/Charged.h +++ b/modules/atom/include/Charged.h @@ -2,7 +2,7 @@ * \file IMP/atom/Charged.h * \brief A decorator for a point particle that has an electrostatic charge. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Copy.h b/modules/atom/include/Copy.h index 3c93b2f0c6..34a98a218b 100644 --- a/modules/atom/include/Copy.h +++ b/modules/atom/include/Copy.h @@ -2,7 +2,7 @@ * \file IMP/atom/Copy.h * \brief A decorator for keeping track of copies of a molecule. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/CoulombPairScore.h b/modules/atom/include/CoulombPairScore.h index d71a030043..2d1cf57451 100644 --- a/modules/atom/include/CoulombPairScore.h +++ b/modules/atom/include/CoulombPairScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/CoulombPairScore.h * \brief Coulomb (electrostatic) score between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_COULOMB_PAIR_SCORE_H diff --git a/modules/atom/include/CoverBond.h b/modules/atom/include/CoverBond.h index e3c3d325c4..ef5ca9f6a4 100644 --- a/modules/atom/include/CoverBond.h +++ b/modules/atom/include/CoverBond.h @@ -2,7 +2,7 @@ * \file IMP/atom/CoverBond.h * \brief Cover a bond with a sphere * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_COVER_BOND_H diff --git a/modules/atom/include/Diffusion.h b/modules/atom/include/Diffusion.h index 6ea5c26727..1e3fed9669 100644 --- a/modules/atom/include/Diffusion.h +++ b/modules/atom/include/Diffusion.h @@ -2,7 +2,7 @@ * \file IMP/atom/Diffusion.h * \brief A decorator for a diffusing particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/DihedralSingletonScore.h b/modules/atom/include/DihedralSingletonScore.h index 45251444d8..ac6eca7619 100644 --- a/modules/atom/include/DihedralSingletonScore.h +++ b/modules/atom/include/DihedralSingletonScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/DihedralSingletonScore.h * \brief A score on a dihedral angle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_DIHEDRAL_SINGLETON_SCORE_H diff --git a/modules/atom/include/Domain.h b/modules/atom/include/Domain.h index 3a97bdc506..e7d758f8d5 100644 --- a/modules/atom/include/Domain.h +++ b/modules/atom/include/Domain.h @@ -2,7 +2,7 @@ * \file IMP/atom/Domain.h * \brief A decorator for associating an atom::Hierarchy piece with a domain * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_DOMAIN_H diff --git a/modules/atom/include/DopePairScore.h b/modules/atom/include/DopePairScore.h index 3e3bf61a18..4e5657f9ad 100644 --- a/modules/atom/include/DopePairScore.h +++ b/modules/atom/include/DopePairScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/DopePairScore.h * \brief Dope scoring * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/EzRestraint.h b/modules/atom/include/EzRestraint.h index 892432725c..f2db065ffc 100644 --- a/modules/atom/include/EzRestraint.h +++ b/modules/atom/include/EzRestraint.h @@ -2,7 +2,7 @@ * \file IMP/atom/EzRestraint.h * \brief Ez potential. A statistical scoring function for atom proteins * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_EZ_RESTRAINT_H diff --git a/modules/atom/include/ForceFieldParameters.h b/modules/atom/include/ForceFieldParameters.h index bb0a68b43f..3697bd6b0f 100644 --- a/modules/atom/include/ForceFieldParameters.h +++ b/modules/atom/include/ForceFieldParameters.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/ForceFieldParameters.h \brief force field base class * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Fragment.h b/modules/atom/include/Fragment.h index c0a35eee3b..e543f25ad6 100644 --- a/modules/atom/include/Fragment.h +++ b/modules/atom/include/Fragment.h @@ -2,7 +2,7 @@ * \file IMP/atom/Fragment.h * \brief A decorator for associating a Hierarchy piece * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_FRAGMENT_H diff --git a/modules/atom/include/HelixRestraint.h b/modules/atom/include/HelixRestraint.h index de040dd246..4dfdbd4fc7 100644 --- a/modules/atom/include/HelixRestraint.h +++ b/modules/atom/include/HelixRestraint.h @@ -2,7 +2,7 @@ * \file IMP/atom/HelixRestraint.h * \brief Class to maintain helix shape (dihedrals + elastic network) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Hierarchy.h b/modules/atom/include/Hierarchy.h index f0b8eef44f..6766653b09 100644 --- a/modules/atom/include/Hierarchy.h +++ b/modules/atom/include/Hierarchy.h @@ -2,7 +2,7 @@ * \file IMP/atom/Hierarchy.h * \brief Decorator for helping deal with a hierarchy of molecules. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/ImproperSingletonScore.h b/modules/atom/include/ImproperSingletonScore.h index 63a4b76c04..02b94ff00f 100644 --- a/modules/atom/include/ImproperSingletonScore.h +++ b/modules/atom/include/ImproperSingletonScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/ImproperSingletonScore.h * \brief A score on the deviation of an improper angle from ideality. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_IMPROPER_SINGLETON_SCORE_H diff --git a/modules/atom/include/LangevinThermostatOptimizerState.h b/modules/atom/include/LangevinThermostatOptimizerState.h index 26261d986b..7f8a3815c1 100644 --- a/modules/atom/include/LangevinThermostatOptimizerState.h +++ b/modules/atom/include/LangevinThermostatOptimizerState.h @@ -3,7 +3,7 @@ * \brief Maintains temperature during molecular dynamics using * a Langevin thermostat. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/LennardJones.h b/modules/atom/include/LennardJones.h index 30145f9b51..6c4e2f3ce1 100644 --- a/modules/atom/include/LennardJones.h +++ b/modules/atom/include/LennardJones.h @@ -2,7 +2,7 @@ * \file IMP/atom/LennardJones.h * \brief A decorator for a particle that has a Lennard-Jones potential well. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/LennardJonesPairScore.h b/modules/atom/include/LennardJonesPairScore.h index c2526864fc..afc4e639f4 100644 --- a/modules/atom/include/LennardJonesPairScore.h +++ b/modules/atom/include/LennardJonesPairScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/LennardJonesPairScore.h * \brief Lennard-Jones score between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_LENNARD_JONES_PAIR_SCORE_H diff --git a/modules/atom/include/LoopStatisticalPairScore.h b/modules/atom/include/LoopStatisticalPairScore.h index 0dba5abfcb..ddf2b9c15a 100644 --- a/modules/atom/include/LoopStatisticalPairScore.h +++ b/modules/atom/include/LoopStatisticalPairScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/LoopStatisticalPairScore.h * \brief Fiser/Melo loop modeling statistical potential * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Mass.h b/modules/atom/include/Mass.h index 07519d1a30..1cfeb3a2da 100644 --- a/modules/atom/include/Mass.h +++ b/modules/atom/include/Mass.h @@ -2,7 +2,7 @@ * \file IMP/atom/Mass.h * \brief A decorator for particles with mass * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_MASS_H diff --git a/modules/atom/include/MolecularDynamics.h b/modules/atom/include/MolecularDynamics.h index 8cda3900a6..0430f82958 100644 --- a/modules/atom/include/MolecularDynamics.h +++ b/modules/atom/include/MolecularDynamics.h @@ -2,7 +2,7 @@ * \file IMP/atom/MolecularDynamics.h * \brief Simple molecular dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Molecule.h b/modules/atom/include/Molecule.h index b3900b71ff..5bf4711598 100644 --- a/modules/atom/include/Molecule.h +++ b/modules/atom/include/Molecule.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/Molecule.h \brief A decorator for Molecules. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/OrientedSoapPairScore.h b/modules/atom/include/OrientedSoapPairScore.h index d796c6979b..6c35844b97 100644 --- a/modules/atom/include/OrientedSoapPairScore.h +++ b/modules/atom/include/OrientedSoapPairScore.h @@ -2,7 +2,7 @@ * \file IMP/atom/OrientedSoapPairScore.h * \brief Orientation-dependent SOAP scoring * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/RemoveRigidMotionOptimizerState.h b/modules/atom/include/RemoveRigidMotionOptimizerState.h index 8819fb6c58..99e3b170aa 100644 --- a/modules/atom/include/RemoveRigidMotionOptimizerState.h +++ b/modules/atom/include/RemoveRigidMotionOptimizerState.h @@ -2,7 +2,7 @@ * \file IMP/atom/RemoveRigidMotionOptimizerState.h * \brief Remove rigid rotation and translation during molecular dynamics. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/RemoveTranslationOptimizerState.h b/modules/atom/include/RemoveTranslationOptimizerState.h index b4dd7bb0c5..3b6d844f8b 100644 --- a/modules/atom/include/RemoveTranslationOptimizerState.h +++ b/modules/atom/include/RemoveTranslationOptimizerState.h @@ -2,7 +2,7 @@ * \file IMP/atom/RemoveTranslationOptimizerState.h * \brief Remove rigid translation during optimization. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Representation.h b/modules/atom/include/Representation.h index 3d424a6ffa..addba1a249 100644 --- a/modules/atom/include/Representation.h +++ b/modules/atom/include/Representation.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/Representation.h \brief A decorator for Representations. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Residue.h b/modules/atom/include/Residue.h index 6b1bf29425..2a3d70e2ed 100644 --- a/modules/atom/include/Residue.h +++ b/modules/atom/include/Residue.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/Residue.h \brief A decorator for Residues. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/SameResiduePairFilter.h b/modules/atom/include/SameResiduePairFilter.h index 2d42ef251d..e34b36658c 100644 --- a/modules/atom/include/SameResiduePairFilter.h +++ b/modules/atom/include/SameResiduePairFilter.h @@ -2,7 +2,7 @@ * \file IMP/atom/SameResiduePairFilter.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_SAME_RESIDUE_PAIR_FILTER_H diff --git a/modules/atom/include/SecondaryStructureResidue.h b/modules/atom/include/SecondaryStructureResidue.h index 7b74ba38bf..ceee890f12 100644 --- a/modules/atom/include/SecondaryStructureResidue.h +++ b/modules/atom/include/SecondaryStructureResidue.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/SecondaryStructureResidue.h * \brief A decorator for storing secondary structure probabilities. - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Selection.h b/modules/atom/include/Selection.h index 6476e5a073..884f767df1 100644 --- a/modules/atom/include/Selection.h +++ b/modules/atom/include/Selection.h @@ -2,7 +2,7 @@ * \file IMP/atom/Selection.h * \brief Select a subset of a hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_SELECTION_H diff --git a/modules/atom/include/Simulator.h b/modules/atom/include/Simulator.h index 1a8e6bbe45..1b0b8f13be 100644 --- a/modules/atom/include/Simulator.h +++ b/modules/atom/include/Simulator.h @@ -2,7 +2,7 @@ * \file IMP/atom/Simulator.h * \brief Simple molecular dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/SoapPairFilter.h b/modules/atom/include/SoapPairFilter.h index 18fd728a4e..db33d16ea2 100644 --- a/modules/atom/include/SoapPairFilter.h +++ b/modules/atom/include/SoapPairFilter.h @@ -2,7 +2,7 @@ * \file IMP/atom/SoapPairFilter.h * \brief PairFilter for SOAP * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/State.h b/modules/atom/include/State.h index c45d757e9c..2f653ff271 100644 --- a/modules/atom/include/State.h +++ b/modules/atom/include/State.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/State.h \brief A decorator for States. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/StereochemistryPairFilter.h b/modules/atom/include/StereochemistryPairFilter.h index 4dde2e4a57..cd500f3948 100644 --- a/modules/atom/include/StereochemistryPairFilter.h +++ b/modules/atom/include/StereochemistryPairFilter.h @@ -2,7 +2,7 @@ * \file IMP/atom/StereochemistryPairFilter.h * \brief A filter that excludes bonds, angles and dihedrals. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_STEREOCHEMISTRY_PAIR_FILTER_H diff --git a/modules/atom/include/StructureSource.h b/modules/atom/include/StructureSource.h index b3592a49f2..912057ab65 100644 --- a/modules/atom/include/StructureSource.h +++ b/modules/atom/include/StructureSource.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/StructureSource.h \brief Add a Structure ID and Chain ID * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/TAMDCentroid.h b/modules/atom/include/TAMDCentroid.h index f773a78979..4920ee8fdd 100644 --- a/modules/atom/include/TAMDCentroid.h +++ b/modules/atom/include/TAMDCentroid.h @@ -2,7 +2,7 @@ * \file IMP/atom/TAMDCentroid.h * \brief A decorator for a particle that is a centroid of TAMD simulations. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/TAMDParticle.h b/modules/atom/include/TAMDParticle.h index 6f3a3ff8c8..a83693e930 100644 --- a/modules/atom/include/TAMDParticle.h +++ b/modules/atom/include/TAMDParticle.h @@ -2,7 +2,7 @@ * \file IMP/atom/TAMDParticle.h * \brief A decorator for a diffusing particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/VelocityScalingOptimizerState.h b/modules/atom/include/VelocityScalingOptimizerState.h index 5c480e591e..9a872ece95 100644 --- a/modules/atom/include/VelocityScalingOptimizerState.h +++ b/modules/atom/include/VelocityScalingOptimizerState.h @@ -2,7 +2,7 @@ * \file IMP/atom/VelocityScalingOptimizerState.h * \brief Maintains temperature during molecular dynamics by velocity scaling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/alignment.h b/modules/atom/include/alignment.h index cf3911b2d0..151d1cffac 100644 --- a/modules/atom/include/alignment.h +++ b/modules/atom/include/alignment.h @@ -2,7 +2,7 @@ * \file IMP/atom/alignment.h * \brief Alignment of structures * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/angle_decorators.h b/modules/atom/include/angle_decorators.h index 9c6f63cff3..c94f059627 100644 --- a/modules/atom/include/angle_decorators.h +++ b/modules/atom/include/angle_decorators.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/angle_decorators.h \brief Decorators for angles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/atom_macros.h b/modules/atom/include/atom_macros.h index dead945777..55cfa8fd00 100644 --- a/modules/atom/include/atom_macros.h +++ b/modules/atom/include/atom_macros.h @@ -2,7 +2,7 @@ * \file IMP/atom/atom_macros.h \brief Various important macros * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/bond_decorators.h b/modules/atom/include/bond_decorators.h index 3eea0e82c9..68faa395f2 100644 --- a/modules/atom/include/bond_decorators.h +++ b/modules/atom/include/bond_decorators.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/bond_decorators.h \brief Contains decorators for a bond * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/bond_graph.h b/modules/atom/include/bond_graph.h index 4831cfcf0f..9b3e5f493f 100644 --- a/modules/atom/include/bond_graph.h +++ b/modules/atom/include/bond_graph.h @@ -2,7 +2,7 @@ * \file IMP/atom/bond_graph.h * \brief Represents a graph of the bonds within an atomic structure * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/charmm_segment_topology.h b/modules/atom/include/charmm_segment_topology.h index 04a9126c57..ffafd8d4b0 100644 --- a/modules/atom/include/charmm_segment_topology.h +++ b/modules/atom/include/charmm_segment_topology.h @@ -2,7 +2,7 @@ * \file IMP/atom/charmm_segment_topology.h * \brief Classes for handling CHARMM-style topology of segments. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/charmm_topology.h b/modules/atom/include/charmm_topology.h index e347fabf11..d8bb48c420 100644 --- a/modules/atom/include/charmm_topology.h +++ b/modules/atom/include/charmm_topology.h @@ -2,7 +2,7 @@ * \file IMP/atom/charmm_topology.h * \brief Classes for handling CHARMM-style topology. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/constants.h b/modules/atom/include/constants.h index 6610d2ff8e..da4d1f6cd8 100644 --- a/modules/atom/include/constants.h +++ b/modules/atom/include/constants.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/constants.h \brief Define the elements used in \imp. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/dihedrals.h b/modules/atom/include/dihedrals.h index 988bf87558..26d229c55b 100644 --- a/modules/atom/include/dihedrals.h +++ b/modules/atom/include/dihedrals.h @@ -2,7 +2,7 @@ * \file IMP/atom/dihedrals.h * \brief Helpers to extract dihedral information. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/distance.h b/modules/atom/include/distance.h index 3e924b8f47..12e1d857f6 100644 --- a/modules/atom/include/distance.h +++ b/modules/atom/include/distance.h @@ -2,7 +2,7 @@ * \file IMP/atom/distance.h * \brief distance metrics * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/element.h b/modules/atom/include/element.h index 0c0009dfd6..409c5bbbf3 100644 --- a/modules/atom/include/element.h +++ b/modules/atom/include/element.h @@ -1,7 +1,7 @@ /** * \file IMP/atom/element.h \brief Define the elements used in \imp. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/estimates.h b/modules/atom/include/estimates.h index 3b877a206c..3ba5a30c3d 100644 --- a/modules/atom/include/estimates.h +++ b/modules/atom/include/estimates.h @@ -2,7 +2,7 @@ * \file IMP/atom/estimates.h * \brief Estimates of various physical quantities. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_ESTIMATES_H diff --git a/modules/atom/include/force_fields.h b/modules/atom/include/force_fields.h index f48ec63635..528267994e 100644 --- a/modules/atom/include/force_fields.h +++ b/modules/atom/include/force_fields.h @@ -2,7 +2,7 @@ * \file IMP/atom/force_fields.h * \brief Define functions to add bonds and radii to atoms. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/hierarchy_tools.h b/modules/atom/include/hierarchy_tools.h index a14a4ef800..09b9f36e90 100644 --- a/modules/atom/include/hierarchy_tools.h +++ b/modules/atom/include/hierarchy_tools.h @@ -2,7 +2,7 @@ * \file IMP/atom/hierarchy_tools.h * \brief A set of useful functionality on IMP::atom::Hierarchy decorators * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_HIERARCHY_TOOLS_H diff --git a/modules/atom/include/internal/ExcludedPair.h b/modules/atom/include/internal/ExcludedPair.h index b1f92038a0..1afde3d97a 100644 --- a/modules/atom/include/internal/ExcludedPair.h +++ b/modules/atom/include/internal/ExcludedPair.h @@ -2,7 +2,7 @@ * \file ExcludedPair.h * \brief A pair of Particles, used for exclusions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_INTERNAL_EXCLUDED_PAIR_H diff --git a/modules/atom/include/internal/Gaussian.h b/modules/atom/include/internal/Gaussian.h index 38478ba5c8..dc854573ad 100644 --- a/modules/atom/include/internal/Gaussian.h +++ b/modules/atom/include/internal/Gaussian.h @@ -1,7 +1,7 @@ /** * \file Gaussian.h \brief Gaussian function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_INTERNAL_GAUSSIAN_H diff --git a/modules/atom/include/internal/SelectionPredicate.h b/modules/atom/include/internal/SelectionPredicate.h index a64012dc69..07815da418 100644 --- a/modules/atom/include/internal/SelectionPredicate.h +++ b/modules/atom/include/internal/SelectionPredicate.h @@ -2,7 +2,7 @@ * \file IMP/atom/internal/SelectionPredicate.h * \brief Predicates for selecting a subset of a hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_SELECTION_PREDICATE_H diff --git a/modules/atom/include/internal/Sigmoid.h b/modules/atom/include/internal/Sigmoid.h index 41ecc65fdb..c87a2452a0 100644 --- a/modules/atom/include/internal/Sigmoid.h +++ b/modules/atom/include/internal/Sigmoid.h @@ -1,7 +1,7 @@ /** * \file Sigmoid.h \brief Sigmoid function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_INTERNAL_SIGMOID_H diff --git a/modules/atom/include/internal/bond_graph_boost_functions.h b/modules/atom/include/internal/bond_graph_boost_functions.h index a976907fc7..e8c553ad0f 100644 --- a/modules/atom/include/internal/bond_graph_boost_functions.h +++ b/modules/atom/include/internal/bond_graph_boost_functions.h @@ -2,7 +2,7 @@ * \file atom/internal/bond_graph_boost_functions.h * \brief Contains decorators for a bond * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/internal/bond_graph_functors.h b/modules/atom/include/internal/bond_graph_functors.h index c18477a8f0..71c4794bcc 100644 --- a/modules/atom/include/internal/bond_graph_functors.h +++ b/modules/atom/include/internal/bond_graph_functors.h @@ -2,7 +2,7 @@ * \file atom/internal/bond_graph_functors.h * \brief Contains decorators for a bond * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/internal/bond_helpers.h b/modules/atom/include/internal/bond_helpers.h index 32d22ab5f3..c8794d9a5f 100644 --- a/modules/atom/include/internal/bond_helpers.h +++ b/modules/atom/include/internal/bond_helpers.h @@ -2,7 +2,7 @@ * \file bond_helpers.h * \brief Helpers for the bond decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/internal/charmm_helpers.h b/modules/atom/include/internal/charmm_helpers.h index 0386950dec..ef6931ff36 100644 --- a/modules/atom/include/internal/charmm_helpers.h +++ b/modules/atom/include/internal/charmm_helpers.h @@ -2,7 +2,7 @@ * \file charmm_helpers.h * \brief Helpers for the CHARMM forcefield support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/internal/mol2.h b/modules/atom/include/internal/mol2.h index a7496e0763..546704b397 100644 --- a/modules/atom/include/internal/mol2.h +++ b/modules/atom/include/internal/mol2.h @@ -2,7 +2,7 @@ * \file internal/mol2.h * \brief a class with static functions for parsing mol2 files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_INTERNAL_MOL_2_H diff --git a/modules/atom/include/internal/pdb.h b/modules/atom/include/internal/pdb.h index 893b06312e..6f96baad60 100644 --- a/modules/atom/include/internal/pdb.h +++ b/modules/atom/include/internal/pdb.h @@ -2,7 +2,7 @@ * \file internal/pdb.h * \brief A class with static functions for parsing PDB files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/internal/soap_bond_separation.h b/modules/atom/include/internal/soap_bond_separation.h index 837f4b81f6..671fcc2d83 100644 --- a/modules/atom/include/internal/soap_bond_separation.h +++ b/modules/atom/include/internal/soap_bond_separation.h @@ -2,7 +2,7 @@ * \file soap_bond_separation.h * \brief SOAP bond separation filter * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/internal/soap_chain_separation.h b/modules/atom/include/internal/soap_chain_separation.h index 8b6d342e8c..8d6391a14a 100644 --- a/modules/atom/include/internal/soap_chain_separation.h +++ b/modules/atom/include/internal/soap_chain_separation.h @@ -2,7 +2,7 @@ * \file soap_chain_separation.h * \brief SOAP chain separation filter * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/mmcif.h b/modules/atom/include/mmcif.h index 6b54e3af68..de61a2f9c4 100644 --- a/modules/atom/include/mmcif.h +++ b/modules/atom/include/mmcif.h @@ -2,7 +2,7 @@ * \file IMP/atom/mmcif.h * \brief Functions to read PDBs in mmCIF format * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/mol2.h b/modules/atom/include/mol2.h index e98204cf25..2068080dab 100644 --- a/modules/atom/include/mol2.h +++ b/modules/atom/include/mol2.h @@ -2,7 +2,7 @@ * \file IMP/atom/mol2.h * \brief Functions to read mol2s * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/pdb.h b/modules/atom/include/pdb.h index 24f7dad37f..648a287076 100644 --- a/modules/atom/include/pdb.h +++ b/modules/atom/include/pdb.h @@ -2,7 +2,7 @@ * \file IMP/atom/pdb.h * \brief Functions to read PDBs * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/protein_ligand_score.h b/modules/atom/include/protein_ligand_score.h index 6c1cc60751..d38ae298ac 100644 --- a/modules/atom/include/protein_ligand_score.h +++ b/modules/atom/include/protein_ligand_score.h @@ -2,7 +2,7 @@ * \file IMP/atom/protein_ligand_score.h * \brief Functions to read mol2s * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/python_only.h b/modules/atom/include/python_only.h index 17d29048d9..24005e698d 100644 --- a/modules/atom/include/python_only.h +++ b/modules/atom/include/python_only.h @@ -2,7 +2,7 @@ * \file IMP/atom/python_only.h * \brief Functionality only available in Python. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/secondary_structure_reader.h b/modules/atom/include/secondary_structure_reader.h index 05bbf77251..ca0f9a853e 100644 --- a/modules/atom/include/secondary_structure_reader.h +++ b/modules/atom/include/secondary_structure_reader.h @@ -2,7 +2,7 @@ * \file IMP/atom/secondary_structure_reader.h * \brief Functions to read PSIPRED/DSSP and encode as SSES * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/smoothing_functions.h b/modules/atom/include/smoothing_functions.h index 4cedbd2578..c7e66698ca 100644 --- a/modules/atom/include/smoothing_functions.h +++ b/modules/atom/include/smoothing_functions.h @@ -2,7 +2,7 @@ * \file IMP/atom/smoothing_functions.h * \brief Classes to smooth nonbonded interactions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPATOM_SMOOTHING_FUNCTIONS_H diff --git a/modules/atom/src/AngleSingletonScore.cpp b/modules/atom/src/AngleSingletonScore.cpp index 93bab62ba7..98e8b285fe 100644 --- a/modules/atom/src/AngleSingletonScore.cpp +++ b/modules/atom/src/AngleSingletonScore.cpp @@ -2,7 +2,7 @@ * \file atom/AngleSingletonScore.h * \brief A score on the deviation of an angle from ideality. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/atom/src/Atom.cpp b/modules/atom/src/Atom.cpp index 46ff78a799..9c3445c51c 100644 --- a/modules/atom/src/Atom.cpp +++ b/modules/atom/src/Atom.cpp @@ -1,7 +1,7 @@ /** * \file Atom.cpp \brief Simple atoms decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/BerendsenThermostatOptimizerState.cpp b/modules/atom/src/BerendsenThermostatOptimizerState.cpp index 51d05f3a5c..acae23e021 100644 --- a/modules/atom/src/BerendsenThermostatOptimizerState.cpp +++ b/modules/atom/src/BerendsenThermostatOptimizerState.cpp @@ -3,7 +3,7 @@ * \brief Maintains temperature during molecular dynamics using a * Berendsen thermostat. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/BondEndpointsRefiner.cpp b/modules/atom/src/BondEndpointsRefiner.cpp index 2b52024b83..ed2446f2e9 100644 --- a/modules/atom/src/BondEndpointsRefiner.cpp +++ b/modules/atom/src/BondEndpointsRefiner.cpp @@ -2,7 +2,7 @@ * \file BondEndpointsRefiner.cpp * \brief Return the hierarchy children of a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/atom/src/BondPairContainer.cpp b/modules/atom/src/BondPairContainer.cpp index 649b37c145..a95cec7eb6 100644 --- a/modules/atom/src/BondPairContainer.cpp +++ b/modules/atom/src/BondPairContainer.cpp @@ -2,7 +2,7 @@ * \file BondPairContainer.cpp * \brief A fake container that returns true if a pair of particles are bonded * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/BondSingletonScore.cpp b/modules/atom/src/BondSingletonScore.cpp index 8b5324fd18..cf5304afe8 100644 --- a/modules/atom/src/BondSingletonScore.cpp +++ b/modules/atom/src/BondSingletonScore.cpp @@ -2,7 +2,7 @@ * \file BondSingletonScore.cpp * \brief A score based a bond decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/atom/BondSingletonScore.h" diff --git a/modules/atom/src/BondedPairFilter.cpp b/modules/atom/src/BondedPairFilter.cpp index 3abe2068a6..7a62b820b8 100644 --- a/modules/atom/src/BondedPairFilter.cpp +++ b/modules/atom/src/BondedPairFilter.cpp @@ -2,7 +2,7 @@ * \file BondPairFilter.cpp * \brief A fake container that returns true if a pair of particles are bonded * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/BrownianDynamics.cpp b/modules/atom/src/BrownianDynamics.cpp index a882e2b0e3..50fabb391c 100644 --- a/modules/atom/src/BrownianDynamics.cpp +++ b/modules/atom/src/BrownianDynamics.cpp @@ -1,7 +1,7 @@ /** * \file BrownianDynamics.cpp \brief Simple Brownian dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/BrownianDynamicsTAMD.cpp b/modules/atom/src/BrownianDynamicsTAMD.cpp index 99090cedcf..78bce4b5cc 100644 --- a/modules/atom/src/BrownianDynamicsTAMD.cpp +++ b/modules/atom/src/BrownianDynamicsTAMD.cpp @@ -2,7 +2,7 @@ * \file BrownianDynamicsTAMD.cpp \brief Simple Brownian dynamics optimizer * with TAMD adjustments. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/CAAngleRestraint.cpp b/modules/atom/src/CAAngleRestraint.cpp index 84f7e9e152..909fca18fc 100644 --- a/modules/atom/src/CAAngleRestraint.cpp +++ b/modules/atom/src/CAAngleRestraint.cpp @@ -2,7 +2,7 @@ * \file CAAngleRestraint.cpp \brief Dihedral restraint between four * particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/CADihedralRestraint.cpp b/modules/atom/src/CADihedralRestraint.cpp index 9eef45862a..6c6e56277b 100644 --- a/modules/atom/src/CADihedralRestraint.cpp +++ b/modules/atom/src/CADihedralRestraint.cpp @@ -2,7 +2,7 @@ * \file CADihedralRestraint.cpp \brief Dihedral restraint between four * particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/CHARMMAtom.cpp b/modules/atom/src/CHARMMAtom.cpp index ec646db6e9..4d4991ab2e 100644 --- a/modules/atom/src/CHARMMAtom.cpp +++ b/modules/atom/src/CHARMMAtom.cpp @@ -2,7 +2,7 @@ * \file atom/CHARMMAtom.h * \brief A decorator for an atom that has a defined CHARMM type. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/CHARMMParameters.cpp b/modules/atom/src/CHARMMParameters.cpp index c85befda92..51a17e738d 100644 --- a/modules/atom/src/CHARMMParameters.cpp +++ b/modules/atom/src/CHARMMParameters.cpp @@ -2,7 +2,7 @@ * \file CHARMMParameters \brief access to CHARMMParameters * force field parameters * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/atom/src/CHARMMStereochemistryRestraint.cpp b/modules/atom/src/CHARMMStereochemistryRestraint.cpp index e5dbee0b05..e189b54aac 100644 --- a/modules/atom/src/CHARMMStereochemistryRestraint.cpp +++ b/modules/atom/src/CHARMMStereochemistryRestraint.cpp @@ -2,7 +2,7 @@ * \file CHARMMStereochemistryRestraint.cpp * \brief Class to maintain CHARMM stereochemistry. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/CenterOfMass.cpp b/modules/atom/src/CenterOfMass.cpp index 6347b7b1ca..200e98d233 100644 --- a/modules/atom/src/CenterOfMass.cpp +++ b/modules/atom/src/CenterOfMass.cpp @@ -2,7 +2,7 @@ * \file CenterOfMass.cpp * \brief Center of mass of a set of particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Chain.cpp b/modules/atom/src/Chain.cpp index 647786484e..8e06616a72 100644 --- a/modules/atom/src/Chain.cpp +++ b/modules/atom/src/Chain.cpp @@ -2,7 +2,7 @@ * \file Chain.cpp * \brief Store info for a protein chain. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Charged.cpp b/modules/atom/src/Charged.cpp index 3e2fd089b8..9d8a9fe6dd 100644 --- a/modules/atom/src/Charged.cpp +++ b/modules/atom/src/Charged.cpp @@ -2,7 +2,7 @@ * \file atom/Charged.cpp * \brief A decorator for a point particle that has an electrostatic charge. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Copy.cpp b/modules/atom/src/Copy.cpp index fb2050d026..62c0fa13a6 100644 --- a/modules/atom/src/Copy.cpp +++ b/modules/atom/src/Copy.cpp @@ -1,7 +1,7 @@ /** * \file Copy.cpp \brief Simple xyz decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/CoulombPairScore.cpp b/modules/atom/src/CoulombPairScore.cpp index 5626f61c92..18ff703986 100644 --- a/modules/atom/src/CoulombPairScore.cpp +++ b/modules/atom/src/CoulombPairScore.cpp @@ -2,7 +2,7 @@ * \file CoulombPairScore.cpp * \brief Coulomb (electrostatic) score between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/atom/src/CoverBond.cpp b/modules/atom/src/CoverBond.cpp index 4a46417bb7..64ce414cdd 100644 --- a/modules/atom/src/CoverBond.cpp +++ b/modules/atom/src/CoverBond.cpp @@ -2,7 +2,7 @@ * \file CoverBond.cpp * \brief Cover a bond with a sphere. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Diffusion.cpp b/modules/atom/src/Diffusion.cpp index 8b9da311e5..fd176ca8a4 100644 --- a/modules/atom/src/Diffusion.cpp +++ b/modules/atom/src/Diffusion.cpp @@ -1,7 +1,7 @@ /** * \file Diffusion.cpp \brief Simple xyzr decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/DihedralSingletonScore.cpp b/modules/atom/src/DihedralSingletonScore.cpp index 968a3e0a4d..05e013dac4 100644 --- a/modules/atom/src/DihedralSingletonScore.cpp +++ b/modules/atom/src/DihedralSingletonScore.cpp @@ -2,7 +2,7 @@ * \file atom/DihedralSingletonScore.h * \brief A score on a dihedral angle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/atom/src/Domain.cpp b/modules/atom/src/Domain.cpp index 0624819978..ac9ba534ba 100644 --- a/modules/atom/src/Domain.cpp +++ b/modules/atom/src/Domain.cpp @@ -2,7 +2,7 @@ * \file Domain.cpp * \brief A decorator for associating a particle with a protein domain. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/DopePairScore.cpp b/modules/atom/src/DopePairScore.cpp index 0cedc4a251..1ebc793f06 100644 --- a/modules/atom/src/DopePairScore.cpp +++ b/modules/atom/src/DopePairScore.cpp @@ -2,7 +2,7 @@ * \file DopePairScore.cpp * \brief Dope score * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/EzRestraint.cpp b/modules/atom/src/EzRestraint.cpp index f397714d1c..47e2682cee 100644 --- a/modules/atom/src/EzRestraint.cpp +++ b/modules/atom/src/EzRestraint.cpp @@ -2,7 +2,7 @@ * \file EzRestraint.cpp \brief * \brief Ez potential. A statistical scoring function for atom proteins * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/ForceFieldParameters.cpp b/modules/atom/src/ForceFieldParameters.cpp index 753da197ab..7809a3ec70 100644 --- a/modules/atom/src/ForceFieldParameters.cpp +++ b/modules/atom/src/ForceFieldParameters.cpp @@ -1,7 +1,7 @@ /** * \file ForceFieldParameters \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Fragment.cpp b/modules/atom/src/Fragment.cpp index a2fca7cb66..b99e78c755 100644 --- a/modules/atom/src/Fragment.cpp +++ b/modules/atom/src/Fragment.cpp @@ -2,7 +2,7 @@ * \file Fragment.cpp * \brief A decorator to associate a particle with a part of a protein/DNA/RNA. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/HelixRestraint.cpp b/modules/atom/src/HelixRestraint.cpp index fc0f099ebc..bf625282cd 100644 --- a/modules/atom/src/HelixRestraint.cpp +++ b/modules/atom/src/HelixRestraint.cpp @@ -2,7 +2,7 @@ * \file IMP/atom/HelixRestraint.cpp * \brief Class to maintain helix shape (dihedrals + elastic network) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/atom/src/Hierarchy.cpp b/modules/atom/src/Hierarchy.cpp index d48bc0ff72..839729f2c7 100644 --- a/modules/atom/src/Hierarchy.cpp +++ b/modules/atom/src/Hierarchy.cpp @@ -1,7 +1,7 @@ /** * \file Hierarchy.cpp \brief Decorator for helping deal with a hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/ImproperSingletonScore.cpp b/modules/atom/src/ImproperSingletonScore.cpp index 79b70b8fee..d02d5d378c 100644 --- a/modules/atom/src/ImproperSingletonScore.cpp +++ b/modules/atom/src/ImproperSingletonScore.cpp @@ -2,7 +2,7 @@ * \file atom/ImproperSingletonScore.h * \brief A score on the deviation of an improper angle from ideality. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/atom/src/LangevinThermostatOptimizerState.cpp b/modules/atom/src/LangevinThermostatOptimizerState.cpp index d0a49f396f..91071c4014 100644 --- a/modules/atom/src/LangevinThermostatOptimizerState.cpp +++ b/modules/atom/src/LangevinThermostatOptimizerState.cpp @@ -2,7 +2,7 @@ * \file VelocityScalingOptimizerState.cpp * \brief Maintains temperature during molecular dynamics by velocity scaling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/LennardJones.cpp b/modules/atom/src/LennardJones.cpp index 83a2eb230f..15b11d675a 100644 --- a/modules/atom/src/LennardJones.cpp +++ b/modules/atom/src/LennardJones.cpp @@ -2,7 +2,7 @@ * \file atom/LennardJones.cpp * \brief A decorator for a particle that has a Lennard-Jones potential well. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/LennardJonesPairScore.cpp b/modules/atom/src/LennardJonesPairScore.cpp index e8f97bede0..d0f6568926 100644 --- a/modules/atom/src/LennardJonesPairScore.cpp +++ b/modules/atom/src/LennardJonesPairScore.cpp @@ -2,7 +2,7 @@ * \file LennardJonesPairScore.cpp * \brief Lennard-Jones score between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/atom/src/LoopStatisticalPairScore.cpp b/modules/atom/src/LoopStatisticalPairScore.cpp index 5593a497bf..f46fae20a3 100644 --- a/modules/atom/src/LoopStatisticalPairScore.cpp +++ b/modules/atom/src/LoopStatisticalPairScore.cpp @@ -2,7 +2,7 @@ * \file LoopStatisticalPairScore.cpp * \brief Fiser/Melo loop modeling statistical potential * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Mass.cpp b/modules/atom/src/Mass.cpp index 7d5fe3d38d..9074cc8585 100644 --- a/modules/atom/src/Mass.cpp +++ b/modules/atom/src/Mass.cpp @@ -2,7 +2,7 @@ * \file Mass.cpp * \brief A decorator for particles with mass. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/MolecularDynamics.cpp b/modules/atom/src/MolecularDynamics.cpp index 8d5df330a5..f23e7c9c91 100644 --- a/modules/atom/src/MolecularDynamics.cpp +++ b/modules/atom/src/MolecularDynamics.cpp @@ -1,7 +1,7 @@ /** * \file MolecularDynamics.cpp \brief Simple molecular dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Molecule.cpp b/modules/atom/src/Molecule.cpp index f38b168c7b..56d4fc746a 100644 --- a/modules/atom/src/Molecule.cpp +++ b/modules/atom/src/Molecule.cpp @@ -1,7 +1,7 @@ /** * \file Atom.cpp \brief Simple atoms decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/RemoveRigidMotionOptimizerState.cpp b/modules/atom/src/RemoveRigidMotionOptimizerState.cpp index 48746252cc..8a72e7ea33 100644 --- a/modules/atom/src/RemoveRigidMotionOptimizerState.cpp +++ b/modules/atom/src/RemoveRigidMotionOptimizerState.cpp @@ -2,7 +2,7 @@ * \file RemoveRigidMOtionOptimizerState.cpp * \brief Maintains temperature during molecular dynamics by velocity scaling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/RemoveTranslationOptimizerState.cpp b/modules/atom/src/RemoveTranslationOptimizerState.cpp index bdc71362f9..ca68a94b2a 100644 --- a/modules/atom/src/RemoveTranslationOptimizerState.cpp +++ b/modules/atom/src/RemoveTranslationOptimizerState.cpp @@ -2,7 +2,7 @@ * \file RemoveTranslationOptimizerState.cpp * \brief Remove rigid translation during optimization. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Representation.cpp b/modules/atom/src/Representation.cpp index 6efa3a1ef2..323843c66c 100644 --- a/modules/atom/src/Representation.cpp +++ b/modules/atom/src/Representation.cpp @@ -1,7 +1,7 @@ /** * \file Atom.cpp \brief Simple atoms decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Residue.cpp b/modules/atom/src/Residue.cpp index 11f37d5495..b11d5d340c 100644 --- a/modules/atom/src/Residue.cpp +++ b/modules/atom/src/Residue.cpp @@ -1,7 +1,7 @@ /** * \file Atom.cpp \brief Simple atoms decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/SameResiduePairFilter.cpp b/modules/atom/src/SameResiduePairFilter.cpp index 92ef38e71d..9af96cfc3f 100644 --- a/modules/atom/src/SameResiduePairFilter.cpp +++ b/modules/atom/src/SameResiduePairFilter.cpp @@ -2,7 +2,7 @@ * \file BondPairFilter.cpp * \brief A fake container that returns true if a pair of particles are bonded * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/SecondaryStructureResidue.cpp b/modules/atom/src/SecondaryStructureResidue.cpp index 268e9d93bd..7f8bea0b08 100644 --- a/modules/atom/src/SecondaryStructureResidue.cpp +++ b/modules/atom/src/SecondaryStructureResidue.cpp @@ -1,7 +1,7 @@ /** * \file atom/SecondaryStructureResidue.cpp * \brief A decorator for storing secondary structure probabilities. - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Selection.cpp b/modules/atom/src/Selection.cpp index fd4806e916..133ba7923d 100644 --- a/modules/atom/src/Selection.cpp +++ b/modules/atom/src/Selection.cpp @@ -2,7 +2,7 @@ * \file IMP/atom/Selection.cpp * \brief Select a subset of a hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/Simulator.cpp b/modules/atom/src/Simulator.cpp index 1a257729ee..dd3bc679cc 100644 --- a/modules/atom/src/Simulator.cpp +++ b/modules/atom/src/Simulator.cpp @@ -1,7 +1,7 @@ /** * \file Simulator.cpp \brief Simple Brownian dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/State.cpp b/modules/atom/src/State.cpp index 51dc591145..0bfa420b17 100644 --- a/modules/atom/src/State.cpp +++ b/modules/atom/src/State.cpp @@ -1,7 +1,7 @@ /** * \file State.cpp \brief Simple xyz decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/StereochemistryPairFilter.cpp b/modules/atom/src/StereochemistryPairFilter.cpp index 983c042d0e..a948377223 100644 --- a/modules/atom/src/StereochemistryPairFilter.cpp +++ b/modules/atom/src/StereochemistryPairFilter.cpp @@ -2,7 +2,7 @@ * \file atom/StereochemistryPairFilter.h * \brief A filter that excludes bonds, angles and dihedrals. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/StructureSource.cpp b/modules/atom/src/StructureSource.cpp index 4360165298..8c97c9c36f 100644 --- a/modules/atom/src/StructureSource.cpp +++ b/modules/atom/src/StructureSource.cpp @@ -2,7 +2,7 @@ * \file atom/StructureSource.cpp * \brief Add a Source Structure ID and Source Chain ID * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/TAMDCentroid.cpp b/modules/atom/src/TAMDCentroid.cpp index 51d303d748..7710a53316 100644 --- a/modules/atom/src/TAMDCentroid.cpp +++ b/modules/atom/src/TAMDCentroid.cpp @@ -1,7 +1,7 @@ /** * \file TAMDCentroid.cpp \brief A centroid for TAMD simulations * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/TAMDParticle.cpp b/modules/atom/src/TAMDParticle.cpp index eecfaec31f..4ef9062809 100644 --- a/modules/atom/src/TAMDParticle.cpp +++ b/modules/atom/src/TAMDParticle.cpp @@ -1,7 +1,7 @@ /** * \file TAMDParticle.cpp \brief Simple xyzr decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/VelocityScalingOptimizerState.cpp b/modules/atom/src/VelocityScalingOptimizerState.cpp index f8c271798a..b01ce395e6 100644 --- a/modules/atom/src/VelocityScalingOptimizerState.cpp +++ b/modules/atom/src/VelocityScalingOptimizerState.cpp @@ -2,7 +2,7 @@ * \file VelocityScalingOptimizerState.cpp * \brief Maintains temperature during molecular dynamics by velocity scaling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/alignment.cpp b/modules/atom/src/alignment.cpp index 8495f4b933..fef7f4071e 100644 --- a/modules/atom/src/alignment.cpp +++ b/modules/atom/src/alignment.cpp @@ -2,7 +2,7 @@ * \file alignment.cpp * \brief Alignment of structures * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/angle_decorators.cpp b/modules/atom/src/angle_decorators.cpp index 6c4e372ef8..c10bd70722 100644 --- a/modules/atom/src/angle_decorators.cpp +++ b/modules/atom/src/angle_decorators.cpp @@ -1,7 +1,7 @@ /** * \file atom/angle_decorators.cpp \brief Decorators for angles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/bond_decorators.cpp b/modules/atom/src/bond_decorators.cpp index 88759b441f..b7f0e78b8e 100644 --- a/modules/atom/src/bond_decorators.cpp +++ b/modules/atom/src/bond_decorators.cpp @@ -1,7 +1,7 @@ /** * \file bond_decorators.cpp \brief Decorators for a bond * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/bond_graph.cpp b/modules/atom/src/bond_graph.cpp index 1eb1100719..e94cdacb57 100644 --- a/modules/atom/src/bond_graph.cpp +++ b/modules/atom/src/bond_graph.cpp @@ -1,7 +1,7 @@ /** * \file bond_graph.cpp \brief Decorators for a bond * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/charmm_topology.cpp b/modules/atom/src/charmm_topology.cpp index 595616b94b..e437ecd8b5 100644 --- a/modules/atom/src/charmm_topology.cpp +++ b/modules/atom/src/charmm_topology.cpp @@ -1,7 +1,7 @@ /** * \file charmm_topology.cpp \brief Classes for handling CHARMM-style topology. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/atom/src/dihedrals.cpp b/modules/atom/src/dihedrals.cpp index 50ac35444b..6408223dde 100644 --- a/modules/atom/src/dihedrals.cpp +++ b/modules/atom/src/dihedrals.cpp @@ -1,7 +1,7 @@ /** * \file dihedrals.cpp \brief Helpers to extract dihedral information. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/distance.cpp b/modules/atom/src/distance.cpp index 98590ca5e9..1d5f3a12fb 100644 --- a/modules/atom/src/distance.cpp +++ b/modules/atom/src/distance.cpp @@ -1,7 +1,7 @@ /** * \file distance.cpp \brief distance measures * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/atom/src/element.cpp b/modules/atom/src/element.cpp index 8cc0b5f6cc..abbff1191c 100644 --- a/modules/atom/src/element.cpp +++ b/modules/atom/src/element.cpp @@ -1,7 +1,7 @@ /** * \file Element \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/estimates.cpp b/modules/atom/src/estimates.cpp index ea2ea0a080..649ddbab06 100644 --- a/modules/atom/src/estimates.cpp +++ b/modules/atom/src/estimates.cpp @@ -2,7 +2,7 @@ * \file estimates.cpp * \brief Estimates of various physical quantities. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/atom/estimates.h" diff --git a/modules/atom/src/force_fields.cpp b/modules/atom/src/force_fields.cpp index 618fa99c5d..872f1ef874 100644 --- a/modules/atom/src/force_fields.cpp +++ b/modules/atom/src/force_fields.cpp @@ -1,7 +1,7 @@ /** * \file force_fields \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/hierarchy_tools.cpp b/modules/atom/src/hierarchy_tools.cpp index 123d31a9ba..851635cfd3 100644 --- a/modules/atom/src/hierarchy_tools.cpp +++ b/modules/atom/src/hierarchy_tools.cpp @@ -2,7 +2,7 @@ * \file atom/hierarchy_tools.cpp * \brief A decorator for a point particle that has an electrostatic charge. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/internal/charmm_helpers.cpp b/modules/atom/src/internal/charmm_helpers.cpp index 9dfa3db467..0b00697d62 100644 --- a/modules/atom/src/internal/charmm_helpers.cpp +++ b/modules/atom/src/internal/charmm_helpers.cpp @@ -2,7 +2,7 @@ * \file charmm_helpers.cpp * \brief Helper functions for CHARMM support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/atom/src/internal/mol2.cpp b/modules/atom/src/internal/mol2.cpp index 0f0216e41e..c66227271b 100644 --- a/modules/atom/src/internal/mol2.cpp +++ b/modules/atom/src/internal/mol2.cpp @@ -2,7 +2,7 @@ * \file mol2 reader * \brief A class with static functions for parsing mol2 file * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/internal/pdb.cpp b/modules/atom/src/internal/pdb.cpp index c1e696eebf..f5397898fe 100644 --- a/modules/atom/src/internal/pdb.cpp +++ b/modules/atom/src/internal/pdb.cpp @@ -2,7 +2,7 @@ * \file PDBParser.h * \brief A class with static functions for parsing PDB files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/mmcif.cpp b/modules/atom/src/mmcif.cpp index baeabeb486..d8a049dd4a 100644 --- a/modules/atom/src/mmcif.cpp +++ b/modules/atom/src/mmcif.cpp @@ -2,7 +2,7 @@ * \file mmcif.cpp * \brief Functions to read PDBs in mmCIF format * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/src/mol2.cpp b/modules/atom/src/mol2.cpp index b39964fd84..efe8ae582d 100644 --- a/modules/atom/src/mol2.cpp +++ b/modules/atom/src/mol2.cpp @@ -1,7 +1,7 @@ /** * \file mol2.cpp \brief A class for reading mol2 files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/atom/src/pdb.cpp b/modules/atom/src/pdb.cpp index 2c78427908..d71f0623d5 100644 --- a/modules/atom/src/pdb.cpp +++ b/modules/atom/src/pdb.cpp @@ -1,7 +1,7 @@ /** * \file PDBParser.h \brief A class for reading PDB files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/atom/src/protein_ligand_score.cpp b/modules/atom/src/protein_ligand_score.cpp index 1a1c2d8e58..31c00c452e 100644 --- a/modules/atom/src/protein_ligand_score.cpp +++ b/modules/atom/src/protein_ligand_score.cpp @@ -1,7 +1,7 @@ /** * \file protein_ligand_score.cpp \brief A class for reading mol2 files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/atom/src/secondary_structure_reader.cpp b/modules/atom/src/secondary_structure_reader.cpp index 3af0f8d728..c09540d88e 100644 --- a/modules/atom/src/secondary_structure_reader.cpp +++ b/modules/atom/src/secondary_structure_reader.cpp @@ -1,7 +1,7 @@ /** * \file secondary_structure_reader.cpp \brief Reading PSIPRED/DSSP results * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/atom/src/smoothing_functions.cpp b/modules/atom/src/smoothing_functions.cpp index 74ad323e7e..b11685ce81 100644 --- a/modules/atom/src/smoothing_functions.cpp +++ b/modules/atom/src/smoothing_functions.cpp @@ -1,7 +1,7 @@ /** * \file smoothing_functions.cpp Classes to smooth nonbonded interactions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/benchmark/benchmark/benchmark_nothing.cpp b/modules/benchmark/benchmark/benchmark_nothing.cpp index 70db4b3be1..7a20f58aed 100644 --- a/modules/benchmark/benchmark/benchmark_nothing.cpp +++ b/modules/benchmark/benchmark/benchmark_nothing.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/benchmark/include/Profiler.h b/modules/benchmark/include/Profiler.h index 5603a067bf..793f96f7bf 100644 --- a/modules/benchmark/include/Profiler.h +++ b/modules/benchmark/include/Profiler.h @@ -2,7 +2,7 @@ * \file IMP/benchmark/Profiler.h * \brief Various utilities for benchmarking * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/benchmark/include/benchmark_macros.h b/modules/benchmark/include/benchmark_macros.h index a1be45ba06..f0a2b3eb0a 100644 --- a/modules/benchmark/include/benchmark_macros.h +++ b/modules/benchmark/include/benchmark_macros.h @@ -2,7 +2,7 @@ * \file IMP/benchmark/benchmark_macros.h * \brief Various general useful macros for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/benchmark/include/internal/control.h b/modules/benchmark/include/internal/control.h index bba4002eee..e8be954933 100644 --- a/modules/benchmark/include/internal/control.h +++ b/modules/benchmark/include/internal/control.h @@ -2,7 +2,7 @@ * \file benchmark/control.h * \brief Various utilities for benchmarking * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/benchmark/include/internal/flags.h b/modules/benchmark/include/internal/flags.h index 4ecebc663a..c7d6d74e17 100644 --- a/modules/benchmark/include/internal/flags.h +++ b/modules/benchmark/include/internal/flags.h @@ -2,7 +2,7 @@ * \file IMP/benchmark/flags.h * \brief Various general useful macros for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/benchmark/include/internal/utility.h b/modules/benchmark/include/internal/utility.h index 5eee588374..cc3fab1a30 100644 --- a/modules/benchmark/include/internal/utility.h +++ b/modules/benchmark/include/internal/utility.h @@ -2,7 +2,7 @@ * \file benchmark/utility.h * \brief Various utilities for benchmarking * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/benchmark/include/utility.h b/modules/benchmark/include/utility.h index 5631b811b8..870870eb75 100644 --- a/modules/benchmark/include/utility.h +++ b/modules/benchmark/include/utility.h @@ -2,7 +2,7 @@ * \file IMP/benchmark/utility.h * \brief Various utilities for benchmarking * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/benchmark/src/Profiler.cpp b/modules/benchmark/src/Profiler.cpp index 161544be1f..ffa779563f 100644 --- a/modules/benchmark/src/Profiler.cpp +++ b/modules/benchmark/src/Profiler.cpp @@ -1,6 +1,6 @@ /** \file utility.cpp Benchmarking utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/benchmark/src/internal/control.cpp b/modules/benchmark/src/internal/control.cpp index 09c2e3fd02..39fd50dc44 100644 --- a/modules/benchmark/src/internal/control.cpp +++ b/modules/benchmark/src/internal/control.cpp @@ -1,6 +1,6 @@ /** \file utility.cpp Benchmarking utilties * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/benchmark/src/internal/flags.cpp b/modules/benchmark/src/internal/flags.cpp index cdfa2336b8..1477de4ee7 100644 --- a/modules/benchmark/src/internal/flags.cpp +++ b/modules/benchmark/src/internal/flags.cpp @@ -1,6 +1,6 @@ /** \file utility.cpp Benchmarking utilties * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/benchmark/src/internal/utility.cpp b/modules/benchmark/src/internal/utility.cpp index 1b9c298b51..4fa0d1a821 100644 --- a/modules/benchmark/src/internal/utility.cpp +++ b/modules/benchmark/src/internal/utility.cpp @@ -1,6 +1,6 @@ /** \file utility.cpp Benchmarking utilties * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/benchmark/src/utility.cpp b/modules/benchmark/src/utility.cpp index 4733f4f2f5..4c836d613a 100644 --- a/modules/benchmark/src/utility.cpp +++ b/modules/benchmark/src/utility.cpp @@ -1,6 +1,6 @@ /** \file utility.cpp Benchmarking utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/cgal/include/internal/bounding_sphere.h b/modules/cgal/include/internal/bounding_sphere.h index bcf1a818ef..2f516e733f 100644 --- a/modules/cgal/include/internal/bounding_sphere.h +++ b/modules/cgal/include/internal/bounding_sphere.h @@ -1,7 +1,7 @@ /** * \file bounding_sphere.h \brief Simple 3D sphere class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cgal/include/internal/knn.h b/modules/cgal/include/internal/knn.h index 0253d86650..4fe5520d34 100644 --- a/modules/cgal/include/internal/knn.h +++ b/modules/cgal/include/internal/knn.h @@ -1,7 +1,7 @@ /** * \file cgal/internal/knn.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCGAL_INTERNAL_KNN_H diff --git a/modules/cgal/include/internal/polygons.h b/modules/cgal/include/internal/polygons.h index 19ad651865..bea8a6c726 100644 --- a/modules/cgal/include/internal/polygons.h +++ b/modules/cgal/include/internal/polygons.h @@ -1,7 +1,7 @@ /** * \file cgal/internal/polygons.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCGAL_INTERNAL_POLYGONS_H diff --git a/modules/cgal/include/internal/polyhedrons.h b/modules/cgal/include/internal/polyhedrons.h index 60c6101de8..a163bbb4e5 100644 --- a/modules/cgal/include/internal/polyhedrons.h +++ b/modules/cgal/include/internal/polyhedrons.h @@ -1,7 +1,7 @@ /** * \file cgal/internal/polyhedrons.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCGAL_INTERNAL_POLYHEDRONS_H diff --git a/modules/cgal/include/internal/sphere_cover.h b/modules/cgal/include/internal/sphere_cover.h index 1e5b912824..bf09036375 100644 --- a/modules/cgal/include/internal/sphere_cover.h +++ b/modules/cgal/include/internal/sphere_cover.h @@ -1,7 +1,7 @@ /** * \file cgal/internal/polyhedrons.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCGAL_INTERNAL_SPHERE_COVER_H diff --git a/modules/cgal/include/internal/union_of_balls.h b/modules/cgal/include/internal/union_of_balls.h index c7819ca3a3..97d1e7359f 100644 --- a/modules/cgal/include/internal/union_of_balls.h +++ b/modules/cgal/include/internal/union_of_balls.h @@ -1,7 +1,7 @@ /** * \file cgal/internal/polyhedrons.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCGAL_INTERNAL_UNION_OF_BALLS_H diff --git a/modules/cgal/src/internal/bounding_sphere.cpp b/modules/cgal/src/internal/bounding_sphere.cpp index d460708cb4..b6a87617de 100644 --- a/modules/cgal/src/internal/bounding_sphere.cpp +++ b/modules/cgal/src/internal/bounding_sphere.cpp @@ -2,7 +2,7 @@ * \file Sphere3D.cpp * \brief simple implementation of spheres in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/cgal/src/internal/errors.cpp b/modules/cgal/src/internal/errors.cpp index 460454f6f3..96a0b7fd5d 100644 --- a/modules/cgal/src/internal/errors.cpp +++ b/modules/cgal/src/internal/errors.cpp @@ -2,7 +2,7 @@ * \file Sphere3D.cpp * \brief simple implementation of spheres in 3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/cgal/src/internal/knn.cpp b/modules/cgal/src/internal/knn.cpp index 3d799976ce..67a66b1912 100644 --- a/modules/cgal/src/internal/knn.cpp +++ b/modules/cgal/src/internal/knn.cpp @@ -1,7 +1,7 @@ /** * \file internal/cgal_knn.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/cgal/src/internal/polygons.cpp b/modules/cgal/src/internal/polygons.cpp index 2bb760ac76..a47257afce 100644 --- a/modules/cgal/src/internal/polygons.cpp +++ b/modules/cgal/src/internal/polygons.cpp @@ -1,7 +1,7 @@ /** * \file internal/cgal_knn.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ // value in Lazy #include diff --git a/modules/cgal/src/internal/polyhedrons.cpp b/modules/cgal/src/internal/polyhedrons.cpp index c5c0544a57..7f1a355f1c 100644 --- a/modules/cgal/src/internal/polyhedrons.cpp +++ b/modules/cgal/src/internal/polyhedrons.cpp @@ -1,7 +1,7 @@ /** * \file internal/cgal_knn.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/cgal/src/internal/sphere_cover.cpp b/modules/cgal/src/internal/sphere_cover.cpp index 0d8fed02fb..36504571c5 100644 --- a/modules/cgal/src/internal/sphere_cover.cpp +++ b/modules/cgal/src/internal/sphere_cover.cpp @@ -1,7 +1,7 @@ /** * \file internal/cgal_knn.h * \brief manipulation of text, and Interconversion between text and numbers - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/cgal/src/internal/union_of_balls.cpp b/modules/cgal/src/internal/union_of_balls.cpp index 56eeb6e04e..f01e94c68a 100644 --- a/modules/cgal/src/internal/union_of_balls.cpp +++ b/modules/cgal/src/internal/union_of_balls.cpp @@ -3,7 +3,7 @@ * \brief computation of molecular volumetrics : * surface and area of an union of balls * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/cnmultifit/include/AlignSymmetric.h b/modules/cnmultifit/include/AlignSymmetric.h index 016fa13e01..e5fd6e6c9a 100644 --- a/modules/cnmultifit/include/AlignSymmetric.h +++ b/modules/cnmultifit/include/AlignSymmetric.h @@ -2,7 +2,7 @@ * \file IMP/cnmultifit/AlignSymmetric.h * \brief Fast alignment of a cyclic model to its density. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/include/CnSymmAxisDetector.h b/modules/cnmultifit/include/CnSymmAxisDetector.h index d583d34b57..231188a0b3 100644 --- a/modules/cnmultifit/include/CnSymmAxisDetector.h +++ b/modules/cnmultifit/include/CnSymmAxisDetector.h @@ -2,7 +2,7 @@ * \file IMP/cnmultifit/CnSymmAxisDetector.h * \brief Detect cn symmetry in proteins and density maps. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/include/MolCnSymmAxisDetector.h b/modules/cnmultifit/include/MolCnSymmAxisDetector.h index c1080a58c4..fd8720d429 100644 --- a/modules/cnmultifit/include/MolCnSymmAxisDetector.h +++ b/modules/cnmultifit/include/MolCnSymmAxisDetector.h @@ -2,7 +2,7 @@ * \file IMP/cnmultifit/MolCnSymmAxisDetector.h * \brief molecule symmetry detector * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/include/cn_rmsd.h b/modules/cnmultifit/include/cn_rmsd.h index a795abc700..27ab28f027 100644 --- a/modules/cnmultifit/include/cn_rmsd.h +++ b/modules/cnmultifit/include/cn_rmsd.h @@ -2,7 +2,7 @@ * \file IMP/cnmultifit/cn_rmsd.h * \brief High-level functions for RMSD calculation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/include/internal/Parameters.h b/modules/cnmultifit/include/internal/Parameters.h index 327505f57e..6eff281373 100644 --- a/modules/cnmultifit/include/internal/Parameters.h +++ b/modules/cnmultifit/include/internal/Parameters.h @@ -2,7 +2,7 @@ * \file Parameters.h * \brief Parameters for symmetric MultiFit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCNMULTIFIT_PARAMETERS_H diff --git a/modules/cnmultifit/include/symmetric_multifit.h b/modules/cnmultifit/include/symmetric_multifit.h index a57e3dfd52..47ace79451 100644 --- a/modules/cnmultifit/include/symmetric_multifit.h +++ b/modules/cnmultifit/include/symmetric_multifit.h @@ -2,7 +2,7 @@ * \file IMP/cnmultifit/symmetric_multifit.h * \brief Build cyclic symmetric complexes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/include/symmetry_utils.h b/modules/cnmultifit/include/symmetry_utils.h index 175abb208f..c86283f290 100644 --- a/modules/cnmultifit/include/symmetry_utils.h +++ b/modules/cnmultifit/include/symmetry_utils.h @@ -2,7 +2,7 @@ * \file IMP/cnmultifit/symmetry_utils.h * \brief Symmetry utilities. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/src/AlignSymmetric.cpp b/modules/cnmultifit/src/AlignSymmetric.cpp index 0c0da82de2..c81add0b5e 100644 --- a/modules/cnmultifit/src/AlignSymmetric.cpp +++ b/modules/cnmultifit/src/AlignSymmetric.cpp @@ -2,7 +2,7 @@ * \file AlignSymmetric.cpp * \brief Fast alignment of a cyclic model to its density. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/src/CnSymmAxisDetector.cpp b/modules/cnmultifit/src/CnSymmAxisDetector.cpp index 61178e4fd4..e5d8e82706 100644 --- a/modules/cnmultifit/src/CnSymmAxisDetector.cpp +++ b/modules/cnmultifit/src/CnSymmAxisDetector.cpp @@ -2,7 +2,7 @@ * \file CnSymmAxisDetector.cpp * \brief Detect cn symmetry in proteins and density maps. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/src/MolCnSymmAxisDetector.cpp b/modules/cnmultifit/src/MolCnSymmAxisDetector.cpp index 1bb7e165cb..dafec0a565 100644 --- a/modules/cnmultifit/src/MolCnSymmAxisDetector.cpp +++ b/modules/cnmultifit/src/MolCnSymmAxisDetector.cpp @@ -2,7 +2,7 @@ * \file MolCnSymmAxisDetector.cpp * \brief molecule symmetry detector * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/cnmultifit/src/cn_rmsd.cpp b/modules/cnmultifit/src/cn_rmsd.cpp index b6951e8f4f..d090b5f7a7 100644 --- a/modules/cnmultifit/src/cn_rmsd.cpp +++ b/modules/cnmultifit/src/cn_rmsd.cpp @@ -1,7 +1,7 @@ /** * \file cn_rmsd.cpp \brief High-level functions for RMSD calculation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/src/internal/Parameters.cpp b/modules/cnmultifit/src/internal/Parameters.cpp index 80f3912869..4b821161c2 100644 --- a/modules/cnmultifit/src/internal/Parameters.cpp +++ b/modules/cnmultifit/src/internal/Parameters.cpp @@ -2,7 +2,7 @@ * \file Parameters.cpp * \brief Parameters for symmetric MultiFit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/cnmultifit/src/symmetric_multifit.cpp b/modules/cnmultifit/src/symmetric_multifit.cpp index e186d1b3d8..9b6b8cc869 100644 --- a/modules/cnmultifit/src/symmetric_multifit.cpp +++ b/modules/cnmultifit/src/symmetric_multifit.cpp @@ -1,7 +1,7 @@ /** * \file symmetric_multifit.cpp \brief Build cyclic symmetric complexes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/cnmultifit/src/symmetry_utils.cpp b/modules/cnmultifit/src/symmetry_utils.cpp index 117b6730e0..1b6d97e769 100644 --- a/modules/cnmultifit/src/symmetry_utils.cpp +++ b/modules/cnmultifit/src/symmetry_utils.cpp @@ -2,7 +2,7 @@ * \file symmetry_utils.cpp * \brief Symmetry utilities. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/benchmark/benchmark_close_pairs_finders.cpp b/modules/container/benchmark/benchmark_close_pairs_finders.cpp index dcef285135..1945f6978f 100644 --- a/modules/container/benchmark/benchmark_close_pairs_finders.cpp +++ b/modules/container/benchmark/benchmark_close_pairs_finders.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/container/benchmark/benchmark_connectivity.cpp b/modules/container/benchmark/benchmark_connectivity.cpp index 4bae1259ca..65fee03229 100644 --- a/modules/container/benchmark/benchmark_connectivity.cpp +++ b/modules/container/benchmark/benchmark_connectivity.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/container/benchmark/benchmark_evaluate.cpp b/modules/container/benchmark/benchmark_evaluate.cpp index 39a69fb2b1..20409887f9 100644 --- a/modules/container/benchmark/benchmark_evaluate.cpp +++ b/modules/container/benchmark/benchmark_evaluate.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/container/benchmark/benchmark_random_collisions.cpp b/modules/container/benchmark/benchmark_random_collisions.cpp index 2d1c785dc2..d9dd13e959 100644 --- a/modules/container/benchmark/benchmark_random_collisions.cpp +++ b/modules/container/benchmark/benchmark_random_collisions.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/container/benchmark/benchmark_rigid_collisions.cpp b/modules/container/benchmark/benchmark_rigid_collisions.cpp index 337d8fa772..d7d1c8869f 100644 --- a/modules/container/benchmark/benchmark_rigid_collisions.cpp +++ b/modules/container/benchmark/benchmark_rigid_collisions.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/container/include/AllBipartitePairContainer.h b/modules/container/include/AllBipartitePairContainer.h index 8262c65e53..714e7ae059 100644 --- a/modules/container/include/AllBipartitePairContainer.h +++ b/modules/container/include/AllBipartitePairContainer.h @@ -2,7 +2,7 @@ * \file IMP/container/AllBipartitePairContainer.h * \brief Return all bipartite pairs between two containers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_ALL_BIPARTITE_PAIR_CONTAINER_H diff --git a/modules/container/include/AllPairContainer.h b/modules/container/include/AllPairContainer.h index 6502ab8679..f9544b3782 100644 --- a/modules/container/include/AllPairContainer.h +++ b/modules/container/include/AllPairContainer.h @@ -2,7 +2,7 @@ * \file IMP/container/AllPairContainer.h * \brief Return all pairs from a SingletonContainer * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_ALL_PAIR_CONTAINER_H diff --git a/modules/container/include/CloseBipartitePairContainer.h b/modules/container/include/CloseBipartitePairContainer.h index 6892688ed7..ffcff80d8a 100644 --- a/modules/container/include/CloseBipartitePairContainer.h +++ b/modules/container/include/CloseBipartitePairContainer.h @@ -2,7 +2,7 @@ * \file IMP/container/CloseBipartitePairContainer.h * \brief Return all pairs from a SingletonContainer * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CLOSE_BIPARTITE_PAIR_CONTAINER_H diff --git a/modules/container/include/ClosePairContainer.h b/modules/container/include/ClosePairContainer.h index 2decd0c6b3..7f67d26200 100644 --- a/modules/container/include/ClosePairContainer.h +++ b/modules/container/include/ClosePairContainer.h @@ -2,7 +2,7 @@ * \file IMP/container/ClosePairContainer.h * \brief Return all pairs from a SingletonContainer * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CLOSE_PAIR_CONTAINER_H diff --git a/modules/container/include/ConnectingPairContainer.h b/modules/container/include/ConnectingPairContainer.h index 0b71fd17a9..420677955b 100644 --- a/modules/container/include/ConnectingPairContainer.h +++ b/modules/container/include/ConnectingPairContainer.h @@ -2,7 +2,7 @@ * \file IMP/container/ConnectingPairContainer.h * \brief A container which has pairs which ensure a set is connected * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CONNECTING_PAIR_CONTAINER_H diff --git a/modules/container/include/ConsecutivePairContainer.h b/modules/container/include/ConsecutivePairContainer.h index f66392b751..792c1f7431 100644 --- a/modules/container/include/ConsecutivePairContainer.h +++ b/modules/container/include/ConsecutivePairContainer.h @@ -2,7 +2,7 @@ * \file IMP/container/ConsecutivePairContainer.h * \brief Return all pairs from a SingletonContainer * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CONSECUTIVE_PAIR_CONTAINER_H diff --git a/modules/container/include/generic.h b/modules/container/include/generic.h index a960640833..feeb9e8da0 100644 --- a/modules/container/include/generic.h +++ b/modules/container/include/generic.h @@ -2,7 +2,7 @@ * \file IMP/container/generic.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/include/internal/CloseBipartitePairContainer.h b/modules/container/include/internal/CloseBipartitePairContainer.h index 3f988e3fb4..d5f31c3376 100644 --- a/modules/container/include/internal/CloseBipartitePairContainer.h +++ b/modules/container/include/internal/CloseBipartitePairContainer.h @@ -2,7 +2,7 @@ * \file container/include/internal/CloseBipartitePairContainer.h * \brief Internal class of close bipartite pair container * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_INTERNAL_CONTAINER_CLOSE_BIPARTITE_PAIR_CONTAINER_H diff --git a/modules/container/include/internal/ClosePairContainer.h b/modules/container/include/internal/ClosePairContainer.h index 232c1124ad..1b4df4da77 100644 --- a/modules/container/include/internal/ClosePairContainer.h +++ b/modules/container/include/internal/ClosePairContainer.h @@ -2,7 +2,7 @@ * \file container/internal/ClosePairContainer.h * \brief Internal class of close pair container * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_INTERNAL_CONTAINER_CLOSE_PAIR_CONTAINER_H diff --git a/modules/container/src/AllBipartitePairContainer.cpp b/modules/container/src/AllBipartitePairContainer.cpp index a701164414..ac9e25fab1 100644 --- a/modules/container/src/AllBipartitePairContainer.cpp +++ b/modules/container/src/AllBipartitePairContainer.cpp @@ -2,7 +2,7 @@ * \file AllBipartitePairContainer.cpp \brief A list of *ParticlePairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/src/AllPairContainer.cpp b/modules/container/src/AllPairContainer.cpp index c1c8f3401c..a2d9a324ba 100644 --- a/modules/container/src/AllPairContainer.cpp +++ b/modules/container/src/AllPairContainer.cpp @@ -1,7 +1,7 @@ /** * \file AllPairContainer.cpp \brief A list of ParticlePairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/src/CloseBipartitePairContainer.cpp b/modules/container/src/CloseBipartitePairContainer.cpp index d516f10478..922b4087ae 100644 --- a/modules/container/src/CloseBipartitePairContainer.cpp +++ b/modules/container/src/CloseBipartitePairContainer.cpp @@ -1,7 +1,7 @@ /** * \file CloseBipartitePairContainer.cpp \brief A list of ParticlePairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/src/ClosePairContainer.cpp b/modules/container/src/ClosePairContainer.cpp index 0bbff44aae..3ee827056a 100644 --- a/modules/container/src/ClosePairContainer.cpp +++ b/modules/container/src/ClosePairContainer.cpp @@ -1,7 +1,7 @@ /** * \file ClosePairContainer.cpp \brief A list of ParticlePairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/src/ConnectingPairContainer.cpp b/modules/container/src/ConnectingPairContainer.cpp index ed8d7911f0..d6d174987f 100644 --- a/modules/container/src/ConnectingPairContainer.cpp +++ b/modules/container/src/ConnectingPairContainer.cpp @@ -1,7 +1,7 @@ /** * \file ConnectingPairContainer.cpp \brief A list of ParticlePairs. * - * Copyright 2007-2021 IMP Inventors. Connecting rights reserved. + * Copyright 2007-2022 IMP Inventors. Connecting rights reserved. * */ diff --git a/modules/container/src/ConsecutivePairContainer.cpp b/modules/container/src/ConsecutivePairContainer.cpp index 0c5c680cf2..6f405d86ec 100644 --- a/modules/container/src/ConsecutivePairContainer.cpp +++ b/modules/container/src/ConsecutivePairContainer.cpp @@ -1,7 +1,7 @@ /** * \file AllPairContainer.cpp \brief A list of ParticlePairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/src/internal/CloseBipartitePairContainer.cpp b/modules/container/src/internal/CloseBipartitePairContainer.cpp index 92cda4f1a9..a8408c1f1b 100644 --- a/modules/container/src/internal/CloseBipartitePairContainer.cpp +++ b/modules/container/src/internal/CloseBipartitePairContainer.cpp @@ -2,7 +2,7 @@ * \file CloseBipartitePairContainer.cpp * \brief internal implementation of close pair container * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/src/internal/ClosePairContainer.cpp b/modules/container/src/internal/ClosePairContainer.cpp index 7473e9266a..34240034be 100644 --- a/modules/container/src/internal/ClosePairContainer.cpp +++ b/modules/container/src/internal/ClosePairContainer.cpp @@ -2,7 +2,7 @@ * \file ClosePairContainer.cpp * \brief internal implementation of close pair container * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/container/test/test_consecutive_pair_container.cpp b/modules/container/test/test_consecutive_pair_container.cpp index e4c94774e9..d17d547e98 100644 --- a/modules/container/test/test_consecutive_pair_container.cpp +++ b/modules/container/test/test_consecutive_pair_container.cpp @@ -1,7 +1,7 @@ /** * \file test_.cpp \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/benchmark/benchmark_omp_evaluate.cpp b/modules/core/benchmark/benchmark_omp_evaluate.cpp index e5ca43b1dc..35dba949cd 100644 --- a/modules/core/benchmark/benchmark_omp_evaluate.cpp +++ b/modules/core/benchmark/benchmark_omp_evaluate.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/core/benchmark/benchmark_xyz_access.cpp b/modules/core/benchmark/benchmark_xyz_access.cpp index 9ae5a0dc6e..46900ddcdf 100644 --- a/modules/core/benchmark/benchmark_xyz_access.cpp +++ b/modules/core/benchmark/benchmark_xyz_access.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/core/include/AngleRestraint.h b/modules/core/include/AngleRestraint.h index 83c64540e4..5f18a75c5a 100644 --- a/modules/core/include/AngleRestraint.h +++ b/modules/core/include/AngleRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/AngleRestraint.h * \brief Angle restraint between three particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/AngleTripletScore.h b/modules/core/include/AngleTripletScore.h index 753652406a..de309fd944 100644 --- a/modules/core/include/AngleTripletScore.h +++ b/modules/core/include/AngleTripletScore.h @@ -2,7 +2,7 @@ * \file IMP/core/AngleTripletScore.h * \brief A Score on the angle between three particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_ANGLE_TRIPLET_SCORE_H diff --git a/modules/core/include/BallMover.h b/modules/core/include/BallMover.h index 01d9288f4f..337be4a646 100644 --- a/modules/core/include/BallMover.h +++ b/modules/core/include/BallMover.h @@ -2,7 +2,7 @@ * \file IMP/core/BallMover.h * \brief A modifier which variables within a ball. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/BoundingBox3DSingletonScore.h b/modules/core/include/BoundingBox3DSingletonScore.h index 59ea86927b..96c9b3cd82 100644 --- a/modules/core/include/BoundingBox3DSingletonScore.h +++ b/modules/core/include/BoundingBox3DSingletonScore.h @@ -2,7 +2,7 @@ * \file IMP/core/BoundingBox3DSingletonScore.h * \brief Score particles based on a bounding box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_BOUNDING_BOX_3DSINGLETON_SCORE_H diff --git a/modules/core/include/BoundingSphere3DSingletonScore.h b/modules/core/include/BoundingSphere3DSingletonScore.h index dc58936c72..454c93eef9 100644 --- a/modules/core/include/BoundingSphere3DSingletonScore.h +++ b/modules/core/include/BoundingSphere3DSingletonScore.h @@ -4,7 +4,7 @@ * increase as particles are exiting the sphere boundaries, and must * be zero within the sphere and positive outside of it. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_BOUNDING_SPHERE_3D_SINGLETON_SCORE_H diff --git a/modules/core/include/BoxSweepClosePairsFinder.h b/modules/core/include/BoxSweepClosePairsFinder.h index 9bc3a0cbf1..2e404afbaf 100644 --- a/modules/core/include/BoxSweepClosePairsFinder.h +++ b/modules/core/include/BoxSweepClosePairsFinder.h @@ -2,7 +2,7 @@ * \file IMP/core/BoxSweepClosePairsFinder.h * \brief Test all pairs of particles to find close pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_BOX_SWEEP_CLOSE_PAIRS_FINDER_H diff --git a/modules/core/include/CentroidOfRefined.h b/modules/core/include/CentroidOfRefined.h index f78c7f4f0c..f9a69451a5 100644 --- a/modules/core/include/CentroidOfRefined.h +++ b/modules/core/include/CentroidOfRefined.h @@ -3,7 +3,7 @@ * \brief Set the coordinates of the particle to be the centroid of the * refined particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_CENTROID_OF_REFINED_H diff --git a/modules/core/include/ChecksScoreState.h b/modules/core/include/ChecksScoreState.h index f326f9f6ca..5f92a476b4 100644 --- a/modules/core/include/ChecksScoreState.h +++ b/modules/core/include/ChecksScoreState.h @@ -1,7 +1,7 @@ /** * \file IMP/core/ChecksScoreState.h \brief Turn checks on and off. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_CHECKS_SCORE_STATE_H diff --git a/modules/core/include/ChildrenRefiner.h b/modules/core/include/ChildrenRefiner.h index 68d3f6b994..4e76d103a6 100644 --- a/modules/core/include/ChildrenRefiner.h +++ b/modules/core/include/ChildrenRefiner.h @@ -2,7 +2,7 @@ * \file IMP/core/ChildrenRefiner.h * \brief Return the hierarchy children of a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_CHILDREN_REFINER_H diff --git a/modules/core/include/ClosePairsFinder.h b/modules/core/include/ClosePairsFinder.h index 5c6b040c70..b97c8e8ffd 100644 --- a/modules/core/include/ClosePairsFinder.h +++ b/modules/core/include/ClosePairsFinder.h @@ -2,7 +2,7 @@ * \file IMP/core/ClosePairsFinder.h * \brief A base class for algorithms to detect proximities. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_CLOSE_PAIRS_FINDER_H diff --git a/modules/core/include/ClosePairsPairScore.h b/modules/core/include/ClosePairsPairScore.h index 6d69862fb5..6a26f06a84 100644 --- a/modules/core/include/ClosePairsPairScore.h +++ b/modules/core/include/ClosePairsPairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/ClosePairsPairScore.h * \brief Apply a PairScore to close pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_CLOSE_PAIRS_PAIR_SCORE_H diff --git a/modules/core/include/ClosedCubicSpline.h b/modules/core/include/ClosedCubicSpline.h index 1b3808acc7..3cc264b342 100644 --- a/modules/core/include/ClosedCubicSpline.h +++ b/modules/core/include/ClosedCubicSpline.h @@ -1,7 +1,7 @@ /** * \file IMP/core/ClosedCubicSpline.h \brief Closed cubic spline function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_CLOSED_CUBIC_SPLINE_H diff --git a/modules/core/include/ConjugateGradients.h b/modules/core/include/ConjugateGradients.h index c1f3a4613e..1a06229e3c 100644 --- a/modules/core/include/ConjugateGradients.h +++ b/modules/core/include/ConjugateGradients.h @@ -2,7 +2,7 @@ * \file IMP/core/ConjugateGradients.h * \brief Simple conjugate gradients optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/ConnectivityRestraint.h b/modules/core/include/ConnectivityRestraint.h index b1d0ac0491..8657aefa4c 100644 --- a/modules/core/include/ConnectivityRestraint.h +++ b/modules/core/include/ConnectivityRestraint.h @@ -4,7 +4,7 @@ * Restrict max distance between at least one pair of particles of any * two distinct types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/ConstantRestraint.h b/modules/core/include/ConstantRestraint.h index b2c3597149..c0b39697f9 100644 --- a/modules/core/include/ConstantRestraint.h +++ b/modules/core/include/ConstantRestraint.h @@ -3,7 +3,7 @@ * * Just return a constant. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/Cosine.h b/modules/core/include/Cosine.h index 976c771b9e..6ea83123fa 100644 --- a/modules/core/include/Cosine.h +++ b/modules/core/include/Cosine.h @@ -1,7 +1,7 @@ /** * \file IMP/core/Cosine.h \brief Cosine function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_COSINE_H diff --git a/modules/core/include/CoverRefined.h b/modules/core/include/CoverRefined.h index f5fe40c674..96fbd21fce 100644 --- a/modules/core/include/CoverRefined.h +++ b/modules/core/include/CoverRefined.h @@ -2,7 +2,7 @@ * \file IMP/core/CoverRefined.h * \brief Set the position and radius of a particle to enclose the refined. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_COVER_REFINED_H diff --git a/modules/core/include/DataObject.h b/modules/core/include/DataObject.h index a008f27c5f..5b08d162ad 100644 --- a/modules/core/include/DataObject.h +++ b/modules/core/include/DataObject.h @@ -2,7 +2,7 @@ * \file IMP/core/DataObject.h * \brief A modifier which variables within a ball. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/DerivativesFromRefined.h b/modules/core/include/DerivativesFromRefined.h index 5ef77bf394..6f2ec76ce7 100644 --- a/modules/core/include/DerivativesFromRefined.h +++ b/modules/core/include/DerivativesFromRefined.h @@ -2,7 +2,7 @@ * \file IMP/core/DerivativesFromRefined.h * \brief Accumulate the derivatives of the refined particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_DERIVATIVES_FROM_REFINED_H diff --git a/modules/core/include/DerivativesToRefined.h b/modules/core/include/DerivativesToRefined.h index d003f4314d..1537c5df43 100644 --- a/modules/core/include/DerivativesToRefined.h +++ b/modules/core/include/DerivativesToRefined.h @@ -2,7 +2,7 @@ * \file IMP/core/DerivativesToRefined.h * \brief Accumulate the derivatives of the refined particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_DERIVATIVES_TO_REFINED_H diff --git a/modules/core/include/DiameterRestraint.h b/modules/core/include/DiameterRestraint.h index dbf86b441f..dc65b3f6dc 100644 --- a/modules/core/include/DiameterRestraint.h +++ b/modules/core/include/DiameterRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/DiameterRestraint.h * \brief A restraint to maintain the diameter of a set of points * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_DIAMETER_RESTRAINT_H diff --git a/modules/core/include/DihedralRestraint.h b/modules/core/include/DihedralRestraint.h index 14941f190d..50e3fe23d7 100644 --- a/modules/core/include/DihedralRestraint.h +++ b/modules/core/include/DihedralRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/DihedralRestraint.h * \brief Dihedral restraint between four particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/DirectionMover.h b/modules/core/include/DirectionMover.h index c787f8e8fd..4b13b958be 100644 --- a/modules/core/include/DirectionMover.h +++ b/modules/core/include/DirectionMover.h @@ -2,7 +2,7 @@ * \file IMP/core/DirectionMover.h * \brief A mover that transforms a Direction. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/DistancePairScore.h b/modules/core/include/DistancePairScore.h index 632b47ad0f..5450931a9d 100644 --- a/modules/core/include/DistancePairScore.h +++ b/modules/core/include/DistancePairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/DistancePairScore.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_DISTANCE_PAIR_SCORE_H diff --git a/modules/core/include/DistanceRestraint.h b/modules/core/include/DistanceRestraint.h index 602d6d2fde..a310899ec2 100644 --- a/modules/core/include/DistanceRestraint.h +++ b/modules/core/include/DistanceRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/DistanceRestraint.h * \brief Distance restraint between two particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/DistanceToSingletonScore.h b/modules/core/include/DistanceToSingletonScore.h index 3ae5ab189a..d94b375ec7 100644 --- a/modules/core/include/DistanceToSingletonScore.h +++ b/modules/core/include/DistanceToSingletonScore.h @@ -2,7 +2,7 @@ * \file IMP/core/DistanceToSingletonScore.h * \brief A Score on the distance to a fixed point. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_DISTANCE_TO_SINGLETON_SCORE_H diff --git a/modules/core/include/ExcludedVolumeRestraint.h b/modules/core/include/ExcludedVolumeRestraint.h index ea68b0d2e3..6e7688fd57 100644 --- a/modules/core/include/ExcludedVolumeRestraint.h +++ b/modules/core/include/ExcludedVolumeRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/ExcludedVolumeRestraint.h * \brief Prevent spheres from inter-penetrating * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_EXCLUDED_VOLUME_RESTRAINT_H diff --git a/modules/core/include/FixedRefiner.h b/modules/core/include/FixedRefiner.h index 7d4e890717..0eadb36e74 100644 --- a/modules/core/include/FixedRefiner.h +++ b/modules/core/include/FixedRefiner.h @@ -2,7 +2,7 @@ * \file IMP/core/FixedRefiner.h * \brief A particle refiner which returns a fixed set of particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_FIXED_REFINER_H diff --git a/modules/core/include/Gaussian.h b/modules/core/include/Gaussian.h index 9e595c4487..a6acc39fe7 100644 --- a/modules/core/include/Gaussian.h +++ b/modules/core/include/Gaussian.h @@ -2,7 +2,7 @@ * \file IMP/core/Gaussian.h * \brief Decorator to hold Gaussian3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/GenericAttributeSingletonScore.h b/modules/core/include/GenericAttributeSingletonScore.h index 9ef38d7aca..a8496416b0 100644 --- a/modules/core/include/GenericAttributeSingletonScore.h +++ b/modules/core/include/GenericAttributeSingletonScore.h @@ -2,7 +2,7 @@ * \file IMP/core/GenericAttributeSingletonScore.h * \brief A score based on the unmodified value of an attribute. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_GENERIC_ATTRIBUTE_SINGLETON_SCORE_H diff --git a/modules/core/include/GridClosePairsFinder.h b/modules/core/include/GridClosePairsFinder.h index a9856cce6b..a91ef2a908 100644 --- a/modules/core/include/GridClosePairsFinder.h +++ b/modules/core/include/GridClosePairsFinder.h @@ -2,7 +2,7 @@ * \file IMP/core/GridClosePairsFinder.h * \brief Use a hierarchy of grids to find close pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_GRID_CLOSE_PAIRS_FINDER_H diff --git a/modules/core/include/Harmonic.h b/modules/core/include/Harmonic.h index 0b4e695007..3d2e4808b5 100644 --- a/modules/core/include/Harmonic.h +++ b/modules/core/include/Harmonic.h @@ -1,7 +1,7 @@ /** * \file IMP/core/Harmonic.h \brief Harmonic function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_HARMONIC_H diff --git a/modules/core/include/HarmonicLowerBound.h b/modules/core/include/HarmonicLowerBound.h index d65359faf7..2a0973e2d9 100644 --- a/modules/core/include/HarmonicLowerBound.h +++ b/modules/core/include/HarmonicLowerBound.h @@ -1,7 +1,7 @@ /** * \file IMP/core/HarmonicLowerBound.h \brief Harmonic lower bound function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_HARMONIC_LOWER_BOUND_H diff --git a/modules/core/include/HarmonicUpperBound.h b/modules/core/include/HarmonicUpperBound.h index d0cd1c442f..041e8d0da2 100644 --- a/modules/core/include/HarmonicUpperBound.h +++ b/modules/core/include/HarmonicUpperBound.h @@ -1,7 +1,7 @@ /** * \file IMP/core/HarmonicUpperBound.h \brief Harmonic upper bound function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_HARMONIC_UPPER_BOUND_H diff --git a/modules/core/include/HarmonicWell.h b/modules/core/include/HarmonicWell.h index ecdced6c8b..bd29f5d0e7 100644 --- a/modules/core/include/HarmonicWell.h +++ b/modules/core/include/HarmonicWell.h @@ -1,7 +1,7 @@ /** * \file IMP/core/HarmonicWell.h \brief Harmonic function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_HARMONIC_WELL_H diff --git a/modules/core/include/Hierarchy.h b/modules/core/include/Hierarchy.h index 4d88e348f3..a696f8af16 100644 --- a/modules/core/include/Hierarchy.h +++ b/modules/core/include/Hierarchy.h @@ -2,7 +2,7 @@ * \file IMP/core/Hierarchy.h \brief Decorator for helping deal with * a hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/IncrementalScoringFunction.h b/modules/core/include/IncrementalScoringFunction.h index 2ae6e694af..ead845262c 100644 --- a/modules/core/include/IncrementalScoringFunction.h +++ b/modules/core/include/IncrementalScoringFunction.h @@ -2,7 +2,7 @@ * \file IMP/core/IncrementalScoringFunction.h * \brief Score model efficiently when a small number of particles are changed. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/LeavesRefiner.h b/modules/core/include/LeavesRefiner.h index b731572d81..03746aae6e 100644 --- a/modules/core/include/LeavesRefiner.h +++ b/modules/core/include/LeavesRefiner.h @@ -2,7 +2,7 @@ * \file IMP/core/LeavesRefiner.h * \brief Return the hierarchy leaves under a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_LEAVES_REFINER_H diff --git a/modules/core/include/Linear.h b/modules/core/include/Linear.h index 503ca8765c..58600160de 100644 --- a/modules/core/include/Linear.h +++ b/modules/core/include/Linear.h @@ -1,7 +1,7 @@ /** * \file IMP/core/Linear.h \brief A linear function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_LINEAR_H diff --git a/modules/core/include/LogNormalMover.h b/modules/core/include/LogNormalMover.h index ead456bc94..73c328c5c6 100644 --- a/modules/core/include/LogNormalMover.h +++ b/modules/core/include/LogNormalMover.h @@ -2,7 +2,7 @@ * \file IMP/core/LogNormalMover.h * \brief A modifier that perturbs a point with a log-normal distribution. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/MCCGSampler.h b/modules/core/include/MCCGSampler.h index 039bea43bc..b982497842 100644 --- a/modules/core/include/MCCGSampler.h +++ b/modules/core/include/MCCGSampler.h @@ -2,7 +2,7 @@ * \file IMP/core/MCCGSampler.h * \brief A Monte Carlo/Conjugate Gradients based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/MSConnectivityRestraint.h b/modules/core/include/MSConnectivityRestraint.h index 402b25d049..e5005d4504 100644 --- a/modules/core/include/MSConnectivityRestraint.h +++ b/modules/core/include/MSConnectivityRestraint.h @@ -5,7 +5,7 @@ * Restrict max distance between at least one pair of particles of any * two distinct types. It also handles multiple copies of the same particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/MinimumRestraint.h b/modules/core/include/MinimumRestraint.h index a954bd1965..452aad0a00 100644 --- a/modules/core/include/MinimumRestraint.h +++ b/modules/core/include/MinimumRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/MinimumRestraint.h * \brief Score based on the k minimum restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/MonteCarlo.h b/modules/core/include/MonteCarlo.h index afdf3ad693..6ca07dc19f 100644 --- a/modules/core/include/MonteCarlo.h +++ b/modules/core/include/MonteCarlo.h @@ -1,7 +1,7 @@ /** * \file IMP/core/MonteCarlo.h \brief Simple Monte Carlo optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/MonteCarloMover.h b/modules/core/include/MonteCarloMover.h index e3f958eed3..087061db70 100644 --- a/modules/core/include/MonteCarloMover.h +++ b/modules/core/include/MonteCarloMover.h @@ -2,7 +2,7 @@ * \file IMP/core/MonteCarloMover.h * \brief The base class for movers for Monte Carlo optimization. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/MoveStatisticsScoreState.h b/modules/core/include/MoveStatisticsScoreState.h index db94e10e5d..8459aade24 100644 --- a/modules/core/include/MoveStatisticsScoreState.h +++ b/modules/core/include/MoveStatisticsScoreState.h @@ -2,7 +2,7 @@ * \file IMP/core/MoveStatisticsScoreState.h * \brief Write geometry to a file during optimization * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_MOVE_STATISTICS_SCORE_STATE_H diff --git a/modules/core/include/MultipleBinormalRestraint.h b/modules/core/include/MultipleBinormalRestraint.h index f3e5b1696d..413f968acf 100644 --- a/modules/core/include/MultipleBinormalRestraint.h +++ b/modules/core/include/MultipleBinormalRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/MultipleBinormalRestraint.h * \brief Modeller-style multiple binormal (phi/psi) restraint. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/NearestNeighborsClosePairsFinder.h b/modules/core/include/NearestNeighborsClosePairsFinder.h index a8bac77139..d40d75369f 100644 --- a/modules/core/include/NearestNeighborsClosePairsFinder.h +++ b/modules/core/include/NearestNeighborsClosePairsFinder.h @@ -2,7 +2,7 @@ * \file IMP/core/NearestNeighborsClosePairsFinder.h * \brief Test all pairs of particles to find close pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_NEAREST_NEIGHBORS_CLOSE_PAIRS_FINDER_H diff --git a/modules/core/include/NeighborsTable.h b/modules/core/include/NeighborsTable.h index 63b057c07c..16fbf10988 100644 --- a/modules/core/include/NeighborsTable.h +++ b/modules/core/include/NeighborsTable.h @@ -2,7 +2,7 @@ * \file IMP/core/NeighborsTable.h * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/NormalMover.h b/modules/core/include/NormalMover.h index 2b88e248c6..5a5a525428 100644 --- a/modules/core/include/NormalMover.h +++ b/modules/core/include/NormalMover.h @@ -2,7 +2,7 @@ * \file IMP/core/NormalMover.h * \brief A modifier which perturbs a point with a normal distribution. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/OpenCubicSpline.h b/modules/core/include/OpenCubicSpline.h index 9a1884bf77..55e024242f 100644 --- a/modules/core/include/OpenCubicSpline.h +++ b/modules/core/include/OpenCubicSpline.h @@ -1,7 +1,7 @@ /** * \file IMP/core/OpenCubicSpline.h \brief Open cubic spline function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_OPEN_CUBIC_SPLINE_H diff --git a/modules/core/include/PeriodicOptimizerState.h b/modules/core/include/PeriodicOptimizerState.h index b1d2c836ad..d91163c2df 100644 --- a/modules/core/include/PeriodicOptimizerState.h +++ b/modules/core/include/PeriodicOptimizerState.h @@ -2,7 +2,7 @@ * \file IMP/core/PeriodicOptimizerState.h * \brief Angle restraint between three particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/QuadraticClosePairsFinder.h b/modules/core/include/QuadraticClosePairsFinder.h index 7fb469f723..06d2868734 100644 --- a/modules/core/include/QuadraticClosePairsFinder.h +++ b/modules/core/include/QuadraticClosePairsFinder.h @@ -2,7 +2,7 @@ * \file IMP/core/QuadraticClosePairsFinder.h * \brief Test all pairs of particles to find close pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_QUADRATIC_CLOSE_PAIRS_FINDER_H diff --git a/modules/core/include/RefinedPairsPairScore.h b/modules/core/include/RefinedPairsPairScore.h index 559776c6f8..f8a3e0ac79 100644 --- a/modules/core/include/RefinedPairsPairScore.h +++ b/modules/core/include/RefinedPairsPairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/RefinedPairsPairScore.h * \brief Generate pairs by applying a Refiner to the particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_REFINED_PAIRS_PAIR_SCORE_H diff --git a/modules/core/include/RestraintsScoringFunction.h b/modules/core/include/RestraintsScoringFunction.h index b6ba71604e..a9a0bded91 100644 --- a/modules/core/include/RestraintsScoringFunction.h +++ b/modules/core/include/RestraintsScoringFunction.h @@ -2,7 +2,7 @@ * \file IMP/core/RestraintsScoringFunction.h * \brief A scoring function on a list of restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/RigidBodyAnglePairScore.h b/modules/core/include/RigidBodyAnglePairScore.h index c6a9f82323..9b12c302ee 100644 --- a/modules/core/include/RigidBodyAnglePairScore.h +++ b/modules/core/include/RigidBodyAnglePairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/RigidBodyAnglePairScore.h * \brief A Score on the crossing angle between two rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_RIGID_BODY_ANGLE_PAIR_SCORE_H diff --git a/modules/core/include/RigidBodyDistancePairScore.h b/modules/core/include/RigidBodyDistancePairScore.h index 1d59a7a36b..a7d5551cff 100644 --- a/modules/core/include/RigidBodyDistancePairScore.h +++ b/modules/core/include/RigidBodyDistancePairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/RigidBodyDistancePairScore.h * \brief Act on the distance between two rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_RIGID_BODY_DISTANCE_PAIR_SCORE_H diff --git a/modules/core/include/RigidBodyMover.h b/modules/core/include/RigidBodyMover.h index f022bc9682..8064df4f2d 100644 --- a/modules/core/include/RigidBodyMover.h +++ b/modules/core/include/RigidBodyMover.h @@ -2,7 +2,7 @@ * \file IMP/core/RigidBodyMover.h * \brief A mover that transforms a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/RigidBodyTunneler.h b/modules/core/include/RigidBodyTunneler.h index 4459e67e24..c6a432ea22 100644 --- a/modules/core/include/RigidBodyTunneler.h +++ b/modules/core/include/RigidBodyTunneler.h @@ -2,7 +2,7 @@ * \file IMP/core/RigidBodyTunneler.h * \brief A mover that transform a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/RigidBodyUmbrella.h b/modules/core/include/RigidBodyUmbrella.h index 779e7f539e..13bd332398 100644 --- a/modules/core/include/RigidBodyUmbrella.h +++ b/modules/core/include/RigidBodyUmbrella.h @@ -2,7 +2,7 @@ * \file IMP/core/RigidBodyUmbrella.h * \brief Distance restraint between two particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/RigidClosePairsFinder.h b/modules/core/include/RigidClosePairsFinder.h index cefb41a8b7..a0e1afb7de 100644 --- a/modules/core/include/RigidClosePairsFinder.h +++ b/modules/core/include/RigidClosePairsFinder.h @@ -2,7 +2,7 @@ * \file IMP/core/RigidClosePairsFinder.h * \brief Handle rigid bodies by looking at their members * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_RIGID_CLOSE_PAIRS_FINDER_H diff --git a/modules/core/include/SerialMover.h b/modules/core/include/SerialMover.h index dad663d8bb..bb2bfe6ee4 100644 --- a/modules/core/include/SerialMover.h +++ b/modules/core/include/SerialMover.h @@ -2,7 +2,7 @@ * \file IMP/core/SerialMover.h * \brief A mover that applies other movers one at a time * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/SphereDistancePairScore.h b/modules/core/include/SphereDistancePairScore.h index 3ab7dee5db..31574e3445 100644 --- a/modules/core/include/SphereDistancePairScore.h +++ b/modules/core/include/SphereDistancePairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/SphereDistancePairScore.h * \brief A score on the distance between the surfaces of two spheres. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_SPHERE_DISTANCE_PAIR_SCORE_H diff --git a/modules/core/include/StatisticalPairScore.h b/modules/core/include/StatisticalPairScore.h index 607ebec483..184e6aa0d3 100644 --- a/modules/core/include/StatisticalPairScore.h +++ b/modules/core/include/StatisticalPairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/StatisticalPairScore.h * \brief Functions to read mol2s * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/SteepestDescent.h b/modules/core/include/SteepestDescent.h index 42fc533256..510b235eea 100644 --- a/modules/core/include/SteepestDescent.h +++ b/modules/core/include/SteepestDescent.h @@ -1,7 +1,7 @@ /** * \file IMP/core/SteepestDescent.h \brief Simple steepest descent optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/SubsetMover.h b/modules/core/include/SubsetMover.h index bda8ed928a..a2b15496c0 100644 --- a/modules/core/include/SubsetMover.h +++ b/modules/core/include/SubsetMover.h @@ -2,7 +2,7 @@ * \file IMP/core/SubsetMover.h * \brief A mover that applies a random subset of movers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/Surface.h b/modules/core/include/Surface.h index f385d768c4..523931fe26 100644 --- a/modules/core/include/Surface.h +++ b/modules/core/include/Surface.h @@ -1,7 +1,7 @@ /** * \file IMP/core/Surface.h \brief Simple surface decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/SurfaceDistancePairScore.h b/modules/core/include/SurfaceDistancePairScore.h index d8532d9893..f05a66c9cc 100644 --- a/modules/core/include/SurfaceDistancePairScore.h +++ b/modules/core/include/SurfaceDistancePairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/SurfaceDistancePairScore.h * \brief A score on the distance between a surface and a sphere. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_SURFACE_DISTANCE_PAIR_SCORE_H diff --git a/modules/core/include/SurfaceMover.h b/modules/core/include/SurfaceMover.h index 2e9f00e91a..0df4230b5e 100644 --- a/modules/core/include/SurfaceMover.h +++ b/modules/core/include/SurfaceMover.h @@ -2,7 +2,7 @@ * \file IMP/core/SurfaceMover.h * \brief A mover that transforms a Surface. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/SurfaceSymmetryConstraint.h b/modules/core/include/SurfaceSymmetryConstraint.h index 1b89263e3b..ad22b91d23 100644 --- a/modules/core/include/SurfaceSymmetryConstraint.h +++ b/modules/core/include/SurfaceSymmetryConstraint.h @@ -2,7 +2,7 @@ * \file IMP/core/SurfaceSymmetryConstraint.h * \brief Constrain orientation of surfaces with respect to rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/SurfaceTetheredChain.h b/modules/core/include/SurfaceTetheredChain.h index da5da511bf..38ef040e82 100644 --- a/modules/core/include/SurfaceTetheredChain.h +++ b/modules/core/include/SurfaceTetheredChain.h @@ -2,7 +2,7 @@ * \file IMP/core/SurfaceTetheredChain.h * \brief Score on surface-to-end distance of chain tethered to impenetrable surface * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_SURFACE_TETHERED_CHAIN_H diff --git a/modules/core/include/TableRefiner.h b/modules/core/include/TableRefiner.h index e6d60a4389..86eb61d443 100644 --- a/modules/core/include/TableRefiner.h +++ b/modules/core/include/TableRefiner.h @@ -2,7 +2,7 @@ * \file IMP/core/TableRefiner.h * \brief A lookup based particle refiner * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_TABLE_REFINER_H diff --git a/modules/core/include/Transform.h b/modules/core/include/Transform.h index 66b0b00058..3bd1305c1c 100644 --- a/modules/core/include/Transform.h +++ b/modules/core/include/Transform.h @@ -1,7 +1,7 @@ /** * \file IMP/core/Transform.h \brief Transform a particle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/TransformedDistancePairScore.h b/modules/core/include/TransformedDistancePairScore.h index 51121cef65..39f61d130b 100644 --- a/modules/core/include/TransformedDistancePairScore.h +++ b/modules/core/include/TransformedDistancePairScore.h @@ -3,7 +3,7 @@ * \brief A score on the distance between a pair of particles * after transforming one. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_TRANSFORMED_DISTANCE_PAIR_SCORE_H diff --git a/modules/core/include/TruncatedHarmonic.h b/modules/core/include/TruncatedHarmonic.h index ff434152c2..dca53b85be 100644 --- a/modules/core/include/TruncatedHarmonic.h +++ b/modules/core/include/TruncatedHarmonic.h @@ -1,7 +1,7 @@ /** * \file IMP/core/TruncatedHarmonic.h \brief Truncated harmonic. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_TRUNCATED_HARMONIC_H diff --git a/modules/core/include/Typed.h b/modules/core/include/Typed.h index afca99ba5c..d2a2911356 100644 --- a/modules/core/include/Typed.h +++ b/modules/core/include/Typed.h @@ -1,7 +1,7 @@ /** * \file IMP/core/Typed.h \brief A particle with a user-defined type. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/TypedPairScore.h b/modules/core/include/TypedPairScore.h index 5c3db4925f..9eb7f2c7a1 100644 --- a/modules/core/include/TypedPairScore.h +++ b/modules/core/include/TypedPairScore.h @@ -2,7 +2,7 @@ * \file IMP/core/TypedPairScore.h * \brief Delegate to another PairScore depending on particle types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_TYPED_PAIR_SCORE_H diff --git a/modules/core/include/VolumeRestraint.h b/modules/core/include/VolumeRestraint.h index 7a37be26a5..7785cd3b8c 100644 --- a/modules/core/include/VolumeRestraint.h +++ b/modules/core/include/VolumeRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/VolumeRestraint.h * \brief A restraint that prevents spheres from inter-penetrating * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_VOLUME_RESTRAINT_H diff --git a/modules/core/include/WeightedDerivativesToRefined.h b/modules/core/include/WeightedDerivativesToRefined.h index 38af3aa88f..28d69ec243 100644 --- a/modules/core/include/WeightedDerivativesToRefined.h +++ b/modules/core/include/WeightedDerivativesToRefined.h @@ -4,7 +4,7 @@ * to its refined set of particles using weights * indicated by a weight key. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_WEIGHTED_DERIVATIVES_TO_REFINED_H diff --git a/modules/core/include/WeightedSum.h b/modules/core/include/WeightedSum.h index 8a9eee1cce..05cc39ba33 100644 --- a/modules/core/include/WeightedSum.h +++ b/modules/core/include/WeightedSum.h @@ -1,7 +1,7 @@ /** * \file IMP/core/WeightedSum.h \brief Weighted sum of unary functions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_WEIGHTED_SUM_H diff --git a/modules/core/include/WeightedSumOfExponential.h b/modules/core/include/WeightedSumOfExponential.h index 90f519d354..ff7a8a9e76 100644 --- a/modules/core/include/WeightedSumOfExponential.h +++ b/modules/core/include/WeightedSumOfExponential.h @@ -2,7 +2,7 @@ * \file IMP/core/WeightedSumOfExponential.h * \brief Negative logarithm of weighted sum of negative exponential of unary functions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_WEIGHTED_SUM_OF_EXPONENTIAL_H diff --git a/modules/core/include/XYZ.h b/modules/core/include/XYZ.h index 405ca6a889..da8bdbaea5 100644 --- a/modules/core/include/XYZ.h +++ b/modules/core/include/XYZ.h @@ -1,7 +1,7 @@ /** * \file IMP/core/XYZ.h \brief Simple XYZ decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/XYZR.h b/modules/core/include/XYZR.h index ce19634906..8440773823 100644 --- a/modules/core/include/XYZR.h +++ b/modules/core/include/XYZR.h @@ -2,7 +2,7 @@ * \file IMP/core/XYZR.h * \brief Decorator for a sphere-like particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/blame.h b/modules/core/include/blame.h index 06232fb44a..6a6666ca5d 100644 --- a/modules/core/include/blame.h +++ b/modules/core/include/blame.h @@ -2,7 +2,7 @@ * \file IMP/core/blame.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/direction.h b/modules/core/include/direction.h index 4beb555131..5eb363b13e 100644 --- a/modules/core/include/direction.h +++ b/modules/core/include/direction.h @@ -2,7 +2,7 @@ * \file IMP/core/direction.h * \brief Decorators for directions and the angle between them. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/generic.h b/modules/core/include/generic.h index 056624417d..fd80cf7670 100644 --- a/modules/core/include/generic.h +++ b/modules/core/include/generic.h @@ -2,7 +2,7 @@ * \file IMP/core/generic.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/internal/MovedSingletonContainer.h b/modules/core/include/internal/MovedSingletonContainer.h index 2867548c32..0e81899fbe 100644 --- a/modules/core/include/internal/MovedSingletonContainer.h +++ b/modules/core/include/internal/MovedSingletonContainer.h @@ -3,7 +3,7 @@ * \brief Keep track of the maximum change of a set of attributes * for e.g., incremental updateing of close pair containers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_INTERNAL_MOVED_SINGLETON_CONTAINER_H diff --git a/modules/core/include/internal/angle_helpers.h b/modules/core/include/internal/angle_helpers.h index f75901a560..47384ad808 100644 --- a/modules/core/include/internal/angle_helpers.h +++ b/modules/core/include/internal/angle_helpers.h @@ -2,7 +2,7 @@ * \file anglel_helpers.h * \brief Helper functions to calculate and handle angles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_ANGLE_HELPERS_H diff --git a/modules/core/include/internal/close_pairs_helpers.h b/modules/core/include/internal/close_pairs_helpers.h index 97fcf4e930..e68a97f772 100644 --- a/modules/core/include/internal/close_pairs_helpers.h +++ b/modules/core/include/internal/close_pairs_helpers.h @@ -2,7 +2,7 @@ * \file internal/close_pairs_helpers.h * \brief utilities for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_INTERNAL_CLOSE_PAIRS_HELPERS_H diff --git a/modules/core/include/internal/container_helpers.h b/modules/core/include/internal/container_helpers.h index 12f9fa195e..0622feeeb1 100644 --- a/modules/core/include/internal/container_helpers.h +++ b/modules/core/include/internal/container_helpers.h @@ -2,7 +2,7 @@ * \file internal/particle_helpers.h * \brief A container for Singletons. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_INTERNAL_CONTAINER_HELPERS_H diff --git a/modules/core/include/internal/dihedral_helpers.h b/modules/core/include/internal/dihedral_helpers.h index 81a57a1f2b..01fe3daeaa 100644 --- a/modules/core/include/internal/dihedral_helpers.h +++ b/modules/core/include/internal/dihedral_helpers.h @@ -2,7 +2,7 @@ * \file dihedral_helpers.h * \brief Helper functions to calculate dihedral angles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_DIHEDRAL_HELPERS_H diff --git a/modules/core/include/internal/evaluate_distance_pair_score.h b/modules/core/include/internal/evaluate_distance_pair_score.h index 295ce80486..5a628c89ac 100644 --- a/modules/core/include/internal/evaluate_distance_pair_score.h +++ b/modules/core/include/internal/evaluate_distance_pair_score.h @@ -2,7 +2,7 @@ * \file evaluate_distance_pair_score.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_EVALUATE_DISTANCE_PAIR_SCORE_H diff --git a/modules/core/include/internal/graph_base.h b/modules/core/include/internal/graph_base.h index 4ca20e0df6..8c9109d6e0 100644 --- a/modules/core/include/internal/graph_base.h +++ b/modules/core/include/internal/graph_base.h @@ -1,7 +1,7 @@ /** * \file graph_base.h \brief Internal use only. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/internal/grid_close_pairs_impl.h b/modules/core/include/internal/grid_close_pairs_impl.h index 055c4c048e..05a19a12f6 100644 --- a/modules/core/include/internal/grid_close_pairs_impl.h +++ b/modules/core/include/internal/grid_close_pairs_impl.h @@ -2,7 +2,7 @@ * \file grid_close_pair_impl.h * \brief Implementation of close pairs finder that is based on a grid hierarchy * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/internal/hierarchy_helpers.h b/modules/core/include/internal/hierarchy_helpers.h index a681f1166c..d94053e846 100644 --- a/modules/core/include/internal/hierarchy_helpers.h +++ b/modules/core/include/internal/hierarchy_helpers.h @@ -2,7 +2,7 @@ * \file hierarchy_helpers.h * \brief Helpers for the Hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/internal/incremental_scoring_function.h b/modules/core/include/internal/incremental_scoring_function.h index be1e37545b..460ef0303a 100644 --- a/modules/core/include/internal/incremental_scoring_function.h +++ b/modules/core/include/internal/incremental_scoring_function.h @@ -1,7 +1,7 @@ /** * \file IncrementalScoringFunction.h \brief Simple Monte Carlo optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/internal/remove_pointers.h b/modules/core/include/internal/remove_pointers.h index 98f2d8881f..e177e7b34f 100644 --- a/modules/core/include/internal/remove_pointers.h +++ b/modules/core/include/internal/remove_pointers.h @@ -3,7 +3,7 @@ * \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/internal/rigid_bodies.h b/modules/core/include/internal/rigid_bodies.h index 2e76ad30a6..5259741630 100644 --- a/modules/core/include/internal/rigid_bodies.h +++ b/modules/core/include/internal/rigid_bodies.h @@ -2,7 +2,7 @@ * \file rigid_bodies.h * \brief utilities for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_INTERNAL_RIGID_BODIES_H diff --git a/modules/core/include/internal/rigid_body_tree.h b/modules/core/include/internal/rigid_body_tree.h index b36e2d4805..fc292690e1 100644 --- a/modules/core/include/internal/rigid_body_tree.h +++ b/modules/core/include/internal/rigid_body_tree.h @@ -2,7 +2,7 @@ * \file rigid_pair_score.h * \brief utilities for rigid pair scores. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_INTERNAL_RIGID_BODY_TREE_H diff --git a/modules/core/include/internal/sinks.h b/modules/core/include/internal/sinks.h index 7bb653180e..d530357ade 100644 --- a/modules/core/include/internal/sinks.h +++ b/modules/core/include/internal/sinks.h @@ -3,7 +3,7 @@ * \brief utilities for output "sink", including classes ParticleSink, * ParticlePairSink, ParticleIndexPairSink, etc. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_INTERNAL_SINKS_H diff --git a/modules/core/include/internal/truncated_harmonic.h b/modules/core/include/internal/truncated_harmonic.h index edaf7f0fc5..3e80dbd4b4 100644 --- a/modules/core/include/internal/truncated_harmonic.h +++ b/modules/core/include/internal/truncated_harmonic.h @@ -2,7 +2,7 @@ * \file truncated_harmonic.h * \brief Helpers for the truncated harmonics. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/internal/tunneler_helpers.h b/modules/core/include/internal/tunneler_helpers.h index 3670e5f1ed..585ca62c0f 100644 --- a/modules/core/include/internal/tunneler_helpers.h +++ b/modules/core/include/internal/tunneler_helpers.h @@ -2,7 +2,7 @@ * \file tunneler_helpers.h * \brief Helper functions for rigid body tunneler * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_TUNNELER_HELPERS_H diff --git a/modules/core/include/model_statistics.h b/modules/core/include/model_statistics.h index f3cb0aa2e1..ba9c8a020c 100644 --- a/modules/core/include/model_statistics.h +++ b/modules/core/include/model_statistics.h @@ -2,7 +2,7 @@ * \file IMP/core/model_statistics.h * \brief Write the scores of the passed restraints to a file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_MODEL_STATISTICS_H diff --git a/modules/core/include/predicates.h b/modules/core/include/predicates.h index 2ee29e30eb..1f2b82a20f 100644 --- a/modules/core/include/predicates.h +++ b/modules/core/include/predicates.h @@ -2,7 +2,7 @@ * \file IMP/core/predicates.h * \brief Score particles based on a bounding box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_PREDICATES_H diff --git a/modules/core/include/provenance.h b/modules/core/include/provenance.h index 720c82d60e..38d9cb2119 100644 --- a/modules/core/include/provenance.h +++ b/modules/core/include/provenance.h @@ -2,7 +2,7 @@ * \file IMP/core/provenance.h * \brief Classes to track how the model was created. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_PROVENANCE_H diff --git a/modules/core/include/python_only.h b/modules/core/include/python_only.h index 8a64c29dfd..b26e0398d8 100644 --- a/modules/core/include/python_only.h +++ b/modules/core/include/python_only.h @@ -2,7 +2,7 @@ * \file IMP/core/python_only.h * \brief Functionality only available in Python. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/rigid_bodies.h b/modules/core/include/rigid_bodies.h index 522ed0dfdd..87466b10df 100644 --- a/modules/core/include/rigid_bodies.h +++ b/modules/core/include/rigid_bodies.h @@ -2,7 +2,7 @@ * \file IMP/core/rigid_bodies.h * \brief functionality for defining rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_RIGID_BODIES_H diff --git a/modules/core/include/rigid_body_geometries.h b/modules/core/include/rigid_body_geometries.h index 70cad663c7..bec69a6b55 100644 --- a/modules/core/include/rigid_body_geometries.h +++ b/modules/core/include/rigid_body_geometries.h @@ -2,7 +2,7 @@ * \file IMP/core/rigid_body_geometries.h * \brief functionality for defining rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_RIGID_BODY_GEOMETRIES_H diff --git a/modules/core/include/symmetry.h b/modules/core/include/symmetry.h index cf2b2e3796..0c481ce79c 100644 --- a/modules/core/include/symmetry.h +++ b/modules/core/include/symmetry.h @@ -1,7 +1,7 @@ /** * \file IMP/core/symmetry.h \brief Implement various types of symmetry * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/include/utility.h b/modules/core/include/utility.h index e2b87c5ab9..907a1e2e2c 100644 --- a/modules/core/include/utility.h +++ b/modules/core/include/utility.h @@ -2,7 +2,7 @@ * \file IMP/core/utility.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/AngleRestraint.cpp b/modules/core/src/AngleRestraint.cpp index 8eb3c0dc31..3919f09fd7 100644 --- a/modules/core/src/AngleRestraint.cpp +++ b/modules/core/src/AngleRestraint.cpp @@ -1,7 +1,7 @@ /** * \file AngleRestraint.cpp \brief Angle restraint between three particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/AngleTripletScore.cpp b/modules/core/src/AngleTripletScore.cpp index ce79b61c7d..10d533339c 100644 --- a/modules/core/src/AngleTripletScore.cpp +++ b/modules/core/src/AngleTripletScore.cpp @@ -2,7 +2,7 @@ * \file AngleTripletScore.cpp * \brief A Score on the angle between a triplet of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/BallMover.cpp b/modules/core/src/BallMover.cpp index 60110ee1b8..d38640c9a1 100644 --- a/modules/core/src/BallMover.cpp +++ b/modules/core/src/BallMover.cpp @@ -1,7 +1,7 @@ /** * \file BallMover.cpp \brief A modifier which perturbs a discrete variable. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/BoundingBox3DSingletonScore.cpp b/modules/core/src/BoundingBox3DSingletonScore.cpp index b2b15cc4e9..6112b22278 100644 --- a/modules/core/src/BoundingBox3DSingletonScore.cpp +++ b/modules/core/src/BoundingBox3DSingletonScore.cpp @@ -2,7 +2,7 @@ * \file BoundingBox3DSingletonScore.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/BoundingSphere3DSingletonScore.cpp b/modules/core/src/BoundingSphere3DSingletonScore.cpp index e04a549374..ac7cea60f2 100644 --- a/modules/core/src/BoundingSphere3DSingletonScore.cpp +++ b/modules/core/src/BoundingSphere3DSingletonScore.cpp @@ -2,7 +2,7 @@ * \file BoundingSphere3DSingletonScore.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/BoxSweepClosePairsFinder.cpp b/modules/core/src/BoxSweepClosePairsFinder.cpp index 38da6572e1..c7c40b719b 100644 --- a/modules/core/src/BoxSweepClosePairsFinder.cpp +++ b/modules/core/src/BoxSweepClosePairsFinder.cpp @@ -2,7 +2,7 @@ * \file BoxSweepClosePairsFinder.cpp * \brief Test all pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/CentroidOfRefined.cpp b/modules/core/src/CentroidOfRefined.cpp index eba61d8a13..0a7024cab5 100644 --- a/modules/core/src/CentroidOfRefined.cpp +++ b/modules/core/src/CentroidOfRefined.cpp @@ -2,7 +2,7 @@ * \file CentroidOfRefined.cpp * \brief CentroidOf a the refined particles with a sphere. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/core/CentroidOfRefined.h" diff --git a/modules/core/src/ChecksScoreState.cpp b/modules/core/src/ChecksScoreState.cpp index 6349e2a49e..abd3afb6dd 100644 --- a/modules/core/src/ChecksScoreState.cpp +++ b/modules/core/src/ChecksScoreState.cpp @@ -2,7 +2,7 @@ * \file ChecksScoreState.cpp * \brief Keep track of the maximum change of a set of attributes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/ChildrenRefiner.cpp b/modules/core/src/ChildrenRefiner.cpp index 1ec95fe83c..f2c82b1ef4 100644 --- a/modules/core/src/ChildrenRefiner.cpp +++ b/modules/core/src/ChildrenRefiner.cpp @@ -2,7 +2,7 @@ * \file ChildrenRefiner.cpp * \brief Return the hierarchy children of a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/ClosePairsFinder.cpp b/modules/core/src/ClosePairsFinder.cpp index 77f5ce3c9b..0e20d8e115 100644 --- a/modules/core/src/ClosePairsFinder.cpp +++ b/modules/core/src/ClosePairsFinder.cpp @@ -2,7 +2,7 @@ * \file ClosePairsFinder.cpp * \brief Algorithm base class to find close pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/ClosePairsPairScore.cpp b/modules/core/src/ClosePairsPairScore.cpp index 761a1429c9..e303ae90e1 100644 --- a/modules/core/src/ClosePairsPairScore.cpp +++ b/modules/core/src/ClosePairsPairScore.cpp @@ -3,7 +3,7 @@ * \brief Iteratively refine to find all close pairs in a tree. * * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/ClosedCubicSpline.cpp b/modules/core/src/ClosedCubicSpline.cpp index 8b0d392dd5..7e2943a483 100644 --- a/modules/core/src/ClosedCubicSpline.cpp +++ b/modules/core/src/ClosedCubicSpline.cpp @@ -1,7 +1,7 @@ /** * \file ClosedCubicSpline.cpp \brief Closed cubic spline function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/ConjugateGradients.cpp b/modules/core/src/ConjugateGradients.cpp index 0500ccf2fd..e7af71b2a2 100644 --- a/modules/core/src/ConjugateGradients.cpp +++ b/modules/core/src/ConjugateGradients.cpp @@ -1,7 +1,7 @@ /** * \file ConjugateGradients.cpp \brief Simple conjugate gradients optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/ConnectivityRestraint.cpp b/modules/core/src/ConnectivityRestraint.cpp index 4cf8c8c35b..3861939201 100644 --- a/modules/core/src/ConnectivityRestraint.cpp +++ b/modules/core/src/ConnectivityRestraint.cpp @@ -4,7 +4,7 @@ * Restrict max distance between at least one pair of particles of any * two distinct types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/ConstantRestraint.cpp b/modules/core/src/ConstantRestraint.cpp index da5ff2c708..606225b40e 100644 --- a/modules/core/src/ConstantRestraint.cpp +++ b/modules/core/src/ConstantRestraint.cpp @@ -1,7 +1,7 @@ /** * \file ConstantRestraint.cpp \brief Don't restrain anything. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/Cosine.cpp b/modules/core/src/Cosine.cpp index 60f6d1a155..0d12e9ce78 100644 --- a/modules/core/src/Cosine.cpp +++ b/modules/core/src/Cosine.cpp @@ -1,7 +1,7 @@ /** * \file Cosine.cpp \brief Cosine function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/CoverRefined.cpp b/modules/core/src/CoverRefined.cpp index 49acef0f29..3b4c56efd8 100644 --- a/modules/core/src/CoverRefined.cpp +++ b/modules/core/src/CoverRefined.cpp @@ -2,7 +2,7 @@ * \file CoverRefined.cpp * \brief Cover a the refined particles with a sphere. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/core/CoverRefined.h" diff --git a/modules/core/src/DerivativesFromRefined.cpp b/modules/core/src/DerivativesFromRefined.cpp index 41fac2d4e9..0c29de95f2 100644 --- a/modules/core/src/DerivativesFromRefined.cpp +++ b/modules/core/src/DerivativesFromRefined.cpp @@ -2,7 +2,7 @@ * \file DerivativesFromRefined.cpp * \brief Cover a bond with a sphere. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/core/DerivativesFromRefined.h" diff --git a/modules/core/src/DerivativesToRefined.cpp b/modules/core/src/DerivativesToRefined.cpp index 7bdf662a70..f6244ccd38 100644 --- a/modules/core/src/DerivativesToRefined.cpp +++ b/modules/core/src/DerivativesToRefined.cpp @@ -2,7 +2,7 @@ * \file DerivativesToRefined.cpp * \brief Copy derivatives from coarse particles to fine particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/core/DerivativesToRefined.h" diff --git a/modules/core/src/DiameterRestraint.cpp b/modules/core/src/DiameterRestraint.cpp index a8f1e218e2..7c3746f233 100644 --- a/modules/core/src/DiameterRestraint.cpp +++ b/modules/core/src/DiameterRestraint.cpp @@ -2,7 +2,7 @@ * \file DiameterRestraint.cpp * \brief A restraint to maintain the diameter of a set of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/DihedralRestraint.cpp b/modules/core/src/DihedralRestraint.cpp index 3c992e7102..bb0ce1093f 100644 --- a/modules/core/src/DihedralRestraint.cpp +++ b/modules/core/src/DihedralRestraint.cpp @@ -2,7 +2,7 @@ * \file DihedralRestraint.cpp \brief Dihedral restraint between four * particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/DirectionMover.cpp b/modules/core/src/DirectionMover.cpp index 6515dff0e0..bedefb698b 100644 --- a/modules/core/src/DirectionMover.cpp +++ b/modules/core/src/DirectionMover.cpp @@ -2,7 +2,7 @@ * \file DirectionMover.cpp * \brief A mover that transforms a Direction * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/DistanceRestraint.cpp b/modules/core/src/DistanceRestraint.cpp index 49b5c9349e..a2e637121c 100644 --- a/modules/core/src/DistanceRestraint.cpp +++ b/modules/core/src/DistanceRestraint.cpp @@ -1,7 +1,7 @@ /** * \file DistanceRestraint.cpp \brief Distance restraint between two particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/DistanceToSingletonScore.cpp b/modules/core/src/DistanceToSingletonScore.cpp index 82655c0d0b..51644807d3 100644 --- a/modules/core/src/DistanceToSingletonScore.cpp +++ b/modules/core/src/DistanceToSingletonScore.cpp @@ -2,7 +2,7 @@ * \file DistanceToSingletonScore.cpp * \brief A Score on the distance to a fixed point. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/ExcludedVolumeRestraint.cpp b/modules/core/src/ExcludedVolumeRestraint.cpp index 728d445bed..360d426b67 100644 --- a/modules/core/src/ExcludedVolumeRestraint.cpp +++ b/modules/core/src/ExcludedVolumeRestraint.cpp @@ -2,7 +2,7 @@ * \file ExcludedVolumeRestraint.cpp * \brief Prevent spheres from inter-penetrating. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/FixedRefiner.cpp b/modules/core/src/FixedRefiner.cpp index aa927207a0..544755f126 100644 --- a/modules/core/src/FixedRefiner.cpp +++ b/modules/core/src/FixedRefiner.cpp @@ -2,7 +2,7 @@ * \file FixedRefiner.cpp * \brief A particle refiner which returns a fixed set of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/Gaussian.cpp b/modules/core/src/Gaussian.cpp index fdf8993504..42843e310a 100644 --- a/modules/core/src/Gaussian.cpp +++ b/modules/core/src/Gaussian.cpp @@ -2,7 +2,7 @@ * \file example/Gaussian.cpp * \brief Decorator to hold Gaussian3D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/GenericAttributeSingletonScore.cpp b/modules/core/src/GenericAttributeSingletonScore.cpp index 021f58ffd9..e39910434f 100644 --- a/modules/core/src/GenericAttributeSingletonScore.cpp +++ b/modules/core/src/GenericAttributeSingletonScore.cpp @@ -2,7 +2,7 @@ * \file GenericAttributeSingletonScore.cpp * \brief A score based on an unmodified attribute value. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/GridClosePairsFinder.cpp b/modules/core/src/GridClosePairsFinder.cpp index ed7e0e1cb2..325ce4ca2f 100644 --- a/modules/core/src/GridClosePairsFinder.cpp +++ b/modules/core/src/GridClosePairsFinder.cpp @@ -2,7 +2,7 @@ * \file GridClosePairsFinder.cpp * \brief Test all pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/Hierarchy.cpp b/modules/core/src/Hierarchy.cpp index 5ab42021ee..3eff7ac534 100644 --- a/modules/core/src/Hierarchy.cpp +++ b/modules/core/src/Hierarchy.cpp @@ -2,7 +2,7 @@ * \file Hierarchy.cpp \brief Decorator for helping deal with * a hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/IncrementalScoringFunction.cpp b/modules/core/src/IncrementalScoringFunction.cpp index 0a14cc1eab..9371ba2a3c 100644 --- a/modules/core/src/IncrementalScoringFunction.cpp +++ b/modules/core/src/IncrementalScoringFunction.cpp @@ -2,7 +2,7 @@ * \file IncrementalScoringFunction.cpp * \brief Score model efficiently when a small number of particles are changed. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/LeavesRefiner.cpp b/modules/core/src/LeavesRefiner.cpp index 80e1b31602..15c1dcd90e 100644 --- a/modules/core/src/LeavesRefiner.cpp +++ b/modules/core/src/LeavesRefiner.cpp @@ -2,7 +2,7 @@ * \file LeavesRefiner.cpp * \brief Return the hierarchy children of a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/LogNormalMover.cpp b/modules/core/src/LogNormalMover.cpp index 082c9bbad6..9d3b517bde 100644 --- a/modules/core/src/LogNormalMover.cpp +++ b/modules/core/src/LogNormalMover.cpp @@ -2,7 +2,7 @@ * \file LogNormalMover.cpp * \brief A modifier that perturbs a point with a log-normal distribution. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/MCCGSampler.cpp b/modules/core/src/MCCGSampler.cpp index c463e3399d..2f74ee584f 100644 --- a/modules/core/src/MCCGSampler.cpp +++ b/modules/core/src/MCCGSampler.cpp @@ -1,7 +1,7 @@ /** * \file ConjugateGradients.cpp \brief Simple conjugate gradients optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/MSConnectivityRestraint.cpp b/modules/core/src/MSConnectivityRestraint.cpp index 332c72c149..817885b555 100644 --- a/modules/core/src/MSConnectivityRestraint.cpp +++ b/modules/core/src/MSConnectivityRestraint.cpp @@ -4,7 +4,7 @@ * Restrict max distance between at least one pair of particles of any * two distinct types. It also handles multiple copies of the same particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/MinimumRestraint.cpp b/modules/core/src/MinimumRestraint.cpp index d777d185a1..a9ad0ce12f 100644 --- a/modules/core/src/MinimumRestraint.cpp +++ b/modules/core/src/MinimumRestraint.cpp @@ -1,7 +1,7 @@ /** * \file MinimumRestraint.cpp \brief Distance restraint between two particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/MonteCarlo.cpp b/modules/core/src/MonteCarlo.cpp index 5e1288aed3..c262580577 100644 --- a/modules/core/src/MonteCarlo.cpp +++ b/modules/core/src/MonteCarlo.cpp @@ -1,7 +1,7 @@ /** * \file MonteCarlo.cpp \brief Simple Monte Carlo optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/MonteCarloMover.cpp b/modules/core/src/MonteCarloMover.cpp index d7f302152b..7affca75d2 100644 --- a/modules/core/src/MonteCarloMover.cpp +++ b/modules/core/src/MonteCarloMover.cpp @@ -1,7 +1,7 @@ /** * \file Mover.cpp \brief Refine a particle into a list of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/MoveStatisticsScoreState.cpp b/modules/core/src/MoveStatisticsScoreState.cpp index d01a090481..6d0b639fde 100644 --- a/modules/core/src/MoveStatisticsScoreState.cpp +++ b/modules/core/src/MoveStatisticsScoreState.cpp @@ -1,7 +1,7 @@ /** * \file Clustering.cpp \brief Holds data points to cluster using k-means * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/MultipleBinormalRestraint.cpp b/modules/core/src/MultipleBinormalRestraint.cpp index c073916091..271bd5e901 100644 --- a/modules/core/src/MultipleBinormalRestraint.cpp +++ b/modules/core/src/MultipleBinormalRestraint.cpp @@ -2,7 +2,7 @@ * \file MultipleBinormalRestraint.cpp * \brief Modeller-style multiple binormal (phi/psi) restraint. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/NearestNeighborsClosePairsFinder.cpp b/modules/core/src/NearestNeighborsClosePairsFinder.cpp index cd4486c7ff..4bc5c3b9d0 100644 --- a/modules/core/src/NearestNeighborsClosePairsFinder.cpp +++ b/modules/core/src/NearestNeighborsClosePairsFinder.cpp @@ -2,7 +2,7 @@ * \file NearestNeighborsClosePairsFinder.cpp * \brief Test all pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/NeighborsTable.cpp b/modules/core/src/NeighborsTable.cpp index 091f1241db..349fde86ce 100644 --- a/modules/core/src/NeighborsTable.cpp +++ b/modules/core/src/NeighborsTable.cpp @@ -2,7 +2,7 @@ * \file NeighborsTable.cpp * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/NormalMover.cpp b/modules/core/src/NormalMover.cpp index 2a845530e7..522df000e5 100644 --- a/modules/core/src/NormalMover.cpp +++ b/modules/core/src/NormalMover.cpp @@ -2,7 +2,7 @@ * \file NormalMover.cpp * \brief A modifier which perturbs a point with a Gaussian. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/QuadraticClosePairsFinder.cpp b/modules/core/src/QuadraticClosePairsFinder.cpp index 815a178c61..20b2e5d5a0 100644 --- a/modules/core/src/QuadraticClosePairsFinder.cpp +++ b/modules/core/src/QuadraticClosePairsFinder.cpp @@ -2,7 +2,7 @@ * \file QuadraticClosePairsFinder.cpp * \brief Test all pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/RefinedPairsPairScore.cpp b/modules/core/src/RefinedPairsPairScore.cpp index 3ddbaa4a25..3f45b464f8 100644 --- a/modules/core/src/RefinedPairsPairScore.cpp +++ b/modules/core/src/RefinedPairsPairScore.cpp @@ -3,7 +3,7 @@ * \brief Refine particles at most once with a Refiner. * * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/RigidBodyAnglePairScore.cpp b/modules/core/src/RigidBodyAnglePairScore.cpp index 7f23c9d0c3..910c103c4c 100644 --- a/modules/core/src/RigidBodyAnglePairScore.cpp +++ b/modules/core/src/RigidBodyAnglePairScore.cpp @@ -2,7 +2,7 @@ * \file RigidBodyAnglePairScore.cpp * \brief A score on the kink angle between two rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/RigidBodyDistancePairScore.cpp b/modules/core/src/RigidBodyDistancePairScore.cpp index aa6fc6249a..a432356280 100644 --- a/modules/core/src/RigidBodyDistancePairScore.cpp +++ b/modules/core/src/RigidBodyDistancePairScore.cpp @@ -2,7 +2,7 @@ * \file RigidBodyDistancePairScore.cpp * \brief Act on the distance between two rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/RigidBodyMover.cpp b/modules/core/src/RigidBodyMover.cpp index aa49f451ac..68f1f521bb 100644 --- a/modules/core/src/RigidBodyMover.cpp +++ b/modules/core/src/RigidBodyMover.cpp @@ -2,7 +2,7 @@ * \file RigidBodyMover.cpp * \brief A mover that transforms a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/RigidBodyTunneler.cpp b/modules/core/src/RigidBodyTunneler.cpp index 7de695a4ef..52d115b66d 100644 --- a/modules/core/src/RigidBodyTunneler.cpp +++ b/modules/core/src/RigidBodyTunneler.cpp @@ -2,7 +2,7 @@ * \file RigidBodyTunneler.cpp * \brief A mover that transforms a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/RigidBodyUmbrella.cpp b/modules/core/src/RigidBodyUmbrella.cpp index 231a77715e..e839da2b69 100644 --- a/modules/core/src/RigidBodyUmbrella.cpp +++ b/modules/core/src/RigidBodyUmbrella.cpp @@ -1,7 +1,7 @@ /** * \file RigidBodyUmbrella.cpp \brief Distance restraint between two particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/RigidClosePairsFinder.cpp b/modules/core/src/RigidClosePairsFinder.cpp index 9c1427cb86..dfb02a6948 100644 --- a/modules/core/src/RigidClosePairsFinder.cpp +++ b/modules/core/src/RigidClosePairsFinder.cpp @@ -2,7 +2,7 @@ * \file RigidClosePairsFinder.cpp * \brief Test all pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/SerialMover.cpp b/modules/core/src/SerialMover.cpp index 511d6e44fa..00644a1d91 100644 --- a/modules/core/src/SerialMover.cpp +++ b/modules/core/src/SerialMover.cpp @@ -2,7 +2,7 @@ * \file SerialMover.cpp * \brief A mover that apply other movers one at a time * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/SphereDistancePairScore.cpp b/modules/core/src/SphereDistancePairScore.cpp index 1c99e2ff8b..cdc223c71c 100644 --- a/modules/core/src/SphereDistancePairScore.cpp +++ b/modules/core/src/SphereDistancePairScore.cpp @@ -2,7 +2,7 @@ * \file SphereDistancePairScore.cpp * \brief A score on the distance between the surfaces of two spheres. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/SteepestDescent.cpp b/modules/core/src/SteepestDescent.cpp index 4b680665f5..0bd1eb283a 100644 --- a/modules/core/src/SteepestDescent.cpp +++ b/modules/core/src/SteepestDescent.cpp @@ -1,7 +1,7 @@ /** * \file SteepestDescent.cpp \brief Simple steepest descent optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/SubsetMover.cpp b/modules/core/src/SubsetMover.cpp index cfd9d86939..3dc00f4f3c 100644 --- a/modules/core/src/SubsetMover.cpp +++ b/modules/core/src/SubsetMover.cpp @@ -2,7 +2,7 @@ * \file SubsetMover.cpp * \brief A mover that applies a random subset of movers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/Surface.cpp b/modules/core/src/Surface.cpp index 4d406ff303..1343e304e1 100644 --- a/modules/core/src/Surface.cpp +++ b/modules/core/src/Surface.cpp @@ -1,7 +1,7 @@ /** * \file Surface.cpp \brief Simple surface decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/SurfaceMover.cpp b/modules/core/src/SurfaceMover.cpp index 2c4903856c..bd7df7beaf 100644 --- a/modules/core/src/SurfaceMover.cpp +++ b/modules/core/src/SurfaceMover.cpp @@ -2,7 +2,7 @@ * \file SurfaceMover.cpp * \brief A mover that transforms a Surface * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/SurfaceSymmetryConstraint.cpp b/modules/core/src/SurfaceSymmetryConstraint.cpp index 0b63440a74..61e70629c9 100644 --- a/modules/core/src/SurfaceSymmetryConstraint.cpp +++ b/modules/core/src/SurfaceSymmetryConstraint.cpp @@ -2,7 +2,7 @@ * \file SurfaceSymmetryConstraint.cpp * \brief Constrain orientation of surfaces with respect to rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/TableRefiner.cpp b/modules/core/src/TableRefiner.cpp index 4096a92f1d..bd3d9721a6 100644 --- a/modules/core/src/TableRefiner.cpp +++ b/modules/core/src/TableRefiner.cpp @@ -2,7 +2,7 @@ * \file TableRefiner.cpp * \brief A particle refiner that uses a table. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/Transform.cpp b/modules/core/src/Transform.cpp index 4e099c30fa..66ee08350b 100644 --- a/modules/core/src/Transform.cpp +++ b/modules/core/src/Transform.cpp @@ -2,7 +2,7 @@ * \file TransformSingletonParticle.cpp * \brief Transform a particle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/TransformedDistancePairScore.cpp b/modules/core/src/TransformedDistancePairScore.cpp index 780a484d89..b2385d59b7 100644 --- a/modules/core/src/TransformedDistancePairScore.cpp +++ b/modules/core/src/TransformedDistancePairScore.cpp @@ -2,7 +2,7 @@ * \file TransformedDistancePairScore.cpp * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/Typed.cpp b/modules/core/src/Typed.cpp index 124412dc58..d203984afc 100644 --- a/modules/core/src/Typed.cpp +++ b/modules/core/src/Typed.cpp @@ -1,7 +1,7 @@ /** * \file Typed.cpp \brief Simple xyz decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/TypedPairScore.cpp b/modules/core/src/TypedPairScore.cpp index 41a411d0ce..c1ef163bba 100644 --- a/modules/core/src/TypedPairScore.cpp +++ b/modules/core/src/TypedPairScore.cpp @@ -2,7 +2,7 @@ * \file TypedPairScore.cpp * \brief Delegate to another PairScore depending on particle types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/VolumeRestraint.cpp b/modules/core/src/VolumeRestraint.cpp index 5e213d23ca..0dfd9d4a0e 100644 --- a/modules/core/src/VolumeRestraint.cpp +++ b/modules/core/src/VolumeRestraint.cpp @@ -2,7 +2,7 @@ * \file VolumeRestraint.cpp * \brief A restraint that prevents spheres from inter-penetrating. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/WeightedDerivativesToRefined.cpp b/modules/core/src/WeightedDerivativesToRefined.cpp index cd94d6b0dc..1af6670e94 100644 --- a/modules/core/src/WeightedDerivativesToRefined.cpp +++ b/modules/core/src/WeightedDerivativesToRefined.cpp @@ -4,7 +4,7 @@ * to its refined set of particles using weights * indicated by a weight key. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/core/WeightedDerivativesToRefined.h" diff --git a/modules/core/src/XYZ.cpp b/modules/core/src/XYZ.cpp index 982fe1009d..70397c2ed9 100644 --- a/modules/core/src/XYZ.cpp +++ b/modules/core/src/XYZ.cpp @@ -1,7 +1,7 @@ /** * \file XYZ.cpp \brief Simple xyz decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/XYZR.cpp b/modules/core/src/XYZR.cpp index 8f191cd06e..96c581bc3f 100644 --- a/modules/core/src/XYZR.cpp +++ b/modules/core/src/XYZR.cpp @@ -1,7 +1,7 @@ /** * \file XYZR.cpp \brief Simple xyzr decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/blame.cpp b/modules/core/src/blame.cpp index 27c6c690b4..7cb239f552 100644 --- a/modules/core/src/blame.cpp +++ b/modules/core/src/blame.cpp @@ -2,7 +2,7 @@ * \file core/utility.cpp * \brief Functions to perform simple functions on a set of particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include "IMP/core/blame.h" diff --git a/modules/core/src/direction.cpp b/modules/core/src/direction.cpp index 6e74cfec23..e2112aafc5 100644 --- a/modules/core/src/direction.cpp +++ b/modules/core/src/direction.cpp @@ -2,7 +2,7 @@ * \file direction.cpp * \brief Decorators for directions and the angle between them. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/src/internal/MovedSingletonContainer.cpp b/modules/core/src/internal/MovedSingletonContainer.cpp index f849b405eb..acec3449f9 100644 --- a/modules/core/src/internal/MovedSingletonContainer.cpp +++ b/modules/core/src/internal/MovedSingletonContainer.cpp @@ -2,7 +2,7 @@ * \file MovedSingletonContainer.cpp * \brief Keep track of the maximum change of a set of attributes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/internal/close_pairs_helpers.cpp b/modules/core/src/internal/close_pairs_helpers.cpp index c53282b970..fcf6e27ead 100644 --- a/modules/core/src/internal/close_pairs_helpers.cpp +++ b/modules/core/src/internal/close_pairs_helpers.cpp @@ -1,7 +1,7 @@ /** * \file close_pairs_helpers.cpp \brief Helper functions for close pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/internal/graph_base.cpp b/modules/core/src/internal/graph_base.cpp index 56290be087..eda31136a4 100644 --- a/modules/core/src/internal/graph_base.cpp +++ b/modules/core/src/internal/graph_base.cpp @@ -1,7 +1,7 @@ /** * \file graph_base.cpp \brief classes for implementing a graph. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/internal/incremental_scoring_function.cpp b/modules/core/src/internal/incremental_scoring_function.cpp index 39fbd93f0a..269888afcc 100644 --- a/modules/core/src/internal/incremental_scoring_function.cpp +++ b/modules/core/src/internal/incremental_scoring_function.cpp @@ -2,7 +2,7 @@ * \file incremental_scoring_function.cpp * \brief Helper functions for incremental scoring functions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/internal/rigid_body_tree.cpp b/modules/core/src/internal/rigid_body_tree.cpp index f0fc646184..caeba85c97 100644 --- a/modules/core/src/internal/rigid_body_tree.cpp +++ b/modules/core/src/internal/rigid_body_tree.cpp @@ -2,7 +2,7 @@ * \file rigid_body_tree.cpp * \brief Handle trees of rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/internal/tunneler_helpers.cpp b/modules/core/src/internal/tunneler_helpers.cpp index 3805acd93b..3682980475 100644 --- a/modules/core/src/internal/tunneler_helpers.cpp +++ b/modules/core/src/internal/tunneler_helpers.cpp @@ -2,7 +2,7 @@ * \file tunneler_helpers.cpp * \brief helper classes for RigidBodyTunneler * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/model_statistics.cpp b/modules/core/src/model_statistics.cpp index bafe8caccd..5bb4aa048c 100644 --- a/modules/core/src/model_statistics.cpp +++ b/modules/core/src/model_statistics.cpp @@ -1,7 +1,7 @@ /** * \file AngleRestraint.cpp \brief Angle restraint between three particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/provenance.cpp b/modules/core/src/provenance.cpp index d9f56c306a..463bf36894 100644 --- a/modules/core/src/provenance.cpp +++ b/modules/core/src/provenance.cpp @@ -2,7 +2,7 @@ * \file provenance.cpp * \brief Classes to track how the model was created. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/rigid_bodies.cpp b/modules/core/src/rigid_bodies.cpp index 8c8522857d..f39e8f41f7 100644 --- a/modules/core/src/rigid_bodies.cpp +++ b/modules/core/src/rigid_bodies.cpp @@ -2,7 +2,7 @@ * \file rigid_bodies.cpp * \brief Support for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/rigid_body_geometries.cpp b/modules/core/src/rigid_body_geometries.cpp index ba20ffdb55..330e438eea 100644 --- a/modules/core/src/rigid_body_geometries.cpp +++ b/modules/core/src/rigid_body_geometries.cpp @@ -2,7 +2,7 @@ * \file rigid_bodies.cpp * \brief Support for rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/core/src/symmetry.cpp b/modules/core/src/symmetry.cpp index 09d575ff16..cb5dab52f9 100644 --- a/modules/core/src/symmetry.cpp +++ b/modules/core/src/symmetry.cpp @@ -2,7 +2,7 @@ * \file symmetry.cpp * \brief Transform a particle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/core/src/utility.cpp b/modules/core/src/utility.cpp index e710963586..15af690e2a 100644 --- a/modules/core/src/utility.cpp +++ b/modules/core/src/utility.cpp @@ -2,7 +2,7 @@ * \file core/utility.cpp * \brief Functions to perform simple functions on a set of particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include "IMP/core/utility.h" diff --git a/modules/core/test/test_generic.cpp b/modules/core/test/test_generic.cpp index 0d4ae840d3..968b6d0ec0 100644 --- a/modules/core/test/test_generic.cpp +++ b/modules/core/test/test_generic.cpp @@ -2,7 +2,7 @@ * \file test_generic.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/core/test/test_soft_sphere.cpp b/modules/core/test/test_soft_sphere.cpp index ca9e16a1eb..6a1e9e9037 100644 --- a/modules/core/test/test_soft_sphere.cpp +++ b/modules/core/test/test_soft_sphere.cpp @@ -2,7 +2,7 @@ * \file test_functor_distance_pair_scores.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/include/Color.h b/modules/display/include/Color.h index c80dc59c2b..32c721c46b 100644 --- a/modules/display/include/Color.h +++ b/modules/display/include/Color.h @@ -2,7 +2,7 @@ * \file IMP/display/Color.h * \brief Represent a color * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_COLOR_H diff --git a/modules/display/include/Colored.h b/modules/display/include/Colored.h index 4f986e3590..854f2a99d0 100644 --- a/modules/display/include/Colored.h +++ b/modules/display/include/Colored.h @@ -2,7 +2,7 @@ * \file IMP/display/Colored.h * \brief A decorator for a particle with a color * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_COLORED_H diff --git a/modules/display/include/FilterGeometry.h b/modules/display/include/FilterGeometry.h index 8990ad265a..d40d25a424 100644 --- a/modules/display/include/FilterGeometry.h +++ b/modules/display/include/FilterGeometry.h @@ -2,7 +2,7 @@ * \file IMP/display/FilterGeometry.h * \brief Remove geometry which is not above a plane. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_FILTER_GEOMETRY_H diff --git a/modules/display/include/GeometryProcessor.h b/modules/display/include/GeometryProcessor.h index bf1eeffd92..783de2e8c4 100644 --- a/modules/display/include/GeometryProcessor.h +++ b/modules/display/include/GeometryProcessor.h @@ -2,7 +2,7 @@ * \file IMP/display/GeometryProcessor.h * \brief Provide a standard geometry processing framework. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_GEOMETRY_PROCESSOR_H diff --git a/modules/display/include/GeometrySet.h b/modules/display/include/GeometrySet.h index a57ddc4406..e2742ff15a 100644 --- a/modules/display/include/GeometrySet.h +++ b/modules/display/include/GeometrySet.h @@ -2,7 +2,7 @@ * \file IMP/display/GeometrySet.h * \brief Implement geometry for the basic shapes from IMP.algebra. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_GEOMETRY_SET_H diff --git a/modules/display/include/LogOptimizerState.h b/modules/display/include/LogOptimizerState.h index bee81f1ea8..ffad7d7304 100644 --- a/modules/display/include/LogOptimizerState.h +++ b/modules/display/include/LogOptimizerState.h @@ -2,7 +2,7 @@ * \file IMP/display/LogOptimizerState.h * \brief Write geometry to a file during optimization * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_LOG_OPTIMIZER_STATE_H diff --git a/modules/display/include/PymolWriter.h b/modules/display/include/PymolWriter.h index c9fdb0a83a..d27267db47 100644 --- a/modules/display/include/PymolWriter.h +++ b/modules/display/include/PymolWriter.h @@ -2,7 +2,7 @@ * \file IMP/display/PymolWriter.h * \brief Write a CGO file with the geometry. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_PYMOL_WRITER_H diff --git a/modules/display/include/Writer.h b/modules/display/include/Writer.h index 5597073702..e352527b85 100644 --- a/modules/display/include/Writer.h +++ b/modules/display/include/Writer.h @@ -2,7 +2,7 @@ * \file IMP/display/Writer.h * \brief Base class for writing geometry to a file * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_WRITER_H diff --git a/modules/display/include/declare_Geometry.h b/modules/display/include/declare_Geometry.h index 6aff52cafd..4caa74e546 100644 --- a/modules/display/include/declare_Geometry.h +++ b/modules/display/include/declare_Geometry.h @@ -2,7 +2,7 @@ * \file IMP/display/declare_Geometry.h * \brief Implement geometry for the basic shapes from IMP.algebra. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_DECLARE_GEOMETRY_H diff --git a/modules/display/include/display_macros.h b/modules/display/include/display_macros.h index 434234991f..9b3c11e5d0 100644 --- a/modules/display/include/display_macros.h +++ b/modules/display/include/display_macros.h @@ -2,7 +2,7 @@ * \file IMP/display/display_macros.h * \brief macros for display classes * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_MACROS_H diff --git a/modules/display/include/geometry.h b/modules/display/include/geometry.h index 9dacf23b30..46a745e169 100644 --- a/modules/display/include/geometry.h +++ b/modules/display/include/geometry.h @@ -2,7 +2,7 @@ * \file IMP/display/geometry.h * \brief Backwards compatibility header. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_GEOMETRY_H diff --git a/modules/display/include/geometry_macros.h b/modules/display/include/geometry_macros.h index 2b8843d89b..3b348d585b 100644 --- a/modules/display/include/geometry_macros.h +++ b/modules/display/include/geometry_macros.h @@ -2,7 +2,7 @@ * \file IMP/display/geometry_macros.h * \brief macros for display classes * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_GEOMETRY_MACROS_H diff --git a/modules/display/include/internal/utility.h b/modules/display/include/internal/utility.h index a1171e1ed2..ddcc9ced2a 100644 --- a/modules/display/include/internal/utility.h +++ b/modules/display/include/internal/utility.h @@ -2,7 +2,7 @@ * \file display/internal/utility.h * \brief Base class for writing geometry to a file * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_INTERNAL_UTILITY_H diff --git a/modules/display/include/internal/writers.h b/modules/display/include/internal/writers.h index 8c843b8758..ea0caa7ca0 100644 --- a/modules/display/include/internal/writers.h +++ b/modules/display/include/internal/writers.h @@ -2,7 +2,7 @@ * \file writers.h * \brief Base class for writing geometry to a file * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_INTERNAL_WRITERS_H diff --git a/modules/display/include/particle_geometry.h b/modules/display/include/particle_geometry.h index e32739d412..689138afb6 100644 --- a/modules/display/include/particle_geometry.h +++ b/modules/display/include/particle_geometry.h @@ -2,7 +2,7 @@ * \file IMP/display/particle_geometry.h * \brief Represent an XYZR particle with a sphere * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_PARTICLE_GEOMETRY_H diff --git a/modules/display/include/primitive_geometries.h b/modules/display/include/primitive_geometries.h index dfda72f16c..91011000ad 100644 --- a/modules/display/include/primitive_geometries.h +++ b/modules/display/include/primitive_geometries.h @@ -2,7 +2,7 @@ * \file IMP/display/primitive_geometries.h * \brief Implement geometry for the basic shapes from IMP.algebra. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_PRIMITIVE_GEOMETRIES_H diff --git a/modules/display/include/python_only.h b/modules/display/include/python_only.h index 6b76212043..ba8c831161 100644 --- a/modules/display/include/python_only.h +++ b/modules/display/include/python_only.h @@ -1,7 +1,7 @@ /** * \file IMP/display/python_only.h \brief Build dependency graphs on models. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/include/restraint_geometry.h b/modules/display/include/restraint_geometry.h index 09cf14cd3c..d62b322374 100644 --- a/modules/display/include/restraint_geometry.h +++ b/modules/display/include/restraint_geometry.h @@ -2,7 +2,7 @@ * \file IMP/display/restraint_geometry.h * \brief Represent an XYZR restraint with a sphere * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_RESTRAINT_GEOMETRY_H diff --git a/modules/display/include/writer_macros.h b/modules/display/include/writer_macros.h index 116c5ae869..447e057441 100644 --- a/modules/display/include/writer_macros.h +++ b/modules/display/include/writer_macros.h @@ -2,7 +2,7 @@ * \file IMP/display/writer_macros.h * \brief macros for display classes * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDISPLAY_WRITER_MACROS_H diff --git a/modules/display/src/Color.cpp b/modules/display/src/Color.cpp index 4ff79a5125..ae96b3dc4a 100644 --- a/modules/display/src/Color.cpp +++ b/modules/display/src/Color.cpp @@ -2,7 +2,7 @@ * \file Color.cpp * \brief Represent an RGB color. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/Colored.cpp b/modules/display/src/Colored.cpp index 85821c40da..bd54bd3b38 100644 --- a/modules/display/src/Colored.cpp +++ b/modules/display/src/Colored.cpp @@ -2,7 +2,7 @@ * \file Colored.cpp * \brief A decorator for a particle with a color. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/FilterGeometry.cpp b/modules/display/src/FilterGeometry.cpp index ee04387960..c5c9d42627 100644 --- a/modules/display/src/FilterGeometry.cpp +++ b/modules/display/src/FilterGeometry.cpp @@ -2,7 +2,7 @@ * \file FilterGeometry.cpp * \brief Remove geometry which is not above a plane. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/GeometryProcessor.cpp b/modules/display/src/GeometryProcessor.cpp index d921bf8331..b7d9518e74 100644 --- a/modules/display/src/GeometryProcessor.cpp +++ b/modules/display/src/GeometryProcessor.cpp @@ -2,7 +2,7 @@ * \file GeometryProcessor.cpp * \brief Provide a standard geometry processing framework. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/LogOptimizerState.cpp b/modules/display/src/LogOptimizerState.cpp index fab97d8693..6db5c9071b 100644 --- a/modules/display/src/LogOptimizerState.cpp +++ b/modules/display/src/LogOptimizerState.cpp @@ -2,7 +2,7 @@ * \file Writer.cpp * \brief Base class for writing geometry to a file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/PymolWriter.cpp b/modules/display/src/PymolWriter.cpp index 35baebb843..9f23132e48 100644 --- a/modules/display/src/PymolWriter.cpp +++ b/modules/display/src/PymolWriter.cpp @@ -2,7 +2,7 @@ * \file PymolWriter.cpp * \brief Write a CGO file with the geometry. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/Writer.cpp b/modules/display/src/Writer.cpp index b7b973f5cf..02fee3f4ec 100644 --- a/modules/display/src/Writer.cpp +++ b/modules/display/src/Writer.cpp @@ -2,7 +2,7 @@ * \file Writer.cpp * \brief Base class for writing geometry to a file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/geometry.cpp b/modules/display/src/geometry.cpp index 206fa3913f..6cc6021a3e 100644 --- a/modules/display/src/geometry.cpp +++ b/modules/display/src/geometry.cpp @@ -2,7 +2,7 @@ * \file Geometry.cpp * \brief Implement geometry for the basic shapes from IMP.algebra. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/internal/utility.cpp b/modules/display/src/internal/utility.cpp index 4da4dd166e..df63085cb0 100644 --- a/modules/display/src/internal/utility.cpp +++ b/modules/display/src/internal/utility.cpp @@ -2,7 +2,7 @@ * \file writers.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/internal/writers.cpp b/modules/display/src/internal/writers.cpp index b883e413e1..3d5bcc62f3 100644 --- a/modules/display/src/internal/writers.cpp +++ b/modules/display/src/internal/writers.cpp @@ -2,7 +2,7 @@ * \file writers.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/particle_geometry.cpp b/modules/display/src/particle_geometry.cpp index ca994d6354..37e95f16ec 100644 --- a/modules/display/src/particle_geometry.cpp +++ b/modules/display/src/particle_geometry.cpp @@ -2,7 +2,7 @@ * \file particle_geometry.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/display/src/restraint_geometry.cpp b/modules/display/src/restraint_geometry.cpp index b2caa78dd9..b7100f570f 100644 --- a/modules/display/src/restraint_geometry.cpp +++ b/modules/display/src/restraint_geometry.cpp @@ -2,7 +2,7 @@ * \file restraint_geometry.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/benchmark/benchmark_domino2.cpp b/modules/domino/benchmark/benchmark_domino2.cpp index 81236177c3..b5a679df6c 100644 --- a/modules/domino/benchmark/benchmark_domino2.cpp +++ b/modules/domino/benchmark/benchmark_domino2.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/domino/benchmark/benchmark_domino_container.cpp b/modules/domino/benchmark/benchmark_domino_container.cpp index d5dea6cd7a..156d045c3b 100644 --- a/modules/domino/benchmark/benchmark_domino_container.cpp +++ b/modules/domino/benchmark/benchmark_domino_container.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/domino/include/Assignment.h b/modules/domino/include/Assignment.h index ef70c010d2..0736371d65 100644 --- a/modules/domino/include/Assignment.h +++ b/modules/domino/include/Assignment.h @@ -2,7 +2,7 @@ * \file IMP/domino/Assignment.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/BranchAndBoundSampler.h b/modules/domino/include/BranchAndBoundSampler.h index 314d0981ab..bbfe5c4acd 100644 --- a/modules/domino/include/BranchAndBoundSampler.h +++ b/modules/domino/include/BranchAndBoundSampler.h @@ -2,7 +2,7 @@ * \file IMP/domino/BranchAndBoundSampler.h * \brief Sample best solutions using BranchAndBound. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/DependencyScoreState.h b/modules/domino/include/DependencyScoreState.h index 8ec5c3315e..e1f4239689 100644 --- a/modules/domino/include/DependencyScoreState.h +++ b/modules/domino/include/DependencyScoreState.h @@ -2,7 +2,7 @@ * \file IMP/domino/DependencyScoreState.h * \brief Add a dependency to the dependency graph. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/DiscreteSampler.h b/modules/domino/include/DiscreteSampler.h index c0c15a91e6..d5aa37e763 100644 --- a/modules/domino/include/DiscreteSampler.h +++ b/modules/domino/include/DiscreteSampler.h @@ -2,7 +2,7 @@ * \file IMP/domino/DiscreteSampler.h * \brief A base class for discrete samplers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/DominoSampler.h b/modules/domino/include/DominoSampler.h index 6070c9b8ea..c8e0c373fd 100644 --- a/modules/domino/include/DominoSampler.h +++ b/modules/domino/include/DominoSampler.h @@ -2,7 +2,7 @@ * \file IMP/domino/DominoSampler.h * \brief Sample best solutions using Domino. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/Order.h b/modules/domino/include/Order.h index 026a5bd596..b57634f515 100644 --- a/modules/domino/include/Order.h +++ b/modules/domino/include/Order.h @@ -2,7 +2,7 @@ * \file IMP/domino/Order.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/Slice.h b/modules/domino/include/Slice.h index c33a7fc0e6..649dea482a 100644 --- a/modules/domino/include/Slice.h +++ b/modules/domino/include/Slice.h @@ -2,7 +2,7 @@ * \file IMP/domino/Slice.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/Subset.h b/modules/domino/include/Subset.h index bf00646054..edb924b85e 100644 --- a/modules/domino/include/Subset.h +++ b/modules/domino/include/Subset.h @@ -2,7 +2,7 @@ * \file IMP/domino/Subset.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/analysis.h b/modules/domino/include/analysis.h index 714be08210..e6bc32797c 100644 --- a/modules/domino/include/analysis.h +++ b/modules/domino/include/analysis.h @@ -2,7 +2,7 @@ * \file IMP/domino/analysis.h * \brief Functions to get report statistics about the used attributes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDOMINO_ANALYSIS_H diff --git a/modules/domino/include/assignment_containers.h b/modules/domino/include/assignment_containers.h index 5e772b3a9b..cc45a50d28 100644 --- a/modules/domino/include/assignment_containers.h +++ b/modules/domino/include/assignment_containers.h @@ -2,7 +2,7 @@ * \file IMP/domino/assignment_containers.h * \brief Container classes to store assignments. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/assignment_tables.h b/modules/domino/include/assignment_tables.h index bea6638553..6ddf7916db 100644 --- a/modules/domino/include/assignment_tables.h +++ b/modules/domino/include/assignment_tables.h @@ -2,7 +2,7 @@ * \file IMP/domino/assignment_tables.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/domino_macros.h b/modules/domino/include/domino_macros.h index 44e32f003a..2a9767282c 100644 --- a/modules/domino/include/domino_macros.h +++ b/modules/domino/include/domino_macros.h @@ -2,7 +2,7 @@ * \file IMP/domino/domino_macros.h \brief Various important macros * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/interactive.h b/modules/domino/include/interactive.h index a3c02ff486..54857f112c 100644 --- a/modules/domino/include/interactive.h +++ b/modules/domino/include/interactive.h @@ -2,7 +2,7 @@ * \file IMP/domino/interactive.h * \brief Functions to get report statistics about the used attributes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDOMINO_INTERACTIVE_H diff --git a/modules/domino/include/internal/inference_utility.h b/modules/domino/include/internal/inference_utility.h index 2694bad010..a5bc84581b 100644 --- a/modules/domino/include/internal/inference_utility.h +++ b/modules/domino/include/internal/inference_utility.h @@ -2,7 +2,7 @@ * \file RestraintGraph.h * \brief creates a MRF from a set of particles and restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/internal/tree_inference.h b/modules/domino/include/internal/tree_inference.h index 2f81ab1815..bdcc917cae 100644 --- a/modules/domino/include/internal/tree_inference.h +++ b/modules/domino/include/internal/tree_inference.h @@ -2,7 +2,7 @@ * \file RestraintGraph.h * \brief creates a MRF from a set of particles and restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/particle_states.h b/modules/domino/include/particle_states.h index 3eef942a60..8902156d47 100644 --- a/modules/domino/include/particle_states.h +++ b/modules/domino/include/particle_states.h @@ -2,7 +2,7 @@ * \file IMP/domino/particle_states.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/subset_filters.h b/modules/domino/include/subset_filters.h index 1bc74da0d6..e6c83259e3 100644 --- a/modules/domino/include/subset_filters.h +++ b/modules/domino/include/subset_filters.h @@ -2,7 +2,7 @@ * \file IMP/domino/subset_filters.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/subset_graphs.h b/modules/domino/include/subset_graphs.h index 091705c044..ee16b4d02d 100644 --- a/modules/domino/include/subset_graphs.h +++ b/modules/domino/include/subset_graphs.h @@ -2,7 +2,7 @@ * \file IMP/domino/subset_graphs.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/subset_scores.h b/modules/domino/include/subset_scores.h index 3c2b55dfc9..e00c752df1 100644 --- a/modules/domino/include/subset_scores.h +++ b/modules/domino/include/subset_scores.h @@ -2,7 +2,7 @@ * \file IMP/domino/subset_scores.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/include/utility.h b/modules/domino/include/utility.h index 6534c925ea..cf018838dd 100644 --- a/modules/domino/include/utility.h +++ b/modules/domino/include/utility.h @@ -2,7 +2,7 @@ * \file IMP/domino/utility.h * \brief Functions for helping optimize and understand DOMINO-based sampling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPDOMINO_UTILITY_H diff --git a/modules/domino/src/Assignment.cpp b/modules/domino/src/Assignment.cpp index f72c77f608..21837349ad 100644 --- a/modules/domino/src/Assignment.cpp +++ b/modules/domino/src/Assignment.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/BranchAndBoundSampler.cpp b/modules/domino/src/BranchAndBoundSampler.cpp index 369858eb95..4564a4abac 100644 --- a/modules/domino/src/BranchAndBoundSampler.cpp +++ b/modules/domino/src/BranchAndBoundSampler.cpp @@ -2,7 +2,7 @@ * \file BranchAndBoundSampler.cpp * \brief Sample best solutions using BranchAndBound. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/src/DependencyScoreState.cpp b/modules/domino/src/DependencyScoreState.cpp index 729b30eef1..e8f5a499e2 100644 --- a/modules/domino/src/DependencyScoreState.cpp +++ b/modules/domino/src/DependencyScoreState.cpp @@ -2,7 +2,7 @@ * \file DependencyScoreState.cpp * \brief Add a dependency to the dependency graph. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/src/DiscreteSampler.cpp b/modules/domino/src/DiscreteSampler.cpp index a25875eb84..0178a09a3e 100644 --- a/modules/domino/src/DiscreteSampler.cpp +++ b/modules/domino/src/DiscreteSampler.cpp @@ -2,7 +2,7 @@ * \file DiscreteSampler.cpp * \brief A base class for discrete samplers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/src/DominoSampler.cpp b/modules/domino/src/DominoSampler.cpp index bc96fb5eec..d11df1f67c 100644 --- a/modules/domino/src/DominoSampler.cpp +++ b/modules/domino/src/DominoSampler.cpp @@ -2,7 +2,7 @@ * \file DominoSampler.cpp * \brief Sample best solutions using Domino. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/src/Order.cpp b/modules/domino/src/Order.cpp index 3fa60ee211..38ddcae528 100644 --- a/modules/domino/src/Order.cpp +++ b/modules/domino/src/Order.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/Slice.cpp b/modules/domino/src/Slice.cpp index 0df8c96e9b..f6d4ad9c7e 100644 --- a/modules/domino/src/Slice.cpp +++ b/modules/domino/src/Slice.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/Subset.cpp b/modules/domino/src/Subset.cpp index 0d0275b0bf..efef4a6410 100644 --- a/modules/domino/src/Subset.cpp +++ b/modules/domino/src/Subset.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/analysis.cpp b/modules/domino/src/analysis.cpp index d22188429c..da1f143d1e 100644 --- a/modules/domino/src/analysis.cpp +++ b/modules/domino/src/analysis.cpp @@ -2,7 +2,7 @@ * \file interaction_graph.cpp * \brief Score particles with respect to a tunnel. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/assignment_containers.cpp b/modules/domino/src/assignment_containers.cpp index be2ec17ed1..27a488579f 100644 --- a/modules/domino/src/assignment_containers.cpp +++ b/modules/domino/src/assignment_containers.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/assignment_tables.cpp b/modules/domino/src/assignment_tables.cpp index 65ac625e77..06a49b5d71 100644 --- a/modules/domino/src/assignment_tables.cpp +++ b/modules/domino/src/assignment_tables.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h \brief A Bayesian inference-based * sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/interactive.cpp b/modules/domino/src/interactive.cpp index eaef4dc30c..3a236f8d9c 100644 --- a/modules/domino/src/interactive.cpp +++ b/modules/domino/src/interactive.cpp @@ -2,7 +2,7 @@ * \file domino/interactive.cpp * \brief Functions to get report statistics about the used attributes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/domino/src/internal/inference_utility.cpp b/modules/domino/src/internal/inference_utility.cpp index 09ce2b953f..886df5cbb2 100644 --- a/modules/domino/src/internal/inference_utility.cpp +++ b/modules/domino/src/internal/inference_utility.cpp @@ -2,7 +2,7 @@ * \file RestraintGraph.cpp * \brief creates a MRF from a set of particles and restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/src/internal/tree_inference.cpp b/modules/domino/src/internal/tree_inference.cpp index 70a694a882..970bc2eb5a 100644 --- a/modules/domino/src/internal/tree_inference.cpp +++ b/modules/domino/src/internal/tree_inference.cpp @@ -2,7 +2,7 @@ * \file RestraintGraph.cpp * \brief creates a MRF from a set of particles and restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/src/particle_states.cpp b/modules/domino/src/particle_states.cpp index e2284bbaeb..6d3559927e 100644 --- a/modules/domino/src/particle_states.cpp +++ b/modules/domino/src/particle_states.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h * \brief A Bayesian inference-based sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/domino/src/subset_filters.cpp b/modules/domino/src/subset_filters.cpp index c872689e0b..816afd51f2 100644 --- a/modules/domino/src/subset_filters.cpp +++ b/modules/domino/src/subset_filters.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h \brief A Bayesian inference-based * sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/subset_graphs.cpp b/modules/domino/src/subset_graphs.cpp index 0956069772..f47866e85d 100644 --- a/modules/domino/src/subset_graphs.cpp +++ b/modules/domino/src/subset_graphs.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h \brief A Bayesian inference-based * sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/subset_scores.cpp b/modules/domino/src/subset_scores.cpp index 97f34aa11b..a801244030 100644 --- a/modules/domino/src/subset_scores.cpp +++ b/modules/domino/src/subset_scores.cpp @@ -2,7 +2,7 @@ * \file domino/DominoSampler.h \brief A Bayesian inference-based * sampler. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/domino/src/utility.cpp b/modules/domino/src/utility.cpp index dc832451f6..42e7cbc37f 100644 --- a/modules/domino/src/utility.cpp +++ b/modules/domino/src/utility.cpp @@ -2,7 +2,7 @@ * \file utility.cpp * \brief Functions for helping optimize and understand DOMINO-based sampling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/benchmark/benchmark_density.cpp b/modules/em/benchmark/benchmark_density.cpp index 7e542b64d7..624c4ba59e 100644 --- a/modules/em/benchmark/benchmark_density.cpp +++ b/modules/em/benchmark/benchmark_density.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/em/include/CoarseCC.h b/modules/em/include/CoarseCC.h index 0cfeb8d376..a7a26369c8 100644 --- a/modules/em/include/CoarseCC.h +++ b/modules/em/include/CoarseCC.h @@ -2,7 +2,7 @@ * \file IMP/em/CoarseCC.h * \brief Perform coarse fitting between two density objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/CoarseCCatIntervals.h b/modules/em/include/CoarseCCatIntervals.h index 947efec72d..ddba55a372 100644 --- a/modules/em/include/CoarseCCatIntervals.h +++ b/modules/em/include/CoarseCCatIntervals.h @@ -2,7 +2,7 @@ * \file IMP/em/CoarseCCatIntervals.h * \brief Cross correlation coefficient calculator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/CoarseConvolution.h b/modules/em/include/CoarseConvolution.h index 63991c54c2..1130d1ef3f 100644 --- a/modules/em/include/CoarseConvolution.h +++ b/modules/em/include/CoarseConvolution.h @@ -2,7 +2,7 @@ * \file IMP/em/CoarseConvolution.h * \brief Convolutes two grids * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/DensityFillingRestraint.h b/modules/em/include/DensityFillingRestraint.h index 0d02984e15..c7e6720a68 100644 --- a/modules/em/include/DensityFillingRestraint.h +++ b/modules/em/include/DensityFillingRestraint.h @@ -2,7 +2,7 @@ * \file IMP/em/DensityFillingRestraint.h * \brief Score how well the particles fill the density * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/DensityHeader.h b/modules/em/include/DensityHeader.h index 56eec51b96..c28ce3580c 100644 --- a/modules/em/include/DensityHeader.h +++ b/modules/em/include/DensityHeader.h @@ -2,7 +2,7 @@ * \file IMP/em/DensityHeader.h * \brief Metadata for a density file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/DensityMap.h b/modules/em/include/DensityMap.h index 935a82ca16..99f75002ad 100644 --- a/modules/em/include/DensityMap.h +++ b/modules/em/include/DensityMap.h @@ -2,7 +2,7 @@ * \file IMP/em/DensityMap.h * \brief Class for handling density maps. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/EMReaderWriter.h b/modules/em/include/EMReaderWriter.h index de111026f7..750e08aadb 100644 --- a/modules/em/include/EMReaderWriter.h +++ b/modules/em/include/EMReaderWriter.h @@ -2,7 +2,7 @@ * \file IMP/em/EMReaderWriter.h * \brief Classes to read or write density files in EM format. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/EnvelopeFitRestraint.h b/modules/em/include/EnvelopeFitRestraint.h index 30823e6e62..adfb2c3b7a 100644 --- a/modules/em/include/EnvelopeFitRestraint.h +++ b/modules/em/include/EnvelopeFitRestraint.h @@ -3,7 +3,7 @@ * \brief score envelope fit based on map distance transform * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/EnvelopePenetrationRestraint.h b/modules/em/include/EnvelopePenetrationRestraint.h index 44a2d61668..b3afa9ff7f 100644 --- a/modules/em/include/EnvelopePenetrationRestraint.h +++ b/modules/em/include/EnvelopePenetrationRestraint.h @@ -2,7 +2,7 @@ * \file IMP/em/EnvelopePenetrationRestraint.h * \brief Score how well a protein is inside its density * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/EnvelopeScore.h b/modules/em/include/EnvelopeScore.h index 1cbb20b050..cce6f8891e 100644 --- a/modules/em/include/EnvelopeScore.h +++ b/modules/em/include/EnvelopeScore.h @@ -2,7 +2,7 @@ * \file IMP/em/EnvelopeScore.h * \brief class for envelope based scoring using MapDistanceTransform * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/FitRestraint.h b/modules/em/include/FitRestraint.h index e6c120ceea..c6914bce32 100644 --- a/modules/em/include/FitRestraint.h +++ b/modules/em/include/FitRestraint.h @@ -2,7 +2,7 @@ * \file IMP/em/FitRestraint.h * \brief Calculate score based on fit to EM map. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/ImageHeader.h b/modules/em/include/ImageHeader.h index 4659fbeb72..774eb05115 100644 --- a/modules/em/include/ImageHeader.h +++ b/modules/em/include/ImageHeader.h @@ -1,7 +1,7 @@ /** * \file IMP/em/ImageHeader.h * \brief Header for EM images. Compatible with Spider and Xmipp formats - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. **/ #ifndef IMPEM_IMAGE_HEADER_H diff --git a/modules/em/include/KernelParameters.h b/modules/em/include/KernelParameters.h index 0f78e33a2e..8bd3f90214 100644 --- a/modules/em/include/KernelParameters.h +++ b/modules/em/include/KernelParameters.h @@ -2,7 +2,7 @@ * \file IMP/em/KernelParameters.h * \brief Calculates and stores Gaussian kernel parameters. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/MRCReaderWriter.h b/modules/em/include/MRCReaderWriter.h index 6cb7e49a83..e8002dc383 100644 --- a/modules/em/include/MRCReaderWriter.h +++ b/modules/em/include/MRCReaderWriter.h @@ -2,7 +2,7 @@ * \file IMP/em/MRCReaderWriter.h * \brief Classes to read or write MRC files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/MapDistanceTransform.h b/modules/em/include/MapDistanceTransform.h index 43aeff5efd..e51fa9fc85 100644 --- a/modules/em/include/MapDistanceTransform.h +++ b/modules/em/include/MapDistanceTransform.h @@ -2,7 +2,7 @@ * \file IMP/em/MapDistanceTransform.h \brief class for computing a distance * transform of the density map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/MapReaderWriter.h b/modules/em/include/MapReaderWriter.h index c64e569b5b..4228e63279 100644 --- a/modules/em/include/MapReaderWriter.h +++ b/modules/em/include/MapReaderWriter.h @@ -2,7 +2,7 @@ * \file IMP/em/MapReaderWriter.h * \brief An abstract class for reading a map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/PCAAligner.h b/modules/em/include/PCAAligner.h index 59f3465446..af12048249 100644 --- a/modules/em/include/PCAAligner.h +++ b/modules/em/include/PCAAligner.h @@ -2,7 +2,7 @@ * \file IMP/em/PCAAligner.h * \brief Fast alignment of points to a density map using principal components * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/PCAFitRestraint.h b/modules/em/include/PCAFitRestraint.h index a59c3d9db8..5c4ade3955 100644 --- a/modules/em/include/PCAFitRestraint.h +++ b/modules/em/include/PCAFitRestraint.h @@ -2,7 +2,7 @@ * \file IMP/em/PCAFitRestraint.h * \brief Calculate match between density map PCA and particles PCA. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/SampledDensityMap.h b/modules/em/include/SampledDensityMap.h index 24451ca70a..f617ccab59 100644 --- a/modules/em/include/SampledDensityMap.h +++ b/modules/em/include/SampledDensityMap.h @@ -2,7 +2,7 @@ * \file IMP/em/SampledDensityMap.h * \brief Sampled density map. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/SpiderHeader.h b/modules/em/include/SpiderHeader.h index 894ae02ba7..491f3a872a 100644 --- a/modules/em/include/SpiderHeader.h +++ b/modules/em/include/SpiderHeader.h @@ -2,7 +2,7 @@ * \file IMP/em/SpiderHeader.h * \brief Header for Spider and Xmipp formats * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM_SPIDER_HEADER_H diff --git a/modules/em/include/SpiderReaderWriter.h b/modules/em/include/SpiderReaderWriter.h index 4d97c5ee7d..3b95698a9e 100644 --- a/modules/em/include/SpiderReaderWriter.h +++ b/modules/em/include/SpiderReaderWriter.h @@ -2,7 +2,7 @@ * \file IMP/em/SpiderReaderWriter.h * \brief Management of Spider Headers Electron Microscopy. Compatible with * Spider and Xmipp formats - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM_SPIDER_READER_WRITER_H diff --git a/modules/em/include/SurfaceShellDensityMap.h b/modules/em/include/SurfaceShellDensityMap.h index 7146b5af18..8666dea385 100644 --- a/modules/em/include/SurfaceShellDensityMap.h +++ b/modules/em/include/SurfaceShellDensityMap.h @@ -2,7 +2,7 @@ * \file IMP/em/SurfaceShellDensityMap.h * \brief Represent a molecule as shells of distance from the surface * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/Voxel.h b/modules/em/include/Voxel.h index f537c9b828..ae842ba7d4 100644 --- a/modules/em/include/Voxel.h +++ b/modules/em/include/Voxel.h @@ -1,7 +1,7 @@ /** * \file IMP/em/Voxel.h \brief voxel decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/XplorReaderWriter.h b/modules/em/include/XplorReaderWriter.h index c73c319297..de58118cc7 100644 --- a/modules/em/include/XplorReaderWriter.h +++ b/modules/em/include/XplorReaderWriter.h @@ -2,7 +2,7 @@ * \file IMP/em/XplorReaderWriter.h * \brief Classes to read or write density files in XPLOR format. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/converters.h b/modules/em/include/converters.h index 7df907e6ed..e7a30ba671 100644 --- a/modules/em/include/converters.h +++ b/modules/em/include/converters.h @@ -2,7 +2,7 @@ * \file IMP/em/converters.h * \brief Converters of density values * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/def.h b/modules/em/include/def.h index f1411c9522..f01e20b4ee 100644 --- a/modules/em/include/def.h +++ b/modules/em/include/def.h @@ -2,7 +2,7 @@ * \file IMP/em/def.h * \brief Definitions for EMBED. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/density_utilities.h b/modules/em/include/density_utilities.h index e076e8a0ca..30ab881210 100644 --- a/modules/em/include/density_utilities.h +++ b/modules/em/include/density_utilities.h @@ -2,7 +2,7 @@ * \file IMP/em/density_utilities.h * \brief density map manipulations * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/embedding.h b/modules/em/include/embedding.h index 913d324352..b62afab104 100644 --- a/modules/em/include/embedding.h +++ b/modules/em/include/embedding.h @@ -2,7 +2,7 @@ * \file IMP/em/embedding.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/envelope_penetration.h b/modules/em/include/envelope_penetration.h index 82831e8585..250e1a435e 100644 --- a/modules/em/include/envelope_penetration.h +++ b/modules/em/include/envelope_penetration.h @@ -2,7 +2,7 @@ * \file IMP/em/envelope_penetration.h * \brief functions for calculation envelope penetration * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/exp.h b/modules/em/include/exp.h index 3059025737..b8521abc5f 100644 --- a/modules/em/include/exp.h +++ b/modules/em/include/exp.h @@ -2,7 +2,7 @@ * \file IMP/em/exp.h * \brief An approximation of the exponential function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/header_converters.h b/modules/em/include/header_converters.h index af9d6a014b..fab1a842d3 100644 --- a/modules/em/include/header_converters.h +++ b/modules/em/include/header_converters.h @@ -1,7 +1,7 @@ /** * \file IMP/em/header_converters.h * \brief Functions to convert between ImageHeader and DensityHeader - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM_HEADER_CONVERTERS_H diff --git a/modules/em/include/internal/EMHeader.h b/modules/em/include/internal/EMHeader.h index 092343e91e..b79fb40491 100644 --- a/modules/em/include/internal/EMHeader.h +++ b/modules/em/include/internal/EMHeader.h @@ -2,7 +2,7 @@ * \file EMHeader.h * \brief Header information for files in EM format. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/internal/MRCHeader.h b/modules/em/include/internal/MRCHeader.h index 02478f43bc..bdf3ecef32 100644 --- a/modules/em/include/internal/MRCHeader.h +++ b/modules/em/include/internal/MRCHeader.h @@ -2,7 +2,7 @@ * \file MRCHeader.h * \brief Header information for an MRC file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/internal/RadiusDependentKernelParameters.h b/modules/em/include/internal/RadiusDependentKernelParameters.h index ca5c659bd2..82e552a109 100644 --- a/modules/em/include/internal/RadiusDependentKernelParameters.h +++ b/modules/em/include/internal/RadiusDependentKernelParameters.h @@ -2,7 +2,7 @@ * \file IMP/em/internal/RadiusDependentKernelParameters.h * \brief Calculates kernel parameters as a function of a specific radius. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/internal/XplorHeader.h b/modules/em/include/internal/XplorHeader.h index 8159a7e847..f7502aaa18 100644 --- a/modules/em/include/internal/XplorHeader.h +++ b/modules/em/include/internal/XplorHeader.h @@ -2,7 +2,7 @@ * \file XplorHeader.h * \brief Header information for an XPLOR file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/masking.h b/modules/em/include/masking.h index f1bac482a3..f1e06e0dd5 100644 --- a/modules/em/include/masking.h +++ b/modules/em/include/masking.h @@ -2,7 +2,7 @@ * \file IMP/em/masking.h * \brief masking tools * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/include/rigid_fitting.h b/modules/em/include/rigid_fitting.h index a00fbddd0f..aeb213691f 100644 --- a/modules/em/include/rigid_fitting.h +++ b/modules/em/include/rigid_fitting.h @@ -2,7 +2,7 @@ * \file IMP/em/rigid_fitting.h * \brief preforms rigid fitting between a set of particles and a density map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM_RIGID_FITTING_H diff --git a/modules/em/src/CoarseCC.cpp b/modules/em/src/CoarseCC.cpp index 65c40b75bc..e652485747 100644 --- a/modules/em/src/CoarseCC.cpp +++ b/modules/em/src/CoarseCC.cpp @@ -2,7 +2,7 @@ * \file CoarseCC.cpp * \brief Perform coarse fitting between two density objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/CoarseCCatIntervals.cpp b/modules/em/src/CoarseCCatIntervals.cpp index a53b1e0134..efacdac101 100644 --- a/modules/em/src/CoarseCCatIntervals.cpp +++ b/modules/em/src/CoarseCCatIntervals.cpp @@ -2,7 +2,7 @@ * \file CoarseCCatIntervals.cpp * \brief Cross correlation coefficient calculator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/CoarseConvolution.cpp b/modules/em/src/CoarseConvolution.cpp index 2874d34ab4..b0931a7d1d 100644 --- a/modules/em/src/CoarseConvolution.cpp +++ b/modules/em/src/CoarseConvolution.cpp @@ -2,7 +2,7 @@ * \file CoarseConvolution.cpp * \brief Convolutes two grids * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/DensityFillingRestraint.cpp b/modules/em/src/DensityFillingRestraint.cpp index b050244320..5a2acdc5a6 100644 --- a/modules/em/src/DensityFillingRestraint.cpp +++ b/modules/em/src/DensityFillingRestraint.cpp @@ -2,7 +2,7 @@ * \file DensityFillingRestraint.cpp * \brief Score how well a protein is inside its density * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/DensityHeader.cpp b/modules/em/src/DensityHeader.cpp index a5f9e8dc3c..675a31c2ad 100644 --- a/modules/em/src/DensityHeader.cpp +++ b/modules/em/src/DensityHeader.cpp @@ -2,7 +2,7 @@ * \file DensityHeader.cpp * \brief Metadata for a density file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/DensityMap.cpp b/modules/em/src/DensityMap.cpp index 737610c8c5..b3d0d6fea5 100644 --- a/modules/em/src/DensityMap.cpp +++ b/modules/em/src/DensityMap.cpp @@ -2,7 +2,7 @@ * \file DensityMap.cpp * \brief Class for handling density maps. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/EMReaderWriter.cpp b/modules/em/src/EMReaderWriter.cpp index 43259ba2fc..cf7d821298 100644 --- a/modules/em/src/EMReaderWriter.cpp +++ b/modules/em/src/EMReaderWriter.cpp @@ -2,7 +2,7 @@ * \file EMReaderWriter.cpp * \brief Classes to read or write density files in EM format. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/EnvelopeFitRestraint.cpp b/modules/em/src/EnvelopeFitRestraint.cpp index d881f16fef..26a1eedf07 100644 --- a/modules/em/src/EnvelopeFitRestraint.cpp +++ b/modules/em/src/EnvelopeFitRestraint.cpp @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/EnvelopePenetrationRestraint.cpp b/modules/em/src/EnvelopePenetrationRestraint.cpp index d7d1ecfd8d..fdca5e78d8 100644 --- a/modules/em/src/EnvelopePenetrationRestraint.cpp +++ b/modules/em/src/EnvelopePenetrationRestraint.cpp @@ -2,7 +2,7 @@ * \file EnvelopePenetrationRestraint.cpp * \brief Score how well a protein is inside its density * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/EnvelopeScore.cpp b/modules/em/src/EnvelopeScore.cpp index 725f85c3a8..e5cd61558c 100644 --- a/modules/em/src/EnvelopeScore.cpp +++ b/modules/em/src/EnvelopeScore.cpp @@ -1,7 +1,7 @@ /** * \file EnvelopeScore.cpp \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/FitRestraint.cpp b/modules/em/src/FitRestraint.cpp index 9a110cfb6a..518b58713e 100644 --- a/modules/em/src/FitRestraint.cpp +++ b/modules/em/src/FitRestraint.cpp @@ -2,7 +2,7 @@ * \file FitRestraint.cpp * \brief Calculate score based on fit to EM map. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/ImageHeader.cpp b/modules/em/src/ImageHeader.cpp index 6cd72bcaae..292df3795f 100644 --- a/modules/em/src/ImageHeader.cpp +++ b/modules/em/src/ImageHeader.cpp @@ -1,7 +1,7 @@ /** * \file ImageHeader.cpp * \brief Header for EM images - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. **/ #include "IMP/em/ImageHeader.h" diff --git a/modules/em/src/KernelParameters.cpp b/modules/em/src/KernelParameters.cpp index 4fb5b7dab5..035b3729d9 100644 --- a/modules/em/src/KernelParameters.cpp +++ b/modules/em/src/KernelParameters.cpp @@ -2,7 +2,7 @@ * \file KernelParameters.cpp * \brief Calculates and stores Gaussian kernel parameters. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/MRCReaderWriter.cpp b/modules/em/src/MRCReaderWriter.cpp index dd1691df2a..905e096343 100644 --- a/modules/em/src/MRCReaderWriter.cpp +++ b/modules/em/src/MRCReaderWriter.cpp @@ -2,7 +2,7 @@ * \file MRCReaderWriter.cpp * \brief Classes to read or write MRC files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/MapDistanceTransform.cpp b/modules/em/src/MapDistanceTransform.cpp index 42f2deb848..14073afe0c 100644 --- a/modules/em/src/MapDistanceTransform.cpp +++ b/modules/em/src/MapDistanceTransform.cpp @@ -2,7 +2,7 @@ * \file MapDistanceTransform \brief class for computing a distance * transform of the density map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/PCAAligner.cpp b/modules/em/src/PCAAligner.cpp index 49caacbd01..302c5770f9 100644 --- a/modules/em/src/PCAAligner.cpp +++ b/modules/em/src/PCAAligner.cpp @@ -1,7 +1,7 @@ /** * \file PCAAligner.cpp \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/PCAFitRestraint.cpp b/modules/em/src/PCAFitRestraint.cpp index a1aa2ccddb..9c845eec74 100644 --- a/modules/em/src/PCAFitRestraint.cpp +++ b/modules/em/src/PCAFitRestraint.cpp @@ -2,7 +2,7 @@ * \file PCAFitRestraint.cpp * \brief Calculate match between density and particle PCA * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/SampledDensityMap.cpp b/modules/em/src/SampledDensityMap.cpp index 65387cadf3..6f9c1f0c79 100644 --- a/modules/em/src/SampledDensityMap.cpp +++ b/modules/em/src/SampledDensityMap.cpp @@ -2,7 +2,7 @@ * \file SampledDensityMap.cpp * \brief Sampled density map. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/SpiderReaderWriter.cpp b/modules/em/src/SpiderReaderWriter.cpp index e65d6a2645..4bad70894a 100644 --- a/modules/em/src/SpiderReaderWriter.cpp +++ b/modules/em/src/SpiderReaderWriter.cpp @@ -2,7 +2,7 @@ * \file SpiderReaderWriter.cpp * \brief Reader and Writer for Spider volumes * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em/SpiderReaderWriter.h" diff --git a/modules/em/src/SurfaceShellDensityMap.cpp b/modules/em/src/SurfaceShellDensityMap.cpp index eedd7d7fd4..ddf5fd5f3f 100644 --- a/modules/em/src/SurfaceShellDensityMap.cpp +++ b/modules/em/src/SurfaceShellDensityMap.cpp @@ -2,7 +2,7 @@ * \file SurfaceShellDensityMap.cpp * \brief Represent a molecule as shells of distance from the surface * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/Voxel.cpp b/modules/em/src/Voxel.cpp index ce22a999a8..b1efd02692 100644 --- a/modules/em/src/Voxel.cpp +++ b/modules/em/src/Voxel.cpp @@ -1,7 +1,7 @@ /** * \file Voxel.cpp \brief Voxel decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/XplorReaderWriter.cpp b/modules/em/src/XplorReaderWriter.cpp index 90283cc1ca..4be7c746df 100644 --- a/modules/em/src/XplorReaderWriter.cpp +++ b/modules/em/src/XplorReaderWriter.cpp @@ -2,7 +2,7 @@ * \file XplorReaderWriter.cpp * \brief Classes to read or write density files in XPLOR format. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/converters.cpp b/modules/em/src/converters.cpp index d3e2552861..1bfa77fba9 100644 --- a/modules/em/src/converters.cpp +++ b/modules/em/src/converters.cpp @@ -1,7 +1,7 @@ /** * \file converters.cpp * \brief impl - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/em/src/density_utilities.cpp b/modules/em/src/density_utilities.cpp index a1c4361a87..e9129f4e4e 100644 --- a/modules/em/src/density_utilities.cpp +++ b/modules/em/src/density_utilities.cpp @@ -2,7 +2,7 @@ * \file density_utilities.cpp * \brief density map manipulations * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/embedding.cpp b/modules/em/src/embedding.cpp index 5312f0b162..cc53fb8c85 100644 --- a/modules/em/src/embedding.cpp +++ b/modules/em/src/embedding.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/envelope_penetration.cpp b/modules/em/src/envelope_penetration.cpp index e650e42025..e341db74d9 100644 --- a/modules/em/src/envelope_penetration.cpp +++ b/modules/em/src/envelope_penetration.cpp @@ -2,7 +2,7 @@ * \file envelope_penetration.cpp * \brief functions for calculation envelope penetration * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/em/src/header_converters.cpp b/modules/em/src/header_converters.cpp index f9a367f830..430d1ba6fe 100644 --- a/modules/em/src/header_converters.cpp +++ b/modules/em/src/header_converters.cpp @@ -2,7 +2,7 @@ * \file header_converters.cpp * \brief Functions to convert between ImageHeader and DensityHeader * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/em/src/internal/EMHeader.cpp b/modules/em/src/internal/EMHeader.cpp index 7230986fb0..3a6274d0d0 100644 --- a/modules/em/src/internal/EMHeader.cpp +++ b/modules/em/src/internal/EMHeader.cpp @@ -2,7 +2,7 @@ * \file EMHeader.cpp * \brief Header information for files in EM format. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/internal/MRCHeader.cpp b/modules/em/src/internal/MRCHeader.cpp index bb5b0933c5..5ae0c43cba 100644 --- a/modules/em/src/internal/MRCHeader.cpp +++ b/modules/em/src/internal/MRCHeader.cpp @@ -2,7 +2,7 @@ * \file MRCHeader.cpp * \brief Header information for an MRC file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/masking.cpp b/modules/em/src/masking.cpp index e3059ddbd9..60afb10807 100644 --- a/modules/em/src/masking.cpp +++ b/modules/em/src/masking.cpp @@ -2,7 +2,7 @@ * \file masking.cpp * \brief masking tools * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em/src/rigid_fitting.cpp b/modules/em/src/rigid_fitting.cpp index 22de13aa7f..1d124c89a5 100644 --- a/modules/em/src/rigid_fitting.cpp +++ b/modules/em/src/rigid_fitting.cpp @@ -2,7 +2,7 @@ * \file rigid_fitting.cpp * \brief Rigid fitting functionality * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/bin/create_single_particle_images.cpp b/modules/em2d/bin/create_single_particle_images.cpp index 61778eca6d..95c6f8c4eb 100644 --- a/modules/em2d/bin/create_single_particle_images.cpp +++ b/modules/em2d/bin/create_single_particle_images.cpp @@ -1,7 +1,7 @@ /** * \file create_single_particle_images.cpp * \brief Generation of projections from models or density maps or pure noisy images - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ diff --git a/modules/em2d/include/CenteredMat.h b/modules/em2d/include/CenteredMat.h index cc6ee7fcc2..a75740bd5e 100644 --- a/modules/em2d/include/CenteredMat.h +++ b/modules/em2d/include/CenteredMat.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/CenteredMat.h * \brief Decorator for OpenCV matrix to use relative coordinates - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_CENTERED_MAT_H diff --git a/modules/em2d/include/CollisionCrossSection.h b/modules/em2d/include/CollisionCrossSection.h index 0e106dc3c5..6116bba294 100644 --- a/modules/em2d/include/CollisionCrossSection.h +++ b/modules/em2d/include/CollisionCrossSection.h @@ -2,7 +2,7 @@ * \file IMP/em2d/CollisionCrossSection.h * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/DummyRestraint.h b/modules/em2d/include/DummyRestraint.h index 823bc74fad..724a877777 100644 --- a/modules/em2d/include/DummyRestraint.h +++ b/modules/em2d/include/DummyRestraint.h @@ -2,7 +2,7 @@ * \file IMP/em2d/DummyRestraint.h * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/Em2DRestraint.h b/modules/em2d/include/Em2DRestraint.h index eecea579fa..8a30048e77 100644 --- a/modules/em2d/include/Em2DRestraint.h +++ b/modules/em2d/include/Em2DRestraint.h @@ -2,7 +2,7 @@ * \file IMP/em2d/Em2DRestraint.h * \brief A restraint to score the fitness of a model to a set of EM images * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/FFToperations.h b/modules/em2d/include/FFToperations.h index 8a4eabe82e..227dd4c07c 100644 --- a/modules/em2d/include/FFToperations.h +++ b/modules/em2d/include/FFToperations.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/FFToperations.h * \brief Operations involving FFT - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_FF_TOPERATIONS_H diff --git a/modules/em2d/include/Fine2DRegistrationRestraint.h b/modules/em2d/include/Fine2DRegistrationRestraint.h index 95f4b59094..281366110c 100644 --- a/modules/em2d/include/Fine2DRegistrationRestraint.h +++ b/modules/em2d/include/Fine2DRegistrationRestraint.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/Fine2DRegistrationRestraint.h * \brief Alignment of 2D projections of a 3D volume - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_FINE_2DREGISTRATION_RESTRAINT_H diff --git a/modules/em2d/include/Image.h b/modules/em2d/include/Image.h index 8e7d509d8a..dc20ca0359 100644 --- a/modules/em2d/include/Image.h +++ b/modules/em2d/include/Image.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/Image.h * \brief IMP images for Electron Microscopy using openCV matrices - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_IMAGE_H diff --git a/modules/em2d/include/ImageReaderWriter.h b/modules/em2d/include/ImageReaderWriter.h index d4b2207b63..715c50232c 100644 --- a/modules/em2d/include/ImageReaderWriter.h +++ b/modules/em2d/include/ImageReaderWriter.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/ImageReaderWriter.h * \brief Virtual class for reader/writers of images - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_IMAGE_READER_WRITER_H diff --git a/modules/em2d/include/JPGImageReaderWriter.h b/modules/em2d/include/JPGImageReaderWriter.h index c048665ec6..0a2511718a 100644 --- a/modules/em2d/include/JPGImageReaderWriter.h +++ b/modules/em2d/include/JPGImageReaderWriter.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/JPGImageReaderWriter.h * \brief Management of JPG format for EM images - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_JPG_IMAGE_READER_WRITER_H diff --git a/modules/em2d/include/PCAFitRestraint.h b/modules/em2d/include/PCAFitRestraint.h index d42531be02..bca92f77e8 100644 --- a/modules/em2d/include/PCAFitRestraint.h +++ b/modules/em2d/include/PCAFitRestraint.h @@ -3,7 +3,7 @@ * \brief fast scoring of fit between Particles in 3D and 2D class averages * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/PolarResamplingParameters.h b/modules/em2d/include/PolarResamplingParameters.h index c04f8417f3..27144dc2f5 100644 --- a/modules/em2d/include/PolarResamplingParameters.h +++ b/modules/em2d/include/PolarResamplingParameters.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/PolarResamplingParameters.h * \brief Functions related with rotations in em2d - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_POLAR_RESAMPLING_PARAMETERS_H diff --git a/modules/em2d/include/ProjectionFinder.h b/modules/em2d/include/ProjectionFinder.h index 2e2fce4a59..bff5369275 100644 --- a/modules/em2d/include/ProjectionFinder.h +++ b/modules/em2d/include/ProjectionFinder.h @@ -2,7 +2,7 @@ * \file IMP/em2d/ProjectionFinder.h * \brief Coarse registration of 2D projections from a 3D volume * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_PROJECTION_FINDER_H diff --git a/modules/em2d/include/ProjectionMask.h b/modules/em2d/include/ProjectionMask.h index 9da93a28b5..039591fd7b 100644 --- a/modules/em2d/include/ProjectionMask.h +++ b/modules/em2d/include/ProjectionMask.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/ProjectionMask.h * \brief projection masks - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_PROJECTION_MASK_H diff --git a/modules/em2d/include/ProjectionParameters.h b/modules/em2d/include/ProjectionParameters.h index 66afd15808..24d2ffbe07 100644 --- a/modules/em2d/include/ProjectionParameters.h +++ b/modules/em2d/include/ProjectionParameters.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/ProjectionParameters.h * \brief Decorator for projection parameters - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_PROJECTION_PARAMETERS_H diff --git a/modules/em2d/include/RegistrationResult.h b/modules/em2d/include/RegistrationResult.h index 151f7a9eeb..7fffa1487a 100644 --- a/modules/em2d/include/RegistrationResult.h +++ b/modules/em2d/include/RegistrationResult.h @@ -1,7 +1,7 @@ /*! * \file IMP/em2d/RegistrationResult.h * \brief Registration results class - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_REGISTRATION_RESULT_H diff --git a/modules/em2d/include/RelativePositionMover.h b/modules/em2d/include/RelativePositionMover.h index 6dba3f63fe..fb00ca8c63 100644 --- a/modules/em2d/include/RelativePositionMover.h +++ b/modules/em2d/include/RelativePositionMover.h @@ -2,7 +2,7 @@ * \file IMP/em2d/RelativePositionMover.h * \brief Mover for Rigid Bodies moving respect to each other * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/RigidBodiesImageFitRestraint.h b/modules/em2d/include/RigidBodiesImageFitRestraint.h index 89e9ad8c64..adbbe3bcaf 100644 --- a/modules/em2d/include/RigidBodiesImageFitRestraint.h +++ b/modules/em2d/include/RigidBodiesImageFitRestraint.h @@ -2,7 +2,7 @@ * \file IMP/em2d/RigidBodiesImageFitRestraint.h * \brief Fit rigid bodies to an image. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/SpiderImageReaderWriter.h b/modules/em2d/include/SpiderImageReaderWriter.h index 39ef27bb21..6ec46f1f02 100644 --- a/modules/em2d/include/SpiderImageReaderWriter.h +++ b/modules/em2d/include/SpiderImageReaderWriter.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/SpiderImageReaderWriter.h * \brief Management of Images in Spider format - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_SPIDER_IMAGE_READER_WRITER_H diff --git a/modules/em2d/include/TIFFImageReaderWriter.h b/modules/em2d/include/TIFFImageReaderWriter.h index e5e82c0d3d..fe18ddae8d 100644 --- a/modules/em2d/include/TIFFImageReaderWriter.h +++ b/modules/em2d/include/TIFFImageReaderWriter.h @@ -2,7 +2,7 @@ * \file IMP/em2d/TIFFImageReaderWriter.h * \brief Management of reading/writing TIFF images * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/align2D.h b/modules/em2d/include/align2D.h index 95999f20e6..82b5aecc85 100644 --- a/modules/em2d/include/align2D.h +++ b/modules/em2d/include/align2D.h @@ -1,7 +1,7 @@ /*! * \file IMP/em2d/align2D.h * \brief Alignment of images in 2D - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_ALIGN_2D_H diff --git a/modules/em2d/include/domino_filter_tables.h b/modules/em2d/include/domino_filter_tables.h index 3b7aa29329..0b8e469bf9 100644 --- a/modules/em2d/include/domino_filter_tables.h +++ b/modules/em2d/include/domino_filter_tables.h @@ -2,7 +2,7 @@ * \file IMP/em2d/domino_filter_tables.h * \brief Managing of projection overlap filter * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/domino_filters.h b/modules/em2d/include/domino_filters.h index 465fc751c2..be383279d6 100644 --- a/modules/em2d/include/domino_filters.h +++ b/modules/em2d/include/domino_filters.h @@ -2,7 +2,7 @@ * \file IMP/em2d/domino_filters.h * \brief SubsetFilter for checking overlap between projections and images * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/domino_particle_states.h b/modules/em2d/include/domino_particle_states.h index 0702ace96d..cbdbfccaa5 100644 --- a/modules/em2d/include/domino_particle_states.h +++ b/modules/em2d/include/domino_particle_states.h @@ -3,7 +3,7 @@ * \brief Particles states for a rigid body that is going to be *projected * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/filenames_manipulation.h b/modules/em2d/include/filenames_manipulation.h index 964749e346..6e75388a44 100644 --- a/modules/em2d/include/filenames_manipulation.h +++ b/modules/em2d/include/filenames_manipulation.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/filenames_manipulation.h * \brief Generation of projections using the central section theorem - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_FILENAMES_MANIPULATION_H diff --git a/modules/em2d/include/hierarchical_clustering.h b/modules/em2d/include/hierarchical_clustering.h index 217452eb6b..6e1748faef 100644 --- a/modules/em2d/include/hierarchical_clustering.h +++ b/modules/em2d/include/hierarchical_clustering.h @@ -2,7 +2,7 @@ * \file IMP/em2d/hierarchical_clustering.h * \brief Agglomerative clustering algorithm * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/image_processing.h b/modules/em2d/include/image_processing.h index 6008663b8e..874c374653 100644 --- a/modules/em2d/include/image_processing.h +++ b/modules/em2d/include/image_processing.h @@ -2,7 +2,7 @@ * \file IMP/em2d/image_processing.h * \brief Image processing functions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_IMAGE_PROCESSING_H diff --git a/modules/em2d/include/internal/Image2D.h b/modules/em2d/include/internal/Image2D.h index 7527643320..1f3fbeeb8e 100644 --- a/modules/em2d/include/internal/Image2D.h +++ b/modules/em2d/include/internal/Image2D.h @@ -3,7 +3,7 @@ * \brief A basic image class * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/internal/ImageTransform.h b/modules/em2d/include/internal/ImageTransform.h index 620ff26cb5..d4772eeda3 100644 --- a/modules/em2d/include/internal/ImageTransform.h +++ b/modules/em2d/include/internal/ImageTransform.h @@ -3,7 +3,7 @@ * \brief stores image transformation * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/internal/Projection.h b/modules/em2d/include/internal/Projection.h index 7eab91f053..3dbf564136 100644 --- a/modules/em2d/include/internal/Projection.h +++ b/modules/em2d/include/internal/Projection.h @@ -1,7 +1,7 @@ /** * \file Projection \brief basic projection class * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/internal/ProjectionSphere.h b/modules/em2d/include/internal/ProjectionSphere.h index a586874126..4ad82eb590 100644 --- a/modules/em2d/include/internal/ProjectionSphere.h +++ b/modules/em2d/include/internal/ProjectionSphere.h @@ -4,7 +4,7 @@ * projection directions on a sphere * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/internal/Projector.h b/modules/em2d/include/internal/Projector.h index 2c03e16e8c..389aaeaa27 100644 --- a/modules/em2d/include/internal/Projector.h +++ b/modules/em2d/include/internal/Projector.h @@ -3,7 +3,7 @@ * \brief projection generation class * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/internal/clustering_helper.h b/modules/em2d/include/internal/clustering_helper.h index 767ae628b2..b4542399d4 100644 --- a/modules/em2d/include/internal/clustering_helper.h +++ b/modules/em2d/include/internal/clustering_helper.h @@ -2,7 +2,7 @@ * \file clustering_helper.h * \brief Implementation details for clustering algorithms * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/internal/image_processing_helper.h b/modules/em2d/include/internal/image_processing_helper.h index 3f23f1bd99..de1b7fd82d 100644 --- a/modules/em2d/include/internal/image_processing_helper.h +++ b/modules/em2d/include/internal/image_processing_helper.h @@ -2,7 +2,7 @@ * \file image_processing_helper.h * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/include/internal/rotation_helper.h b/modules/em2d/include/internal/rotation_helper.h index 9db246f763..b3e787a7d6 100644 --- a/modules/em2d/include/internal/rotation_helper.h +++ b/modules/em2d/include/internal/rotation_helper.h @@ -2,7 +2,7 @@ * \file rotation_helper.h * \brief Funtions related with rotations in em2d * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_INTERNAL_ROTATION_HELPER_H diff --git a/modules/em2d/include/model_interaction.h b/modules/em2d/include/model_interaction.h index c83be3ad83..7db83477fb 100644 --- a/modules/em2d/include/model_interaction.h +++ b/modules/em2d/include/model_interaction.h @@ -2,7 +2,7 @@ * \file IMP/em2d/model_interaction.h * \brief operations implying interaction of models and the EM module * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_MODEL_INTERACTION_H diff --git a/modules/em2d/include/opencv_interface.h b/modules/em2d/include/opencv_interface.h index 97ba799648..96230bbec9 100644 --- a/modules/em2d/include/opencv_interface.h +++ b/modules/em2d/include/opencv_interface.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/opencv_interface.h * \brief Interface with OpenCV - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_OPENCV_INTERFACE_H diff --git a/modules/em2d/include/project.h b/modules/em2d/include/project.h index ace9115ab0..f90bb56b61 100644 --- a/modules/em2d/include/project.h +++ b/modules/em2d/include/project.h @@ -1,7 +1,7 @@ /** * \file IMP/em2d/project.h * \brief Generation of projections from models or density maps - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_PROJECT_H diff --git a/modules/em2d/include/scores2D.h b/modules/em2d/include/scores2D.h index e386a800d9..8b63eddc73 100644 --- a/modules/em2d/include/scores2D.h +++ b/modules/em2d/include/scores2D.h @@ -1,7 +1,7 @@ /*! * \file IMP/em2d/scores2D.h * \brief Scoring functions for 2D - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEM2D_SCORES_2D_H diff --git a/modules/em2d/src/CollisionCrossSection.cpp b/modules/em2d/src/CollisionCrossSection.cpp index 07c05cfd5f..aa76aeeb5d 100644 --- a/modules/em2d/src/CollisionCrossSection.cpp +++ b/modules/em2d/src/CollisionCrossSection.cpp @@ -2,7 +2,7 @@ * \file CollisionCrossSection * \brief Routines for Ion Mobility Mass Spectrometry * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/DummyRestraint.cpp b/modules/em2d/src/DummyRestraint.cpp index 7434b20aba..5d45b35355 100644 --- a/modules/em2d/src/DummyRestraint.cpp +++ b/modules/em2d/src/DummyRestraint.cpp @@ -2,7 +2,7 @@ * \file DummyRestraint.cpp * \brief Dummy restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/Em2DRestraint.cpp b/modules/em2d/src/Em2DRestraint.cpp index aaa0d46b17..b57a89e574 100644 --- a/modules/em2d/src/Em2DRestraint.cpp +++ b/modules/em2d/src/Em2DRestraint.cpp @@ -2,7 +2,7 @@ * \file Em2DRestraint.cpp * \brief A restraint to score the fitness of a model to a set of EM images * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/FFToperations.cpp b/modules/em2d/src/FFToperations.cpp index be5f04fd80..4b5ae1b9ed 100644 --- a/modules/em2d/src/FFToperations.cpp +++ b/modules/em2d/src/FFToperations.cpp @@ -1,7 +1,7 @@ /** * \file FFToperations.cpp * \brief operations involving FFT - Copyright 2007-2021 IMP Inventors. All rights reserved. + Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/FFToperations.h" diff --git a/modules/em2d/src/Fine2DRegistrationRestraint.cpp b/modules/em2d/src/Fine2DRegistrationRestraint.cpp index 72d1469225..9413e15cdd 100644 --- a/modules/em2d/src/Fine2DRegistrationRestraint.cpp +++ b/modules/em2d/src/Fine2DRegistrationRestraint.cpp @@ -1,7 +1,7 @@ /** * \file Fine2DRegistrationRestraint.cpp * \brief Finely refine the angles and translations of a set of subject images - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/Fine2DRegistrationRestraint.h" diff --git a/modules/em2d/src/Image.cpp b/modules/em2d/src/Image.cpp index 6a383c5319..fbb12b72a1 100644 --- a/modules/em2d/src/Image.cpp +++ b/modules/em2d/src/Image.cpp @@ -1,7 +1,7 @@ /*! * \file Image.cpp * \brief Management of IMP images for Electron Microscopy - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/Image.h" diff --git a/modules/em2d/src/PCAFitRestraint.cpp b/modules/em2d/src/PCAFitRestraint.cpp index bd158f245b..3181a009f5 100644 --- a/modules/em2d/src/PCAFitRestraint.cpp +++ b/modules/em2d/src/PCAFitRestraint.cpp @@ -3,7 +3,7 @@ * \brief fast scoring of fit between Particles in 3D and 2D class averages * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/ProjectionFinder.cpp b/modules/em2d/src/ProjectionFinder.cpp index 0b814136f2..c1580db3e4 100644 --- a/modules/em2d/src/ProjectionFinder.cpp +++ b/modules/em2d/src/ProjectionFinder.cpp @@ -2,7 +2,7 @@ * \file ProjectionFinder.cpp * \brief Coarse registration of 2D projections from a 3D volume * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/ProjectionFinder.h" diff --git a/modules/em2d/src/ProjectionMask.cpp b/modules/em2d/src/ProjectionMask.cpp index 0e2f142d77..d234ba22f3 100644 --- a/modules/em2d/src/ProjectionMask.cpp +++ b/modules/em2d/src/ProjectionMask.cpp @@ -1,7 +1,7 @@ /** * \file ProjectionMask.cpp * \brief projection masks - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/ProjectionMask.h" diff --git a/modules/em2d/src/ProjectionParameters.cpp b/modules/em2d/src/ProjectionParameters.cpp index 8123881cea..842459d042 100644 --- a/modules/em2d/src/ProjectionParameters.cpp +++ b/modules/em2d/src/ProjectionParameters.cpp @@ -1,7 +1,7 @@ /** * \file ProjectionParameters.cpp * \brief Decorator for projection parameters - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/ProjectionParameters.h" diff --git a/modules/em2d/src/RegistrationResult.cpp b/modules/em2d/src/RegistrationResult.cpp index 7c7618cf31..54185c1f67 100644 --- a/modules/em2d/src/RegistrationResult.cpp +++ b/modules/em2d/src/RegistrationResult.cpp @@ -1,7 +1,7 @@ /** * \file RegistrationResult.cpp * \brief Registration results class - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/RegistrationResult.h" diff --git a/modules/em2d/src/RelativePositionMover.cpp b/modules/em2d/src/RelativePositionMover.cpp index abfa549ef4..276079f58b 100644 --- a/modules/em2d/src/RelativePositionMover.cpp +++ b/modules/em2d/src/RelativePositionMover.cpp @@ -2,7 +2,7 @@ * \file RelativePositionMover.cpp * \brief Mover for Rigid Bodies moving respect to each other * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/RigidBodiesImageFitRestraint.cpp b/modules/em2d/src/RigidBodiesImageFitRestraint.cpp index 5f966c3a66..994936e04c 100644 --- a/modules/em2d/src/RigidBodiesImageFitRestraint.cpp +++ b/modules/em2d/src/RigidBodiesImageFitRestraint.cpp @@ -2,7 +2,7 @@ * \file RigidBodiesImageFitRestraint * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/align2D.cpp b/modules/em2d/src/align2D.cpp index 824843f6c4..e365cbd1c7 100644 --- a/modules/em2d/src/align2D.cpp +++ b/modules/em2d/src/align2D.cpp @@ -2,7 +2,7 @@ * \file align2D.cpp * \brief Align operations for EM images * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/align2D.h" diff --git a/modules/em2d/src/domino_filter_tables.cpp b/modules/em2d/src/domino_filter_tables.cpp index df99321340..e6ffa9b7d1 100644 --- a/modules/em2d/src/domino_filter_tables.cpp +++ b/modules/em2d/src/domino_filter_tables.cpp @@ -2,7 +2,7 @@ * \file domino_filter_tables.cpp * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/domino_filters.cpp b/modules/em2d/src/domino_filters.cpp index 81a383b0b6..3fb65fb7ac 100644 --- a/modules/em2d/src/domino_filters.cpp +++ b/modules/em2d/src/domino_filters.cpp @@ -2,7 +2,7 @@ * \file domino_filters.cpp * \brief SubsetFilter for checking overlap between projections and images * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/domino_particle_states.cpp b/modules/em2d/src/domino_particle_states.cpp index df7de735a3..942e9fae80 100644 --- a/modules/em2d/src/domino_particle_states.cpp +++ b/modules/em2d/src/domino_particle_states.cpp @@ -2,7 +2,7 @@ * \file domino_particle_states.cpp * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/hierarchical_clustering.cpp b/modules/em2d/src/hierarchical_clustering.cpp index 246fcf228c..bda2293c70 100644 --- a/modules/em2d/src/hierarchical_clustering.cpp +++ b/modules/em2d/src/hierarchical_clustering.cpp @@ -2,7 +2,7 @@ * \file hierarchical_clustering.cpp * \brief Agglomerative clustering algorithm * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/image_processing.cpp b/modules/em2d/src/image_processing.cpp index 0ed45c8000..0565846999 100644 --- a/modules/em2d/src/image_processing.cpp +++ b/modules/em2d/src/image_processing.cpp @@ -1,7 +1,7 @@ /** * \file image_processing.cpp * \brief image processing for EM - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/image_processing.h" diff --git a/modules/em2d/src/internal/Image2D.cpp b/modules/em2d/src/internal/Image2D.cpp index 0a193d344c..c404b3bae5 100644 --- a/modules/em2d/src/internal/Image2D.cpp +++ b/modules/em2d/src/internal/Image2D.cpp @@ -2,7 +2,7 @@ * \file IMP/em2d/internal/Image2D.cpp * \brief A basic image class * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/internal/Projection.cpp b/modules/em2d/src/internal/Projection.cpp index 1280386647..9d113b54d8 100644 --- a/modules/em2d/src/internal/Projection.cpp +++ b/modules/em2d/src/internal/Projection.cpp @@ -3,7 +3,7 @@ * \brief A class for generation and storage of projections * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/internal/ProjectionSphere.cpp b/modules/em2d/src/internal/ProjectionSphere.cpp index f8cf671317..aa95a5a24b 100644 --- a/modules/em2d/src/internal/ProjectionSphere.cpp +++ b/modules/em2d/src/internal/ProjectionSphere.cpp @@ -4,7 +4,7 @@ * projection directions on a sphere * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/internal/Projector.cpp b/modules/em2d/src/internal/Projector.cpp index 70f585c57e..5d18853ccb 100644 --- a/modules/em2d/src/internal/Projector.cpp +++ b/modules/em2d/src/internal/Projector.cpp @@ -3,7 +3,7 @@ * \brief projection generation class * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/internal/image_processing_helper.cpp b/modules/em2d/src/internal/image_processing_helper.cpp index fbe8dedfc9..9dda6b356e 100644 --- a/modules/em2d/src/internal/image_processing_helper.cpp +++ b/modules/em2d/src/internal/image_processing_helper.cpp @@ -2,7 +2,7 @@ * \file image_processing_helper.cpp * \brief Helper functions for the image_processing main file * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/em2d/src/internal/rotation_helper.cpp b/modules/em2d/src/internal/rotation_helper.cpp index 193366bb27..9deb1941e9 100644 --- a/modules/em2d/src/internal/rotation_helper.cpp +++ b/modules/em2d/src/internal/rotation_helper.cpp @@ -2,7 +2,7 @@ * \file rotation_helper.cp * \brief Funtions related with rotations in em2d * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/internal/rotation_helper.h" diff --git a/modules/em2d/src/model_interaction.cpp b/modules/em2d/src/model_interaction.cpp index 15ccdfadb4..d9e91102a6 100644 --- a/modules/em2d/src/model_interaction.cpp +++ b/modules/em2d/src/model_interaction.cpp @@ -2,7 +2,7 @@ * \file model_interaction.cpp * \brief operations implying interaction of models and the EM module * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/model_interaction.h" diff --git a/modules/em2d/src/opencv_interface.cpp b/modules/em2d/src/opencv_interface.cpp index f6f6571bd2..7769197680 100644 --- a/modules/em2d/src/opencv_interface.cpp +++ b/modules/em2d/src/opencv_interface.cpp @@ -1,7 +1,7 @@ /** * \file opencv_interface.h * \brief Interface with OpenCV - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/opencv_interface.h" diff --git a/modules/em2d/src/project.cpp b/modules/em2d/src/project.cpp index 5ab1151fa5..6b8d08cd92 100644 --- a/modules/em2d/src/project.cpp +++ b/modules/em2d/src/project.cpp @@ -1,7 +1,7 @@ /** * \file project.cpp * \brief Generation of projections from models or density maps - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/project.h" diff --git a/modules/em2d/src/scores2D.cpp b/modules/em2d/src/scores2D.cpp index fd1baae4f4..16f83bc2d0 100644 --- a/modules/em2d/src/scores2D.cpp +++ b/modules/em2d/src/scores2D.cpp @@ -2,7 +2,7 @@ * \file scores2D.cpp * \brief Scoring functions for 2D * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/scores2D.h" diff --git a/modules/em2d/utility/process_pdb.cpp b/modules/em2d/utility/process_pdb.cpp index e2cc9f998b..c44476b8d6 100644 --- a/modules/em2d/utility/process_pdb.cpp +++ b/modules/em2d/utility/process_pdb.cpp @@ -2,7 +2,7 @@ * \file main.cpp * \brief PDB processing * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/em2d_config.h" diff --git a/modules/em2d/utility/score_model.cpp b/modules/em2d/utility/score_model.cpp index bc44cc2da4..83f7359f73 100644 --- a/modules/em2d/utility/score_model.cpp +++ b/modules/em2d/utility/score_model.cpp @@ -2,7 +2,7 @@ * \file main.cpp * \brief Scoring of models against 2D-EM projections * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/em2d/em2d_config.h" diff --git a/modules/example/include/ExampleComplexRestraint.h b/modules/example/include/ExampleComplexRestraint.h index 9021eb7298..7d6013edcf 100644 --- a/modules/example/include/ExampleComplexRestraint.h +++ b/modules/example/include/ExampleComplexRestraint.h @@ -2,7 +2,7 @@ * \file IMP/example/ExampleComplexRestraint.h * \brief A restraint to maintain the diameter of a set of points * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEXAMPLE_EXAMPLE_COMPLEX_RESTRAINT_H diff --git a/modules/example/include/ExampleConstraint.h b/modules/example/include/ExampleConstraint.h index 116ffcc317..c1c2ba0dc4 100644 --- a/modules/example/include/ExampleConstraint.h +++ b/modules/example/include/ExampleConstraint.h @@ -2,7 +2,7 @@ * \file IMP/example/ExampleConstraint.h * \brief A restraint on a list of particle pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/ExampleDecorator.h b/modules/example/include/ExampleDecorator.h index e358fb3dac..cd5764136c 100644 --- a/modules/example/include/ExampleDecorator.h +++ b/modules/example/include/ExampleDecorator.h @@ -1,7 +1,7 @@ /** * \file IMP/example/ExampleDecorator.h \brief Add a name to a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/ExampleObject.h b/modules/example/include/ExampleObject.h index b42ffcaa75..e37bccf405 100644 --- a/modules/example/include/ExampleObject.h +++ b/modules/example/include/ExampleObject.h @@ -2,7 +2,7 @@ * \file IMP/example/ExampleObject.h * \brief An example showing how to make a simple ref counted object * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEXAMPLE_EXAMPLE_OBJECT_H diff --git a/modules/example/include/ExamplePairScore.h b/modules/example/include/ExamplePairScore.h index 4596992e65..8702bd0ed2 100644 --- a/modules/example/include/ExamplePairScore.h +++ b/modules/example/include/ExamplePairScore.h @@ -2,7 +2,7 @@ * \file IMP/example/ExamplePairScore.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEXAMPLE_EXAMPLE_PAIR_SCORE_H diff --git a/modules/example/include/ExampleRestraint.h b/modules/example/include/ExampleRestraint.h index bade33f111..72490f2230 100644 --- a/modules/example/include/ExampleRestraint.h +++ b/modules/example/include/ExampleRestraint.h @@ -2,7 +2,7 @@ * \file IMP/example/ExampleRestraint.h * \brief A restraint on a list of particle pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/ExampleSingletonModifier.h b/modules/example/include/ExampleSingletonModifier.h index 1b8836ee8e..9d71653cbc 100644 --- a/modules/example/include/ExampleSingletonModifier.h +++ b/modules/example/include/ExampleSingletonModifier.h @@ -3,7 +3,7 @@ * \brief A singleton modifier which wraps an attribute into a * given range. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEXAMPLE_EXAMPLE_SINGLETON_MODIFIER_H diff --git a/modules/example/include/ExampleSubsetFilterTable.h b/modules/example/include/ExampleSubsetFilterTable.h index ce5da68c99..78c1cd5150 100644 --- a/modules/example/include/ExampleSubsetFilterTable.h +++ b/modules/example/include/ExampleSubsetFilterTable.h @@ -2,7 +2,7 @@ * \file IMP/example/ExampleSubsetFilterTable.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPEXAMPLE_EXAMPLE_SUBSET_FILTER_TABLE_H diff --git a/modules/example/include/ExampleTemplateClass.h b/modules/example/include/ExampleTemplateClass.h index f27a1f44c6..f72bac937a 100644 --- a/modules/example/include/ExampleTemplateClass.h +++ b/modules/example/include/ExampleTemplateClass.h @@ -2,7 +2,7 @@ * \file IMP/example/ExampleTemplateClass.h * \brief Show how to manage a template class with Python. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/ExampleUnaryFunction.h b/modules/example/include/ExampleUnaryFunction.h index 95cdc01656..06148edc5c 100644 --- a/modules/example/include/ExampleUnaryFunction.h +++ b/modules/example/include/ExampleUnaryFunction.h @@ -2,7 +2,7 @@ * \file IMP/example/ExampleUnaryFunction.h * \brief A simple unary function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/complex_assembly.h b/modules/example/include/complex_assembly.h index 6b0f8c0e14..00b197747d 100644 --- a/modules/example/include/complex_assembly.h +++ b/modules/example/include/complex_assembly.h @@ -2,7 +2,7 @@ * \file IMP/example/complex_assembly.h * \brief A simple unary function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/counting.h b/modules/example/include/counting.h index 9305ce94ae..5e06e60f94 100644 --- a/modules/example/include/counting.h +++ b/modules/example/include/counting.h @@ -2,7 +2,7 @@ * \file IMP/example/counting.h * \brief A simple unary function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/creating_restraints.h b/modules/example/include/creating_restraints.h index ea1f18fae9..22057b9d2e 100644 --- a/modules/example/include/creating_restraints.h +++ b/modules/example/include/creating_restraints.h @@ -2,7 +2,7 @@ * \file IMP/example/creating_restraints.h * \brief A simple unary function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/optimizing.h b/modules/example/include/optimizing.h index 4cfe171a3b..bd0d836a97 100644 --- a/modules/example/include/optimizing.h +++ b/modules/example/include/optimizing.h @@ -2,7 +2,7 @@ * \file IMP/example/optimizing.h * \brief A simple unary function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/include/randomizing.h b/modules/example/include/randomizing.h index 69853f96f8..25395e86cc 100644 --- a/modules/example/include/randomizing.h +++ b/modules/example/include/randomizing.h @@ -2,7 +2,7 @@ * \file IMP/example/randomizing.h * \brief A simple unary function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/src/ExampleComplexRestraint.cpp b/modules/example/src/ExampleComplexRestraint.cpp index 45da5fd0e8..73f4c777e6 100644 --- a/modules/example/src/ExampleComplexRestraint.cpp +++ b/modules/example/src/ExampleComplexRestraint.cpp @@ -2,7 +2,7 @@ * \file example/ExampleComplexRestraint.cpp * \brief Restrain the diameter of a set of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/src/ExampleConstraint.cpp b/modules/example/src/ExampleConstraint.cpp index 466f10e6e9..fca0d99014 100644 --- a/modules/example/src/ExampleConstraint.cpp +++ b/modules/example/src/ExampleConstraint.cpp @@ -2,7 +2,7 @@ * \file example/ExampleConstraint.cpp * \brief Restrain a list of particle pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/src/ExampleDecorator.cpp b/modules/example/src/ExampleDecorator.cpp index e48ca05fd3..39447c4450 100644 --- a/modules/example/src/ExampleDecorator.cpp +++ b/modules/example/src/ExampleDecorator.cpp @@ -2,7 +2,7 @@ * \file example/ExampleDecorator.cpp * \brief Add a name to a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/src/ExampleObject.cpp b/modules/example/src/ExampleObject.cpp index b94f4f7f78..99d9281f93 100644 --- a/modules/example/src/ExampleObject.cpp +++ b/modules/example/src/ExampleObject.cpp @@ -2,7 +2,7 @@ * \file ExampleObject.cpp * \brief An example reference counted object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/src/ExamplePairScore.cpp b/modules/example/src/ExamplePairScore.cpp index 58e4084e33..1634281d2d 100644 --- a/modules/example/src/ExamplePairScore.cpp +++ b/modules/example/src/ExamplePairScore.cpp @@ -2,7 +2,7 @@ * \file ExamplePairScore.cpp * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/example/src/ExampleRestraint.cpp b/modules/example/src/ExampleRestraint.cpp index 7ac45a101c..e01133e12a 100644 --- a/modules/example/src/ExampleRestraint.cpp +++ b/modules/example/src/ExampleRestraint.cpp @@ -2,7 +2,7 @@ * \file example/ExampleRestraint.cpp * \brief Restrain a list of particle pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/src/ExampleSingletonModifier.cpp b/modules/example/src/ExampleSingletonModifier.cpp index 0869f8498a..05d6bd441a 100644 --- a/modules/example/src/ExampleSingletonModifier.cpp +++ b/modules/example/src/ExampleSingletonModifier.cpp @@ -3,7 +3,7 @@ * \brief A singleton modifier which wraps an attribute into a * given range. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/example/src/ExampleSubsetFilterTable.cpp b/modules/example/src/ExampleSubsetFilterTable.cpp index fa287194ac..d1d9d97d0c 100644 --- a/modules/example/src/ExampleSubsetFilterTable.cpp +++ b/modules/example/src/ExampleSubsetFilterTable.cpp @@ -2,7 +2,7 @@ * \file ExampleSubsetFilterTable.cpp * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/example/src/complex_assembly.cpp b/modules/example/src/complex_assembly.cpp index ea932f2c70..e05212f015 100644 --- a/modules/example/src/complex_assembly.cpp +++ b/modules/example/src/complex_assembly.cpp @@ -2,7 +2,7 @@ * \file complex_assembly.cpp * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/example/src/optimize_balls.cpp b/modules/example/src/optimize_balls.cpp index e31df0b7a1..50a91bf184 100644 --- a/modules/example/src/optimize_balls.cpp +++ b/modules/example/src/optimize_balls.cpp @@ -2,7 +2,7 @@ * \file optimize_balls.cpp * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/example/src/use_example_dependency.cpp b/modules/example/src/use_example_dependency.cpp index 6f8ec8a012..4d10ba3101 100644 --- a/modules/example/src/use_example_dependency.cpp +++ b/modules/example/src/use_example_dependency.cpp @@ -2,7 +2,7 @@ * \file use_example_dependency.cpp * \brief A simple unary function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include "IMP/example/example_config.h" diff --git a/modules/example/utility/example_program.cpp b/modules/example/utility/example_program.cpp index 69a998b3db..379f871f0e 100644 --- a/modules/example/utility/example_program.cpp +++ b/modules/example/utility/example_program.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/foxs/bin/foxs.cpp b/modules/foxs/bin/foxs.cpp index dec8867310..f7b5178633 100644 --- a/modules/foxs/bin/foxs.cpp +++ b/modules/foxs/bin/foxs.cpp @@ -49,7 +49,7 @@ int main(int argc, char** argv) { "\nAny number of input PDBs and profiles is supported.\n" "Each PDB will be fitted against each profile.\n\n" "This program is part of IMP, the Integrative Modeling Platform,\n" - "which is Copyright 2007-2021 IMP Inventors.\n\n" + "which is Copyright 2007-2022 IMP Inventors.\n\n" "Options"); desc.add_options() ("help", "Show command line arguments and exit.") diff --git a/modules/foxs/include/internal/ColorCoder.h b/modules/foxs/include/internal/ColorCoder.h index eec0ae8c3d..bdaf87d15c 100644 --- a/modules/foxs/include/internal/ColorCoder.h +++ b/modules/foxs/include/internal/ColorCoder.h @@ -1,7 +1,7 @@ /** * \file IMP/foxs/ColorCoder.h \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/foxs/include/internal/Gnuplot.h b/modules/foxs/include/internal/Gnuplot.h index d13839b2d7..9038a47a3c 100644 --- a/modules/foxs/include/internal/Gnuplot.h +++ b/modules/foxs/include/internal/Gnuplot.h @@ -2,7 +2,7 @@ * \file IMP/foxs/Gnuplot.h \brief A class for printing gnuplot scripts * for profile viewing * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/foxs/include/internal/JmolWriter.h b/modules/foxs/include/internal/JmolWriter.h index 2b8d36394b..74a4e260b4 100644 --- a/modules/foxs/include/internal/JmolWriter.h +++ b/modules/foxs/include/internal/JmolWriter.h @@ -1,7 +1,7 @@ /** * \file IMP/foxs/JmolWriter.h \brief outputs javascript for jmol display * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/foxs/src/internal/ColorCoder.cpp b/modules/foxs/src/internal/ColorCoder.cpp index 1169ccb00a..911e760326 100644 --- a/modules/foxs/src/internal/ColorCoder.cpp +++ b/modules/foxs/src/internal/ColorCoder.cpp @@ -1,7 +1,7 @@ /** * \file IMP/foxs/ColorCoder.cpp \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/foxs/src/internal/Gnuplot.cpp b/modules/foxs/src/internal/Gnuplot.cpp index be5853a77d..afd40431a2 100644 --- a/modules/foxs/src/internal/Gnuplot.cpp +++ b/modules/foxs/src/internal/Gnuplot.cpp @@ -2,7 +2,7 @@ * \file IMP/foxs/Gnuplot.h \brief A class for printing gnuplot scripts * for profile viewing * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/foxs/src/internal/JmolWriter.cpp b/modules/foxs/src/internal/JmolWriter.cpp index 436283362d..da70efffa7 100644 --- a/modules/foxs/src/internal/JmolWriter.cpp +++ b/modules/foxs/src/internal/JmolWriter.cpp @@ -1,7 +1,7 @@ /** * \file IMP/foxs/JmolWriter.cpp \brief outputs javascript for jmol display * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/gsl/include/ConjugateGradients.h b/modules/gsl/include/ConjugateGradients.h index 0fad57d39c..470c820d21 100644 --- a/modules/gsl/include/ConjugateGradients.h +++ b/modules/gsl/include/ConjugateGradients.h @@ -2,7 +2,7 @@ * \file IMP/gsl/ConjugateGradients.h * \brief A conjugate gradients optimizer from GSL * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPGSL_CONJUGATE_GRADIENTS_H diff --git a/modules/gsl/include/GSLOptimizer.h b/modules/gsl/include/GSLOptimizer.h index 087f86f343..b37f806e88 100644 --- a/modules/gsl/include/GSLOptimizer.h +++ b/modules/gsl/include/GSLOptimizer.h @@ -2,7 +2,7 @@ * \file IMP/gsl/GSLOptimizer.h * \brief A base class for GSL-based optimizers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPGSL_GSL_OPTIMIZER_H diff --git a/modules/gsl/include/QuasiNewton.h b/modules/gsl/include/QuasiNewton.h index d94120909c..5007d2371e 100644 --- a/modules/gsl/include/QuasiNewton.h +++ b/modules/gsl/include/QuasiNewton.h @@ -2,7 +2,7 @@ * \file IMP/gsl/QuasiNewton.h * \brief A GSL-based Quasi-Newton optimizer * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPGSL_QUASI_NEWTON_H diff --git a/modules/gsl/include/Simplex.h b/modules/gsl/include/Simplex.h index 75cc46f121..da477d5bdd 100644 --- a/modules/gsl/include/Simplex.h +++ b/modules/gsl/include/Simplex.h @@ -2,7 +2,7 @@ * \file IMP/gsl/Simplex.h * \brief The simplex algorithm from GSL. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPGSL_SIMPLEX_H diff --git a/modules/gsl/include/internal/helpers.h b/modules/gsl/include/internal/helpers.h index f07dc2dbcc..d4420031ba 100644 --- a/modules/gsl/include/internal/helpers.h +++ b/modules/gsl/include/internal/helpers.h @@ -2,7 +2,7 @@ * \file gsl/internal/helpers.h * \brief Helpers for using IMP with GSL * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/gsl/src/ConjugateGradients.cpp b/modules/gsl/src/ConjugateGradients.cpp index 33dbfd8c3c..0d87cf96e1 100644 --- a/modules/gsl/src/ConjugateGradients.cpp +++ b/modules/gsl/src/ConjugateGradients.cpp @@ -2,7 +2,7 @@ * \file ConjugateGradients.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/gsl/src/GSLOptimizer.cpp b/modules/gsl/src/GSLOptimizer.cpp index b1613f1a2a..93ac435ff9 100644 --- a/modules/gsl/src/GSLOptimizer.cpp +++ b/modules/gsl/src/GSLOptimizer.cpp @@ -2,7 +2,7 @@ * \file GSLOptimizer.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/gsl/src/QuasiNewton.cpp b/modules/gsl/src/QuasiNewton.cpp index e05a5b558f..7be52d7315 100644 --- a/modules/gsl/src/QuasiNewton.cpp +++ b/modules/gsl/src/QuasiNewton.cpp @@ -2,7 +2,7 @@ * \file QuasiNewton.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/gsl/src/Simplex.cpp b/modules/gsl/src/Simplex.cpp index fbfa3be7a9..fcbb1a3d5a 100644 --- a/modules/gsl/src/Simplex.cpp +++ b/modules/gsl/src/Simplex.cpp @@ -2,7 +2,7 @@ * \file Simplex.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/gsl/src/internal/helpers.cpp b/modules/gsl/src/internal/helpers.cpp index 44424f5e6b..a38e291250 100644 --- a/modules/gsl/src/internal/helpers.cpp +++ b/modules/gsl/src/internal/helpers.cpp @@ -2,7 +2,7 @@ * \file gsl/internal/helpers.cpp * \brief Helpers for using IMP with GSL * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/bin/combine_scores.cpp b/modules/integrative_docking/bin/combine_scores.cpp index d5285504ed..7957c7d75e 100644 --- a/modules/integrative_docking/bin/combine_scores.cpp +++ b/modules/integrative_docking/bin/combine_scores.cpp @@ -1,7 +1,7 @@ /** * \file combine_scores.cpp \brief A program for combination of score files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/bin/cross_links_score.cpp b/modules/integrative_docking/bin/cross_links_score.cpp index afc3e357f6..23f933e4d1 100644 --- a/modules/integrative_docking/bin/cross_links_score.cpp +++ b/modules/integrative_docking/bin/cross_links_score.cpp @@ -2,7 +2,7 @@ * \file cross_link_score.cpp \brief A program for scoring of docking models * with cross linking data * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/cross_links_single_score.cpp b/modules/integrative_docking/bin/cross_links_single_score.cpp index 8a328abc2d..217743ca5e 100644 --- a/modules/integrative_docking/bin/cross_links_single_score.cpp +++ b/modules/integrative_docking/bin/cross_links_single_score.cpp @@ -2,7 +2,7 @@ * \file cross_link_score.cpp \brief A program for scoring of docking models * with cross linking data * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/em2d_score.cpp b/modules/integrative_docking/bin/em2d_score.cpp index cefa131970..a92572187a 100644 --- a/modules/integrative_docking/bin/em2d_score.cpp +++ b/modules/integrative_docking/bin/em2d_score.cpp @@ -2,7 +2,7 @@ * \file em2d_score.cpp \brief A program to score docking models given a list * of transformations for a ligand * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/bin/em2d_single_score.cpp b/modules/integrative_docking/bin/em2d_single_score.cpp index bc76750be7..9f7fcd1cb8 100644 --- a/modules/integrative_docking/bin/em2d_single_score.cpp +++ b/modules/integrative_docking/bin/em2d_single_score.cpp @@ -2,7 +2,7 @@ * \file em2d_single_score.cpp \brief A program to score a single * docking model in PDB file * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/bin/em3d_score.cpp b/modules/integrative_docking/bin/em3d_score.cpp index 0ebaf45fd4..b274a5e6dd 100644 --- a/modules/integrative_docking/bin/em3d_score.cpp +++ b/modules/integrative_docking/bin/em3d_score.cpp @@ -2,7 +2,7 @@ * \file em3d_score.cpp \brief A program to score docking models given a list * of transformations for a ligand * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/em3d_single_score.cpp b/modules/integrative_docking/bin/em3d_single_score.cpp index 22e805ac0f..8678409812 100644 --- a/modules/integrative_docking/bin/em3d_single_score.cpp +++ b/modules/integrative_docking/bin/em3d_single_score.cpp @@ -2,7 +2,7 @@ * \file em3d_single_score.cpp \brief A program to score a single * docking model in PDB file * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/interface_cross_links.cpp b/modules/integrative_docking/bin/interface_cross_links.cpp index e14a689835..d5c509d79b 100644 --- a/modules/integrative_docking/bin/interface_cross_links.cpp +++ b/modules/integrative_docking/bin/interface_cross_links.cpp @@ -2,7 +2,7 @@ * \file interface_rtc.cpp \brief A program for computing NMR residue * type content of a single interface. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/interface_rtc.cpp b/modules/integrative_docking/bin/interface_rtc.cpp index 61d73d690b..30b31cfc16 100644 --- a/modules/integrative_docking/bin/interface_rtc.cpp +++ b/modules/integrative_docking/bin/interface_rtc.cpp @@ -2,7 +2,7 @@ * \file interface_rtc.cpp \brief A program for computing NMR residue * type content of a single interface. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/nmr_rtc_score.cpp b/modules/integrative_docking/bin/nmr_rtc_score.cpp index 430d5a3928..dac4a765d7 100644 --- a/modules/integrative_docking/bin/nmr_rtc_score.cpp +++ b/modules/integrative_docking/bin/nmr_rtc_score.cpp @@ -2,7 +2,7 @@ * \file nmr_rtc_score.cpp \brief A program for NMR residue type content \ * scoring of docking models. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/recompute_zscore.cpp b/modules/integrative_docking/bin/recompute_zscore.cpp index 1ac3a1e51c..31de4a619c 100644 --- a/modules/integrative_docking/bin/recompute_zscore.cpp +++ b/modules/integrative_docking/bin/recompute_zscore.cpp @@ -1,7 +1,7 @@ /** * \file recompute_zscore.cpp \brief A program for combination of score files * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/saxs_score.cpp b/modules/integrative_docking/bin/saxs_score.cpp index 3180725a37..5c93fba0c5 100644 --- a/modules/integrative_docking/bin/saxs_score.cpp +++ b/modules/integrative_docking/bin/saxs_score.cpp @@ -1,7 +1,7 @@ /** * \file saxs_score.cpp \brief A program for SAXS scoring of docking models. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/bin/soap_score.cpp b/modules/integrative_docking/bin/soap_score.cpp index 8e148723b8..7bad0b18a6 100644 --- a/modules/integrative_docking/bin/soap_score.cpp +++ b/modules/integrative_docking/bin/soap_score.cpp @@ -2,7 +2,7 @@ * \file soap_score.cpp \brief A program for scoring of docking models * with SOAP statistical potentials * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/CrossLink.h b/modules/integrative_docking/include/internal/CrossLink.h index a977dc0588..43ab7995c8 100644 --- a/modules/integrative_docking/include/internal/CrossLink.h +++ b/modules/integrative_docking/include/internal/CrossLink.h @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/CrossLink.h \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/CrossLinkingResult.h b/modules/integrative_docking/include/internal/CrossLinkingResult.h index c116096816..5678482c82 100644 --- a/modules/integrative_docking/include/internal/CrossLinkingResult.h +++ b/modules/integrative_docking/include/internal/CrossLinkingResult.h @@ -3,7 +3,7 @@ * \brief A class that stores one docking model with cross linking scores * * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/DockingDistanceRestraint.h b/modules/integrative_docking/include/internal/DockingDistanceRestraint.h index 59763940fa..2d665a9123 100644 --- a/modules/integrative_docking/include/internal/DockingDistanceRestraint.h +++ b/modules/integrative_docking/include/internal/DockingDistanceRestraint.h @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/DockingDistanceRestraint.h \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/EM2DFitResult.h b/modules/integrative_docking/include/internal/EM2DFitResult.h index 6f7fcf17f0..450dcdfc17 100644 --- a/modules/integrative_docking/include/internal/EM2DFitResult.h +++ b/modules/integrative_docking/include/internal/EM2DFitResult.h @@ -2,7 +2,7 @@ * \file IMP/integrative_docking/EM2DFitResult.h * \brief A class that stores one docking model with the related scores * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/EM3DFitResult.h b/modules/integrative_docking/include/internal/EM3DFitResult.h index d9d9b95cc8..3ee438df2a 100644 --- a/modules/integrative_docking/include/internal/EM3DFitResult.h +++ b/modules/integrative_docking/include/internal/EM3DFitResult.h @@ -2,7 +2,7 @@ * \file IMP/integrative_docking/EM3DFitResult.h * \brief A class that stores one docking model with the related scores * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/EMFit.h b/modules/integrative_docking/include/internal/EMFit.h index ff8a8b0964..d317a124b1 100644 --- a/modules/integrative_docking/include/internal/EMFit.h +++ b/modules/integrative_docking/include/internal/EMFit.h @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/EMFit.h \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/MapScorer.h b/modules/integrative_docking/include/internal/MapScorer.h index 9d2a721ede..2eac227788 100644 --- a/modules/integrative_docking/include/internal/MapScorer.h +++ b/modules/integrative_docking/include/internal/MapScorer.h @@ -2,7 +2,7 @@ * \file IMP/integrative_docking/MapScorer.h * \brief A class for fast cc scoring of docking models * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/NMR_RTCResult.h b/modules/integrative_docking/include/internal/NMR_RTCResult.h index adc270fc0c..47525a51e5 100644 --- a/modules/integrative_docking/include/internal/NMR_RTCResult.h +++ b/modules/integrative_docking/include/internal/NMR_RTCResult.h @@ -3,7 +3,7 @@ * \brief A class that stores one docking model with NMR_RTC related scores * * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/Normalization.h b/modules/integrative_docking/include/internal/Normalization.h index 79bb3086f5..eb393b207c 100644 --- a/modules/integrative_docking/include/internal/Normalization.h +++ b/modules/integrative_docking/include/internal/Normalization.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/ResidueContent.h b/modules/integrative_docking/include/internal/ResidueContent.h index 1562088677..2b86ef1124 100644 --- a/modules/integrative_docking/include/internal/ResidueContent.h +++ b/modules/integrative_docking/include/internal/ResidueContent.h @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/ResidueContent.h \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/Result.h b/modules/integrative_docking/include/internal/Result.h index caee831b84..93b6fcca74 100644 --- a/modules/integrative_docking/include/internal/Result.h +++ b/modules/integrative_docking/include/internal/Result.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/SAXSResult.h b/modules/integrative_docking/include/internal/SAXSResult.h index f12568baae..062f05b32f 100644 --- a/modules/integrative_docking/include/internal/SAXSResult.h +++ b/modules/integrative_docking/include/internal/SAXSResult.h @@ -2,7 +2,7 @@ * \file IMP/integrative_docking/SAXSResult.h * \brief A class that stores one docking model with SAXS related scores * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/SOAPResult.h b/modules/integrative_docking/include/internal/SOAPResult.h index f30929ab00..7acef82141 100644 --- a/modules/integrative_docking/include/internal/SOAPResult.h +++ b/modules/integrative_docking/include/internal/SOAPResult.h @@ -3,7 +3,7 @@ * \brief store SOAP scores for a docking model * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/helpers.h b/modules/integrative_docking/include/internal/helpers.h index d7a5b96a06..3240df6be3 100644 --- a/modules/integrative_docking/include/internal/helpers.h +++ b/modules/integrative_docking/include/internal/helpers.h @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/helpers.h \brief A set of helper functions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/include/internal/soap_score.h b/modules/integrative_docking/include/internal/soap_score.h index abd7b8e577..196eb3359e 100644 --- a/modules/integrative_docking/include/internal/soap_score.h +++ b/modules/integrative_docking/include/internal/soap_score.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/src/internal/CrossLink.cpp b/modules/integrative_docking/src/internal/CrossLink.cpp index 3ae5aaf639..ea2d07566a 100644 --- a/modules/integrative_docking/src/internal/CrossLink.cpp +++ b/modules/integrative_docking/src/internal/CrossLink.cpp @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/CrossLink.cpp \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/src/internal/EMFit.cpp b/modules/integrative_docking/src/internal/EMFit.cpp index 5811061e56..59aa1caeaa 100644 --- a/modules/integrative_docking/src/internal/EMFit.cpp +++ b/modules/integrative_docking/src/internal/EMFit.cpp @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/EMFit.cpp \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/src/internal/MapScorer.cpp b/modules/integrative_docking/src/internal/MapScorer.cpp index 8812db8539..5e64ad028b 100644 --- a/modules/integrative_docking/src/internal/MapScorer.cpp +++ b/modules/integrative_docking/src/internal/MapScorer.cpp @@ -2,7 +2,7 @@ * \file IMP/integrative_docking/MapScorer.cpp * \brief A class for fast cc scoring of docking models * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/integrative_docking/src/internal/Normalization.cpp b/modules/integrative_docking/src/internal/Normalization.cpp index 99591a3d26..6d07f1a963 100644 --- a/modules/integrative_docking/src/internal/Normalization.cpp +++ b/modules/integrative_docking/src/internal/Normalization.cpp @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/src/internal/ResidueContent.cpp b/modules/integrative_docking/src/internal/ResidueContent.cpp index 36e3908151..4019511eda 100644 --- a/modules/integrative_docking/src/internal/ResidueContent.cpp +++ b/modules/integrative_docking/src/internal/ResidueContent.cpp @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/ResidueContent.cpp \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/src/internal/Result.cpp b/modules/integrative_docking/src/internal/Result.cpp index 0886604c04..7e38b010ef 100644 --- a/modules/integrative_docking/src/internal/Result.cpp +++ b/modules/integrative_docking/src/internal/Result.cpp @@ -2,7 +2,7 @@ * \file IMP/integrative_docking/Result.cpp * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/src/internal/helpers.cpp b/modules/integrative_docking/src/internal/helpers.cpp index 5ce0a89d3a..fa79ed43b8 100644 --- a/modules/integrative_docking/src/internal/helpers.cpp +++ b/modules/integrative_docking/src/internal/helpers.cpp @@ -1,7 +1,7 @@ /** * \file IMP/integrative_docking/helpers.cpp \brief A set of helper functions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/integrative_docking/src/internal/soap_score.cpp b/modules/integrative_docking/src/internal/soap_score.cpp index 2cf9241f9d..2d24b30c26 100644 --- a/modules/integrative_docking/src/internal/soap_score.cpp +++ b/modules/integrative_docking/src/internal/soap_score.cpp @@ -2,7 +2,7 @@ * \file IMP/integrative_docking/soap_score.cpp * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/AmbiguousNOERestraint.h b/modules/isd/include/AmbiguousNOERestraint.h index 8243789fd1..873615c26d 100644 --- a/modules/isd/include/AmbiguousNOERestraint.h +++ b/modules/isd/include/AmbiguousNOERestraint.h @@ -3,7 +3,7 @@ * \brief A lognormal restraint that uses the ISPA model to model NOE-derived * distance fit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/AmbiguousRestraint.h b/modules/isd/include/AmbiguousRestraint.h index 1d10a7a32d..1e8c8c9e30 100644 --- a/modules/isd/include/AmbiguousRestraint.h +++ b/modules/isd/include/AmbiguousRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/AmbiguousRestraint.h * \brief An implementation of the d-norm to make an ambiguous restraint. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/AtomicCrossLinkMSRestraint.h b/modules/isd/include/AtomicCrossLinkMSRestraint.h index b48bd21be8..2cf8a2d15c 100644 --- a/modules/isd/include/AtomicCrossLinkMSRestraint.h +++ b/modules/isd/include/AtomicCrossLinkMSRestraint.h @@ -3,7 +3,7 @@ * \brief A pmf based likelihood function * with prior knowledge on the false positive rate. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/CrossLinkData.h b/modules/isd/include/CrossLinkData.h index e483ccc10d..f9b05c9efe 100644 --- a/modules/isd/include/CrossLinkData.h +++ b/modules/isd/include/CrossLinkData.h @@ -1,7 +1,7 @@ /** * \file IMP/isd/CrossLinkData.h \brief Normal distribution of Function * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_CROSS_LINK_DATA_H diff --git a/modules/isd/include/CrossLinkMSRestraint.h b/modules/isd/include/CrossLinkMSRestraint.h index c2151d1e69..7866902866 100644 --- a/modules/isd/include/CrossLinkMSRestraint.h +++ b/modules/isd/include/CrossLinkMSRestraint.h @@ -3,7 +3,7 @@ * \brief A pmf based likelihood function * with prior knowledge on the false positive rate. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/CysteineCrossLinkData.h b/modules/isd/include/CysteineCrossLinkData.h index b7685221d1..755ae36a76 100644 --- a/modules/isd/include/CysteineCrossLinkData.h +++ b/modules/isd/include/CysteineCrossLinkData.h @@ -1,7 +1,7 @@ /** * \file IMP/isd/CysteineCrossLinkData.h \brief Normal distribution of Function * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_CYSTEINE_CROSS_LINK_DATA_H diff --git a/modules/isd/include/CysteineCrossLinkRestraint.h b/modules/isd/include/CysteineCrossLinkRestraint.h index 8bd0628e38..fccf7088dc 100644 --- a/modules/isd/include/CysteineCrossLinkRestraint.h +++ b/modules/isd/include/CysteineCrossLinkRestraint.h @@ -5,7 +5,7 @@ * and ambiguous assignment. To be used with * cross-linking mass-spectrometry data. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/FNormal.h b/modules/isd/include/FNormal.h index 06b89bcb67..926b5e2498 100644 --- a/modules/isd/include/FNormal.h +++ b/modules/isd/include/FNormal.h @@ -1,7 +1,7 @@ /** * \file IMP/isd/FNormal.h \brief Normal distribution of Function * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_FNORMAL_H diff --git a/modules/isd/include/FStudentT.h b/modules/isd/include/FStudentT.h index c69bc5510b..e8266f3eee 100644 --- a/modules/isd/include/FStudentT.h +++ b/modules/isd/include/FStudentT.h @@ -2,7 +2,7 @@ * \file IMP/isd/FStudentT.h * \brief Joint Student's t-distribution of Function * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_F_STUDENT_T_H diff --git a/modules/isd/include/FretData.h b/modules/isd/include/FretData.h index 80e235d53d..303a662169 100644 --- a/modules/isd/include/FretData.h +++ b/modules/isd/include/FretData.h @@ -1,7 +1,7 @@ /** * \file IMP/isd/FretData.h \brief Auxiliary class useful for FRET_R restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_FRET_DATA_H diff --git a/modules/isd/include/FretRestraint.h b/modules/isd/include/FretRestraint.h index 76e6dabb7b..d77f6f390f 100644 --- a/modules/isd/include/FretRestraint.h +++ b/modules/isd/include/FretRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/FretRestraint.h * \brief FRET_R restraint to use in vivo FRET data. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/GammaPrior.h b/modules/isd/include/GammaPrior.h index c126406235..117c0bdda3 100644 --- a/modules/isd/include/GammaPrior.h +++ b/modules/isd/include/GammaPrior.h @@ -2,7 +2,7 @@ * \file IMP/isd/GammaPrior.h * \brief A restraint on a scale parameter. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/GaussianAnchorEMRestraint.h b/modules/isd/include/GaussianAnchorEMRestraint.h index f70a433e46..5f1735b12e 100644 --- a/modules/isd/include/GaussianAnchorEMRestraint.h +++ b/modules/isd/include/GaussianAnchorEMRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/GaussianAnchorEMRestraint.h * \brief Restraint between two sets of anchor points "model" and "EM density" * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/GaussianEMRestraint.h b/modules/isd/include/GaussianEMRestraint.h index 7ec321a8fa..63f3286a97 100644 --- a/modules/isd/include/GaussianEMRestraint.h +++ b/modules/isd/include/GaussianEMRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/GaussianEMRestraint.h * \brief Restrain two sets of Gaussians (model and GMM derived from EM map) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/GaussianProcessInterpolation.h b/modules/isd/include/GaussianProcessInterpolation.h index 1474bca81f..6cf4b2ad14 100644 --- a/modules/isd/include/GaussianProcessInterpolation.h +++ b/modules/isd/include/GaussianProcessInterpolation.h @@ -2,7 +2,7 @@ * \file IMP/isd/GaussianProcessInterpolation.h * \brief Normal distribution of Function * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_GAUSSIAN_PROCESS_INTERPOLATION_H diff --git a/modules/isd/include/GaussianProcessInterpolationRestraint.h b/modules/isd/include/GaussianProcessInterpolationRestraint.h index fc95e04bee..fd79f4aa3d 100644 --- a/modules/isd/include/GaussianProcessInterpolationRestraint.h +++ b/modules/isd/include/GaussianProcessInterpolationRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/GaussianProcessInterpolationRestraint.h * \brief Restraint and ScoreState for GaussianProcessInterpolation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_GAUSSIAN_PROCESS_INTERPOLATION_RESTRAINT_H diff --git a/modules/isd/include/GaussianRestraint.h b/modules/isd/include/GaussianRestraint.h index 2486a1b06e..7a4e56254d 100644 --- a/modules/isd/include/GaussianRestraint.h +++ b/modules/isd/include/GaussianRestraint.h @@ -3,7 +3,7 @@ * \brief A lognormal restraint that uses the ISPA model to model NOE-derived * distance fit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/HybridMonteCarlo.h b/modules/isd/include/HybridMonteCarlo.h index a199026898..3bf9a134f0 100644 --- a/modules/isd/include/HybridMonteCarlo.h +++ b/modules/isd/include/HybridMonteCarlo.h @@ -2,7 +2,7 @@ * \file IMP/isd/HybridMonteCarlo.h * \brief A hybrid monte carlo implementation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/ISDRestraint.h b/modules/isd/include/ISDRestraint.h index dd8d401278..2d2e1e5726 100644 --- a/modules/isd/include/ISDRestraint.h +++ b/modules/isd/include/ISDRestraint.h @@ -1,7 +1,7 @@ /** * \file IMP/isd/ISDRestraint.h * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/JeffreysRestraint.h b/modules/isd/include/JeffreysRestraint.h index 10300d4c54..9b62a519ca 100644 --- a/modules/isd/include/JeffreysRestraint.h +++ b/modules/isd/include/JeffreysRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/JeffreysRestraint.h * \brief A restraint on a scale parameter. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/LogWrapper.h b/modules/isd/include/LogWrapper.h index 51ff37a2b6..0a98981ac0 100644 --- a/modules/isd/include/LogWrapper.h +++ b/modules/isd/include/LogWrapper.h @@ -2,7 +2,7 @@ * \file IMP/isd/LogWrapper.h * \brief Calculate the -Log of a list of restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/LognormalAmbiguousRestraint.h b/modules/isd/include/LognormalAmbiguousRestraint.h index 001cfbdada..59c865b6f7 100644 --- a/modules/isd/include/LognormalAmbiguousRestraint.h +++ b/modules/isd/include/LognormalAmbiguousRestraint.h @@ -5,7 +5,7 @@ * and ambiguous assignment. To be used with * cross-linking mass-spectrometry data. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/LognormalRestraint.h b/modules/isd/include/LognormalRestraint.h index 74e9c72a9b..45a9a9447d 100644 --- a/modules/isd/include/LognormalRestraint.h +++ b/modules/isd/include/LognormalRestraint.h @@ -3,7 +3,7 @@ * \brief A lognormal restraint that uses the ISPA model to model NOE-derived * distance fit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/MarginalHBondRestraint.h b/modules/isd/include/MarginalHBondRestraint.h index 5fa2a0ce76..6aff30755d 100644 --- a/modules/isd/include/MarginalHBondRestraint.h +++ b/modules/isd/include/MarginalHBondRestraint.h @@ -3,7 +3,7 @@ * \brief A lognormal restraint that uses the ISPA model to model HBond-derived * distance fit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/MarginalNOERestraint.h b/modules/isd/include/MarginalNOERestraint.h index b2582ecb9c..fed56de4a7 100644 --- a/modules/isd/include/MarginalNOERestraint.h +++ b/modules/isd/include/MarginalNOERestraint.h @@ -3,7 +3,7 @@ * \brief A lognormal restraint that uses the ISPA model to model NOE-derived * distance fit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/MolecularDynamics.h b/modules/isd/include/MolecularDynamics.h index ebcad32a85..090a642dcb 100644 --- a/modules/isd/include/MolecularDynamics.h +++ b/modules/isd/include/MolecularDynamics.h @@ -2,7 +2,7 @@ * \file IMP/isd/MolecularDynamics.h * \brief Simple molecular dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/MolecularDynamicsMover.h b/modules/isd/include/MolecularDynamicsMover.h index 4fe072b1ac..78e61c55a4 100644 --- a/modules/isd/include/MolecularDynamicsMover.h +++ b/modules/isd/include/MolecularDynamicsMover.h @@ -3,7 +3,7 @@ * \brief A modifier which perturbs XYZs or Nuisances with a constant energy * MD simulation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/MultivariateFNormalSufficient.h b/modules/isd/include/MultivariateFNormalSufficient.h index 7b0884544c..644a3e6a0f 100644 --- a/modules/isd/include/MultivariateFNormalSufficient.h +++ b/modules/isd/include/MultivariateFNormalSufficient.h @@ -2,7 +2,7 @@ * \file IMP/isd/MultivariateFNormalSufficient.h * \brief Normal distribution of Function * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_MULTIVARIATE_FNORMAL_SUFFICIENT_H diff --git a/modules/isd/include/NOERestraint.h b/modules/isd/include/NOERestraint.h index 7546044b8b..0d8ee6ed53 100644 --- a/modules/isd/include/NOERestraint.h +++ b/modules/isd/include/NOERestraint.h @@ -3,7 +3,7 @@ * \brief A lognormal restraint that uses the ISPA model to model NOE-derived * distance fit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/NormalSigmaPCRestraint.h b/modules/isd/include/NormalSigmaPCRestraint.h index c4e0fd85ff..f87acbc3ce 100644 --- a/modules/isd/include/NormalSigmaPCRestraint.h +++ b/modules/isd/include/NormalSigmaPCRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/NormalSigmaPCRestraint.h * \brief A Penalized Complexity prior on sigma of a normal distribution. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/Nuisance.h b/modules/isd/include/Nuisance.h index 03e0fdf623..533057196d 100644 --- a/modules/isd/include/Nuisance.h +++ b/modules/isd/include/Nuisance.h @@ -2,7 +2,7 @@ * \file IMP/isd/Nuisance.h * \brief A decorator for nuisance parameters particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_NUISANCE_H diff --git a/modules/isd/include/PenalizedComplexityPrior.h b/modules/isd/include/PenalizedComplexityPrior.h index 1910dbd415..be76d56ac6 100644 --- a/modules/isd/include/PenalizedComplexityPrior.h +++ b/modules/isd/include/PenalizedComplexityPrior.h @@ -2,7 +2,7 @@ * \file IMP/isd/PenalizedComplexityPrior.h * \brief Penalized complexity prior. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_PENALIZED_COMPLEXITY_PRIOR_H diff --git a/modules/isd/include/RepulsiveDistancePairScore.h b/modules/isd/include/RepulsiveDistancePairScore.h index 6183b1da08..5bc60c8720 100644 --- a/modules/isd/include/RepulsiveDistancePairScore.h +++ b/modules/isd/include/RepulsiveDistancePairScore.h @@ -3,7 +3,7 @@ * \brief A simple quadric repulsive term between two atoms. Restraint is zero * when the distance equals the sum of the radii plus the shift. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_REPULSIVE_DISTANCE_PAIR_SCORE_H diff --git a/modules/isd/include/Scale.h b/modules/isd/include/Scale.h index 29606d84d5..8aba6300d8 100644 --- a/modules/isd/include/Scale.h +++ b/modules/isd/include/Scale.h @@ -2,7 +2,7 @@ * \file IMP/isd/Scale.h * \brief A decorator for scale parameters particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_SCALE_H diff --git a/modules/isd/include/StudentTRestraint.h b/modules/isd/include/StudentTRestraint.h index de9317a5f8..a2067e41d4 100644 --- a/modules/isd/include/StudentTRestraint.h +++ b/modules/isd/include/StudentTRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/StudentTRestraint.h * \brief A Student-t distribution restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/Switching.h b/modules/isd/include/Switching.h index 46ca060a96..0e44cf4e57 100644 --- a/modules/isd/include/Switching.h +++ b/modules/isd/include/Switching.h @@ -2,7 +2,7 @@ * \file IMP/isd/Switching.h * \brief A decorator for switching parameters particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_SWITCHING_H diff --git a/modules/isd/include/TALOSRestraint.h b/modules/isd/include/TALOSRestraint.h index 36ffc8315a..10bcc765fb 100644 --- a/modules/isd/include/TALOSRestraint.h +++ b/modules/isd/include/TALOSRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/TALOSRestraint.h * \brief TALOS dihedral restraint between four particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/UniformPrior.h b/modules/isd/include/UniformPrior.h index 733d56d460..6bb05d061c 100644 --- a/modules/isd/include/UniformPrior.h +++ b/modules/isd/include/UniformPrior.h @@ -2,7 +2,7 @@ * \file IMP/isd/UniformPrior.h * \brief A restraint on a scale parameter. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/Weight.h b/modules/isd/include/Weight.h index 9bb12cbcc8..3458de36a2 100755 --- a/modules/isd/include/Weight.h +++ b/modules/isd/include/Weight.h @@ -2,7 +2,7 @@ * \file IMP/isd/Weight.h * \brief Add weights constrained to the unit simplex to a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/WeightMover.h b/modules/isd/include/WeightMover.h index ed521fe83e..7a2de229b4 100644 --- a/modules/isd/include/WeightMover.h +++ b/modules/isd/include/WeightMover.h @@ -2,7 +2,7 @@ * \file IMP/isd/WeightMover.h * \brief A mover that perturbs a Weight particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/WeightRestraint.h b/modules/isd/include/WeightRestraint.h index bec1b6159b..ea2c783e67 100644 --- a/modules/isd/include/WeightRestraint.h +++ b/modules/isd/include/WeightRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/WeightRestraint.h * \brief Put description here * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/bivariate_functions.h b/modules/isd/include/bivariate_functions.h index 462d094b54..1c1bbaa2bd 100644 --- a/modules/isd/include/bivariate_functions.h +++ b/modules/isd/include/bivariate_functions.h @@ -2,7 +2,7 @@ * \file IMP/isd/bivariate_functions.h * \brief Classes for general functions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_BIVARIATE_FUNCTIONS_H diff --git a/modules/isd/include/distribution.h b/modules/isd/include/distribution.h index 5aa24ba1f8..143217e503 100644 --- a/modules/isd/include/distribution.h +++ b/modules/isd/include/distribution.h @@ -2,7 +2,7 @@ * \file IMP/isd/distribution.h * \brief Base class for probability distributions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_DISTRIBUTION_H diff --git a/modules/isd/include/em_utilities.h b/modules/isd/include/em_utilities.h index 6cfbe2dc1f..8aa1c5f7a9 100644 --- a/modules/isd/include/em_utilities.h +++ b/modules/isd/include/em_utilities.h @@ -2,7 +2,7 @@ * \file IMP/isd/em_utilities.h * \brief Common scoring functions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/internal/cg_eigen.h b/modules/isd/include/internal/cg_eigen.h index d0b4863ca5..9bec0f452b 100644 --- a/modules/isd/include/internal/cg_eigen.h +++ b/modules/isd/include/internal/cg_eigen.h @@ -1,6 +1,6 @@ /** testing of the Eigen CG. tests return true when they succeed. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_INTERNAL_CG_EIGEN_H diff --git a/modules/isd/include/internal/timer.h b/modules/isd/include/internal/timer.h index 1769e4c232..d71a27bbc4 100644 --- a/modules/isd/include/internal/timer.h +++ b/modules/isd/include/internal/timer.h @@ -1,7 +1,7 @@ /** * \brief A timer class to time function calls * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/univariate_functions.h b/modules/isd/include/univariate_functions.h index 568e26c61c..56f9b79932 100644 --- a/modules/isd/include/univariate_functions.h +++ b/modules/isd/include/univariate_functions.h @@ -2,7 +2,7 @@ * \file IMP/isd/univariate_functions.h * \brief Classes for general functions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_UNIVARIATE_FUNCTIONS_H diff --git a/modules/isd/include/vonMises.h b/modules/isd/include/vonMises.h index c4893d4c61..fda046c519 100644 --- a/modules/isd/include/vonMises.h +++ b/modules/isd/include/vonMises.h @@ -1,7 +1,7 @@ /** * \file IMP/isd/vonMises.h \brief Normal distribution of Function * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_VON_MISES_H diff --git a/modules/isd/include/vonMisesKappaConjugateRestraint.h b/modules/isd/include/vonMisesKappaConjugateRestraint.h index 2ec0aa1019..f6e5201042 100644 --- a/modules/isd/include/vonMisesKappaConjugateRestraint.h +++ b/modules/isd/include/vonMisesKappaConjugateRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/vonMisesKappaConjugateRestraint.h * \brief Conjugate prior for \f$\kappa\f$ in the von Mises distribution. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/vonMisesKappaJeffreysRestraint.h b/modules/isd/include/vonMisesKappaJeffreysRestraint.h index 2f2b1d6292..2c24566f56 100644 --- a/modules/isd/include/vonMisesKappaJeffreysRestraint.h +++ b/modules/isd/include/vonMisesKappaJeffreysRestraint.h @@ -2,7 +2,7 @@ * \file IMP/isd/vonMisesKappaJeffreysRestraint.h * \brief Jeffreys prior for \f$\kappa\f$ in the von Mises distribution. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/include/vonMisesSufficient.h b/modules/isd/include/vonMisesSufficient.h index ba4883211f..505df92efb 100644 --- a/modules/isd/include/vonMisesSufficient.h +++ b/modules/isd/include/vonMisesSufficient.h @@ -1,7 +1,7 @@ /** * \file IMP/isd/vonMisesSufficient.h \brief Normal distribution of Function * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPISD_VON_MISES_SUFFICIENT_H diff --git a/modules/isd/src/AmbiguousNOERestraint.cpp b/modules/isd/src/AmbiguousNOERestraint.cpp index 58c4906617..28e355b2c8 100644 --- a/modules/isd/src/AmbiguousNOERestraint.cpp +++ b/modules/isd/src/AmbiguousNOERestraint.cpp @@ -3,7 +3,7 @@ * \brief Restrain a list of particle pairs with a lognormal+ISPA. * NOTE: for now, the derivatives are written to all variables. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/AmbiguousRestraint.cpp b/modules/isd/src/AmbiguousRestraint.cpp index 8f8e12f588..0052fbce2d 100644 --- a/modules/isd/src/AmbiguousRestraint.cpp +++ b/modules/isd/src/AmbiguousRestraint.cpp @@ -3,7 +3,7 @@ * \brief Restrain a list of particle pairs with a lognormal+ISPA. * NOTE: for now, the derivatives are written to all variables. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/AtomicCrossLinkMSRestraint.cpp b/modules/isd/src/AtomicCrossLinkMSRestraint.cpp index 331be7b01b..c0f53e684e 100644 --- a/modules/isd/src/AtomicCrossLinkMSRestraint.cpp +++ b/modules/isd/src/AtomicCrossLinkMSRestraint.cpp @@ -5,7 +5,7 @@ * and ambiguous assignment. To be used with * cross-linking mass-spectrometry data. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/CrossLinkData.cpp b/modules/isd/src/CrossLinkData.cpp index 2aebf44038..a3aa8dd344 100644 --- a/modules/isd/src/CrossLinkData.cpp +++ b/modules/isd/src/CrossLinkData.cpp @@ -1,7 +1,7 @@ /** * \file CrossLinkData.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/CrossLinkMSRestraint.cpp b/modules/isd/src/CrossLinkMSRestraint.cpp index 73b35ac235..a94993c5d7 100644 --- a/modules/isd/src/CrossLinkMSRestraint.cpp +++ b/modules/isd/src/CrossLinkMSRestraint.cpp @@ -5,7 +5,7 @@ * and ambiguous assignment. To be used with * cross-linking mass-spectrometry data. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/CysteineCrossLinkData.cpp b/modules/isd/src/CysteineCrossLinkData.cpp index bbf8b9f4e6..8504124436 100644 --- a/modules/isd/src/CysteineCrossLinkData.cpp +++ b/modules/isd/src/CysteineCrossLinkData.cpp @@ -1,7 +1,7 @@ /** * \file CysteineCrossLinkData.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/CysteineCrossLinkRestraint.cpp b/modules/isd/src/CysteineCrossLinkRestraint.cpp index 55110fcb36..833d119807 100644 --- a/modules/isd/src/CysteineCrossLinkRestraint.cpp +++ b/modules/isd/src/CysteineCrossLinkRestraint.cpp @@ -5,7 +5,7 @@ * and ambiguous assignment. To be used with * cross-linking mass-spectrometry data. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/isd/src/FStudentT.cpp b/modules/isd/src/FStudentT.cpp index c264f834d4..e0cc3d5e72 100644 --- a/modules/isd/src/FStudentT.cpp +++ b/modules/isd/src/FStudentT.cpp @@ -1,7 +1,7 @@ /** * \file FStudentT.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/FretData.cpp b/modules/isd/src/FretData.cpp index 928bf46430..6a4ae8824d 100644 --- a/modules/isd/src/FretData.cpp +++ b/modules/isd/src/FretData.cpp @@ -2,7 +2,7 @@ * \file isd/FretData.cpp * \brief Auxiliary class useful for FRET_R restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/isd/src/FretRestraint.cpp b/modules/isd/src/FretRestraint.cpp index 93a4953a7a..cb65393f32 100644 --- a/modules/isd/src/FretRestraint.cpp +++ b/modules/isd/src/FretRestraint.cpp @@ -3,7 +3,7 @@ * \brief FRET_R restraint * to use in vivo FRET data [Muller et al. Mol Biol Cell 16, 3341, 2005] * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/isd/src/GammaPrior.cpp b/modules/isd/src/GammaPrior.cpp index 77c3557090..6a71012a0f 100644 --- a/modules/isd/src/GammaPrior.cpp +++ b/modules/isd/src/GammaPrior.cpp @@ -2,7 +2,7 @@ * \file IMP/isd/GammaPrior.cpp * \brief Restrain a scale particle with a gamma distribution * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/GaussianAnchorEMRestraint.cpp b/modules/isd/src/GaussianAnchorEMRestraint.cpp index 4eb668ecbf..4cc1193a94 100644 --- a/modules/isd/src/GaussianAnchorEMRestraint.cpp +++ b/modules/isd/src/GaussianAnchorEMRestraint.cpp @@ -3,7 +3,7 @@ * \brief Restrain two sets of anchor points (e.g. protein and EM map) * NOTE: derivitives not implemented * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/GaussianEMRestraint.cpp b/modules/isd/src/GaussianEMRestraint.cpp index 9d848b0f2c..6a09457f60 100644 --- a/modules/isd/src/GaussianEMRestraint.cpp +++ b/modules/isd/src/GaussianEMRestraint.cpp @@ -2,7 +2,7 @@ * \file isd/GaussianEMRestraint.cpp * \brief Restrain two sets of Gaussians (model and GMM derived from EM map) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/GaussianProcessInterpolation.cpp b/modules/isd/src/GaussianProcessInterpolation.cpp index 5d5037732a..aeecaf94d7 100644 --- a/modules/isd/src/GaussianProcessInterpolation.cpp +++ b/modules/isd/src/GaussianProcessInterpolation.cpp @@ -1,7 +1,7 @@ /** * \file GaussianProcessInterpolation.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/GaussianProcessInterpolationRestraint.cpp b/modules/isd/src/GaussianProcessInterpolationRestraint.cpp index 5cdf763a0e..37ac43d36f 100644 --- a/modules/isd/src/GaussianProcessInterpolationRestraint.cpp +++ b/modules/isd/src/GaussianProcessInterpolationRestraint.cpp @@ -1,7 +1,7 @@ /** * \file GaussianProcessInterpolationRestraint.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/GaussianRestraint.cpp b/modules/isd/src/GaussianRestraint.cpp index 9a76adc8d3..4ea1603b60 100644 --- a/modules/isd/src/GaussianRestraint.cpp +++ b/modules/isd/src/GaussianRestraint.cpp @@ -3,7 +3,7 @@ * \brief Restrain a list of particle pairs with a lognormal+ISPA. * NOTE: for now, the derivatives are written to all variables. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/HybridMonteCarlo.cpp b/modules/isd/src/HybridMonteCarlo.cpp index 3c1b11a6cf..c45593e28d 100644 --- a/modules/isd/src/HybridMonteCarlo.cpp +++ b/modules/isd/src/HybridMonteCarlo.cpp @@ -2,7 +2,7 @@ * \file isd/HybridMonteCarlo.cpp * \brief The hybrid monte carlo algorithm * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/ISDRestraint.cpp b/modules/isd/src/ISDRestraint.cpp index d280f6f700..c710a93824 100644 --- a/modules/isd/src/ISDRestraint.cpp +++ b/modules/isd/src/ISDRestraint.cpp @@ -1,7 +1,7 @@ /** * \file IMP/isd/ISDRestraint.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/JeffreysRestraint.cpp b/modules/isd/src/JeffreysRestraint.cpp index 5d83dd2dea..5ca633c886 100644 --- a/modules/isd/src/JeffreysRestraint.cpp +++ b/modules/isd/src/JeffreysRestraint.cpp @@ -2,7 +2,7 @@ * \file isd/JeffreysRestraint.cpp * \brief Restrain a scale particle with log(scale) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/LogWrapper.cpp b/modules/isd/src/LogWrapper.cpp index 4c728139af..d2798e8579 100644 --- a/modules/isd/src/LogWrapper.cpp +++ b/modules/isd/src/LogWrapper.cpp @@ -2,7 +2,7 @@ * \file isd/LogWrapper.cpp * \brief Calculate the -Log of a list of restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/LognormalAmbiguousRestraint.cpp b/modules/isd/src/LognormalAmbiguousRestraint.cpp index d533bd6e12..5ad424c254 100644 --- a/modules/isd/src/LognormalAmbiguousRestraint.cpp +++ b/modules/isd/src/LognormalAmbiguousRestraint.cpp @@ -5,7 +5,7 @@ * and ambiguous assignment. To be used with * cross-linking mass-spectrometry data. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/LognormalRestraint.cpp b/modules/isd/src/LognormalRestraint.cpp index 33dfe170dc..f024fbb0f9 100644 --- a/modules/isd/src/LognormalRestraint.cpp +++ b/modules/isd/src/LognormalRestraint.cpp @@ -3,7 +3,7 @@ * \brief Restrain a list of particle pairs with a lognormal+ISPA. * NOTE: for now, the derivatives are written to all variables. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/MarginalHBondRestraint.cpp b/modules/isd/src/MarginalHBondRestraint.cpp index ff39aacc7d..691d4679ca 100644 --- a/modules/isd/src/MarginalHBondRestraint.cpp +++ b/modules/isd/src/MarginalHBondRestraint.cpp @@ -3,7 +3,7 @@ * \brief Restrain a list of particle pairs with a lognormal+ISPA. * NOTE: for now, the derivatives are written to all variables. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/MarginalNOERestraint.cpp b/modules/isd/src/MarginalNOERestraint.cpp index e363bdf3d5..1cf27625be 100644 --- a/modules/isd/src/MarginalNOERestraint.cpp +++ b/modules/isd/src/MarginalNOERestraint.cpp @@ -3,7 +3,7 @@ * \brief Restrain a list of particle pairs with a lognormal+ISPA. * NOTE: for now, the derivatives are written to all variables. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/MolecularDynamics.cpp b/modules/isd/src/MolecularDynamics.cpp index e0c629ca2c..7c282b9bd8 100644 --- a/modules/isd/src/MolecularDynamics.cpp +++ b/modules/isd/src/MolecularDynamics.cpp @@ -1,7 +1,7 @@ /** * \file MolecularDynamics.cpp \brief 1-D and 3-D MD optimizer * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/MolecularDynamicsMover.cpp b/modules/isd/src/MolecularDynamicsMover.cpp index 190afae45b..28ae544d65 100644 --- a/modules/isd/src/MolecularDynamicsMover.cpp +++ b/modules/isd/src/MolecularDynamicsMover.cpp @@ -3,7 +3,7 @@ * \brief A modifier which perturbs XYZs or Nuisances with a constant energy * MD simulation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/MultivariateFNormalSufficient.cpp b/modules/isd/src/MultivariateFNormalSufficient.cpp index 81ed07e5cf..1245e18061 100644 --- a/modules/isd/src/MultivariateFNormalSufficient.cpp +++ b/modules/isd/src/MultivariateFNormalSufficient.cpp @@ -1,7 +1,7 @@ /** * \file MultivariateFNormalSufficient.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/NOERestraint.cpp b/modules/isd/src/NOERestraint.cpp index 918aae95c3..a85e507314 100644 --- a/modules/isd/src/NOERestraint.cpp +++ b/modules/isd/src/NOERestraint.cpp @@ -3,7 +3,7 @@ * \brief Restrain a list of particle pairs with a lognormal+ISPA. * NOTE: for now, the derivatives are written to all variables. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/NormalSigmaPCRestraint.cpp b/modules/isd/src/NormalSigmaPCRestraint.cpp index 4b4b331252..2ef4d960bc 100644 --- a/modules/isd/src/NormalSigmaPCRestraint.cpp +++ b/modules/isd/src/NormalSigmaPCRestraint.cpp @@ -2,7 +2,7 @@ * \file isd/NormalSigmaPCRestraint.cpp * \brief A Penalized Complexity prior on sigma of a normal distribution. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/Nuisance.cpp b/modules/isd/src/Nuisance.cpp index bcb274d565..bc90e737ef 100644 --- a/modules/isd/src/Nuisance.cpp +++ b/modules/isd/src/Nuisance.cpp @@ -2,7 +2,7 @@ * \file Nuisance.cpp * \brief defines a one-dimensional nuisance parameter (sigma, gamma, ...) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/PenalizedComplexityPrior.cpp b/modules/isd/src/PenalizedComplexityPrior.cpp index 5eee69018d..330dfd1543 100644 --- a/modules/isd/src/PenalizedComplexityPrior.cpp +++ b/modules/isd/src/PenalizedComplexityPrior.cpp @@ -1,7 +1,7 @@ /** * \file PenalizedComplexityPrior.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/RepulsiveDistancePairScore.cpp b/modules/isd/src/RepulsiveDistancePairScore.cpp index 7fd61bbce0..08b75b7ea6 100644 --- a/modules/isd/src/RepulsiveDistancePairScore.cpp +++ b/modules/isd/src/RepulsiveDistancePairScore.cpp @@ -3,7 +3,7 @@ * \brief A simple quadric repulsive term between two atoms. Restraint is zero * when the distance equals the sum of the radii plus the shift. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/isd/RepulsiveDistancePairScore.h" diff --git a/modules/isd/src/Scale.cpp b/modules/isd/src/Scale.cpp index b8d8db055f..8c47419b87 100644 --- a/modules/isd/src/Scale.cpp +++ b/modules/isd/src/Scale.cpp @@ -2,7 +2,7 @@ * \file Scale.h * \brief A decorator for scale parameters particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/StudentTRestraint.cpp b/modules/isd/src/StudentTRestraint.cpp index 9b3e0429ea..cc13079321 100644 --- a/modules/isd/src/StudentTRestraint.cpp +++ b/modules/isd/src/StudentTRestraint.cpp @@ -2,7 +2,7 @@ * \file isd/StudentTRestraint.cpp * \brief A Student-t distribution restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/Switching.cpp b/modules/isd/src/Switching.cpp index d42ac9ccdc..b3d5b86971 100644 --- a/modules/isd/src/Switching.cpp +++ b/modules/isd/src/Switching.cpp @@ -2,7 +2,7 @@ * \file Switching.h * \brief A decorator for switching parameters particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/TALOSRestraint.cpp b/modules/isd/src/TALOSRestraint.cpp index cd26e97b6c..4f3359b9f2 100644 --- a/modules/isd/src/TALOSRestraint.cpp +++ b/modules/isd/src/TALOSRestraint.cpp @@ -2,7 +2,7 @@ * \file TALOSRestraint.cpp \brief TALOS dihedral restraint between four * particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/UniformPrior.cpp b/modules/isd/src/UniformPrior.cpp index 6dba25d28f..517df66790 100644 --- a/modules/isd/src/UniformPrior.cpp +++ b/modules/isd/src/UniformPrior.cpp @@ -2,7 +2,7 @@ * \file IMP/isd/UniformPrior.cpp * \brief Restrain a scale particle with log(scale) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/Weight.cpp b/modules/isd/src/Weight.cpp index dfac36ea70..f7ddfc8528 100644 --- a/modules/isd/src/Weight.cpp +++ b/modules/isd/src/Weight.cpp @@ -2,7 +2,7 @@ * \file isd/Weight.cpp * \brief Add weights constrained to the unit simplex to a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/WeightMover.cpp b/modules/isd/src/WeightMover.cpp index b9a2d4fb06..34a6279a8c 100644 --- a/modules/isd/src/WeightMover.cpp +++ b/modules/isd/src/WeightMover.cpp @@ -1,7 +1,7 @@ /** * \file WeightMover.cpp \brief A modifier which perturbs a Weight particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/WeightRestraint.cpp b/modules/isd/src/WeightRestraint.cpp index a7fb5a12ff..1c72b44577 100644 --- a/modules/isd/src/WeightRestraint.cpp +++ b/modules/isd/src/WeightRestraint.cpp @@ -3,7 +3,7 @@ * \brief * Put description here * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/isd/src/distribution.cpp b/modules/isd/src/distribution.cpp index ff5569da78..dee776931f 100644 --- a/modules/isd/src/distribution.cpp +++ b/modules/isd/src/distribution.cpp @@ -1,7 +1,7 @@ /** * \file distribution.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/isd/src/vonMisesKappaConjugateRestraint.cpp b/modules/isd/src/vonMisesKappaConjugateRestraint.cpp index 03d15c0c23..16f4033a7c 100644 --- a/modules/isd/src/vonMisesKappaConjugateRestraint.cpp +++ b/modules/isd/src/vonMisesKappaConjugateRestraint.cpp @@ -2,7 +2,7 @@ * \file isd/vonMisesKappaConjugateRestraint.cpp * \brief Restrain a scale particle with log(scale) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/src/vonMisesKappaJeffreysRestraint.cpp b/modules/isd/src/vonMisesKappaJeffreysRestraint.cpp index 9de5ab3c8c..a4ea0d50bd 100644 --- a/modules/isd/src/vonMisesKappaJeffreysRestraint.cpp +++ b/modules/isd/src/vonMisesKappaJeffreysRestraint.cpp @@ -2,7 +2,7 @@ * \file isd/vonMisesKappaJeffreysRestraint.cpp * \brief Restrain a scale particle with log(scale) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/isd/test/test_MultivariateFNormalSufficient.cpp b/modules/isd/test/test_MultivariateFNormalSufficient.cpp index 53ba743ac4..20531c3d9c 100644 --- a/modules/isd/test/test_MultivariateFNormalSufficient.cpp +++ b/modules/isd/test/test_MultivariateFNormalSufficient.cpp @@ -2,7 +2,7 @@ * \file test_MultivariateFNormalSufficient.cpp * \brief testing of the Multivariate FNormal. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/kernel/compiler/has_auto.cpp b/modules/kernel/compiler/has_auto.cpp index 7557249be9..ef9c0cbf82 100644 --- a/modules/kernel/compiler/has_auto.cpp +++ b/modules/kernel/compiler/has_auto.cpp @@ -2,7 +2,7 @@ * \file nothing.cpp * \brief nothing * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/compiler/has_debug_vector.cpp b/modules/kernel/compiler/has_debug_vector.cpp index 267f4895bc..1b5f481ae3 100644 --- a/modules/kernel/compiler/has_debug_vector.cpp +++ b/modules/kernel/compiler/has_debug_vector.cpp @@ -2,7 +2,7 @@ * \file nothing.cpp * \brief nothing * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/compiler/has_unique_ptr.cpp b/modules/kernel/compiler/has_unique_ptr.cpp index 7ef1c0ef58..7b375ef4db 100644 --- a/modules/kernel/compiler/has_unique_ptr.cpp +++ b/modules/kernel/compiler/has_unique_ptr.cpp @@ -2,7 +2,7 @@ * \file nothing.cpp * \brief nothing * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Array.h b/modules/kernel/include/Array.h index 9b37e0d13e..8c364216ca 100644 --- a/modules/kernel/include/Array.h +++ b/modules/kernel/include/Array.h @@ -2,7 +2,7 @@ * \file IMP/Array.h * \brief Classes to handle static sized arrays of things. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/AttributeOptimizer.h b/modules/kernel/include/AttributeOptimizer.h index 30f6d8109c..d717d61dd5 100644 --- a/modules/kernel/include/AttributeOptimizer.h +++ b/modules/kernel/include/AttributeOptimizer.h @@ -2,7 +2,7 @@ * \file IMP/AttributeOptimizer.h * \brief Base class for optimizers that act on individual attributes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Configuration.h b/modules/kernel/include/Configuration.h index fa762c0c32..31f4b93196 100644 --- a/modules/kernel/include/Configuration.h +++ b/modules/kernel/include/Configuration.h @@ -2,7 +2,7 @@ * \file IMP/Configuration.h * \brief Store a set of configurations of the model. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/ConfigurationSet.h b/modules/kernel/include/ConfigurationSet.h index 88ee18dcf1..26787e6285 100644 --- a/modules/kernel/include/ConfigurationSet.h +++ b/modules/kernel/include/ConfigurationSet.h @@ -2,7 +2,7 @@ * \file IMP/ConfigurationSet.h * \brief Store a set of configurations of the model. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/ConstVector.h b/modules/kernel/include/ConstVector.h index 474e6f9a7a..cd059079c8 100644 --- a/modules/kernel/include/ConstVector.h +++ b/modules/kernel/include/ConstVector.h @@ -2,7 +2,7 @@ * \file IMP/ConstVector.h * \brief Store an array of values of the same type. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Constraint.h b/modules/kernel/include/Constraint.h index b7b0b85ed7..5933fc54bf 100644 --- a/modules/kernel/include/Constraint.h +++ b/modules/kernel/include/Constraint.h @@ -1,7 +1,7 @@ /** * \file IMP/Constraint.h \brief A base class for constraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/CreateLogContext.h b/modules/kernel/include/CreateLogContext.h index a2327edec2..8ad42d28f8 100644 --- a/modules/kernel/include/CreateLogContext.h +++ b/modules/kernel/include/CreateLogContext.h @@ -2,7 +2,7 @@ * \file IMP/CreateLogContext.h * \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Decorator.h b/modules/kernel/include/Decorator.h index 9f5aef8b25..0df1dc1b3c 100644 --- a/modules/kernel/include/Decorator.h +++ b/modules/kernel/include/Decorator.h @@ -1,7 +1,7 @@ /** * \file IMP/Decorator.h \brief The base class for decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/DerivativeAccumulator.h b/modules/kernel/include/DerivativeAccumulator.h index b911905b0a..0edb2a16ff 100644 --- a/modules/kernel/include/DerivativeAccumulator.h +++ b/modules/kernel/include/DerivativeAccumulator.h @@ -2,7 +2,7 @@ * \file IMP/DerivativeAccumulator.h * \brief Class for adding derivatives from restraints to the model. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Flag.h b/modules/kernel/include/Flag.h index c83561a337..fcfe8b42c1 100644 --- a/modules/kernel/include/Flag.h +++ b/modules/kernel/include/Flag.h @@ -2,7 +2,7 @@ * \file IMP/Flag.h * \brief Utility classes to add command line flags. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/FloatIndex.h b/modules/kernel/include/FloatIndex.h index dfcc094c25..f28f9ca6f5 100644 --- a/modules/kernel/include/FloatIndex.h +++ b/modules/kernel/include/FloatIndex.h @@ -2,7 +2,7 @@ * \file IMP/FloatIndex.h * \brief A FloatIndex identifies an optimized attribute in a model. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Index.h b/modules/kernel/include/Index.h index b951d14aee..a2671df008 100644 --- a/modules/kernel/include/Index.h +++ b/modules/kernel/include/Index.h @@ -2,7 +2,7 @@ * \file IMP/Index.h * \brief Utility types to refer to various types of indices * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/InputAdaptor.h b/modules/kernel/include/InputAdaptor.h index a169c70f2e..2f27e9bba1 100644 --- a/modules/kernel/include/InputAdaptor.h +++ b/modules/kernel/include/InputAdaptor.h @@ -2,7 +2,7 @@ * \file IMP/InputAdaptor.h * \brief Convenience class to accept multiple input types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Key.h b/modules/kernel/include/Key.h index 3cc2668002..bca90ae7ae 100644 --- a/modules/kernel/include/Key.h +++ b/modules/kernel/include/Key.h @@ -1,7 +1,7 @@ /** * \file IMP/Key.h \brief Keys to cache lookup of attribute strings. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Model.h b/modules/kernel/include/Model.h index 3fcac8352e..1c4b65a213 100644 --- a/modules/kernel/include/Model.h +++ b/modules/kernel/include/Model.h @@ -2,7 +2,7 @@ * \file IMP/Model.h * \brief Storage of a model, its restraints, constraints and particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/ModelObject.h b/modules/kernel/include/ModelObject.h index f340e0aacf..6db7b332c8 100644 --- a/modules/kernel/include/ModelObject.h +++ b/modules/kernel/include/ModelObject.h @@ -2,7 +2,7 @@ * \file IMP/ModelObject.h * \brief Base class for objects in a Model that depend on other objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_MODEL_OBJECT_H diff --git a/modules/kernel/include/NonCopyable.h b/modules/kernel/include/NonCopyable.h index da160363ce..f3651811ca 100644 --- a/modules/kernel/include/NonCopyable.h +++ b/modules/kernel/include/NonCopyable.h @@ -2,7 +2,7 @@ * \file IMP/NonCopyable.h * \brief Base class for all objects that cannot be copied. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Object.h b/modules/kernel/include/Object.h index 2ca23f1ff9..2bbaf08f25 100644 --- a/modules/kernel/include/Object.h +++ b/modules/kernel/include/Object.h @@ -2,7 +2,7 @@ * \file IMP/Object.h * \brief A shared base class to help in debugging and things. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Optimizer.h b/modules/kernel/include/Optimizer.h index 17e373e265..53f8a3e9cd 100644 --- a/modules/kernel/include/Optimizer.h +++ b/modules/kernel/include/Optimizer.h @@ -1,7 +1,7 @@ /** * \file IMP/Optimizer.h \brief Base class for all optimizers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/OptimizerState.h b/modules/kernel/include/OptimizerState.h index 8768a250e6..d36bf0f72e 100644 --- a/modules/kernel/include/OptimizerState.h +++ b/modules/kernel/include/OptimizerState.h @@ -1,7 +1,7 @@ /** * \file IMP/OptimizerState.h \brief Shared optimizer state. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Particle.h b/modules/kernel/include/Particle.h index 6170d80bba..b64ba64340 100644 --- a/modules/kernel/include/Particle.h +++ b/modules/kernel/include/Particle.h @@ -3,7 +3,7 @@ * \brief Classes to handle individual model particles. * (Note that implementation of inline functions is in internal) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Pointer.h b/modules/kernel/include/Pointer.h index b156d8b411..ad1d50943a 100644 --- a/modules/kernel/include/Pointer.h +++ b/modules/kernel/include/Pointer.h @@ -2,7 +2,7 @@ * \file IMP/Pointer.h * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/RAII.h b/modules/kernel/include/RAII.h index 9af680a6e7..c55696e111 100644 --- a/modules/kernel/include/RAII.h +++ b/modules/kernel/include/RAII.h @@ -2,7 +2,7 @@ * \file IMP/RAII.h \brief Basic types used by IMP. * \brief Temporarily change something; undo the change when object destroyed * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Refiner.h b/modules/kernel/include/Refiner.h index 96e654175e..d245075d2d 100644 --- a/modules/kernel/include/Refiner.h +++ b/modules/kernel/include/Refiner.h @@ -2,7 +2,7 @@ * \file IMP/Refiner.h * \brief Refine a particle into a list of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_REFINER_H diff --git a/modules/kernel/include/Restraint.h b/modules/kernel/include/Restraint.h index 9a1aef74d9..3c6fdb2525 100644 --- a/modules/kernel/include/Restraint.h +++ b/modules/kernel/include/Restraint.h @@ -2,7 +2,7 @@ * \file IMP/Restraint.h * \brief Abstract base class for all restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/RestraintInfo.h b/modules/kernel/include/RestraintInfo.h index b753c5ed53..c92196401e 100644 --- a/modules/kernel/include/RestraintInfo.h +++ b/modules/kernel/include/RestraintInfo.h @@ -2,7 +2,7 @@ * \file IMP/RestraintInfo.h * \brief Report key:value information on restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/RestraintSet.h b/modules/kernel/include/RestraintSet.h index f0a3e91521..93b55f7f0e 100644 --- a/modules/kernel/include/RestraintSet.h +++ b/modules/kernel/include/RestraintSet.h @@ -2,7 +2,7 @@ * \file IMP/RestraintSet.h * \brief Used to hold a set of related restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Sampler.h b/modules/kernel/include/Sampler.h index 653b0d6858..86dc5bf515 100644 --- a/modules/kernel/include/Sampler.h +++ b/modules/kernel/include/Sampler.h @@ -1,7 +1,7 @@ /** * \file IMP/Sampler.h \brief Base class for all samplers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/ScoreAccumulator.h b/modules/kernel/include/ScoreAccumulator.h index 6584f0dfd4..0d29a7bec0 100644 --- a/modules/kernel/include/ScoreAccumulator.h +++ b/modules/kernel/include/ScoreAccumulator.h @@ -2,7 +2,7 @@ * \file IMP/ScoreAccumulator.h \brief Class for adding scores from * restraints to the model. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/ScoreState.h b/modules/kernel/include/ScoreState.h index 2fc3c524b3..37ee2ef749 100644 --- a/modules/kernel/include/ScoreState.h +++ b/modules/kernel/include/ScoreState.h @@ -1,7 +1,7 @@ /** * \file IMP/ScoreState.h \brief Shared score state. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/ScoringFunction.h b/modules/kernel/include/ScoringFunction.h index 4b5afc15ff..e9f6964022 100644 --- a/modules/kernel/include/ScoringFunction.h +++ b/modules/kernel/include/ScoringFunction.h @@ -2,7 +2,7 @@ * \file IMP/ScoringFunction.h * \brief Represents a scoring function on the model. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/SetCheckState.h b/modules/kernel/include/SetCheckState.h index 0ce26a2680..20cc82cdf0 100644 --- a/modules/kernel/include/SetCheckState.h +++ b/modules/kernel/include/SetCheckState.h @@ -2,7 +2,7 @@ * \file IMP/SetCheckState.h * \brief Checking and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/SetLogState.h b/modules/kernel/include/SetLogState.h index 6209efe7a4..115ce98405 100644 --- a/modules/kernel/include/SetLogState.h +++ b/modules/kernel/include/SetLogState.h @@ -1,7 +1,7 @@ /** * \file IMP/SetLogState.h \brief A class to change and restore log state * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Showable.h b/modules/kernel/include/Showable.h index 6bde9ef613..2174521805 100644 --- a/modules/kernel/include/Showable.h +++ b/modules/kernel/include/Showable.h @@ -2,7 +2,7 @@ * \file IMP/Showable.h * \brief Helper class to aid in output of \imp classes to streams. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/UnaryFunction.h b/modules/kernel/include/UnaryFunction.h index 12d8f47a2f..1759798777 100644 --- a/modules/kernel/include/UnaryFunction.h +++ b/modules/kernel/include/UnaryFunction.h @@ -1,7 +1,7 @@ /** * \file IMP/UnaryFunction.h \brief Single variable function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_UNARY_FUNCTION_H diff --git a/modules/kernel/include/Undecorator.h b/modules/kernel/include/Undecorator.h index 67ae450e29..e2df5e4af7 100644 --- a/modules/kernel/include/Undecorator.h +++ b/modules/kernel/include/Undecorator.h @@ -1,7 +1,7 @@ /** * \file IMP/Undecorator.h \brief The base class for undecorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Value.h b/modules/kernel/include/Value.h index 36b489059b..a3766dcf33 100644 --- a/modules/kernel/include/Value.h +++ b/modules/kernel/include/Value.h @@ -2,7 +2,7 @@ * \file IMP/Value.h * \brief Base class for a simple primitive-like type. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/Vector.h b/modules/kernel/include/Vector.h index 6a64ccdc23..e6b01f1aa2 100644 --- a/modules/kernel/include/Vector.h +++ b/modules/kernel/include/Vector.h @@ -2,7 +2,7 @@ * \file IMP/Vector.h * \brief A class for storing lists of IMP items. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/VersionInfo.h b/modules/kernel/include/VersionInfo.h index 4fd587c655..429382b614 100644 --- a/modules/kernel/include/VersionInfo.h +++ b/modules/kernel/include/VersionInfo.h @@ -1,7 +1,7 @@ /** * \file IMP/VersionInfo.h \brief Version and authorship of IMP objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/WarningContext.h b/modules/kernel/include/WarningContext.h index 07660cefd5..cac85a3d0c 100644 --- a/modules/kernel/include/WarningContext.h +++ b/modules/kernel/include/WarningContext.h @@ -2,7 +2,7 @@ * \file IMP/WarningContext.h * \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/WeakPointer.h b/modules/kernel/include/WeakPointer.h index faddb986a7..7827ce42fd 100644 --- a/modules/kernel/include/WeakPointer.h +++ b/modules/kernel/include/WeakPointer.h @@ -2,7 +2,7 @@ * \file IMP/WeakPointer.h * \brief A weak pointer to an Object or RefCountedObject. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/base_macros.h b/modules/kernel/include/base_macros.h index fe89da85ec..32d54adb36 100644 --- a/modules/kernel/include/base_macros.h +++ b/modules/kernel/include/base_macros.h @@ -2,7 +2,7 @@ * \file IMP/base_macros.h * \brief Various general useful macros for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/base_types.h b/modules/kernel/include/base_types.h index a096b14c89..f0617f0eff 100644 --- a/modules/kernel/include/base_types.h +++ b/modules/kernel/include/base_types.h @@ -1,7 +1,7 @@ /** * \file IMP/base_types.h \brief Basic types used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/base_utility.h b/modules/kernel/include/base_utility.h index 470f2c577a..5fb8d67ca0 100644 --- a/modules/kernel/include/base_utility.h +++ b/modules/kernel/include/base_utility.h @@ -2,7 +2,7 @@ * \file IMP/base_utility.h * \brief Various general useful functions for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/bracket_macros.h b/modules/kernel/include/bracket_macros.h index 1e01713ccc..6dd82835c6 100644 --- a/modules/kernel/include/bracket_macros.h +++ b/modules/kernel/include/bracket_macros.h @@ -2,7 +2,7 @@ * \file IMP/bracket_macros.h * \brief Macros to handle array indexing. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/cache.h b/modules/kernel/include/cache.h index b1df9a396f..fceeab35f3 100644 --- a/modules/kernel/include/cache.h +++ b/modules/kernel/include/cache.h @@ -2,7 +2,7 @@ * \file IMP/cache.h * \brief Helper classes for various types of caching * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/check_macros.h b/modules/kernel/include/check_macros.h index 7a76d9962c..cc8c30085f 100644 --- a/modules/kernel/include/check_macros.h +++ b/modules/kernel/include/check_macros.h @@ -2,7 +2,7 @@ * \file IMP/check_macros.h * \brief Helper macros for throwing and handling exceptions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/comparison_macros.h b/modules/kernel/include/comparison_macros.h index 48b661ad5e..bf926a391a 100644 --- a/modules/kernel/include/comparison_macros.h +++ b/modules/kernel/include/comparison_macros.h @@ -2,7 +2,7 @@ * \file IMP/comparison_macros.h * \brief Helper macros for implementing comparisons of \imp objects * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/compiler_macros.h b/modules/kernel/include/compiler_macros.h index 10e6f1ac48..27dfe212cc 100644 --- a/modules/kernel/include/compiler_macros.h +++ b/modules/kernel/include/compiler_macros.h @@ -2,7 +2,7 @@ * \file IMP/compiler_macros.h * \brief Various compiler workarounds * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_COMPILER_MACROS_H diff --git a/modules/kernel/include/constants.h b/modules/kernel/include/constants.h index 4eef192d2c..92a155aaed 100644 --- a/modules/kernel/include/constants.h +++ b/modules/kernel/include/constants.h @@ -1,7 +1,7 @@ /** * \file IMP/constants.h \brief Various useful constants. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/container_base.h b/modules/kernel/include/container_base.h index 6600eba6b3..eae19a4485 100644 --- a/modules/kernel/include/container_base.h +++ b/modules/kernel/include/container_base.h @@ -2,7 +2,7 @@ * \file IMP/container_base.h * \brief Abstract base class for containers of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/container_macros.h b/modules/kernel/include/container_macros.h index 04c735364a..2f80b06ae9 100644 --- a/modules/kernel/include/container_macros.h +++ b/modules/kernel/include/container_macros.h @@ -2,7 +2,7 @@ * \file IMP/container_macros.h * \brief Macros to define containers of objects * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/decorator_macros.h b/modules/kernel/include/decorator_macros.h index 8a09e1645d..b24bb4b0ae 100644 --- a/modules/kernel/include/decorator_macros.h +++ b/modules/kernel/include/decorator_macros.h @@ -2,7 +2,7 @@ * \file IMP/decorator_macros.h * \brief Helper macros for implementing Decorators * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/dependency_graph.h b/modules/kernel/include/dependency_graph.h index 0bb45cba4b..3968072749 100644 --- a/modules/kernel/include/dependency_graph.h +++ b/modules/kernel/include/dependency_graph.h @@ -2,7 +2,7 @@ * \file IMP/dependency_graph.h * \brief Build dependency graphs on models. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/deprecation.h b/modules/kernel/include/deprecation.h index c6aeae34de..3bc4ecfc0e 100644 --- a/modules/kernel/include/deprecation.h +++ b/modules/kernel/include/deprecation.h @@ -2,7 +2,7 @@ * \file IMP/deprecation.h * \brief Control display of deprecation information. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/deprecation_macros.h b/modules/kernel/include/deprecation_macros.h index 2fa0dd9e01..6a52b7ecd4 100644 --- a/modules/kernel/include/deprecation_macros.h +++ b/modules/kernel/include/deprecation_macros.h @@ -2,7 +2,7 @@ * \file IMP/deprecation_macros.h * \brief Control display of deprecation information. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/doxygen_macros.h b/modules/kernel/include/doxygen_macros.h index c4fcc653e6..f9689b91c8 100644 --- a/modules/kernel/include/doxygen_macros.h +++ b/modules/kernel/include/doxygen_macros.h @@ -2,7 +2,7 @@ * \file IMP/doxygen_macros.h * \brief Helper macros for writing doxygen documentation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/enums.h b/modules/kernel/include/enums.h index efc158fab5..70ec0ef03a 100644 --- a/modules/kernel/include/enums.h +++ b/modules/kernel/include/enums.h @@ -1,7 +1,7 @@ /** * \file IMP/enums.h \brief Basic enumeration types used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/exception.h b/modules/kernel/include/exception.h index 9260c90347..4fd7d84b73 100644 --- a/modules/kernel/include/exception.h +++ b/modules/kernel/include/exception.h @@ -2,7 +2,7 @@ * \file IMP/exception.h * \brief Exception definitions and assertions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/file.h b/modules/kernel/include/file.h index bd4eadab50..2d0f5164bf 100644 --- a/modules/kernel/include/file.h +++ b/modules/kernel/include/file.h @@ -2,7 +2,7 @@ * \file IMP/file.h * \brief Handling of file input/output * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/flags.h b/modules/kernel/include/flags.h index 0b77bf7578..b9dc2cbe48 100644 --- a/modules/kernel/include/flags.h +++ b/modules/kernel/include/flags.h @@ -2,7 +2,7 @@ * \file IMP/flags.h * \brief Support for shared command line flags. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/functor.h b/modules/kernel/include/functor.h index a66b251629..b51738c789 100644 --- a/modules/kernel/include/functor.h +++ b/modules/kernel/include/functor.h @@ -2,7 +2,7 @@ * \file IMP/functor.h * \brief Helper functionality for functors. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/generic.h b/modules/kernel/include/generic.h index 1cf25b98e3..26fc4a1b01 100644 --- a/modules/kernel/include/generic.h +++ b/modules/kernel/include/generic.h @@ -2,7 +2,7 @@ * \file IMP/generic.h * \brief Compile-time generic restraint and constraint support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/graph_macros.h b/modules/kernel/include/graph_macros.h index 365290e18a..da06ad097d 100644 --- a/modules/kernel/include/graph_macros.h +++ b/modules/kernel/include/graph_macros.h @@ -2,7 +2,7 @@ * \file IMP/graph_macros.h * \brief Helper macros for handling graphs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/hash.h b/modules/kernel/include/hash.h index 2074462901..bd028ca540 100644 --- a/modules/kernel/include/hash.h +++ b/modules/kernel/include/hash.h @@ -2,7 +2,7 @@ * \file IMP/hash.h * \brief Helper functions for implementing hashes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/hash_macros.h b/modules/kernel/include/hash_macros.h index 9e8ba8a929..cbb5cecfb7 100644 --- a/modules/kernel/include/hash_macros.h +++ b/modules/kernel/include/hash_macros.h @@ -2,7 +2,7 @@ * \file IMP/hash_macros.h * \brief Helper macros for implementing hashable classes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/input_output.h b/modules/kernel/include/input_output.h index c533e3f71b..3ba7102bba 100644 --- a/modules/kernel/include/input_output.h +++ b/modules/kernel/include/input_output.h @@ -2,7 +2,7 @@ * \file IMP/input_output.h * \brief Utility functions to track input/output particles of model objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INPUT_OUTPUT_H diff --git a/modules/kernel/include/internal/AccumulatorScoreModifier.h b/modules/kernel/include/internal/AccumulatorScoreModifier.h index 88fd79a6c0..47412e2a1f 100644 --- a/modules/kernel/include/internal/AccumulatorScoreModifier.h +++ b/modules/kernel/include/internal/AccumulatorScoreModifier.h @@ -2,7 +2,7 @@ * \file generic.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/AttributeTable.h b/modules/kernel/include/internal/AttributeTable.h index 58321ddda8..094811a944 100644 --- a/modules/kernel/include/internal/AttributeTable.h +++ b/modules/kernel/include/internal/AttributeTable.h @@ -1,7 +1,7 @@ /** * \file AttributeTable.h \brief Keys to cache lookup of attribute strings. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/ContainerConstraint.h b/modules/kernel/include/internal/ContainerConstraint.h index 917cbb9b57..66ab6146f7 100644 --- a/modules/kernel/include/internal/ContainerConstraint.h +++ b/modules/kernel/include/internal/ContainerConstraint.h @@ -2,7 +2,7 @@ * \file core/generic.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/ContainerRestraint.h b/modules/kernel/include/internal/ContainerRestraint.h index 138e48e6f2..d67d867bf1 100644 --- a/modules/kernel/include/internal/ContainerRestraint.h +++ b/modules/kernel/include/internal/ContainerRestraint.h @@ -2,7 +2,7 @@ * \file core/generic.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/ContainerScoreState.h b/modules/kernel/include/internal/ContainerScoreState.h index d047d8144f..60cf36aef5 100644 --- a/modules/kernel/include/internal/ContainerScoreState.h +++ b/modules/kernel/include/internal/ContainerScoreState.h @@ -2,7 +2,7 @@ * \file generic.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/DynamicListContainer.h b/modules/kernel/include/internal/DynamicListContainer.h index 9ec89e2bbb..38c62b2090 100644 --- a/modules/kernel/include/internal/DynamicListContainer.h +++ b/modules/kernel/include/internal/DynamicListContainer.h @@ -4,7 +4,7 @@ * * BLURB * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_DYNAMIC_LIST_CONTAINER_H diff --git a/modules/kernel/include/internal/ExponentialNumber.h b/modules/kernel/include/internal/ExponentialNumber.h index 1b60f7b41a..cb81096ba0 100644 --- a/modules/kernel/include/internal/ExponentialNumber.h +++ b/modules/kernel/include/internal/ExponentialNumber.h @@ -2,7 +2,7 @@ * \file ExponentialNumber.h * \brief Classes to add compile time exponents to numbers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/Flag.h b/modules/kernel/include/internal/Flag.h index 9d1fd15644..48a9416a92 100644 --- a/modules/kernel/include/internal/Flag.h +++ b/modules/kernel/include/internal/Flag.h @@ -2,7 +2,7 @@ * \file IMP/Flag.h * \brief Various general useful macros for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/IndexingIterator.h b/modules/kernel/include/internal/IndexingIterator.h index 11af0f0a9c..73c5d8dc1d 100644 --- a/modules/kernel/include/internal/IndexingIterator.h +++ b/modules/kernel/include/internal/IndexingIterator.h @@ -1,7 +1,7 @@ /** * \file IndexingIterator.h \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/ListLikeContainer.h b/modules/kernel/include/internal/ListLikeContainer.h index 80d71f0edd..a62fecb5f7 100644 --- a/modules/kernel/include/internal/ListLikeContainer.h +++ b/modules/kernel/include/internal/ListLikeContainer.h @@ -5,7 +5,7 @@ * * BLURB * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_LIST_LIKE_CONTAINER_H diff --git a/modules/kernel/include/internal/NestedIterator.h b/modules/kernel/include/internal/NestedIterator.h index a242349a9c..47a3432aed 100644 --- a/modules/kernel/include/internal/NestedIterator.h +++ b/modules/kernel/include/internal/NestedIterator.h @@ -1,7 +1,7 @@ /** * \file NestedIterator.h \brief A class to represent a voxel grid. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/PointerBase.h b/modules/kernel/include/internal/PointerBase.h index 2a4cdd5956..796838b727 100644 --- a/modules/kernel/include/internal/PointerBase.h +++ b/modules/kernel/include/internal/PointerBase.h @@ -2,7 +2,7 @@ * \file base/internal/PointerBase.h * \brief A nullptr-initialized pointer to an IMP ref-counted Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/PrefixStream.h b/modules/kernel/include/internal/PrefixStream.h index 1106d6cc74..c5a920e018 100644 --- a/modules/kernel/include/internal/PrefixStream.h +++ b/modules/kernel/include/internal/PrefixStream.h @@ -2,7 +2,7 @@ * \file PrefixStream.h * \brief A stream which prefixes each line with a string. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/RestraintsScoringFunction.h b/modules/kernel/include/internal/RestraintsScoringFunction.h index 84bbfb418e..7f4fbb9071 100644 --- a/modules/kernel/include/internal/RestraintsScoringFunction.h +++ b/modules/kernel/include/internal/RestraintsScoringFunction.h @@ -2,7 +2,7 @@ * \file IMP/internal/RestraintsScoringFunction.h * \brief A scoring function on a list of restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/StaticListContainer.h b/modules/kernel/include/internal/StaticListContainer.h index 1491e131c5..bda4949398 100644 --- a/modules/kernel/include/internal/StaticListContainer.h +++ b/modules/kernel/include/internal/StaticListContainer.h @@ -3,7 +3,7 @@ * * BLURB * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_STATIC_LIST_CONTAINER_H diff --git a/modules/kernel/include/internal/TupleConstraint.h b/modules/kernel/include/internal/TupleConstraint.h index db36fc2595..3635da9e5d 100644 --- a/modules/kernel/include/internal/TupleConstraint.h +++ b/modules/kernel/include/internal/TupleConstraint.h @@ -2,7 +2,7 @@ * \file generic.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/TupleRestraint.h b/modules/kernel/include/internal/TupleRestraint.h index 777198ee58..b0e2f2988b 100644 --- a/modules/kernel/include/internal/TupleRestraint.h +++ b/modules/kernel/include/internal/TupleRestraint.h @@ -2,7 +2,7 @@ * \file generic.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/Unit.h b/modules/kernel/include/internal/Unit.h index 3964ccb463..121760aa71 100644 --- a/modules/kernel/include/internal/Unit.h +++ b/modules/kernel/include/internal/Unit.h @@ -1,7 +1,7 @@ /** * \file Unit.h \brief Classes to help with converting between units. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/Vector.h b/modules/kernel/include/internal/Vector.h index e17ebdab1b..75d97082d6 100644 --- a/modules/kernel/include/internal/Vector.h +++ b/modules/kernel/include/internal/Vector.h @@ -1,7 +1,7 @@ /** * \file Vector.h \brief A bounds checked vector. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/attribute_tables.h b/modules/kernel/include/internal/attribute_tables.h index a98b5f5a1d..4adb7945ec 100644 --- a/modules/kernel/include/internal/attribute_tables.h +++ b/modules/kernel/include/internal/attribute_tables.h @@ -2,7 +2,7 @@ * \file internal/attribute_tables.h * \brief Access to particle attributes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/base_graph_utility.h b/modules/kernel/include/internal/base_graph_utility.h index f260229a64..196b508a45 100644 --- a/modules/kernel/include/internal/base_graph_utility.h +++ b/modules/kernel/include/internal/base_graph_utility.h @@ -2,7 +2,7 @@ * \file internal/graph_utility.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_BASE_GRAPH_UTILITY_H diff --git a/modules/kernel/include/internal/base_static.h b/modules/kernel/include/internal/base_static.h index ffbe48ffb1..bed7aeb4ee 100644 --- a/modules/kernel/include/internal/base_static.h +++ b/modules/kernel/include/internal/base_static.h @@ -2,7 +2,7 @@ * \file internal/static.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_BASE_STATIC_H diff --git a/modules/kernel/include/internal/cache.h b/modules/kernel/include/internal/cache.h index f12053d042..6a991e8b7b 100644 --- a/modules/kernel/include/internal/cache.h +++ b/modules/kernel/include/internal/cache.h @@ -2,7 +2,7 @@ * \file internal/cache.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_CACHE_H diff --git a/modules/kernel/include/internal/constants.h b/modules/kernel/include/internal/constants.h index ed810a44da..6fc893dfd7 100644 --- a/modules/kernel/include/internal/constants.h +++ b/modules/kernel/include/internal/constants.h @@ -1,7 +1,7 @@ /** * \file interna/constants.h \brief Various useful constants. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/container_helpers.h b/modules/kernel/include/internal/container_helpers.h index 60e81b9fdf..112740817f 100644 --- a/modules/kernel/include/internal/container_helpers.h +++ b/modules/kernel/include/internal/container_helpers.h @@ -2,7 +2,7 @@ * \file container_helpers.h * \brief Internal helpers for container classes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/create_decomposition.h b/modules/kernel/include/internal/create_decomposition.h index 6bcbab59f9..9fc2e03377 100644 --- a/modules/kernel/include/internal/create_decomposition.h +++ b/modules/kernel/include/internal/create_decomposition.h @@ -2,7 +2,7 @@ * \file internal/utility.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_CREATE_DECOMPOSITION_H diff --git a/modules/kernel/include/internal/cuda_helper_functions.h b/modules/kernel/include/internal/cuda_helper_functions.h index 8f0d5002f6..8622116e1d 100644 --- a/modules/kernel/include/internal/cuda_helper_functions.h +++ b/modules/kernel/include/internal/cuda_helper_functions.h @@ -2,7 +2,7 @@ * \file IMP/kernel/random_number_generation.h * \brief GPU or CPU pooled random number generation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/deprecation.h b/modules/kernel/include/internal/deprecation.h index 1e8e6a7307..c0a345ca7f 100644 --- a/modules/kernel/include/internal/deprecation.h +++ b/modules/kernel/include/internal/deprecation.h @@ -2,7 +2,7 @@ * \file internal/deprecation.h * \brief Macros to mark a class as deprecated. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/directories.h b/modules/kernel/include/internal/directories.h index 6cdea93c30..21e3492c03 100644 --- a/modules/kernel/include/internal/directories.h +++ b/modules/kernel/include/internal/directories.h @@ -2,7 +2,7 @@ * \file directories.h * \brief Get directories used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/eat.h b/modules/kernel/include/internal/eat.h index 0b6f051f0f..c44d6018dc 100644 --- a/modules/kernel/include/internal/eat.h +++ b/modules/kernel/include/internal/eat.h @@ -2,7 +2,7 @@ * \file internal/log.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_EAT_H diff --git a/modules/kernel/include/internal/evaluate_utility.h b/modules/kernel/include/internal/evaluate_utility.h index 70985d1dc2..3e494388c9 100644 --- a/modules/kernel/include/internal/evaluate_utility.h +++ b/modules/kernel/include/internal/evaluate_utility.h @@ -2,7 +2,7 @@ * \file internal/utility.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_EVALUATE_UTILITY_H diff --git a/modules/kernel/include/internal/functors.h b/modules/kernel/include/internal/functors.h index 5d3bdb275c..af65752c77 100644 --- a/modules/kernel/include/internal/functors.h +++ b/modules/kernel/include/internal/functors.h @@ -2,7 +2,7 @@ * \file IMP/functor.h \brief Various important functionality * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/graph_utility.h b/modules/kernel/include/internal/graph_utility.h index 779eca587d..6ad7fb089d 100644 --- a/modules/kernel/include/internal/graph_utility.h +++ b/modules/kernel/include/internal/graph_utility.h @@ -2,7 +2,7 @@ * \file internal/graph_utility.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_GRAPH_UTILITY_H diff --git a/modules/kernel/include/internal/ifile.h b/modules/kernel/include/internal/ifile.h index f8e2ce292c..bcc80a2fc6 100644 --- a/modules/kernel/include/internal/ifile.h +++ b/modules/kernel/include/internal/ifile.h @@ -2,7 +2,7 @@ * \file internal/ifile.h * \brief Control display of deprecation information. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/input_output_exception.h b/modules/kernel/include/internal/input_output_exception.h index 3b20421fa2..30a3577f90 100644 --- a/modules/kernel/include/internal/input_output_exception.h +++ b/modules/kernel/include/internal/input_output_exception.h @@ -2,7 +2,7 @@ * \file IMP/exception.h * \brief Exception definitions and assertions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/key_helpers.h b/modules/kernel/include/internal/key_helpers.h index 8190fc4edd..3e4fd16e96 100644 --- a/modules/kernel/include/internal/key_helpers.h +++ b/modules/kernel/include/internal/key_helpers.h @@ -2,7 +2,7 @@ * \file key_helpers.h \brief helpers for declaring keys * such as classes KeyData, KeyTable and method get_key_data() * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/log.h b/modules/kernel/include/internal/log.h index 7d18b7862c..d98b5060c9 100644 --- a/modules/kernel/include/internal/log.h +++ b/modules/kernel/include/internal/log.h @@ -2,7 +2,7 @@ * \file internal/log.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_LOG_H diff --git a/modules/kernel/include/internal/log_stream.h b/modules/kernel/include/internal/log_stream.h index 3ddcb5f9ef..bec7a165fa 100644 --- a/modules/kernel/include/internal/log_stream.h +++ b/modules/kernel/include/internal/log_stream.h @@ -2,7 +2,7 @@ * \file internal/utility.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_LOG_STREAM_H diff --git a/modules/kernel/include/internal/moved_particles_cache.h b/modules/kernel/include/internal/moved_particles_cache.h index 944909edd5..ca7a19d137 100644 --- a/modules/kernel/include/internal/moved_particles_cache.h +++ b/modules/kernel/include/internal/moved_particles_cache.h @@ -3,7 +3,7 @@ * \brief Cache ModelObjects that change when a Particle moves * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_MOVED_PARTICLES_CACHE_H diff --git a/modules/kernel/include/internal/pdb.h b/modules/kernel/include/internal/pdb.h index 60aff187ee..7b8271718f 100644 --- a/modules/kernel/include/internal/pdb.h +++ b/modules/kernel/include/internal/pdb.h @@ -2,7 +2,7 @@ * \file internal/pdb.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_PDB_H diff --git a/modules/kernel/include/internal/random_number_generation_boost.h b/modules/kernel/include/internal/random_number_generation_boost.h index f64258be4b..d94e854530 100644 --- a/modules/kernel/include/internal/random_number_generation_boost.h +++ b/modules/kernel/include/internal/random_number_generation_boost.h @@ -2,7 +2,7 @@ * \file IMP/kernel/internal/random_number_generation_boost.h * \brief GPU or CPU pooled random number generation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/random_number_generation_cuda.h b/modules/kernel/include/internal/random_number_generation_cuda.h index 5af3e72c91..f5eb9ac7f8 100644 --- a/modules/kernel/include/internal/random_number_generation_cuda.h +++ b/modules/kernel/include/internal/random_number_generation_cuda.h @@ -2,7 +2,7 @@ * \file IMP/kernel/random_number_generation.h * \brief GPU or CPU pooled random number generation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/range.h b/modules/kernel/include/internal/range.h index f9f6cfdc80..2cf47e29fa 100644 --- a/modules/kernel/include/internal/range.h +++ b/modules/kernel/include/internal/range.h @@ -2,7 +2,7 @@ * \file internal/log.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_RANGE_H diff --git a/modules/kernel/include/internal/restraint_evaluation.h b/modules/kernel/include/internal/restraint_evaluation.h index 86c5209130..31658e86e7 100644 --- a/modules/kernel/include/internal/restraint_evaluation.h +++ b/modules/kernel/include/internal/restraint_evaluation.h @@ -2,7 +2,7 @@ * \file internal/restraint_evaluation.h * \brief Utility functions to get restraint scores * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_RESTRAINT_EVALUATION_H diff --git a/modules/kernel/include/internal/scoring_functions.h b/modules/kernel/include/internal/scoring_functions.h index 048717e3c1..5238122e3d 100644 --- a/modules/kernel/include/internal/scoring_functions.h +++ b/modules/kernel/include/internal/scoring_functions.h @@ -2,7 +2,7 @@ * \file internal/utility.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_SCORING_FUNCTIONS_H diff --git a/modules/kernel/include/internal/static.h b/modules/kernel/include/internal/static.h index a8a18fcf15..147adb2714 100644 --- a/modules/kernel/include/internal/static.h +++ b/modules/kernel/include/internal/static.h @@ -2,7 +2,7 @@ * \file internal/utility.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_STATIC_H diff --git a/modules/kernel/include/internal/swig.h b/modules/kernel/include/internal/swig.h index 2512c82c8e..2467dcfeef 100644 --- a/modules/kernel/include/internal/swig.h +++ b/modules/kernel/include/internal/swig.h @@ -2,7 +2,7 @@ * \file internal/swig.h * \brief Functions for use in swig wrappers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_SWIG_H diff --git a/modules/kernel/include/internal/swig_base.h b/modules/kernel/include/internal/swig_base.h index 1528eb46d0..f39234a74a 100644 --- a/modules/kernel/include/internal/swig_base.h +++ b/modules/kernel/include/internal/swig_base.h @@ -2,7 +2,7 @@ * \file internal/swig.h * \brief Functions for use in swig wrappers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_SWIG_BASE_H diff --git a/modules/kernel/include/internal/swig_helpers.h b/modules/kernel/include/internal/swig_helpers.h index 187d847d02..2b0914b766 100644 --- a/modules/kernel/include/internal/swig_helpers.h +++ b/modules/kernel/include/internal/swig_helpers.h @@ -2,7 +2,7 @@ * \file internal/swig_helpers.h * \brief Functions for use in swig wrappers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_SWIG_HELPERS_H diff --git a/modules/kernel/include/internal/swig_helpers_base.h b/modules/kernel/include/internal/swig_helpers_base.h index e6f534c965..7f3d228ea2 100644 --- a/modules/kernel/include/internal/swig_helpers_base.h +++ b/modules/kernel/include/internal/swig_helpers_base.h @@ -2,7 +2,7 @@ * \file internal/swig_helpers.h * \brief Functions for use in swig wrappers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_SWIG_HELPERS_BASE_H diff --git a/modules/kernel/include/internal/units.h b/modules/kernel/include/internal/units.h index 6bc887e89b..493c20d7d2 100644 --- a/modules/kernel/include/internal/units.h +++ b/modules/kernel/include/internal/units.h @@ -1,7 +1,7 @@ /** * \file units.h \brief Classes to help with converting between units. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/internal/utility.h b/modules/kernel/include/internal/utility.h index 217151b629..bab3b86d4b 100644 --- a/modules/kernel/include/internal/utility.h +++ b/modules/kernel/include/internal/utility.h @@ -2,7 +2,7 @@ * \file internal/utility.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_INTERNAL_UTILITY_H diff --git a/modules/kernel/include/io.h b/modules/kernel/include/io.h index 63b5a9a9ee..5b91f2f165 100644 --- a/modules/kernel/include/io.h +++ b/modules/kernel/include/io.h @@ -2,7 +2,7 @@ * \file IMP/io.h * \brief Write/read the state of the particles to/from a buffer in memory. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/live_objects.h b/modules/kernel/include/live_objects.h index 5194293f4b..6181c63c03 100644 --- a/modules/kernel/include/live_objects.h +++ b/modules/kernel/include/live_objects.h @@ -2,7 +2,7 @@ * \file IMP/live_objects.h * \brief A shared base class to help in debugging and things. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/log.h b/modules/kernel/include/log.h index 2d16e49132..611270ad90 100644 --- a/modules/kernel/include/log.h +++ b/modules/kernel/include/log.h @@ -2,7 +2,7 @@ * \file IMP/log.h * \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/log_macros.h b/modules/kernel/include/log_macros.h index 6b674322f9..a5164f384d 100644 --- a/modules/kernel/include/log_macros.h +++ b/modules/kernel/include/log_macros.h @@ -2,7 +2,7 @@ * \file IMP/log_macros.h * \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/macros.h b/modules/kernel/include/macros.h index bd96489fcc..655c581973 100644 --- a/modules/kernel/include/macros.h +++ b/modules/kernel/include/macros.h @@ -1,7 +1,7 @@ /** * \file IMP/macros.h \brief Various general useful macros for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/math.h b/modules/kernel/include/math.h index 77fb8743b4..843f86727e 100644 --- a/modules/kernel/include/math.h +++ b/modules/kernel/include/math.h @@ -2,7 +2,7 @@ * \file IMP/math.h * \brief Helper functions to check for NaN or infinity * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_BASE_MATH_H diff --git a/modules/kernel/include/model_object_helpers.h b/modules/kernel/include/model_object_helpers.h index 32ed0bb58c..c37139de0e 100644 --- a/modules/kernel/include/model_object_helpers.h +++ b/modules/kernel/include/model_object_helpers.h @@ -2,7 +2,7 @@ * \file IMP/model_object_helpers.h * \brief Classes used in the construction of ModelObjects * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_MODEL_OBJECT_HELPERS_H diff --git a/modules/kernel/include/nullptr.h b/modules/kernel/include/nullptr.h index dbd36b8f97..989ffa1174 100644 --- a/modules/kernel/include/nullptr.h +++ b/modules/kernel/include/nullptr.h @@ -2,7 +2,7 @@ * \file IMP/nullptr.h * \brief Provide a nullptr keyword analog. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_NULLPTR_H diff --git a/modules/kernel/include/nullptr_macros.h b/modules/kernel/include/nullptr_macros.h index 95e242e1f4..cc11a85ce1 100644 --- a/modules/kernel/include/nullptr_macros.h +++ b/modules/kernel/include/nullptr_macros.h @@ -2,7 +2,7 @@ * \file IMP/nullptr_macros.h * \brief Provide a nullptr keyword analog. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_NULLPTR_MACROS_H diff --git a/modules/kernel/include/object_cast.h b/modules/kernel/include/object_cast.h index 2145969bfb..5249697516 100644 --- a/modules/kernel/include/object_cast.h +++ b/modules/kernel/include/object_cast.h @@ -2,7 +2,7 @@ * \file IMP/object_cast.h * \brief Up (or down) cast an \imp Object-derived class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/object_macros.h b/modules/kernel/include/object_macros.h index 5054a787a5..bac3751e87 100644 --- a/modules/kernel/include/object_macros.h +++ b/modules/kernel/include/object_macros.h @@ -2,7 +2,7 @@ * \file IMP/object_macros.h * \brief Helper macros for implementing \imp Objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/particle_index.h b/modules/kernel/include/particle_index.h index 77bb401fda..53703b4a7e 100644 --- a/modules/kernel/include/particle_index.h +++ b/modules/kernel/include/particle_index.h @@ -2,7 +2,7 @@ * \file IMP/particle_index.h * \brief Functions and adaptors for dealing with particle indexes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/python_only.h b/modules/kernel/include/python_only.h index f62d5a56f6..63d74eef77 100644 --- a/modules/kernel/include/python_only.h +++ b/modules/kernel/include/python_only.h @@ -2,7 +2,7 @@ * \file IMP/python_only.h * \brief Helper functions for Python. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/raii_macros.h b/modules/kernel/include/raii_macros.h index 9ad146de7c..bd7dff570d 100644 --- a/modules/kernel/include/raii_macros.h +++ b/modules/kernel/include/raii_macros.h @@ -2,7 +2,7 @@ * \file IMP/raii_macros.h * \brief Macros to aid in writing RAII-style classes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/random.h b/modules/kernel/include/random.h index be68398b8b..6bb4af26a0 100644 --- a/modules/kernel/include/random.h +++ b/modules/kernel/include/random.h @@ -1,7 +1,7 @@ /** * \file IMP/random.h \brief Random number generators used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/random_utils.h b/modules/kernel/include/random_utils.h index 6c6d6d03bf..7cebb06b55 100644 --- a/modules/kernel/include/random_utils.h +++ b/modules/kernel/include/random_utils.h @@ -2,7 +2,7 @@ * \file IMP/random_utils.h * \brief Random number utility functions used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/ref_counted_macros.h b/modules/kernel/include/ref_counted_macros.h index 1760e6b0da..488f246ac3 100644 --- a/modules/kernel/include/ref_counted_macros.h +++ b/modules/kernel/include/ref_counted_macros.h @@ -2,7 +2,7 @@ * \file IMP/ref_counted_macros.h * \brief Macros to help with reference counting. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/scoped.h b/modules/kernel/include/scoped.h index 2159c9b5f2..d089d426e7 100644 --- a/modules/kernel/include/scoped.h +++ b/modules/kernel/include/scoped.h @@ -2,7 +2,7 @@ * \file IMP/scoped.h * \brief Temporarily set particle attributes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/set_map_macros.h b/modules/kernel/include/set_map_macros.h index 2150f76d7e..e239966096 100644 --- a/modules/kernel/include/set_map_macros.h +++ b/modules/kernel/include/set_map_macros.h @@ -2,7 +2,7 @@ * \file IMP/set_map_macros.h * \brief Macros to choose the best set or map for different purposes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/showable_macros.h b/modules/kernel/include/showable_macros.h index 406794f171..1d1bfffaf4 100644 --- a/modules/kernel/include/showable_macros.h +++ b/modules/kernel/include/showable_macros.h @@ -2,7 +2,7 @@ * \file IMP/showable_macros.h * \brief Macros to help with objects that can be printed to a stream. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/swap_macros.h b/modules/kernel/include/swap_macros.h index 2941885fbf..a2dce2617d 100644 --- a/modules/kernel/include/swap_macros.h +++ b/modules/kernel/include/swap_macros.h @@ -2,7 +2,7 @@ * \file IMP/swap_macros.h * \brief Macros to help with swapping two objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/swig_macros.h b/modules/kernel/include/swig_macros.h index f955acaf79..223080de3a 100644 --- a/modules/kernel/include/swig_macros.h +++ b/modules/kernel/include/swig_macros.h @@ -2,7 +2,7 @@ * \file IMP/swig_macros.h * \brief Macros to hide code from SWIG. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/thread_macros.h b/modules/kernel/include/thread_macros.h index 4137686732..11e798ad42 100644 --- a/modules/kernel/include/thread_macros.h +++ b/modules/kernel/include/thread_macros.h @@ -2,7 +2,7 @@ * \file IMP/thread_macros.h * \brief Control for OpenMP * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/threads.h b/modules/kernel/include/threads.h index 757ceb88a6..3df396b1ff 100644 --- a/modules/kernel/include/threads.h +++ b/modules/kernel/include/threads.h @@ -2,7 +2,7 @@ * \file IMP/threads.h * \brief Control for using multiple threads in IMP * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/tuple_macros.h b/modules/kernel/include/tuple_macros.h index 56f2ad728b..f3b46e4677 100644 --- a/modules/kernel/include/tuple_macros.h +++ b/modules/kernel/include/tuple_macros.h @@ -2,7 +2,7 @@ * \file IMP/tuple_macros.h * \brief Macros to help in defining tuple classes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/types.h b/modules/kernel/include/types.h index 78010e133c..cda7ead07b 100644 --- a/modules/kernel/include/types.h +++ b/modules/kernel/include/types.h @@ -1,7 +1,7 @@ /** * \file IMP/types.h \brief Basic types used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/utility.h b/modules/kernel/include/utility.h index b949ddec1d..fcab1201d9 100644 --- a/modules/kernel/include/utility.h +++ b/modules/kernel/include/utility.h @@ -2,7 +2,7 @@ * \file IMP/utility.h * \brief For backwards compatibility. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/utility_macros.h b/modules/kernel/include/utility_macros.h index 10b3c7c9a5..008f68edbe 100644 --- a/modules/kernel/include/utility_macros.h +++ b/modules/kernel/include/utility_macros.h @@ -2,7 +2,7 @@ * \file IMP/utility_macros.h * \brief Various general useful macros for IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/value_macros.h b/modules/kernel/include/value_macros.h index 4278e1d34a..7e6508ec09 100644 --- a/modules/kernel/include/value_macros.h +++ b/modules/kernel/include/value_macros.h @@ -2,7 +2,7 @@ * \file IMP/value_macros.h * \brief Macros to help in implementing Value objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/include/vector_property_map.h b/modules/kernel/include/vector_property_map.h index e390d8c563..fdd04fdad7 100644 --- a/modules/kernel/include/vector_property_map.h +++ b/modules/kernel/include/vector_property_map.h @@ -6,7 +6,7 @@ * in the boost versions supported by \imp. This header makes sure the correct * file is included. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_VECTOR_PROPERTY_MAP_H diff --git a/modules/kernel/include/warning_macros.h b/modules/kernel/include/warning_macros.h index c3d490971b..e00fdd7979 100644 --- a/modules/kernel/include/warning_macros.h +++ b/modules/kernel/include/warning_macros.h @@ -2,7 +2,7 @@ * \file IMP/warning_macros.h * \brief Macros to control compiler warnings. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/pyext/IMP_kernel.dispatcher.i b/modules/kernel/pyext/IMP_kernel.dispatcher.i index 97b1b179e3..4627ce2668 100644 --- a/modules/kernel/pyext/IMP_kernel.dispatcher.i +++ b/modules/kernel/pyext/IMP_kernel.dispatcher.i @@ -82,7 +82,7 @@ class CommandDispatcher(object): print(self.long_help + """ This program is part of IMP, the Integrative Modeling Platform, -which is Copyright 2007-2021 IMP Inventors. +which is Copyright 2007-2022 IMP Inventors. For additional information about IMP, see . Usage: %s [options] [args] diff --git a/modules/kernel/src/AttributeOptimizer.cpp b/modules/kernel/src/AttributeOptimizer.cpp index fff21ab83d..c21b1136e2 100644 --- a/modules/kernel/src/AttributeOptimizer.cpp +++ b/modules/kernel/src/AttributeOptimizer.cpp @@ -1,7 +1,7 @@ /** * \file Optimizer.cpp \brief Base class for all optimizers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Configuration.cpp b/modules/kernel/src/Configuration.cpp index e4484d30fa..77e967d416 100644 --- a/modules/kernel/src/Configuration.cpp +++ b/modules/kernel/src/Configuration.cpp @@ -3,7 +3,7 @@ * \brief Storage of a model, its restraints, * constraints and particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/ConfigurationSet.cpp b/modules/kernel/src/ConfigurationSet.cpp index 125813c638..147ca41a6c 100644 --- a/modules/kernel/src/ConfigurationSet.cpp +++ b/modules/kernel/src/ConfigurationSet.cpp @@ -3,7 +3,7 @@ * \brief Storage of a model, its restraints, * constraints and particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Constraint.cpp b/modules/kernel/src/Constraint.cpp index 9840727c9d..fb006566a4 100644 --- a/modules/kernel/src/Constraint.cpp +++ b/modules/kernel/src/Constraint.cpp @@ -1,7 +1,7 @@ /** * \file Constraint.cpp \brief Shared score state. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Container.cpp b/modules/kernel/src/Container.cpp index 304aec6d39..035972a36c 100644 --- a/modules/kernel/src/Container.cpp +++ b/modules/kernel/src/Container.cpp @@ -1,7 +1,7 @@ /** * \file Restraint.cpp \brief Abstract base class for all restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Decorator.cpp b/modules/kernel/src/Decorator.cpp index 49dfbce4f4..862126961d 100644 --- a/modules/kernel/src/Decorator.cpp +++ b/modules/kernel/src/Decorator.cpp @@ -1,7 +1,7 @@ /** * \file Restraint.cpp \brief Abstract base class for all restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Model.cpp b/modules/kernel/src/Model.cpp index 341aaa1857..d3c8198a83 100644 --- a/modules/kernel/src/Model.cpp +++ b/modules/kernel/src/Model.cpp @@ -2,7 +2,7 @@ * \file Model.cpp \brief Storage of a model, its restraints, * constraints and particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/ModelObject.cpp b/modules/kernel/src/ModelObject.cpp index 704f3925f2..d8d79eaa70 100644 --- a/modules/kernel/src/ModelObject.cpp +++ b/modules/kernel/src/ModelObject.cpp @@ -1,7 +1,7 @@ /** * \file ModelObject.cpp \brief Single variable function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kernel/src/Model_dependencies.cpp b/modules/kernel/src/Model_dependencies.cpp index f27eae9cab..084b61911c 100644 --- a/modules/kernel/src/Model_dependencies.cpp +++ b/modules/kernel/src/Model_dependencies.cpp @@ -2,7 +2,7 @@ * \file Model_dependencies.cpp * \brief Logic to track dependencies between ModelObjects * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Model_evaluate.cpp b/modules/kernel/src/Model_evaluate.cpp index 98cd03826d..9e9dea8bd8 100644 --- a/modules/kernel/src/Model_evaluate.cpp +++ b/modules/kernel/src/Model_evaluate.cpp @@ -2,7 +2,7 @@ * \file Model.cpp \brief Storage of a model, its restraints, * constraints and particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Object.cpp b/modules/kernel/src/Object.cpp index ea317b4bcf..3b0efc2354 100644 --- a/modules/kernel/src/Object.cpp +++ b/modules/kernel/src/Object.cpp @@ -2,7 +2,7 @@ * \file Object.cpp * \brief A shared base class to help in debugging and things. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Optimizer.cpp b/modules/kernel/src/Optimizer.cpp index ef046ef015..650027634f 100644 --- a/modules/kernel/src/Optimizer.cpp +++ b/modules/kernel/src/Optimizer.cpp @@ -1,7 +1,7 @@ /** * \file Optimizer.cpp \brief Base class for all optimizers. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/OptimizerState.cpp b/modules/kernel/src/OptimizerState.cpp index 74fc103762..28fade0b83 100644 --- a/modules/kernel/src/OptimizerState.cpp +++ b/modules/kernel/src/OptimizerState.cpp @@ -1,7 +1,7 @@ /** * \file OptimizerState.cpp \brief Shared optimizer state. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Particle.cpp b/modules/kernel/src/Particle.cpp index 6d8a5f959a..1923c333fd 100644 --- a/modules/kernel/src/Particle.cpp +++ b/modules/kernel/src/Particle.cpp @@ -1,7 +1,7 @@ /** * \file Particle.cpp \brief Classes to handle individual model particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Refiner.cpp b/modules/kernel/src/Refiner.cpp index 9d5ffa8a01..6e8ba92247 100644 --- a/modules/kernel/src/Refiner.cpp +++ b/modules/kernel/src/Refiner.cpp @@ -1,7 +1,7 @@ /** * \file Refiner.cpp \brief Refine a particle into a list of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Restraint.cpp b/modules/kernel/src/Restraint.cpp index 7b33bb5bf8..d4d3ed03e9 100644 --- a/modules/kernel/src/Restraint.cpp +++ b/modules/kernel/src/Restraint.cpp @@ -1,7 +1,7 @@ /** * \file Restraint.cpp \brief Abstract base class for all restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/RestraintInfo.cpp b/modules/kernel/src/RestraintInfo.cpp index 54760816c6..c0e757b6e7 100644 --- a/modules/kernel/src/RestraintInfo.cpp +++ b/modules/kernel/src/RestraintInfo.cpp @@ -2,7 +2,7 @@ * \file RestraintInfo.cpp * \brief Report key:value information on restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/RestraintSet.cpp b/modules/kernel/src/RestraintSet.cpp index d708ac9886..26fe028b55 100644 --- a/modules/kernel/src/RestraintSet.cpp +++ b/modules/kernel/src/RestraintSet.cpp @@ -1,7 +1,7 @@ /** * \file RestraintSet.cpp \brief Used to hold a set of related restraints. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Sampler.cpp b/modules/kernel/src/Sampler.cpp index 2459b05d18..b38d422209 100644 --- a/modules/kernel/src/Sampler.cpp +++ b/modules/kernel/src/Sampler.cpp @@ -3,7 +3,7 @@ * \brief Storage of a model, its restraints, * constraints and particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/ScoreAccumulator.cpp b/modules/kernel/src/ScoreAccumulator.cpp index 35c8ca96b4..ace196c4dc 100644 --- a/modules/kernel/src/ScoreAccumulator.cpp +++ b/modules/kernel/src/ScoreAccumulator.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/ScoreState.cpp b/modules/kernel/src/ScoreState.cpp index 3cf96ebb0a..f413bb4ad1 100644 --- a/modules/kernel/src/ScoreState.cpp +++ b/modules/kernel/src/ScoreState.cpp @@ -1,7 +1,7 @@ /** * \file ScoreState.cpp \brief Shared score state. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/ScoringFunction.cpp b/modules/kernel/src/ScoringFunction.cpp index e1272192ad..23c5ae365d 100644 --- a/modules/kernel/src/ScoringFunction.cpp +++ b/modules/kernel/src/ScoringFunction.cpp @@ -2,7 +2,7 @@ * \file Model.cpp \brief Storage of a model, its restraints, * constraints and particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/SetCheckState.cpp b/modules/kernel/src/SetCheckState.cpp index b3a61ac269..9444f1ee97 100644 --- a/modules/kernel/src/SetCheckState.cpp +++ b/modules/kernel/src/SetCheckState.cpp @@ -1,7 +1,7 @@ /** * \file Check.cpp \brief Checking and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/SetLogState.cpp b/modules/kernel/src/SetLogState.cpp index d66c230f30..ab777bfe22 100644 --- a/modules/kernel/src/SetLogState.cpp +++ b/modules/kernel/src/SetLogState.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/Showable.cpp b/modules/kernel/src/Showable.cpp index 36e47a15e0..cfcf102918 100644 --- a/modules/kernel/src/Showable.cpp +++ b/modules/kernel/src/Showable.cpp @@ -2,7 +2,7 @@ * \file file.cpp * \brief Get directories used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/UnaryFunction.cpp b/modules/kernel/src/UnaryFunction.cpp index bb1f727972..2117715b08 100644 --- a/modules/kernel/src/UnaryFunction.cpp +++ b/modules/kernel/src/UnaryFunction.cpp @@ -1,7 +1,7 @@ /** * \file UnaryFunction.cpp \brief Single variable function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kernel/src/VersionInfo.cpp b/modules/kernel/src/VersionInfo.cpp index 6a8bee7cb3..27f1f7d4da 100644 --- a/modules/kernel/src/VersionInfo.cpp +++ b/modules/kernel/src/VersionInfo.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/WarningContext.cpp b/modules/kernel/src/WarningContext.cpp index 76a841f1c8..6b160f04ba 100644 --- a/modules/kernel/src/WarningContext.cpp +++ b/modules/kernel/src/WarningContext.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/base_types.cpp b/modules/kernel/src/base_types.cpp index 3e6674cfd0..9fe14b209a 100644 --- a/modules/kernel/src/base_types.cpp +++ b/modules/kernel/src/base_types.cpp @@ -1,7 +1,7 @@ /** * \file base_types.cpp \brief Base types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/base_utility.cpp b/modules/kernel/src/base_utility.cpp index db3bd67473..a245051a76 100644 --- a/modules/kernel/src/base_utility.cpp +++ b/modules/kernel/src/base_utility.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/dependency_graph.cpp b/modules/kernel/src/dependency_graph.cpp index a1436e43d3..6751731d8b 100644 --- a/modules/kernel/src/dependency_graph.cpp +++ b/modules/kernel/src/dependency_graph.cpp @@ -2,7 +2,7 @@ * \file Model.cpp \brief Storage of a model, its restraints, * constraints and particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/deprecation.cpp b/modules/kernel/src/deprecation.cpp index 04e4a5c9cb..951a0d7f47 100644 --- a/modules/kernel/src/deprecation.cpp +++ b/modules/kernel/src/deprecation.cpp @@ -1,7 +1,7 @@ /** * \file exception.cpp \brief Check handling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/enums.cpp b/modules/kernel/src/enums.cpp index 10416ff8b4..ae46f683e9 100644 --- a/modules/kernel/src/enums.cpp +++ b/modules/kernel/src/enums.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/exception.cpp b/modules/kernel/src/exception.cpp index 51e29cddbf..cce0b2d4bc 100644 --- a/modules/kernel/src/exception.cpp +++ b/modules/kernel/src/exception.cpp @@ -1,7 +1,7 @@ /** * \file exception.cpp \brief Check handling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/file.cpp b/modules/kernel/src/file.cpp index db6f104d5c..4e1466c061 100644 --- a/modules/kernel/src/file.cpp +++ b/modules/kernel/src/file.cpp @@ -2,7 +2,7 @@ * \file file.cpp * \brief Get directories used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/flags.cpp b/modules/kernel/src/flags.cpp index a145d2194a..4b50fa7f7b 100644 --- a/modules/kernel/src/flags.cpp +++ b/modules/kernel/src/flags.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ @@ -152,7 +152,7 @@ void write_help(std::ostream &out) { } out << "This program is part of IMP, the Integrative Modeling Platform," << std::endl; - out << "which is Copyright 2007-2021 IMP Inventors." << std::endl; + out << "which is Copyright 2007-2022 IMP Inventors." << std::endl; out << "For additional information about IMP, " << "see ." << std::endl; } diff --git a/modules/kernel/src/internal/PrefixStream.cpp b/modules/kernel/src/internal/PrefixStream.cpp index 7eeac589f3..5220cf4fe3 100644 --- a/modules/kernel/src/internal/PrefixStream.cpp +++ b/modules/kernel/src/internal/PrefixStream.cpp @@ -1,7 +1,7 @@ /** * \file PrefixStreak.cpp \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/base_static.cpp b/modules/kernel/src/internal/base_static.cpp index e0a356cf04..8403ab6e93 100644 --- a/modules/kernel/src/internal/base_static.cpp +++ b/modules/kernel/src/internal/base_static.cpp @@ -1,7 +1,7 @@ /** * \file static.cpp \brief all static data for module. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/base_static.h b/modules/kernel/src/internal/base_static.h index 5e79c6646c..5bc6cad776 100644 --- a/modules/kernel/src/internal/base_static.h +++ b/modules/kernel/src/internal/base_static.h @@ -2,7 +2,7 @@ * \file internal/static.h * \brief Various useful utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_BASE_STATIC_H diff --git a/modules/kernel/src/internal/constants.cpp b/modules/kernel/src/internal/constants.cpp index be421bb69b..a57dc36bad 100644 --- a/modules/kernel/src/internal/constants.cpp +++ b/modules/kernel/src/internal/constants.cpp @@ -1,7 +1,7 @@ /** * \file constants.cpp \brief Various useful constants. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/directories.cpp b/modules/kernel/src/internal/directories.cpp index c2d2099bd7..e181a91113 100644 --- a/modules/kernel/src/internal/directories.cpp +++ b/modules/kernel/src/internal/directories.cpp @@ -3,7 +3,7 @@ * \brief Get directories used by IMP. * \note @AUTOGEN@ * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/graph_utility.cpp b/modules/kernel/src/internal/graph_utility.cpp index b6fcd996a8..c1a2fee45d 100644 --- a/modules/kernel/src/internal/graph_utility.cpp +++ b/modules/kernel/src/internal/graph_utility.cpp @@ -1,7 +1,7 @@ /** * \file constants.cpp \brief Various useful constants. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/input_output_exception.cpp b/modules/kernel/src/internal/input_output_exception.cpp index 48b4061dd0..3ae6299d8e 100644 --- a/modules/kernel/src/internal/input_output_exception.cpp +++ b/modules/kernel/src/internal/input_output_exception.cpp @@ -1,7 +1,7 @@ /** * \file exception.cpp \brief Check handling. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/key_helpers.cpp b/modules/kernel/src/internal/key_helpers.cpp index 65907685e2..24d9097bcf 100644 --- a/modules/kernel/src/internal/key_helpers.cpp +++ b/modules/kernel/src/internal/key_helpers.cpp @@ -1,7 +1,7 @@ /** * \file key_helpers.cpp \brief Internal workings of keys. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/log_stream.cpp b/modules/kernel/src/internal/log_stream.cpp index c9ed8e098b..76dac5ad4c 100644 --- a/modules/kernel/src/internal/log_stream.cpp +++ b/modules/kernel/src/internal/log_stream.cpp @@ -1,7 +1,7 @@ /** * \file static.cpp \brief all static data for module. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/moved_particles_cache.cpp b/modules/kernel/src/internal/moved_particles_cache.cpp index 9175ddd7ea..c928c7445b 100644 --- a/modules/kernel/src/internal/moved_particles_cache.cpp +++ b/modules/kernel/src/internal/moved_particles_cache.cpp @@ -3,7 +3,7 @@ * \brief Cache ModelObjects that change when a Particle moves * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kernel/src/internal/pdb.cpp b/modules/kernel/src/internal/pdb.cpp index cba5c67cd1..01b3f14a80 100644 --- a/modules/kernel/src/internal/pdb.cpp +++ b/modules/kernel/src/internal/pdb.cpp @@ -1,7 +1,7 @@ /** * \file deprecation.cpp \brief classes for deprecation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/random_number_generation_cuda.cu b/modules/kernel/src/internal/random_number_generation_cuda.cu index 2ad9264380..7afbae44c8 100644 --- a/modules/kernel/src/internal/random_number_generation_cuda.cu +++ b/modules/kernel/src/internal/random_number_generation_cuda.cu @@ -2,7 +2,7 @@ * \file IMP/kernel/src/internal/random_number_generation_cuda.cu * \brief GPU or CPU pooled random number generation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/restraint_evaluation.cpp b/modules/kernel/src/internal/restraint_evaluation.cpp index b67d1f6930..948af1c0d0 100644 --- a/modules/kernel/src/internal/restraint_evaluation.cpp +++ b/modules/kernel/src/internal/restraint_evaluation.cpp @@ -2,7 +2,7 @@ * \file internal/restraint_evaluation.cpp * \brief Utility functions to get restraint scores * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/static.cpp b/modules/kernel/src/internal/static.cpp index 1803633371..8052da3e6d 100644 --- a/modules/kernel/src/internal/static.cpp +++ b/modules/kernel/src/internal/static.cpp @@ -1,7 +1,7 @@ /** * \file static.cpp \brief all static data for module. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/swig.cpp b/modules/kernel/src/internal/swig.cpp index f9a2a43e16..df5319174a 100644 --- a/modules/kernel/src/internal/swig.cpp +++ b/modules/kernel/src/internal/swig.cpp @@ -2,7 +2,7 @@ * \file internal/swig.cpp * \brief Functions for use in swig wrappers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/kernel/src/internal/swig_base.cpp b/modules/kernel/src/internal/swig_base.cpp index f402871e25..163755a336 100644 --- a/modules/kernel/src/internal/swig_base.cpp +++ b/modules/kernel/src/internal/swig_base.cpp @@ -1,7 +1,7 @@ /** * \file static.cpp \brief all static data for module. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/internal/utility.cpp b/modules/kernel/src/internal/utility.cpp index c4d492b295..510e827d7a 100644 --- a/modules/kernel/src/internal/utility.cpp +++ b/modules/kernel/src/internal/utility.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/io.cpp b/modules/kernel/src/io.cpp index 2957fed8b4..f88f5a363c 100644 --- a/modules/kernel/src/io.cpp +++ b/modules/kernel/src/io.cpp @@ -2,7 +2,7 @@ * \file file.cpp * \brief Get directories used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/log.cpp b/modules/kernel/src/log.cpp index d1a2c20052..fd5dcf6e45 100644 --- a/modules/kernel/src/log.cpp +++ b/modules/kernel/src/log.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/model_object_helpers.cpp b/modules/kernel/src/model_object_helpers.cpp index e2fba5d687..e226525161 100644 --- a/modules/kernel/src/model_object_helpers.cpp +++ b/modules/kernel/src/model_object_helpers.cpp @@ -1,7 +1,7 @@ /** * \file ModelObject.cpp \brief Single variable function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kernel/src/nullptr.cpp b/modules/kernel/src/nullptr.cpp index f64d192741..75022aa179 100644 --- a/modules/kernel/src/nullptr.cpp +++ b/modules/kernel/src/nullptr.cpp @@ -1,7 +1,7 @@ /** * \file base_types.cpp \brief Base types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/particle_index.cpp b/modules/kernel/src/particle_index.cpp index 99b0199c26..8df16ca4e6 100644 --- a/modules/kernel/src/particle_index.cpp +++ b/modules/kernel/src/particle_index.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/random.cpp b/modules/kernel/src/random.cpp index 5810321437..6018cc219a 100644 --- a/modules/kernel/src/random.cpp +++ b/modules/kernel/src/random.cpp @@ -1,7 +1,7 @@ /** * \file random.cpp \brief Random number generators used by IMP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/threads.cpp b/modules/kernel/src/threads.cpp index 4b9c09aec1..5c5069acf0 100644 --- a/modules/kernel/src/threads.cpp +++ b/modules/kernel/src/threads.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/src/utility.cpp b/modules/kernel/src/utility.cpp index cec6902427..5ddfe38eda 100644 --- a/modules/kernel/src/utility.cpp +++ b/modules/kernel/src/utility.cpp @@ -1,7 +1,7 @@ /** * \file Log.cpp \brief Logging and error reporting support. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kernel/test/test_cache.cpp b/modules/kernel/test/test_cache.cpp index 4a52c23276..e9b8485adc 100644 --- a/modules/kernel/test/test_cache.cpp +++ b/modules/kernel/test/test_cache.cpp @@ -2,7 +2,7 @@ * \file test_cache.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/kernel/test/test_get_has_attribute.cpp b/modules/kernel/test/test_get_has_attribute.cpp index 9b8926edf4..03a9b58c30 100644 --- a/modules/kernel/test/test_get_has_attribute.cpp +++ b/modules/kernel/test/test_get_has_attribute.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved + * Copyright 2007-2022 IMP Inventors. All rights reserved */ #include #include diff --git a/modules/kernel/test/test_memory.cpp b/modules/kernel/test/test_memory.cpp index 9a661a511c..62b6070dce 100644 --- a/modules/kernel/test/test_memory.cpp +++ b/modules/kernel/test/test_memory.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved + * Copyright 2007-2022 IMP Inventors. All rights reserved */ #include #include diff --git a/modules/kernel/test/test_pair_memoizer.cpp b/modules/kernel/test/test_pair_memoizer.cpp index 39d7b6ef82..333480e9c6 100644 --- a/modules/kernel/test/test_pair_memoizer.cpp +++ b/modules/kernel/test/test_pair_memoizer.cpp @@ -2,7 +2,7 @@ * \file test_cache.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/kernel/test/test_pdb.cpp b/modules/kernel/test/test_pdb.cpp index 2680479574..31278feb72 100644 --- a/modules/kernel/test/test_pdb.cpp +++ b/modules/kernel/test/test_pdb.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved + * Copyright 2007-2022 IMP Inventors. All rights reserved */ #include #include diff --git a/modules/kernel/test/test_protection.cpp b/modules/kernel/test/test_protection.cpp index bba6725c03..e9aaad9ef0 100644 --- a/modules/kernel/test/test_protection.cpp +++ b/modules/kernel/test/test_protection.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved + * Copyright 2007-2022 IMP Inventors. All rights reserved */ #include #include diff --git a/modules/kernel/test/test_set_internal_coordinates.cpp b/modules/kernel/test/test_set_internal_coordinates.cpp index 745371880e..a6b3305ae0 100644 --- a/modules/kernel/test/test_set_internal_coordinates.cpp +++ b/modules/kernel/test/test_set_internal_coordinates.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved + * Copyright 2007-2022 IMP Inventors. All rights reserved */ #include #include diff --git a/modules/kernel/test/test_show.cpp b/modules/kernel/test/test_show.cpp index 1588a90993..3d7b63201a 100644 --- a/modules/kernel/test/test_show.cpp +++ b/modules/kernel/test/test_show.cpp @@ -2,7 +2,7 @@ * \file test_cache.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/kernel/test/test_stream_io.cpp b/modules/kernel/test/test_stream_io.cpp index 1ad5d12d29..69bba98216 100644 --- a/modules/kernel/test/test_stream_io.cpp +++ b/modules/kernel/test/test_stream_io.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved + * Copyright 2007-2022 IMP Inventors. All rights reserved */ #include #include diff --git a/modules/kinematics/bin/rrt_ccd.cpp b/modules/kinematics/bin/rrt_ccd.cpp index 9164ab39f8..d4bcaf4e27 100644 --- a/modules/kinematics/bin/rrt_ccd.cpp +++ b/modules/kinematics/bin/rrt_ccd.cpp @@ -54,7 +54,7 @@ int main(int argc, char **argv) po::options_description desc( "Usage: \n\n" "This program is part of IMP, the Integrative Modeling Platform,\n" - "which is Copyright 2007-2021 IMP Inventors.\n\n" + "which is Copyright 2007-2022 IMP Inventors.\n\n" "Options"); desc.add_options() ("help", "Show command line arguments and exit.") diff --git a/modules/kinematics/bin/rrt_sample.cpp b/modules/kinematics/bin/rrt_sample.cpp index 1dc7b4fe9b..3efc83ee29 100644 --- a/modules/kinematics/bin/rrt_sample.cpp +++ b/modules/kinematics/bin/rrt_sample.cpp @@ -53,7 +53,7 @@ int rrt_sample(int argc, char **argv) po::options_description desc( "Usage: \n\n" "This program is part of IMP, the Integrative Modeling Platform,\n" - "which is Copyright 2007-2021 IMP Inventors.\n\n" + "which is Copyright 2007-2022 IMP Inventors.\n\n" "Options"); desc.add_options() ("help", "Show command line arguments and exit.") diff --git a/modules/kinematics/include/CCDLoopClosure.h b/modules/kinematics/include/CCDLoopClosure.h index 1d9586cb78..92117465ab 100644 --- a/modules/kinematics/include/CCDLoopClosure.h +++ b/modules/kinematics/include/CCDLoopClosure.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman, Yannick Spill - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/CompositeJoint.h b/modules/kinematics/include/CompositeJoint.h index 9e9fcc9468..0bc7288bfb 100644 --- a/modules/kinematics/include/CompositeJoint.h +++ b/modules/kinematics/include/CompositeJoint.h @@ -5,7 +5,7 @@ * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_COMPOSITE_JOINT_H diff --git a/modules/kinematics/include/DOF.h b/modules/kinematics/include/DOF.h index 57f9a94b56..c331ed4f5c 100644 --- a/modules/kinematics/include/DOF.h +++ b/modules/kinematics/include/DOF.h @@ -3,7 +3,7 @@ * \brief single degree of freedom * * \authors Dina Schneidman, Barak Raveh - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/DOFValues.h b/modules/kinematics/include/DOFValues.h index 8fea83be23..85bd307ab0 100644 --- a/modules/kinematics/include/DOFValues.h +++ b/modules/kinematics/include/DOFValues.h @@ -4,7 +4,7 @@ * * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/DOFsSampler.h b/modules/kinematics/include/DOFsSampler.h index 49bc428f77..88a2bc4fca 100644 --- a/modules/kinematics/include/DOFsSampler.h +++ b/modules/kinematics/include/DOFsSampler.h @@ -1,7 +1,7 @@ /** * \file IMP/kinematics/DOFsSampler.h \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/Joint.h b/modules/kinematics/include/Joint.h index 459de878fd..1e31c06b9a 100644 --- a/modules/kinematics/include/Joint.h +++ b/modules/kinematics/include/Joint.h @@ -5,7 +5,7 @@ \authors Dina Schneidman, Barak Raveh - Copyright 2007-2021 IMP Inventors. All rights reserved. + Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_JOINT_H diff --git a/modules/kinematics/include/KinematicForest.h b/modules/kinematics/include/KinematicForest.h index 50f1c26e3b..83a7ba666e 100644 --- a/modules/kinematics/include/KinematicForest.h +++ b/modules/kinematics/include/KinematicForest.h @@ -3,7 +3,7 @@ * \brief Define and manipulate a kinematic structure over a model. * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_KINEMATIC_FOREST_H diff --git a/modules/kinematics/include/KinematicForestScoreState.h b/modules/kinematics/include/KinematicForestScoreState.h index 36e9aea8dd..2fef8ea99d 100644 --- a/modules/kinematics/include/KinematicForestScoreState.h +++ b/modules/kinematics/include/KinematicForestScoreState.h @@ -3,7 +3,7 @@ \brief \authors Dina Schneidman, Barak Raveh - Copyright 2007-2021 IMP Inventors. All rights reserved. + Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_KINEMATIC_FOREST_SCORE_STATE_H diff --git a/modules/kinematics/include/KinematicNode.h b/modules/kinematics/include/KinematicNode.h index 24ea1fa2d3..2615b810b0 100644 --- a/modules/kinematics/include/KinematicNode.h +++ b/modules/kinematics/include/KinematicNode.h @@ -3,7 +3,7 @@ * \brief functionality for defining nodes on a kinematic chain * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_KINEMATIC_NODE_H diff --git a/modules/kinematics/include/PrismaticJoint.h b/modules/kinematics/include/PrismaticJoint.h index c03a0b8770..926d757f0f 100644 --- a/modules/kinematics/include/PrismaticJoint.h +++ b/modules/kinematics/include/PrismaticJoint.h @@ -3,7 +3,7 @@ * \brief a prismatic joint between rigid bodies as part of a kinematic tree * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_PRISMATIC_JOINT_H diff --git a/modules/kinematics/include/ProteinKinematics.h b/modules/kinematics/include/ProteinKinematics.h index 29895bd7e1..5e01001c32 100644 --- a/modules/kinematics/include/ProteinKinematics.h +++ b/modules/kinematics/include/ProteinKinematics.h @@ -2,7 +2,7 @@ * \file IMP/kinematics/ProteinKinematics.h * \brief functionality for defining a kinematic forest for proteins * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * \authors Dina Schneidman, Barak Raveh * */ diff --git a/modules/kinematics/include/RMSDClustering.h b/modules/kinematics/include/RMSDClustering.h index 5afe97170d..e5908d6c37 100644 --- a/modules/kinematics/include/RMSDClustering.h +++ b/modules/kinematics/include/RMSDClustering.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/RRT.h b/modules/kinematics/include/RRT.h index 605971445c..149b1df38c 100644 --- a/modules/kinematics/include/RRT.h +++ b/modules/kinematics/include/RRT.h @@ -4,7 +4,7 @@ * * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/RevoluteJointMover.h b/modules/kinematics/include/RevoluteJointMover.h index 5e018418b6..f2bd3c6b0c 100644 --- a/modules/kinematics/include/RevoluteJointMover.h +++ b/modules/kinematics/include/RevoluteJointMover.h @@ -2,7 +2,7 @@ * \file IMP/kinematics/RevoluteJointMover.h * \brief A modifier which perturbs a point with a normal distribution. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/TransformationJoint.h b/modules/kinematics/include/TransformationJoint.h index 826e7c479b..f016fb5278 100644 --- a/modules/kinematics/include/TransformationJoint.h +++ b/modules/kinematics/include/TransformationJoint.h @@ -5,7 +5,7 @@ * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_TRANSFORMATION_JOINT_H diff --git a/modules/kinematics/include/UniformBackboneSampler.h b/modules/kinematics/include/UniformBackboneSampler.h index 7ceb04cda8..d04d5ef1c7 100644 --- a/modules/kinematics/include/UniformBackboneSampler.h +++ b/modules/kinematics/include/UniformBackboneSampler.h @@ -3,7 +3,7 @@ \brief A class for uniform sampling of backbone angles \authors Dina Schneidman, Barak Raveh - Copyright 2007-2021 IMP Inventors. All rights reserved. + Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_UNIFORM_BACKBONE_SAMPLER_H diff --git a/modules/kinematics/include/directional_DOFs.h b/modules/kinematics/include/directional_DOFs.h index ef2baa685d..9691373697 100644 --- a/modules/kinematics/include/directional_DOFs.h +++ b/modules/kinematics/include/directional_DOFs.h @@ -3,7 +3,7 @@ * \brief * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/helpers.h b/modules/kinematics/include/helpers.h index 14298ad70c..074d55a9ad 100644 --- a/modules/kinematics/include/helpers.h +++ b/modules/kinematics/include/helpers.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/internal/graph_helpers.h b/modules/kinematics/include/internal/graph_helpers.h index c516413855..2be16d1640 100644 --- a/modules/kinematics/include/internal/graph_helpers.h +++ b/modules/kinematics/include/internal/graph_helpers.h @@ -2,7 +2,7 @@ * \file IMP/kinematics/internal/graph_helpers.h * \brief Helper functions to deal with graphs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/local_planners.h b/modules/kinematics/include/local_planners.h index fd23bf590b..9b522c135d 100644 --- a/modules/kinematics/include/local_planners.h +++ b/modules/kinematics/include/local_planners.h @@ -2,7 +2,7 @@ * \file IMP/kinematics/local_planners.h * \brief Planners * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/include/revolute_joints.h b/modules/kinematics/include/revolute_joints.h index 8b7ee36aed..f229b6106e 100644 --- a/modules/kinematics/include/revolute_joints.h +++ b/modules/kinematics/include/revolute_joints.h @@ -7,7 +7,7 @@ * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKINEMATICS_REVOLUTE_JOINTS_H diff --git a/modules/kinematics/src/CCDLoopClosure.cpp b/modules/kinematics/src/CCDLoopClosure.cpp index 19edeb45b4..5cfdd411a2 100644 --- a/modules/kinematics/src/CCDLoopClosure.cpp +++ b/modules/kinematics/src/CCDLoopClosure.cpp @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman, Yannick Spill - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/src/CompositeJoint.cpp b/modules/kinematics/src/CompositeJoint.cpp index 706d984520..5a837aef51 100644 --- a/modules/kinematics/src/CompositeJoint.cpp +++ b/modules/kinematics/src/CompositeJoint.cpp @@ -4,7 +4,7 @@ * pair of rigid bodies * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kinematics/src/DOF.cpp b/modules/kinematics/src/DOF.cpp index 933135cc7e..a9503c072f 100644 --- a/modules/kinematics/src/DOF.cpp +++ b/modules/kinematics/src/DOF.cpp @@ -3,7 +3,7 @@ * \brief single degree of freedom * * \authors Dina Schneidman, Barak Raveh - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/src/Joint.cpp b/modules/kinematics/src/Joint.cpp index 9a8d316dc6..8925d20267 100644 --- a/modules/kinematics/src/Joint.cpp +++ b/modules/kinematics/src/Joint.cpp @@ -4,7 +4,7 @@ * as part of a kinematic tree * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kinematics/src/KinematicForest.cpp b/modules/kinematics/src/KinematicForest.cpp index 2da403bf7b..977cc33b2b 100644 --- a/modules/kinematics/src/KinematicForest.cpp +++ b/modules/kinematics/src/KinematicForest.cpp @@ -6,7 +6,7 @@ interconversion between internal and external coordinates. * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kinematics/src/KinematicForestScoreState.cpp b/modules/kinematics/src/KinematicForestScoreState.cpp index 143d15a2fb..3dc3b72433 100644 --- a/modules/kinematics/src/KinematicForestScoreState.cpp +++ b/modules/kinematics/src/KinematicForestScoreState.cpp @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman, Barak Raveh - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/src/KinematicNode.cpp b/modules/kinematics/src/KinematicNode.cpp index 007cea966a..304db4c623 100644 --- a/modules/kinematics/src/KinematicNode.cpp +++ b/modules/kinematics/src/KinematicNode.cpp @@ -3,7 +3,7 @@ * \brief functionality for defining nodes on a kinematic chain * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kinematics/src/PrismaticJoint.cpp b/modules/kinematics/src/PrismaticJoint.cpp index 0736ae5314..90afd1294a 100644 --- a/modules/kinematics/src/PrismaticJoint.cpp +++ b/modules/kinematics/src/PrismaticJoint.cpp @@ -3,7 +3,7 @@ * \brief a prismatic joint between rigid bodies * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kinematics/src/ProteinKinematics.cpp b/modules/kinematics/src/ProteinKinematics.cpp index 1d47d3f699..bfa5907261 100644 --- a/modules/kinematics/src/ProteinKinematics.cpp +++ b/modules/kinematics/src/ProteinKinematics.cpp @@ -2,7 +2,7 @@ * \file ProteinKinematics * \brief functionality for defining a kinematic forest for proteins * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * \authors Dina Schneidman, Barak Raveh * */ diff --git a/modules/kinematics/src/RMSDClustering.cpp b/modules/kinematics/src/RMSDClustering.cpp index 25760e5438..ed23abd59b 100644 --- a/modules/kinematics/src/RMSDClustering.cpp +++ b/modules/kinematics/src/RMSDClustering.cpp @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/src/RRT.cpp b/modules/kinematics/src/RRT.cpp index 7710a616bf..f45b86b39f 100644 --- a/modules/kinematics/src/RRT.cpp +++ b/modules/kinematics/src/RRT.cpp @@ -2,7 +2,7 @@ * \file RRT * \brief implementation of Randomly-Exploring Random Trees * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/kinematics/src/RevoluteJointMover.cpp b/modules/kinematics/src/RevoluteJointMover.cpp index c9925ab124..5fd4a287ac 100644 --- a/modules/kinematics/src/RevoluteJointMover.cpp +++ b/modules/kinematics/src/RevoluteJointMover.cpp @@ -2,7 +2,7 @@ * \file RevoluteJointMover.cpp * \brief A mover which perturbs a joint with a gaussian. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/src/TransformationJoint.cpp b/modules/kinematics/src/TransformationJoint.cpp index c91cb64916..e697ce55af 100644 --- a/modules/kinematics/src/TransformationJoint.cpp +++ b/modules/kinematics/src/TransformationJoint.cpp @@ -4,7 +4,7 @@ * transformation * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kinematics/src/UniformBackboneSampler.cpp b/modules/kinematics/src/UniformBackboneSampler.cpp index 195246ff2c..2b85058c63 100644 --- a/modules/kinematics/src/UniformBackboneSampler.cpp +++ b/modules/kinematics/src/UniformBackboneSampler.cpp @@ -3,7 +3,7 @@ * \brief A class for uniform sampling of backbone angles * * \authors Dina Schneidman, Barak Raveh - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/src/helpers.cpp b/modules/kinematics/src/helpers.cpp index 3be91c0fec..64bce83ff5 100644 --- a/modules/kinematics/src/helpers.cpp +++ b/modules/kinematics/src/helpers.cpp @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/src/local_planners.cpp b/modules/kinematics/src/local_planners.cpp index 4614315848..9a87c8194a 100644 --- a/modules/kinematics/src/local_planners.cpp +++ b/modules/kinematics/src/local_planners.cpp @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman, Barak Raveh - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/kinematics/src/revolute_joints.cpp b/modules/kinematics/src/revolute_joints.cpp index be748716fb..7fcabc0502 100644 --- a/modules/kinematics/src/revolute_joints.cpp +++ b/modules/kinematics/src/revolute_joints.cpp @@ -6,7 +6,7 @@ * BondAngleRevoluteJoint * \authors Dina Schneidman, Barak Raveh * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/kmeans/include/KMeans.h b/modules/kmeans/include/KMeans.h index 9ad506ae4c..d301fbc6a6 100644 --- a/modules/kmeans/include/KMeans.h +++ b/modules/kmeans/include/KMeans.h @@ -2,7 +2,7 @@ * \file IMP/kmeans/KMeans.h * \brief an interface to k-means open source library (stored internally) * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKMEANS_KMEANS_H diff --git a/modules/kmeans/src/KMeans.cpp b/modules/kmeans/src/KMeans.cpp index b561ae1861..a18462bbbf 100644 --- a/modules/kmeans/src/KMeans.cpp +++ b/modules/kmeans/src/KMeans.cpp @@ -2,7 +2,7 @@ * \file KMeans.cpp * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/kmeans/KMeans.h" diff --git a/modules/misc/include/CommonEndpointPairFilter.h b/modules/misc/include/CommonEndpointPairFilter.h index e4ff0eeb7e..98d7d00023 100644 --- a/modules/misc/include/CommonEndpointPairFilter.h +++ b/modules/misc/include/CommonEndpointPairFilter.h @@ -2,7 +2,7 @@ * \file IMP/misc/CommonEndpointPairFilter.h * \brief Return true for any pair of bonds sharing an endpoint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMISC_COMMON_ENDPOINT_PAIR_FILTER_H diff --git a/modules/misc/include/CustomXYZR.h b/modules/misc/include/CustomXYZR.h index f6bd883092..6162cfb470 100644 --- a/modules/misc/include/CustomXYZR.h +++ b/modules/misc/include/CustomXYZR.h @@ -2,7 +2,7 @@ * \file IMP/misc/CustomXYZR.h * \brief Decorator for a sphere-like particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/misc/include/DecayPairContainerOptimizerState.h b/modules/misc/include/DecayPairContainerOptimizerState.h index a60590a5d1..7af2109691 100644 --- a/modules/misc/include/DecayPairContainerOptimizerState.h +++ b/modules/misc/include/DecayPairContainerOptimizerState.h @@ -2,7 +2,7 @@ * \file IMP/misc/DecayPairContainerOptimizerState.h * \brief A pair container with a decaying list of pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMISC_DECAY_PAIR_CONTAINER_OPTIMIZER_STATE_H diff --git a/modules/misc/include/FreelyJointedChain.h b/modules/misc/include/FreelyJointedChain.h index 69bae8886a..411bf4eb53 100644 --- a/modules/misc/include/FreelyJointedChain.h +++ b/modules/misc/include/FreelyJointedChain.h @@ -2,7 +2,7 @@ * \file IMP/misc/FreelyJointedChain.h * \brief Score on end-to-end distance of freely jointed chain * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMISC_FREELY_JOINTED_CHAIN_H diff --git a/modules/misc/include/LogPairScore.h b/modules/misc/include/LogPairScore.h index ba3b9d4630..29a7d634e9 100644 --- a/modules/misc/include/LogPairScore.h +++ b/modules/misc/include/LogPairScore.h @@ -2,7 +2,7 @@ * \file IMP/misc/LogPairScore.h * \brief Track the particles pairs passed to the pair score. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMISC_LOG_PAIR_SCORE_H diff --git a/modules/misc/include/LowestRefinedPairScore.h b/modules/misc/include/LowestRefinedPairScore.h index 142ac60662..be548f4f24 100644 --- a/modules/misc/include/LowestRefinedPairScore.h +++ b/modules/misc/include/LowestRefinedPairScore.h @@ -2,7 +2,7 @@ * \file IMP/misc/LowestRefinedPairScore.h * \brief Score on the lowest scoring pair of the refined pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMISC_LOWEST_REFINED_PAIR_SCORE_H diff --git a/modules/misc/include/MetricClosePairsFinder.h b/modules/misc/include/MetricClosePairsFinder.h index 7bb49ee5c6..e42c2f6d1a 100644 --- a/modules/misc/include/MetricClosePairsFinder.h +++ b/modules/misc/include/MetricClosePairsFinder.h @@ -2,7 +2,7 @@ * \file IMP/misc/MetricClosePairsFinder.h * \brief Decorator for a sphere-like particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/misc/include/SoftCylinderPairScore.h b/modules/misc/include/SoftCylinderPairScore.h index 45b0ff6dde..e78234a2cd 100644 --- a/modules/misc/include/SoftCylinderPairScore.h +++ b/modules/misc/include/SoftCylinderPairScore.h @@ -2,7 +2,7 @@ * \file IMP/misc/SoftCylinderPairScore.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMISC_SOFT_CYLINDER_PAIR_SCORE_H diff --git a/modules/misc/include/StateAdaptor.h b/modules/misc/include/StateAdaptor.h index fa55c3563b..f5700bd6cd 100644 --- a/modules/misc/include/StateAdaptor.h +++ b/modules/misc/include/StateAdaptor.h @@ -2,7 +2,7 @@ * \file IMP/misc/StateAdaptor.h * \brief XXXXXXXXXXXXXX * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMISC_STATE_ADAPTOR_H diff --git a/modules/misc/include/WormLikeChain.h b/modules/misc/include/WormLikeChain.h index 0fdfa1ee93..71656a80a1 100644 --- a/modules/misc/include/WormLikeChain.h +++ b/modules/misc/include/WormLikeChain.h @@ -2,7 +2,7 @@ * \file IMP/misc/WormLikeChain.h * \brief Worm-like-chain score for polymer chains. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMISC_WORM_LIKE_CHAIN_H diff --git a/modules/misc/src/CommonEndpointPairFilter.cpp b/modules/misc/src/CommonEndpointPairFilter.cpp index 5c412f6950..f2f41497ff 100644 --- a/modules/misc/src/CommonEndpointPairFilter.cpp +++ b/modules/misc/src/CommonEndpointPairFilter.cpp @@ -2,7 +2,7 @@ * \file CommonEndpointPairFilter.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/misc/src/CustomXYZR.cpp b/modules/misc/src/CustomXYZR.cpp index 9f8c06a8c1..af8066a0c6 100644 --- a/modules/misc/src/CustomXYZR.cpp +++ b/modules/misc/src/CustomXYZR.cpp @@ -1,7 +1,7 @@ /** * \file XYZR.cpp \brief Simple xyzr decorator. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/misc/src/DecayPairContainerOptimizerState.cpp b/modules/misc/src/DecayPairContainerOptimizerState.cpp index bc0a59db4e..1293fc65db 100644 --- a/modules/misc/src/DecayPairContainerOptimizerState.cpp +++ b/modules/misc/src/DecayPairContainerOptimizerState.cpp @@ -2,7 +2,7 @@ * \file DecayPairContainerOptimizerState.cpp * \brief A pair container with a decaying list of pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/misc/src/LowestRefinedPairScore.cpp b/modules/misc/src/LowestRefinedPairScore.cpp index 47f6a432ee..40f7a2faf7 100644 --- a/modules/misc/src/LowestRefinedPairScore.cpp +++ b/modules/misc/src/LowestRefinedPairScore.cpp @@ -2,7 +2,7 @@ * \file LowestRefinedPairScore.cpp * \brief Score on the lowest scoring pair of the refined pairs. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/misc/src/SoftCylinderPairScore.cpp b/modules/misc/src/SoftCylinderPairScore.cpp index a015914720..5ba7128c13 100644 --- a/modules/misc/src/SoftCylinderPairScore.cpp +++ b/modules/misc/src/SoftCylinderPairScore.cpp @@ -2,7 +2,7 @@ * \file DistancePairScore.cpp * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/misc/src/StateAdaptor.cpp b/modules/misc/src/StateAdaptor.cpp index 135015e05a..803d04ee3a 100644 --- a/modules/misc/src/StateAdaptor.cpp +++ b/modules/misc/src/StateAdaptor.cpp @@ -2,7 +2,7 @@ * \file StateAdaptor.cpp * \brief XXXX. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/misc/test/test_metric_close_pairs.cpp b/modules/misc/test/test_metric_close_pairs.cpp index 6491d2260e..556cb75dd5 100644 --- a/modules/misc/test/test_metric_close_pairs.cpp +++ b/modules/misc/test/test_metric_close_pairs.cpp @@ -2,7 +2,7 @@ * \file test_cache.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/mpi/include/ReplicaExchange.h b/modules/mpi/include/ReplicaExchange.h index 9e8ba42347..1556a8adc7 100644 --- a/modules/mpi/include/ReplicaExchange.h +++ b/modules/mpi/include/ReplicaExchange.h @@ -2,7 +2,7 @@ * \file IMP/mpi/ReplicaExchange.h * \brief A class to do replica exchange in a generic Hamiltonian parameter * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMPI_REPLICA_EXCHANGE_H diff --git a/modules/mpi/include/internal/mpi_helpers.h b/modules/mpi/include/internal/mpi_helpers.h index 381e3b266d..23a7f62e9a 100644 --- a/modules/mpi/include/internal/mpi_helpers.h +++ b/modules/mpi/include/internal/mpi_helpers.h @@ -2,7 +2,7 @@ * \file mpi_helpers.h * \brief Helper functions to set up MPI. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMPI_MPI_HELPERS_H diff --git a/modules/mpi/src/ReplicaExchange.cpp b/modules/mpi/src/ReplicaExchange.cpp index 8a93864afe..583dcc095f 100644 --- a/modules/mpi/src/ReplicaExchange.cpp +++ b/modules/mpi/src/ReplicaExchange.cpp @@ -2,7 +2,7 @@ * \file ReplicaExchange.cpp * \brief Replica Exchange * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/mpi/src/internal/mpi_helpers.cpp b/modules/mpi/src/internal/mpi_helpers.cpp index f6c887c39e..bf3a54cd6d 100644 --- a/modules/mpi/src/internal/mpi_helpers.cpp +++ b/modules/mpi/src/internal/mpi_helpers.cpp @@ -2,7 +2,7 @@ * \file mpi_helpers.cpp * \brief Helper functions to set up MPI. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/mpi/utility/hello_world.cpp b/modules/mpi/utility/hello_world.cpp index 3204ef5c09..6692dac550 100644 --- a/modules/mpi/utility/hello_world.cpp +++ b/modules/mpi/utility/hello_world.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/multi_state/bin/multi_foxs.cpp b/modules/multi_state/bin/multi_foxs.cpp index c7263f9a93..999619d7d7 100644 --- a/modules/multi_state/bin/multi_foxs.cpp +++ b/modules/multi_state/bin/multi_foxs.cpp @@ -4,7 +4,7 @@ * \brief Multiple states generation for multiple SAXS profiles * * Author: Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include @@ -172,7 +172,7 @@ int main(int argc, char* argv[]) { "The weights are computed to minimize the chi between the first profile\n" "and a weighted average of the rest.\n\n" "This program is part of IMP, the Integrative Modeling Platform,\n" - "which is Copyright 2007-2021 IMP Inventors.\n\n" + "which is Copyright 2007-2022 IMP Inventors.\n\n" "Options"); desc.add_options() ("help", "Show command line arguments and exit.") diff --git a/modules/multi_state/include/EnsembleGenerator.h b/modules/multi_state/include/EnsembleGenerator.h index 1100cb0eaa..e6c6dfa954 100644 --- a/modules/multi_state/include/EnsembleGenerator.h +++ b/modules/multi_state/include/EnsembleGenerator.h @@ -3,7 +3,7 @@ * \brief Enumeration of an ensemble of good scoring MultiStateModels * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multi_state/include/MultiStateModel.h b/modules/multi_state/include/MultiStateModel.h index 42a6e2bacc..5b2e8d8074 100644 --- a/modules/multi_state/include/MultiStateModel.h +++ b/modules/multi_state/include/MultiStateModel.h @@ -3,7 +3,7 @@ * \brief Keep track of multiple states * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multi_state/include/MultiStateModelScore.h b/modules/multi_state/include/MultiStateModelScore.h index c9ccf1a25a..c579d92581 100644 --- a/modules/multi_state/include/MultiStateModelScore.h +++ b/modules/multi_state/include/MultiStateModelScore.h @@ -3,7 +3,7 @@ * \brief base class for MultiStateModel scoring classes * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multi_state/include/SAXSMultiStateModelScore.h b/modules/multi_state/include/SAXSMultiStateModelScore.h index cd502fb761..cc7a43fd76 100644 --- a/modules/multi_state/include/SAXSMultiStateModelScore.h +++ b/modules/multi_state/include/SAXSMultiStateModelScore.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multi_state/include/stat_helpers.h b/modules/multi_state/include/stat_helpers.h index ec56a46edd..874560c3a1 100644 --- a/modules/multi_state/include/stat_helpers.h +++ b/modules/multi_state/include/stat_helpers.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multi_state/src/EnsembleGenerator.cpp b/modules/multi_state/src/EnsembleGenerator.cpp index 2050944001..20222e2a1b 100644 --- a/modules/multi_state/src/EnsembleGenerator.cpp +++ b/modules/multi_state/src/EnsembleGenerator.cpp @@ -3,7 +3,7 @@ * * \brief A class for storing and generation of ensembles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multi_state/src/stat_helpers.cpp b/modules/multi_state/src/stat_helpers.cpp index 90859e9abd..840764b878 100644 --- a/modules/multi_state/src/stat_helpers.cpp +++ b/modules/multi_state/src/stat_helpers.cpp @@ -1,7 +1,7 @@ /** * \file IMP/multi_state/stat_helpers.cpp * \brief basic stat functions - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/multifit/benchmark/benchmark_excluded_volume.cpp b/modules/multifit/benchmark/benchmark_excluded_volume.cpp index 7da25fc486..b28155157c 100644 --- a/modules/multifit/benchmark/benchmark_excluded_volume.cpp +++ b/modules/multifit/benchmark/benchmark_excluded_volume.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "benchmark_excluded_volume.h" diff --git a/modules/multifit/benchmark/benchmark_excluded_volume.h b/modules/multifit/benchmark/benchmark_excluded_volume.h index 7c02e509b9..6934cf5383 100644 --- a/modules/multifit/benchmark/benchmark_excluded_volume.h +++ b/modules/multifit/benchmark/benchmark_excluded_volume.h @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMULTIFIT_BENCHMARK_EXCLUDED_VOLUME_H diff --git a/modules/multifit/benchmark/benchmark_excluded_volume_close_pair.cpp b/modules/multifit/benchmark/benchmark_excluded_volume_close_pair.cpp index 2f4fafb133..5c03a27b3b 100644 --- a/modules/multifit/benchmark/benchmark_excluded_volume_close_pair.cpp +++ b/modules/multifit/benchmark/benchmark_excluded_volume_close_pair.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "benchmark_excluded_volume.h" diff --git a/modules/multifit/benchmark/benchmark_excluded_volume_pairs.cpp b/modules/multifit/benchmark/benchmark_excluded_volume_pairs.cpp index 7529d383a0..5c59828890 100644 --- a/modules/multifit/benchmark/benchmark_excluded_volume_pairs.cpp +++ b/modules/multifit/benchmark/benchmark_excluded_volume_pairs.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "benchmark_excluded_volume.h" diff --git a/modules/multifit/benchmark/benchmark_excluded_volume_wev3.cpp b/modules/multifit/benchmark/benchmark_excluded_volume_wev3.cpp index f4c17b1b1c..82e8f94f1a 100644 --- a/modules/multifit/benchmark/benchmark_excluded_volume_wev3.cpp +++ b/modules/multifit/benchmark/benchmark_excluded_volume_wev3.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "benchmark_excluded_volume.h" diff --git a/modules/multifit/benchmark/benchmark_geometric_complementarity.py b/modules/multifit/benchmark/benchmark_geometric_complementarity.py index 46870efd45..9789cc3489 100755 --- a/modules/multifit/benchmark/benchmark_geometric_complementarity.py +++ b/modules/multifit/benchmark/benchmark_geometric_complementarity.py @@ -5,7 +5,7 @@ # Output: # ComplementarityRestraint, (time in sec/score computation), (percentage error) # -# Copyright 2007-2021 IMP Inventors. All rights reserved. +# Copyright 2007-2022 IMP Inventors. All rights reserved. # import sys diff --git a/modules/multifit/include/AlignmentParams.h b/modules/multifit/include/AlignmentParams.h index d93a20403a..dd2c4ddc2d 100644 --- a/modules/multifit/include/AlignmentParams.h +++ b/modules/multifit/include/AlignmentParams.h @@ -2,7 +2,7 @@ * \file IMP/multifit/AlignmentParams.h * \brief Parameters for alignments. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMULTIFIT_ALIGNMENT_PARAMS_H diff --git a/modules/multifit/include/ComplementarityRestraint.h b/modules/multifit/include/ComplementarityRestraint.h index a79fc6ea60..ec683cb5cf 100644 --- a/modules/multifit/include/ComplementarityRestraint.h +++ b/modules/multifit/include/ComplementarityRestraint.h @@ -2,7 +2,7 @@ * \file IMP/multifit/ComplementarityRestraint.h * \brief Calculate weighted excluded volume between rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/DataPointsAssignment.h b/modules/multifit/include/DataPointsAssignment.h index 174a85b050..f4b446eba5 100644 --- a/modules/multifit/include/DataPointsAssignment.h +++ b/modules/multifit/include/DataPointsAssignment.h @@ -2,7 +2,7 @@ * \file IMP/multifit/DataPointsAssignment.h * \brief Tools for data points assignment, after anchor point segmentation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/DensityDataPoints.h b/modules/multifit/include/DensityDataPoints.h index 16b233c9bd..8a1940ece2 100644 --- a/modules/multifit/include/DensityDataPoints.h +++ b/modules/multifit/include/DensityDataPoints.h @@ -2,7 +2,7 @@ * \file IMP/multifit/DensityDataPoints.h * \brief Handling of data for anchor points segmentation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/FittingSolutionRecord.h b/modules/multifit/include/FittingSolutionRecord.h index f6d6f37c8e..96f3cff408 100644 --- a/modules/multifit/include/FittingSolutionRecord.h +++ b/modules/multifit/include/FittingSolutionRecord.h @@ -2,7 +2,7 @@ * \file IMP/multifit/FittingSolutionRecord.h * \brief stored a multifit fitting solution * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/GeometricHash.h b/modules/multifit/include/GeometricHash.h index 9e658e4bca..5f28960cb7 100644 --- a/modules/multifit/include/GeometricHash.h +++ b/modules/multifit/include/GeometricHash.h @@ -1,7 +1,7 @@ /** * \file IMP/multifit/GeometricHash.h \brief Geometric Hashing class. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/RadiusOfGyrationRestraint.h b/modules/multifit/include/RadiusOfGyrationRestraint.h index 7be65ac0bf..fa88441949 100644 --- a/modules/multifit/include/RadiusOfGyrationRestraint.h +++ b/modules/multifit/include/RadiusOfGyrationRestraint.h @@ -4,7 +4,7 @@ * * Restrict max distance between every pair of particle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/RigidLeavesRefiner.h b/modules/multifit/include/RigidLeavesRefiner.h index 2894f6ef92..2edc9328cc 100644 --- a/modules/multifit/include/RigidLeavesRefiner.h +++ b/modules/multifit/include/RigidLeavesRefiner.h @@ -2,7 +2,7 @@ * \file IMP/multifit/RigidLeavesRefiner.h * \brief Return all rigid body members that are also hierarchy leaves. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/SettingsData.h b/modules/multifit/include/SettingsData.h index 7c10f2318f..83318a4f38 100644 --- a/modules/multifit/include/SettingsData.h +++ b/modules/multifit/include/SettingsData.h @@ -2,7 +2,7 @@ * \file IMP/multifit/SettingsData.h * \brief stored multifit settings data * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/WeightedExcludedVolumeRestraint.h b/modules/multifit/include/WeightedExcludedVolumeRestraint.h index e9e03dad53..d8fd1da3db 100644 --- a/modules/multifit/include/WeightedExcludedVolumeRestraint.h +++ b/modules/multifit/include/WeightedExcludedVolumeRestraint.h @@ -2,7 +2,7 @@ * \file IMP/multifit/WeightedExcludedVolumeRestraint.h * \brief Calculate weighted excluded volume between rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/anchor_graph.h b/modules/multifit/include/anchor_graph.h index 7dee37299e..8d02f34c11 100644 --- a/modules/multifit/include/anchor_graph.h +++ b/modules/multifit/include/anchor_graph.h @@ -2,7 +2,7 @@ * \file IMP/multifit/anchor_graph.h * \brief anchor graph utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/anchor_utilities.h b/modules/multifit/include/anchor_utilities.h index fe13a1947f..b43fc5b528 100644 --- a/modules/multifit/include/anchor_utilities.h +++ b/modules/multifit/include/anchor_utilities.h @@ -2,7 +2,7 @@ * \file IMP/multifit/anchor_utilities.h * \brief Common functions in anchor calculations * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/anchors_reader.h b/modules/multifit/include/anchors_reader.h index ff8276c325..405e28c048 100644 --- a/modules/multifit/include/anchors_reader.h +++ b/modules/multifit/include/anchors_reader.h @@ -2,7 +2,7 @@ * \file IMP/multifit/anchors_reader.h * \brief handles reading of anchors data * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/coarse_molecule.h b/modules/multifit/include/coarse_molecule.h index 5581605327..5d0575a9ba 100644 --- a/modules/multifit/include/coarse_molecule.h +++ b/modules/multifit/include/coarse_molecule.h @@ -2,7 +2,7 @@ * \file IMP/multifit/coarse_molecule.h * \brief coarsen molecule by clustering * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/connolly_surface.h b/modules/multifit/include/connolly_surface.h index 3b5de34233..59658be159 100644 --- a/modules/multifit/include/connolly_surface.h +++ b/modules/multifit/include/connolly_surface.h @@ -2,7 +2,7 @@ * \file IMP/multifit/connolly_surface.h * \brief Generate surface for a set of atoms * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/density_analysis.h b/modules/multifit/include/density_analysis.h index 94ce7dbfc2..05ac522944 100644 --- a/modules/multifit/include/density_analysis.h +++ b/modules/multifit/include/density_analysis.h @@ -2,7 +2,7 @@ * \file IMP/multifit/density_analysis.h * \brief density analysis tools, such as segmentation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/ensemble_analysis.h b/modules/multifit/include/ensemble_analysis.h index af8855540e..bf64a3551a 100644 --- a/modules/multifit/include/ensemble_analysis.h +++ b/modules/multifit/include/ensemble_analysis.h @@ -1,7 +1,7 @@ /** * \file IMP/multifit/ensemble_analysis.h * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMULTIFIT_ENSEMBLE_ANALYSIS_H diff --git a/modules/multifit/include/fft_based_rigid_fitting.h b/modules/multifit/include/fft_based_rigid_fitting.h index c09be51383..ad9c93dca3 100644 --- a/modules/multifit/include/fft_based_rigid_fitting.h +++ b/modules/multifit/include/fft_based_rigid_fitting.h @@ -2,7 +2,7 @@ * \file IMP/multifit/fft_based_rigid_fitting.h * \brief FFT based fitting * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/fitting_solutions_reader_writer.h b/modules/multifit/include/fitting_solutions_reader_writer.h index 867709dec2..71674cbbd1 100644 --- a/modules/multifit/include/fitting_solutions_reader_writer.h +++ b/modules/multifit/include/fitting_solutions_reader_writer.h @@ -2,7 +2,7 @@ * \file IMP/multifit/fitting_solutions_reader_writer.h * \brief handles reading and writing MultiFit fitting solutions file * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/fitting_states.h b/modules/multifit/include/fitting_states.h index eb4f18da72..9ea05313b8 100644 --- a/modules/multifit/include/fitting_states.h +++ b/modules/multifit/include/fitting_states.h @@ -2,7 +2,7 @@ * \file IMP/multifit/fitting_states.h * \brief Fitting states * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/fitting_tools.h b/modules/multifit/include/fitting_tools.h index 051207c3d9..c8e3dc46a4 100644 --- a/modules/multifit/include/fitting_tools.h +++ b/modules/multifit/include/fitting_tools.h @@ -2,7 +2,7 @@ * \file IMP/multifit/fitting_tools.h * \brief tools for handling fitting records * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/fitting_utils.h b/modules/multifit/include/fitting_utils.h index 0081320b01..1765d38f5e 100644 --- a/modules/multifit/include/fitting_utils.h +++ b/modules/multifit/include/fitting_utils.h @@ -2,7 +2,7 @@ * \file IMP/multifit/fitting_utils.h * \brief fitting utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/internal/FFTWGrid.h b/modules/multifit/include/internal/FFTWGrid.h index 7fd4701ff7..2f3faa97e9 100644 --- a/modules/multifit/include/internal/FFTWGrid.h +++ b/modules/multifit/include/internal/FFTWGrid.h @@ -1,7 +1,7 @@ /** * \file FFTWGrid.h \brief C++ smart pointer wrapper to fftw_malloc/free * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/internal/FFTWPlan.h b/modules/multifit/include/internal/FFTWPlan.h index c8d3bd4c78..4ee77cbbc6 100644 --- a/modules/multifit/include/internal/FFTWPlan.h +++ b/modules/multifit/include/internal/FFTWPlan.h @@ -1,7 +1,7 @@ /** * \file FFTWPlan.h \brief C++ smart pointer to FFTW plans. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/internal/GeometricComplementarity.h b/modules/multifit/include/internal/GeometricComplementarity.h index 32f1010024..c192f1eedc 100644 --- a/modules/multifit/include/internal/GeometricComplementarity.h +++ b/modules/multifit/include/internal/GeometricComplementarity.h @@ -1,7 +1,7 @@ /** * \file GeometricComplementarity.h \brief Geometric complementarity. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/internal/SurfaceMatching.h b/modules/multifit/include/internal/SurfaceMatching.h index cf2043691e..985ce90ac3 100644 --- a/modules/multifit/include/internal/SurfaceMatching.h +++ b/modules/multifit/include/internal/SurfaceMatching.h @@ -1,7 +1,7 @@ /** * \file SurfaceMatching.h \brief Surface matching. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/internal/fft_fitting_utils.h b/modules/multifit/include/internal/fft_fitting_utils.h index 09438b6f97..7e81f2d331 100644 --- a/modules/multifit/include/internal/fft_fitting_utils.h +++ b/modules/multifit/include/internal/fft_fitting_utils.h @@ -1,7 +1,7 @@ /** * \file fft_fitting_utils.h \brief masking function for fft fitting * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/internal/reader_writer_utility.h b/modules/multifit/include/internal/reader_writer_utility.h index 6871007b78..c3f08ab76d 100644 --- a/modules/multifit/include/internal/reader_writer_utility.h +++ b/modules/multifit/include/internal/reader_writer_utility.h @@ -1,7 +1,7 @@ /** * \file fft_fitting_utils.h \brief masking function for fft fitting * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/merge_tree_utils.h b/modules/multifit/include/merge_tree_utils.h index 924f1188c3..9d009f77d2 100644 --- a/modules/multifit/include/merge_tree_utils.h +++ b/modules/multifit/include/merge_tree_utils.h @@ -1,7 +1,7 @@ /** * \file IMP/multifit/merge_tree_utils.h * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMULTIFIT_MERGE_TREE_UTILS_H diff --git a/modules/multifit/include/path_reader_writer.h b/modules/multifit/include/path_reader_writer.h index cdb4746d14..dc2d0dca8d 100644 --- a/modules/multifit/include/path_reader_writer.h +++ b/modules/multifit/include/path_reader_writer.h @@ -2,7 +2,7 @@ * \file IMP/multifit/path_reader_writer.h * \brief Read and write paths. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/pca_based_rigid_fitting.h b/modules/multifit/include/pca_based_rigid_fitting.h index e5fbd1a23c..32e9f321c8 100644 --- a/modules/multifit/include/pca_based_rigid_fitting.h +++ b/modules/multifit/include/pca_based_rigid_fitting.h @@ -2,7 +2,7 @@ * \file IMP/multifit/pca_based_rigid_fitting.h * \brief preforms rigid fitting between a set of particles and a density map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPMULTIFIT_PCA_BASED_RIGID_FITTING_H diff --git a/modules/multifit/include/protein_anchors_mapping_reader.h b/modules/multifit/include/protein_anchors_mapping_reader.h index 56858715b0..bef7d8e1d5 100644 --- a/modules/multifit/include/protein_anchors_mapping_reader.h +++ b/modules/multifit/include/protein_anchors_mapping_reader.h @@ -2,7 +2,7 @@ * \file IMP/multifit/protein_anchors_mapping_reader.h * \brief handles reading matches between a protein and its anchors * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/proteomics_em_alignment_atomic.h b/modules/multifit/include/proteomics_em_alignment_atomic.h index 0c953fc582..8101f6b82b 100644 --- a/modules/multifit/include/proteomics_em_alignment_atomic.h +++ b/modules/multifit/include/proteomics_em_alignment_atomic.h @@ -2,7 +2,7 @@ * \file IMP/multifit/proteomics_em_alignment_atomic.h * \brief align proteomics graph to em density map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/proteomics_reader.h b/modules/multifit/include/proteomics_reader.h index d69743d320..9d1757c127 100644 --- a/modules/multifit/include/proteomics_reader.h +++ b/modules/multifit/include/proteomics_reader.h @@ -2,7 +2,7 @@ * \file IMP/multifit/proteomics_reader.h * \brief handles reading of proteomics data * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/include/weighted_excluded_volume.h b/modules/multifit/include/weighted_excluded_volume.h index 37fae46fc0..f0f47b279f 100644 --- a/modules/multifit/include/weighted_excluded_volume.h +++ b/modules/multifit/include/weighted_excluded_volume.h @@ -3,7 +3,7 @@ * \brief handles low resolution weighted excluded * volume calculation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/AlignmentParams.cpp b/modules/multifit/src/AlignmentParams.cpp index e9904ddaa6..c7e30a78bc 100644 --- a/modules/multifit/src/AlignmentParams.cpp +++ b/modules/multifit/src/AlignmentParams.cpp @@ -2,7 +2,7 @@ * \file AlignmentParams.cpp * \brief Parameters for alignments. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/multifit/src/ComplementarityRestraint.cpp b/modules/multifit/src/ComplementarityRestraint.cpp index 49cd1ba6c3..4c0f5a69ef 100644 --- a/modules/multifit/src/ComplementarityRestraint.cpp +++ b/modules/multifit/src/ComplementarityRestraint.cpp @@ -2,7 +2,7 @@ * \file WeighedExcludedVolumeRestraint2.cpp * \brief Calculate excluded volume between rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/DataPointsAssignment.cpp b/modules/multifit/src/DataPointsAssignment.cpp index 89ae47411f..6a3a5f5c99 100644 --- a/modules/multifit/src/DataPointsAssignment.cpp +++ b/modules/multifit/src/DataPointsAssignment.cpp @@ -2,7 +2,7 @@ * \file DataPointsAssignment.cpp * \brief Tools for data points assignment, after anchor point segmentation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/DensityDataPoints.cpp b/modules/multifit/src/DensityDataPoints.cpp index 0d236308ed..6057ae2508 100644 --- a/modules/multifit/src/DensityDataPoints.cpp +++ b/modules/multifit/src/DensityDataPoints.cpp @@ -2,7 +2,7 @@ * \file DataPoints.cpp * \brief Handling of data for anchor points segmentation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multifit/src/FittingSolutionRecord.cpp b/modules/multifit/src/FittingSolutionRecord.cpp index 4501005d11..e1a8a99d7a 100644 --- a/modules/multifit/src/FittingSolutionRecord.cpp +++ b/modules/multifit/src/FittingSolutionRecord.cpp @@ -2,7 +2,7 @@ * \file FittingSolutionRecord.cpp * \brief stored a multifit fitting solution * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/RadiusOfGyrationRestraint.cpp b/modules/multifit/src/RadiusOfGyrationRestraint.cpp index 905b1e978b..09c3a56a6f 100644 --- a/modules/multifit/src/RadiusOfGyrationRestraint.cpp +++ b/modules/multifit/src/RadiusOfGyrationRestraint.cpp @@ -3,7 +3,7 @@ * * Restrict max distance between every pair of particle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/RigidLeavesRefiner.cpp b/modules/multifit/src/RigidLeavesRefiner.cpp index 42c4c6f485..91d31ffbb0 100644 --- a/modules/multifit/src/RigidLeavesRefiner.cpp +++ b/modules/multifit/src/RigidLeavesRefiner.cpp @@ -2,7 +2,7 @@ * \file IMP/multifit/RigidLeavesRefiner.cpp * \brief Return all rigid body members that are also hierarchy leaves. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/SettingsData.cpp b/modules/multifit/src/SettingsData.cpp index 6eb1b5840d..8858b583ad 100644 --- a/modules/multifit/src/SettingsData.cpp +++ b/modules/multifit/src/SettingsData.cpp @@ -2,7 +2,7 @@ * \file SettingsData.cpp * \brief stored a multifit settings data * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/WeightedExcludedVolumeRestraint.cpp b/modules/multifit/src/WeightedExcludedVolumeRestraint.cpp index e030f6daeb..fd97ddacb0 100644 --- a/modules/multifit/src/WeightedExcludedVolumeRestraint.cpp +++ b/modules/multifit/src/WeightedExcludedVolumeRestraint.cpp @@ -2,7 +2,7 @@ * \file WeightedExcludedVolumeRestraint.cpp * \brief Calculate excluded volume between rigid bodies. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/anchor_graph.cpp b/modules/multifit/src/anchor_graph.cpp index e0d3190f6f..1ce0151593 100644 --- a/modules/multifit/src/anchor_graph.cpp +++ b/modules/multifit/src/anchor_graph.cpp @@ -2,7 +2,7 @@ * \file anchor_graph.cpp * \brief anchor graph utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multifit/src/anchor_utilities.cpp b/modules/multifit/src/anchor_utilities.cpp index 7b3d51e3dc..693d3bf416 100644 --- a/modules/multifit/src/anchor_utilities.cpp +++ b/modules/multifit/src/anchor_utilities.cpp @@ -2,7 +2,7 @@ * \file anchor_utilities.cpp * \brief Tools for handling anchors. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/multifit/src/anchors_reader.cpp b/modules/multifit/src/anchors_reader.cpp index adf359f576..a0e0a4a851 100644 --- a/modules/multifit/src/anchors_reader.cpp +++ b/modules/multifit/src/anchors_reader.cpp @@ -2,7 +2,7 @@ * \file anchors_reader.cpp * \brief handles reading of anchors data * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/coarse_molecule.cpp b/modules/multifit/src/coarse_molecule.cpp index 44361160e0..5e325b4e87 100644 --- a/modules/multifit/src/coarse_molecule.cpp +++ b/modules/multifit/src/coarse_molecule.cpp @@ -2,7 +2,7 @@ * \file coarse_molecule.cpp * \brief coarsen molecule by clustering * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multifit/src/connolly_surface.cpp b/modules/multifit/src/connolly_surface.cpp index 041daab2d5..17926e1f72 100644 --- a/modules/multifit/src/connolly_surface.cpp +++ b/modules/multifit/src/connolly_surface.cpp @@ -1,7 +1,7 @@ /** * \file connolly_surface.cpp \brief Generate surface for a set of atoms * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/density_analysis.cpp b/modules/multifit/src/density_analysis.cpp index a80f4e33b4..6822e45ba3 100644 --- a/modules/multifit/src/density_analysis.cpp +++ b/modules/multifit/src/density_analysis.cpp @@ -2,7 +2,7 @@ * \file density_analysis.cpp * \brief tools for analyzing density maps * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/ensemble_analysis.cpp b/modules/multifit/src/ensemble_analysis.cpp index eaedff1ebb..21e7158fdb 100644 --- a/modules/multifit/src/ensemble_analysis.cpp +++ b/modules/multifit/src/ensemble_analysis.cpp @@ -1,7 +1,7 @@ /** * \file ensemble_analysis.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/multifit/src/fft_based_rigid_fitting.cpp b/modules/multifit/src/fft_based_rigid_fitting.cpp index fa0405ca7f..230aa927c5 100644 --- a/modules/multifit/src/fft_based_rigid_fitting.cpp +++ b/modules/multifit/src/fft_based_rigid_fitting.cpp @@ -2,7 +2,7 @@ * \file FFTFitting.cpp * \brief FFT based fitting * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multifit/src/fitting_solutions_reader_writer.cpp b/modules/multifit/src/fitting_solutions_reader_writer.cpp index 0da8ebe838..2d794579cc 100644 --- a/modules/multifit/src/fitting_solutions_reader_writer.cpp +++ b/modules/multifit/src/fitting_solutions_reader_writer.cpp @@ -3,7 +3,7 @@ * \brief handles reading and writing of fitting solutions * volume calculation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/fitting_states.cpp b/modules/multifit/src/fitting_states.cpp index 1c544e6c5c..d69dae0ac2 100644 --- a/modules/multifit/src/fitting_states.cpp +++ b/modules/multifit/src/fitting_states.cpp @@ -2,7 +2,7 @@ * \file multifit/fitting_states.cpp * \brief Fitting states * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/fitting_tools.cpp b/modules/multifit/src/fitting_tools.cpp index bf1fe745d2..ca6879de99 100644 --- a/modules/multifit/src/fitting_tools.cpp +++ b/modules/multifit/src/fitting_tools.cpp @@ -2,7 +2,7 @@ * \file fitting_tools.cpp * \brief tools for handling fitting records * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multifit/src/fitting_utils.cpp b/modules/multifit/src/fitting_utils.cpp index 247dd949f6..34ad10b180 100644 --- a/modules/multifit/src/fitting_utils.cpp +++ b/modules/multifit/src/fitting_utils.cpp @@ -2,7 +2,7 @@ * \file fitting_utils.cpp * \brief fitting utilities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multifit/src/internal/FFTWPlan.cpp b/modules/multifit/src/internal/FFTWPlan.cpp index 323affcb23..39f5f9d4a8 100644 --- a/modules/multifit/src/internal/FFTWPlan.cpp +++ b/modules/multifit/src/internal/FFTWPlan.cpp @@ -1,7 +1,7 @@ /** * \file FFTWPlan.cpp \brief C++ smart pointer to FFTW plans. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/internal/GeometricComplementarity.cpp b/modules/multifit/src/internal/GeometricComplementarity.cpp index 74bc9d5eb8..d60623e79a 100644 --- a/modules/multifit/src/internal/GeometricComplementarity.cpp +++ b/modules/multifit/src/internal/GeometricComplementarity.cpp @@ -1,7 +1,7 @@ /** * \file GeometricComplementarity.cpp \brief Geometric complementarity. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/internal/SurfaceMatching.cpp b/modules/multifit/src/internal/SurfaceMatching.cpp index da0c63ea7f..0275ba3c76 100644 --- a/modules/multifit/src/internal/SurfaceMatching.cpp +++ b/modules/multifit/src/internal/SurfaceMatching.cpp @@ -1,7 +1,7 @@ /** * \file SurfaceMatching.cpp \brief Surface matching. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multifit/src/internal/fft_fitting_utils.cpp b/modules/multifit/src/internal/fft_fitting_utils.cpp index d51236ea6a..66ae528c55 100644 --- a/modules/multifit/src/internal/fft_fitting_utils.cpp +++ b/modules/multifit/src/internal/fft_fitting_utils.cpp @@ -1,7 +1,7 @@ /** * \file fft_fitting_utils.cpp \brief masking function for fft fitting * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/merge_tree_utils.cpp b/modules/multifit/src/merge_tree_utils.cpp index faa62a34cb..42c550d40e 100644 --- a/modules/multifit/src/merge_tree_utils.cpp +++ b/modules/multifit/src/merge_tree_utils.cpp @@ -1,7 +1,7 @@ /** * \file merge_tree_utils.cpp * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/multifit/src/path_reader_writer.cpp b/modules/multifit/src/path_reader_writer.cpp index 5785e85ad9..4eb6693ad7 100644 --- a/modules/multifit/src/path_reader_writer.cpp +++ b/modules/multifit/src/path_reader_writer.cpp @@ -2,7 +2,7 @@ * \file path_reader_writer.cpp * \brief Read and write paths. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/pca_based_rigid_fitting.cpp b/modules/multifit/src/pca_based_rigid_fitting.cpp index 1215e5eae7..80138b0680 100644 --- a/modules/multifit/src/pca_based_rigid_fitting.cpp +++ b/modules/multifit/src/pca_based_rigid_fitting.cpp @@ -2,7 +2,7 @@ * \file pca_based_rigid_fitting.cpp * \brief Fast Rigid fitting functionalities * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/protein_anchors_mapping_reader.cpp b/modules/multifit/src/protein_anchors_mapping_reader.cpp index c7389989f4..e33f11ad0f 100644 --- a/modules/multifit/src/protein_anchors_mapping_reader.cpp +++ b/modules/multifit/src/protein_anchors_mapping_reader.cpp @@ -2,7 +2,7 @@ * \file protein_anchors_mapping_reader.cpp * \brief handles reading matches between a protein and its anchors * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/proteomics_em_alignment_atomic.cpp b/modules/multifit/src/proteomics_em_alignment_atomic.cpp index fe6519eba5..80cd3570d1 100644 --- a/modules/multifit/src/proteomics_em_alignment_atomic.cpp +++ b/modules/multifit/src/proteomics_em_alignment_atomic.cpp @@ -2,7 +2,7 @@ * \file proteomics_em_alignment_atomic.cpp * \brief align proteomics graph to em density map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/proteomics_reader.cpp b/modules/multifit/src/proteomics_reader.cpp index 73be097316..56db2ec903 100644 --- a/modules/multifit/src/proteomics_reader.cpp +++ b/modules/multifit/src/proteomics_reader.cpp @@ -2,7 +2,7 @@ * \file proteomics_reader.cpp * \brief handles reading proteomics data * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/multifit/src/weighted_excluded_volume.cpp b/modules/multifit/src/weighted_excluded_volume.cpp index b7947d5bc1..a840fd92b1 100644 --- a/modules/multifit/src/weighted_excluded_volume.cpp +++ b/modules/multifit/src/weighted_excluded_volume.cpp @@ -3,7 +3,7 @@ * \brief handles low resolution weighted excluded * volume calculation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/multifit/test/medium_test_match_transformations.cpp b/modules/multifit/test/medium_test_match_transformations.cpp index 69877a8b00..fe6c69cb03 100644 --- a/modules/multifit/test/medium_test_match_transformations.cpp +++ b/modules/multifit/test/medium_test_match_transformations.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved + * Copyright 2007-2022 IMP Inventors. All rights reserved */ #include #include diff --git a/modules/multifit/test/test_geometric_complementarity.cpp b/modules/multifit/test/test_geometric_complementarity.cpp index 3c5d52b1e1..6ac8920083 100644 --- a/modules/multifit/test/test_geometric_complementarity.cpp +++ b/modules/multifit/test/test_geometric_complementarity.cpp @@ -3,7 +3,7 @@ * intersection volume and compares it with the 'exact' volume. * Print a nice table results and errors in the end. * - * Copyright 2007-2021 IMP Inventors. All rights reserved + * Copyright 2007-2022 IMP Inventors. All rights reserved */ #include #include diff --git a/modules/multifit/test/test_geometric_hash.cpp b/modules/multifit/test/test_geometric_hash.cpp index 8b364b270e..ea7dad1800 100644 --- a/modules/multifit/test/test_geometric_hash.cpp +++ b/modules/multifit/test/test_geometric_hash.cpp @@ -1,7 +1,7 @@ /* Test the GeometricHash class by comparing its results to those obtained * by simple distance calculation. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/multifit/utility/atoms2anchors.cpp b/modules/multifit/utility/atoms2anchors.cpp index 34c3851356..09ffbdf534 100644 --- a/modules/multifit/utility/atoms2anchors.cpp +++ b/modules/multifit/utility/atoms2anchors.cpp @@ -2,7 +2,7 @@ * \fileatoms2anchors.cpp * \brief Find an anchor graph segmentation of a protein * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. **/ #include diff --git a/modules/multifit/utility/single_prot_fft_fit.cpp b/modules/multifit/utility/single_prot_fft_fit.cpp index 5a5215c777..d08fe5475f 100644 --- a/modules/multifit/utility/single_prot_fft_fit.cpp +++ b/modules/multifit/utility/single_prot_fft_fit.cpp @@ -2,7 +2,7 @@ * \file single_prot_fft_fit.cpp * \brief Fit a single protein to a density map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. **/ #include #include diff --git a/modules/multifit/utility/single_prot_pca_fit.cpp b/modules/multifit/utility/single_prot_pca_fit.cpp index 3d9d585c39..2d91be4fb2 100644 --- a/modules/multifit/utility/single_prot_pca_fit.cpp +++ b/modules/multifit/utility/single_prot_pca_fit.cpp @@ -2,7 +2,7 @@ * \file single_prot_pca_fit.cpp * \brief Fit a single protein to a density map * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. **/ // others #include diff --git a/modules/npc/include/CompositeRestraint.h b/modules/npc/include/CompositeRestraint.h index 47b7fc124c..02e66161cc 100644 --- a/modules/npc/include/CompositeRestraint.h +++ b/modules/npc/include/CompositeRestraint.h @@ -1,7 +1,7 @@ /** * \file IMP/npc/CompositeRestraint.h \brief Composite restraint. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/npc/include/MinimumSphereDistancePairScore.h b/modules/npc/include/MinimumSphereDistancePairScore.h index cb8672ade8..73429167de 100644 --- a/modules/npc/include/MinimumSphereDistancePairScore.h +++ b/modules/npc/include/MinimumSphereDistancePairScore.h @@ -2,7 +2,7 @@ * \file IMP/npc/MinimumSphereDistancePairScore.h * \brief Apply a UnaryFunction to the minimum transformed distance * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPNPC_MINIMUM_SPHERE_DISTANCE_PAIR_SCORE_H diff --git a/modules/npc/include/ProteinLocalizationRestraint.h b/modules/npc/include/ProteinLocalizationRestraint.h index 889fc4dfe0..1c3d74d155 100644 --- a/modules/npc/include/ProteinLocalizationRestraint.h +++ b/modules/npc/include/ProteinLocalizationRestraint.h @@ -5,7 +5,7 @@ * Restrict max distance between at least one pair of particles of any * two distinct types. It also handles multiple copies of the same particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/npc/src/CompositeRestraint.cpp b/modules/npc/src/CompositeRestraint.cpp index 651286bb16..b3e0e64e6f 100644 --- a/modules/npc/src/CompositeRestraint.cpp +++ b/modules/npc/src/CompositeRestraint.cpp @@ -1,7 +1,7 @@ /** * \file CompositeRestraint.cpp \brief Composite restraint. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/npc/src/MinimumSphereDistancePairScore.cpp b/modules/npc/src/MinimumSphereDistancePairScore.cpp index 43671dda26..529fc7bbec 100644 --- a/modules/npc/src/MinimumSphereDistancePairScore.cpp +++ b/modules/npc/src/MinimumSphereDistancePairScore.cpp @@ -2,7 +2,7 @@ * \file MinimumSphereDistancePairScore.cpp * \brief Apply a UnaryFunction to the minimum transformed distance * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/npc/src/ProteinLocalizationRestraint.cpp b/modules/npc/src/ProteinLocalizationRestraint.cpp index 304a3238db..5f2aa10285 100644 --- a/modules/npc/src/ProteinLocalizationRestraint.cpp +++ b/modules/npc/src/ProteinLocalizationRestraint.cpp @@ -4,7 +4,7 @@ * Restrict max distance between at least one pair of particles of any * two distinct types. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/benchmark/benchmark_brownian.cpp b/modules/rmf/benchmark/benchmark_brownian.cpp index de9aaf77d7..30d9eeeb03 100644 --- a/modules/rmf/benchmark/benchmark_brownian.cpp +++ b/modules/rmf/benchmark/benchmark_brownian.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/rmf/benchmark/benchmark_load.cpp b/modules/rmf/benchmark/benchmark_load.cpp index f6d1aba909..45471c76ad 100644 --- a/modules/rmf/benchmark/benchmark_load.cpp +++ b/modules/rmf/benchmark/benchmark_load.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/rmf/benchmark/benchmark_save.cpp b/modules/rmf/benchmark/benchmark_save.cpp index 34e1646f72..8c06d197b3 100644 --- a/modules/rmf/benchmark/benchmark_save.cpp +++ b/modules/rmf/benchmark/benchmark_save.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/rmf/bin/pdb_rmf.cpp b/modules/rmf/bin/pdb_rmf.cpp index 0a377494dd..d0e7ea000d 100644 --- a/modules/rmf/bin/pdb_rmf.cpp +++ b/modules/rmf/bin/pdb_rmf.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/bin/rmf_display.cpp b/modules/rmf/bin/rmf_display.cpp index 17b28cbb9f..15b7446dfe 100644 --- a/modules/rmf/bin/rmf_display.cpp +++ b/modules/rmf/bin/rmf_display.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/rmf/bin/rmf_simplify.cpp b/modules/rmf/bin/rmf_simplify.cpp index eadbe91588..f86c6239bd 100644 --- a/modules/rmf/bin/rmf_simplify.cpp +++ b/modules/rmf/bin/rmf_simplify.cpp @@ -1,5 +1,5 @@ /** - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include #include diff --git a/modules/rmf/include/HierarchyLoadLink.h b/modules/rmf/include/HierarchyLoadLink.h index 3db5db101e..7fc0a4b00e 100644 --- a/modules/rmf/include/HierarchyLoadLink.h +++ b/modules/rmf/include/HierarchyLoadLink.h @@ -2,7 +2,7 @@ * \file IMP/rmf/HierarchyLoadLink.h * \brief Manages loading links from an RMF file to an atom::Hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/HierarchySaveLink.h b/modules/rmf/include/HierarchySaveLink.h index fc9fafb1bc..cd42850d0e 100644 --- a/modules/rmf/include/HierarchySaveLink.h +++ b/modules/rmf/include/HierarchySaveLink.h @@ -2,7 +2,7 @@ * \file IMP/rmf/HierarchySaveLink.h * \brief Manage saving links to an RMF file from an atom::Hierarchy. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/RMFWriter.h b/modules/rmf/include/RMFWriter.h index 767776a5ab..6da7f6bb02 100644 --- a/modules/rmf/include/RMFWriter.h +++ b/modules/rmf/include/RMFWriter.h @@ -2,7 +2,7 @@ * \file IMP/rmf/RMFWriter.h * \brief Write geometry to an RMF file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/SaveOptimizerState.h b/modules/rmf/include/SaveOptimizerState.h index acd61e7b1b..76284e2074 100644 --- a/modules/rmf/include/SaveOptimizerState.h +++ b/modules/rmf/include/SaveOptimizerState.h @@ -2,7 +2,7 @@ * \file IMP/rmf/SaveOptimizerState.h * \brief Dump the state of all associated objects into the RMF file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/associations.h b/modules/rmf/include/associations.h index 378af45777..edcc640147 100644 --- a/modules/rmf/include/associations.h +++ b/modules/rmf/include/associations.h @@ -2,7 +2,7 @@ * \file IMP/rmf/associations.h * \brief Track associations between an RMF file and native objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/atom_io.h b/modules/rmf/include/atom_io.h index db11962c43..2d4a0e3e4b 100644 --- a/modules/rmf/include/atom_io.h +++ b/modules/rmf/include/atom_io.h @@ -2,7 +2,7 @@ * \file IMP/rmf/atom_io.h * \brief Input/output of IMP::atom::Hierarchy information. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/atom_links.h b/modules/rmf/include/atom_links.h index 286309b733..4cd4d4449d 100644 --- a/modules/rmf/include/atom_links.h +++ b/modules/rmf/include/atom_links.h @@ -5,7 +5,7 @@ * HierarchySaveLink - the name is misleading and may be * changed to atom_hierarchy_links.h in future. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/frames.h b/modules/rmf/include/frames.h index b16e77c2d6..4e7e64edfc 100644 --- a/modules/rmf/include/frames.h +++ b/modules/rmf/include/frames.h @@ -2,7 +2,7 @@ * \file IMP/rmf/frames.h * \brief Read or write RMF frames. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/geometry_io.h b/modules/rmf/include/geometry_io.h index 3269555307..96643d5d7d 100644 --- a/modules/rmf/include/geometry_io.h +++ b/modules/rmf/include/geometry_io.h @@ -2,7 +2,7 @@ * \file IMP/rmf/geometry_io.h * \brief Handle read/write of geometry data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/internal/atom_links_coordinate_helpers.h b/modules/rmf/include/internal/atom_links_coordinate_helpers.h index 1c94425318..52bf034a7f 100644 --- a/modules/rmf/include/internal/atom_links_coordinate_helpers.h +++ b/modules/rmf/include/internal/atom_links_coordinate_helpers.h @@ -2,7 +2,7 @@ * \file IMP/rmf/atom_links.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/internal/atom_links_gaussians.h b/modules/rmf/include/internal/atom_links_gaussians.h index 79659c37b0..69b9b194b6 100644 --- a/modules/rmf/include/internal/atom_links_gaussians.h +++ b/modules/rmf/include/internal/atom_links_gaussians.h @@ -2,7 +2,7 @@ * \file IMP/rmf/atom_links.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/internal/atom_links_rigid_bodies.h b/modules/rmf/include/internal/atom_links_rigid_bodies.h index 666d991a5f..bf77bbe488 100644 --- a/modules/rmf/include/internal/atom_links_rigid_bodies.h +++ b/modules/rmf/include/internal/atom_links_rigid_bodies.h @@ -2,7 +2,7 @@ * \file IMP/rmf/atom_links.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/internal/atom_links_static.h b/modules/rmf/include/internal/atom_links_static.h index 2df6a4898a..07be32f4c8 100644 --- a/modules/rmf/include/internal/atom_links_static.h +++ b/modules/rmf/include/internal/atom_links_static.h @@ -2,7 +2,7 @@ * \file IMP/rmf/atom_links.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/internal/atom_links_xyzs.h b/modules/rmf/include/internal/atom_links_xyzs.h index d8042e2624..69b9fd52ce 100644 --- a/modules/rmf/include/internal/atom_links_xyzs.h +++ b/modules/rmf/include/internal/atom_links_xyzs.h @@ -2,7 +2,7 @@ * \file IMP/rmf/atom_links.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/internal/hierarchy_links_helpers.h b/modules/rmf/include/internal/hierarchy_links_helpers.h index a76a65bcee..d28544c1e4 100644 --- a/modules/rmf/include/internal/hierarchy_links_helpers.h +++ b/modules/rmf/include/internal/hierarchy_links_helpers.h @@ -2,7 +2,7 @@ * \file IMP/rmf/hierarchy_links_helpers.h * \brief Helper functions for HierarchyLoad/SaveLink.h * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/internal/link_helpers.h b/modules/rmf/include/internal/link_helpers.h index e0cdff52f4..c4659c92b0 100644 --- a/modules/rmf/include/internal/link_helpers.h +++ b/modules/rmf/include/internal/link_helpers.h @@ -2,7 +2,7 @@ * \file IMP/rmf/link_macros.h * \brief macros for display classes * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPRMF_LINK_HELPERS_H diff --git a/modules/rmf/include/link_macros.h b/modules/rmf/include/link_macros.h index 4e8b07f753..bffe8c4e19 100644 --- a/modules/rmf/include/link_macros.h +++ b/modules/rmf/include/link_macros.h @@ -2,7 +2,7 @@ * \file IMP/rmf/link_macros.h * \brief macros for display classes * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPRMF_LINK_MACROS_H diff --git a/modules/rmf/include/links.h b/modules/rmf/include/links.h index 0e8c7ad8bc..5b114bfce0 100644 --- a/modules/rmf/include/links.h +++ b/modules/rmf/include/links.h @@ -2,7 +2,7 @@ * \file IMP/rmf/links.h * \brief Manage links between \imp objects and a part of the RMF file. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/particle_io.h b/modules/rmf/include/particle_io.h index e1a029c936..b250bac8d6 100644 --- a/modules/rmf/include/particle_io.h +++ b/modules/rmf/include/particle_io.h @@ -2,7 +2,7 @@ * \file IMP/rmf/particle_io.h * \brief Manage read/write of particles from/to RMF files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/restraint_io.h b/modules/rmf/include/restraint_io.h index 1093e914ab..0fb8f2088d 100644 --- a/modules/rmf/include/restraint_io.h +++ b/modules/rmf/include/restraint_io.h @@ -2,7 +2,7 @@ * \file IMP/rmf/restraint_io.h * \brief Manage read/write of Restraints from/to RMF files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/include/simple_links.h b/modules/rmf/include/simple_links.h index 2dd2b83d44..423f0d20ea 100644 --- a/modules/rmf/include/simple_links.h +++ b/modules/rmf/include/simple_links.h @@ -2,7 +2,7 @@ * \file IMP/rmf/simple_links.h * \brief Manage links between IMP objects and RMF nodes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/HierarchyLoadLink.cpp b/modules/rmf/src/HierarchyLoadLink.cpp index c12c482eff..64f3a55af4 100644 --- a/modules/rmf/src/HierarchyLoadLink.cpp +++ b/modules/rmf/src/HierarchyLoadLink.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/HierarchyLoadLink.h * \brief Handle read of atom hierarchy from rmf files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/HierarchySaveLink.cpp b/modules/rmf/src/HierarchySaveLink.cpp index 4c5c0d2097..6e3919af25 100644 --- a/modules/rmf/src/HierarchySaveLink.cpp +++ b/modules/rmf/src/HierarchySaveLink.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/HierarchySaveLink.cpp * \brief Handle writing of atom hierarchy to rmf files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/RMFWriter.cpp b/modules/rmf/src/RMFWriter.cpp index a9457fbc39..1413eec40d 100644 --- a/modules/rmf/src/RMFWriter.cpp +++ b/modules/rmf/src/RMFWriter.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/RMFWriter.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/SaveOptimizerState.cpp b/modules/rmf/src/SaveOptimizerState.cpp index d779b761a1..bbb389a146 100644 --- a/modules/rmf/src/SaveOptimizerState.cpp +++ b/modules/rmf/src/SaveOptimizerState.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/SaveOptimizerState.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/associations.cpp b/modules/rmf/src/associations.cpp index 2ed5db52d9..33e9cda91f 100644 --- a/modules/rmf/src/associations.cpp +++ b/modules/rmf/src/associations.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/associations.cpp * \brief Track associations between an RMF file and native objects. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/atom_io.cpp b/modules/rmf/src/atom_io.cpp index bba56d629f..f9e1441d43 100644 --- a/modules/rmf/src/atom_io.cpp +++ b/modules/rmf/src/atom_io.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/atom_io.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/frames.cpp b/modules/rmf/src/frames.cpp index 5139400433..dc9157fd8a 100644 --- a/modules/rmf/src/frames.cpp +++ b/modules/rmf/src/frames.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/frames.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/geometry_io.cpp b/modules/rmf/src/geometry_io.cpp index fc10124ab9..0823cee980 100644 --- a/modules/rmf/src/geometry_io.cpp +++ b/modules/rmf/src/geometry_io.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/geometry_io.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/internal/atom_links_gaussians.cpp b/modules/rmf/src/internal/atom_links_gaussians.cpp index 1bf5fea027..8fc6fbf27d 100644 --- a/modules/rmf/src/internal/atom_links_gaussians.cpp +++ b/modules/rmf/src/internal/atom_links_gaussians.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/internal/atom_links_rigid_bodies.cpp b/modules/rmf/src/internal/atom_links_rigid_bodies.cpp index 7ba41b7efd..8e94bae16e 100644 --- a/modules/rmf/src/internal/atom_links_rigid_bodies.cpp +++ b/modules/rmf/src/internal/atom_links_rigid_bodies.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/internal/atom_links_static.cpp b/modules/rmf/src/internal/atom_links_static.cpp index 128cd6bec2..47b1250742 100644 --- a/modules/rmf/src/internal/atom_links_static.cpp +++ b/modules/rmf/src/internal/atom_links_static.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/internal/atom_links_xyzs.cpp b/modules/rmf/src/internal/atom_links_xyzs.cpp index dc860db451..bbcce0d53e 100644 --- a/modules/rmf/src/internal/atom_links_xyzs.cpp +++ b/modules/rmf/src/internal/atom_links_xyzs.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/internal/hierarchy_links_helpers.cpp b/modules/rmf/src/internal/hierarchy_links_helpers.cpp index 4c6000a071..ad52418757 100644 --- a/modules/rmf/src/internal/hierarchy_links_helpers.cpp +++ b/modules/rmf/src/internal/hierarchy_links_helpers.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/internal/hierarchy_links_helpers.cpp * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/src/internal/link_helpers.cpp b/modules/rmf/src/internal/link_helpers.cpp index fcf888beb1..25160a972b 100644 --- a/modules/rmf/src/internal/link_helpers.cpp +++ b/modules/rmf/src/internal/link_helpers.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/link_macros.h * \brief macros for display classes * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/rmf/src/links.cpp b/modules/rmf/src/links.cpp index 80624c6a2f..aa800d1b2a 100644 --- a/modules/rmf/src/links.cpp +++ b/modules/rmf/src/links.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/links.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/particle_io.cpp b/modules/rmf/src/particle_io.cpp index 815337ba98..b021f7f5fc 100644 --- a/modules/rmf/src/particle_io.cpp +++ b/modules/rmf/src/particle_io.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/particle_io.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/src/restraint_io.cpp b/modules/rmf/src/restraint_io.cpp index 10c3c54cba..759739631d 100644 --- a/modules/rmf/src/restraint_io.cpp +++ b/modules/rmf/src/restraint_io.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/restraint_io.cpp * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rmf/test/test_errors.cpp b/modules/rmf/test/test_errors.cpp index 6b7b776075..e5455f283c 100644 --- a/modules/rmf/test/test_errors.cpp +++ b/modules/rmf/test/test_errors.cpp @@ -2,7 +2,7 @@ * \file IMP/rmf/Category.h * \brief Handle read/write of Model data from/to files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/rotamer/include/RotamerCalculator.h b/modules/rotamer/include/RotamerCalculator.h index 386612994b..5f5956d0f1 100644 --- a/modules/rotamer/include/RotamerCalculator.h +++ b/modules/rotamer/include/RotamerCalculator.h @@ -2,7 +2,7 @@ * \file IMP/rotamer/RotamerCalculator.h * \brief Object performing rotations by Chi angles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rotamer/include/RotamerLibrary.h b/modules/rotamer/include/RotamerLibrary.h index 36a3269d31..8f83eb4163 100644 --- a/modules/rotamer/include/RotamerLibrary.h +++ b/modules/rotamer/include/RotamerLibrary.h @@ -2,7 +2,7 @@ * \file IMP/rotamer/RotamerLibrary.h * \brief Object representing rotamer library. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rotamer/src/RotamerCalculator.cpp b/modules/rotamer/src/RotamerCalculator.cpp index a0f86d7df5..5f57353ee7 100644 --- a/modules/rotamer/src/RotamerCalculator.cpp +++ b/modules/rotamer/src/RotamerCalculator.cpp @@ -2,7 +2,7 @@ * \file RotamerCalculator.cpp * \brief Object calculating coordinates based on rotamer library. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/rotamer/src/RotamerLibrary.cpp b/modules/rotamer/src/RotamerLibrary.cpp index 54f2f68764..4fa5915368 100644 --- a/modules/rotamer/src/RotamerLibrary.cpp +++ b/modules/rotamer/src/RotamerLibrary.cpp @@ -1,7 +1,7 @@ /** * \file RotamerLibrary.cpp \brief Access to RotamerLibrary. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/saxs/include/ChiFreeScore.h b/modules/saxs/include/ChiFreeScore.h index 6d9c1640dc..e465f33801 100644 --- a/modules/saxs/include/ChiFreeScore.h +++ b/modules/saxs/include/ChiFreeScore.h @@ -1,7 +1,7 @@ /** * \file IMP/saxs/ChiFreeScore.h \brief Chi free score implementation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * TODO: add reference */ diff --git a/modules/saxs/include/ChiScore.h b/modules/saxs/include/ChiScore.h index 32925580bb..dbd305f17c 100644 --- a/modules/saxs/include/ChiScore.h +++ b/modules/saxs/include/ChiScore.h @@ -1,7 +1,7 @@ /** * \file IMP/saxs/ChiScore.h \brief Basic chi score implementation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/ChiScoreLog.h b/modules/saxs/include/ChiScoreLog.h index 43c6581083..04a774e5a5 100644 --- a/modules/saxs/include/ChiScoreLog.h +++ b/modules/saxs/include/ChiScoreLog.h @@ -1,7 +1,7 @@ /** * \file IMP/saxs/ChiScoreLog.h \brief scoring with log intensity * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/DerivativeCalculator.h b/modules/saxs/include/DerivativeCalculator.h index 54d5c40a21..ffc9fc5904 100644 --- a/modules/saxs/include/DerivativeCalculator.h +++ b/modules/saxs/include/DerivativeCalculator.h @@ -2,7 +2,7 @@ * \file IMP/saxs/DerivativeCalculator.h * \brief A class for computing SAXS derivatives * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/Distribution.h b/modules/saxs/include/Distribution.h index 1166116d69..54238146e3 100644 --- a/modules/saxs/include/Distribution.h +++ b/modules/saxs/include/Distribution.h @@ -5,7 +5,7 @@ * RadialDistributionFunction required for calculation of SAXS profile * DeltaDistributionFunction requires for chi-square derivatives * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/FitParameters.h b/modules/saxs/include/FitParameters.h index e0a1385330..3062ef18e2 100644 --- a/modules/saxs/include/FitParameters.h +++ b/modules/saxs/include/FitParameters.h @@ -1,7 +1,7 @@ /** * \file IMP/saxs/FitParameters.h \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/FormFactorTable.h b/modules/saxs/include/FormFactorTable.h index ef8b6517af..76bf6e6662 100644 --- a/modules/saxs/include/FormFactorTable.h +++ b/modules/saxs/include/FormFactorTable.h @@ -2,7 +2,7 @@ * \file IMP/saxs/FormFactorTable.h \brief A class for computation of * atomic and residue level form factors for SAXS calculations * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/Profile.h b/modules/saxs/include/Profile.h index 2ecee71c02..9fd095c84c 100644 --- a/modules/saxs/include/Profile.h +++ b/modules/saxs/include/Profile.h @@ -2,7 +2,7 @@ * \file IMP/saxs/Profile.h * \brief A class for profile storing and computation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/ProfileClustering.h b/modules/saxs/include/ProfileClustering.h index b6429a6f54..17a847a7d1 100644 --- a/modules/saxs/include/ProfileClustering.h +++ b/modules/saxs/include/ProfileClustering.h @@ -3,7 +3,7 @@ * \brief A class for profile clustering * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/ProfileFitter.h b/modules/saxs/include/ProfileFitter.h index 3ba7b63c6f..35f6aa6286 100644 --- a/modules/saxs/include/ProfileFitter.h +++ b/modules/saxs/include/ProfileFitter.h @@ -1,7 +1,7 @@ /** * \file IMP/saxs/ProfileFitter.h \brief a class for fitting two profiles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/RadiusOfGyrationRestraint.h b/modules/saxs/include/RadiusOfGyrationRestraint.h index 35b6196e37..d22dd490e4 100644 --- a/modules/saxs/include/RadiusOfGyrationRestraint.h +++ b/modules/saxs/include/RadiusOfGyrationRestraint.h @@ -2,7 +2,7 @@ * \file IMP/saxs/RadiusOfGyrationRestraint.h * \brief Calculate score based on fit to SAXS profile. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/RatioVolatilityScore.h b/modules/saxs/include/RatioVolatilityScore.h index 85d58149ee..eebb1a4472 100644 --- a/modules/saxs/include/RatioVolatilityScore.h +++ b/modules/saxs/include/RatioVolatilityScore.h @@ -3,7 +3,7 @@ * * Hura et al. Nature Methods 2013 * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/Restraint.h b/modules/saxs/include/Restraint.h index afbbdf0310..7643983e04 100644 --- a/modules/saxs/include/Restraint.h +++ b/modules/saxs/include/Restraint.h @@ -2,7 +2,7 @@ * \file IMP/saxs/Restraint.h * \brief Calculate score based on fit to SAXS profile. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/RigidBodiesProfileHandler.h b/modules/saxs/include/RigidBodiesProfileHandler.h index 637b2c6181..8d539d83c8 100644 --- a/modules/saxs/include/RigidBodiesProfileHandler.h +++ b/modules/saxs/include/RigidBodiesProfileHandler.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/SolventAccessibleSurface.h b/modules/saxs/include/SolventAccessibleSurface.h index 67b20406d9..d387988587 100644 --- a/modules/saxs/include/SolventAccessibleSurface.h +++ b/modules/saxs/include/SolventAccessibleSurface.h @@ -1,7 +1,7 @@ /** * \file IMP/saxs/SolventAccessibleSurface.h \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/WeightedFitParameters.h b/modules/saxs/include/WeightedFitParameters.h index a1283b707c..f6431dd4d3 100644 --- a/modules/saxs/include/WeightedFitParameters.h +++ b/modules/saxs/include/WeightedFitParameters.h @@ -1,7 +1,7 @@ /** * \file IMP/saxs/WeightedFitParameters.h * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/WeightedProfileFitter.h b/modules/saxs/include/WeightedProfileFitter.h index 4c89c7b8e4..60367d7136 100644 --- a/modules/saxs/include/WeightedProfileFitter.h +++ b/modules/saxs/include/WeightedProfileFitter.h @@ -5,7 +5,7 @@ * non-negative least squares fitting (NNLS) * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/internal/exp_function.h b/modules/saxs/include/internal/exp_function.h index 0438994e12..ce800fd43b 100644 --- a/modules/saxs/include/internal/exp_function.h +++ b/modules/saxs/include/internal/exp_function.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/internal/sinc_function.h b/modules/saxs/include/internal/sinc_function.h index 89228feb1e..f47c22babc 100644 --- a/modules/saxs/include/internal/sinc_function.h +++ b/modules/saxs/include/internal/sinc_function.h @@ -1,7 +1,7 @@ /** * \file sinc_function \brief caching of sinc values * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/internal/variance_helpers.h b/modules/saxs/include/internal/variance_helpers.h index 314c6b9220..739814c8b7 100644 --- a/modules/saxs/include/internal/variance_helpers.h +++ b/modules/saxs/include/internal/variance_helpers.h @@ -1,7 +1,7 @@ /** * \file sinc_function \brief caching of sinc values * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/nnls.h b/modules/saxs/include/nnls.h index 0a72bbcb59..35ac46c1a5 100644 --- a/modules/saxs/include/nnls.h +++ b/modules/saxs/include/nnls.h @@ -3,7 +3,7 @@ * \brief * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/include/utility.h b/modules/saxs/include/utility.h index cfa3757fe4..bfa1a23b6c 100644 --- a/modules/saxs/include/utility.h +++ b/modules/saxs/include/utility.h @@ -1,7 +1,7 @@ /** * \file IMP/saxs/utility.h * \brief Functions to deal with very common saxs operations - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSAXS_UTILITY_H diff --git a/modules/saxs/src/ChiFreeScore.cpp b/modules/saxs/src/ChiFreeScore.cpp index 40d6c3c4cb..50ea100b12 100644 --- a/modules/saxs/src/ChiFreeScore.cpp +++ b/modules/saxs/src/ChiFreeScore.cpp @@ -1,7 +1,7 @@ /** * \file ChiFreeScore.h \brief Chi free SAXS score * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/ChiScore.cpp b/modules/saxs/src/ChiScore.cpp index 95cb4e8cba..334e109375 100644 --- a/modules/saxs/src/ChiScore.cpp +++ b/modules/saxs/src/ChiScore.cpp @@ -1,7 +1,7 @@ /** * \file ChiScore.h \brief Basic SAXS scoring * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/ChiScoreLog.cpp b/modules/saxs/src/ChiScoreLog.cpp index 4a24795639..24199ce017 100644 --- a/modules/saxs/src/ChiScoreLog.cpp +++ b/modules/saxs/src/ChiScoreLog.cpp @@ -1,7 +1,7 @@ /** * \file ChiScoreLog \brief scoring with log intensity * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/DerivativeCalculator.cpp b/modules/saxs/src/DerivativeCalculator.cpp index f48452b5fb..e0d5abaaa0 100644 --- a/modules/saxs/src/DerivativeCalculator.cpp +++ b/modules/saxs/src/DerivativeCalculator.cpp @@ -1,7 +1,7 @@ /** * \file DerivativeCalculator \brief A class for computing SAXS derivatives * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/Distribution.cpp b/modules/saxs/src/Distribution.cpp index cc9273355c..751a7d675b 100644 --- a/modules/saxs/src/Distribution.cpp +++ b/modules/saxs/src/Distribution.cpp @@ -3,7 +3,7 @@ * * distribution classes implementation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/saxs/src/FormFactorTable.cpp b/modules/saxs/src/FormFactorTable.cpp index fcb0dde0b7..1853c68a91 100644 --- a/modules/saxs/src/FormFactorTable.cpp +++ b/modules/saxs/src/FormFactorTable.cpp @@ -2,7 +2,7 @@ * \file FormFactorTable.h \brief A class for computation of * atomic and residue level form factors for SAXS calculations * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/Profile.cpp b/modules/saxs/src/Profile.cpp index f07f815171..202fd118a1 100644 --- a/modules/saxs/src/Profile.cpp +++ b/modules/saxs/src/Profile.cpp @@ -1,7 +1,7 @@ /** * \file Profile.cpp \brief A class for profile storing and computation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/saxs/src/ProfileClustering.cpp b/modules/saxs/src/ProfileClustering.cpp index 4c9f25e17b..b7398c4830 100644 --- a/modules/saxs/src/ProfileClustering.cpp +++ b/modules/saxs/src/ProfileClustering.cpp @@ -4,7 +4,7 @@ * \brief A class for profiles clustering * * Author: Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/saxs/src/RadiusOfGyrationRestraint.cpp b/modules/saxs/src/RadiusOfGyrationRestraint.cpp index 6ebbb72b6d..8277e2f267 100644 --- a/modules/saxs/src/RadiusOfGyrationRestraint.cpp +++ b/modules/saxs/src/RadiusOfGyrationRestraint.cpp @@ -2,7 +2,7 @@ * \file RadiusOfGyrationRestraint.h * \brief Calculate score based on fit to SAXS profile. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/RatioVolatilityScore.cpp b/modules/saxs/src/RatioVolatilityScore.cpp index 0f818e1e14..fa3da59888 100644 --- a/modules/saxs/src/RatioVolatilityScore.cpp +++ b/modules/saxs/src/RatioVolatilityScore.cpp @@ -1,7 +1,7 @@ /** * \file RatioVolatilityScore.h \brief Chi free SAXS score * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/Restraint.cpp b/modules/saxs/src/Restraint.cpp index 3d1516a00b..bf8ed613c1 100644 --- a/modules/saxs/src/Restraint.cpp +++ b/modules/saxs/src/Restraint.cpp @@ -2,7 +2,7 @@ * \file saxs::Restraint.h * \brief Calculate score based on fit to SAXS profile. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/RigidBodiesProfileHandler.cpp b/modules/saxs/src/RigidBodiesProfileHandler.cpp index c0c99819b5..ace873c162 100644 --- a/modules/saxs/src/RigidBodiesProfileHandler.cpp +++ b/modules/saxs/src/RigidBodiesProfileHandler.cpp @@ -2,7 +2,7 @@ * \file saxs::RigidBodiesProfileHandler.cpp * \brief Calculate score based on fit to SAXS profile. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/SolventAccessibleSurface.cpp b/modules/saxs/src/SolventAccessibleSurface.cpp index c327461356..2f96ef991c 100644 --- a/modules/saxs/src/SolventAccessibleSurface.cpp +++ b/modules/saxs/src/SolventAccessibleSurface.cpp @@ -1,7 +1,7 @@ /** * \file SolventAccessibleSurface \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/saxs/src/utility.cpp b/modules/saxs/src/utility.cpp index 37af33848a..d52a99e4dc 100644 --- a/modules/saxs/src/utility.cpp +++ b/modules/saxs/src/utility.cpp @@ -1,7 +1,7 @@ /** * \file IMP/saxs/utility.cpp * \brief Functions to deal with very common saxs operations - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/score_functor/include/AddScores.h b/modules/score_functor/include/AddScores.h index bfc7254850..920810563f 100644 --- a/modules/score_functor/include/AddScores.h +++ b/modules/score_functor/include/AddScores.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/AddScores.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_ADD_SCORES_H diff --git a/modules/score_functor/include/DistancePairScore.h b/modules/score_functor/include/DistancePairScore.h index cb530d85c6..bb600e3f45 100644 --- a/modules/score_functor/include/DistancePairScore.h +++ b/modules/score_functor/include/DistancePairScore.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/DistancePairScore.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_DISTANCE_PAIR_SCORE_H diff --git a/modules/score_functor/include/DistancePairScoreWithCache.h b/modules/score_functor/include/DistancePairScoreWithCache.h index cc1994d8a4..edc1c1cc2d 100644 --- a/modules/score_functor/include/DistancePairScoreWithCache.h +++ b/modules/score_functor/include/DistancePairScoreWithCache.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/DistancePairScoreWithCache.h * \brief A Score on the distance between a pair of particles, using cache. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_DISTANCE_PAIR_SCORE_WITH_CACHE_H diff --git a/modules/score_functor/include/Dope.h b/modules/score_functor/include/Dope.h index 6c4f60fe57..8986995fae 100644 --- a/modules/score_functor/include/Dope.h +++ b/modules/score_functor/include/Dope.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/Dope.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_DOPE_H diff --git a/modules/score_functor/include/Harmonic.h b/modules/score_functor/include/Harmonic.h index 6a650cf995..9c2b9eb78c 100644 --- a/modules/score_functor/include/Harmonic.h +++ b/modules/score_functor/include/Harmonic.h @@ -3,7 +3,7 @@ * \brief A harmonic score on the directed distance between a pair of particles, * centered at 0. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_HARMONIC_H diff --git a/modules/score_functor/include/HarmonicLowerBound.h b/modules/score_functor/include/HarmonicLowerBound.h index 0d2d806889..d98109f731 100644 --- a/modules/score_functor/include/HarmonicLowerBound.h +++ b/modules/score_functor/include/HarmonicLowerBound.h @@ -5,7 +5,7 @@ * non-negative directed distances. * . * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_HARMONIC_LOWER_BOUND_H diff --git a/modules/score_functor/include/HarmonicUpperBound.h b/modules/score_functor/include/HarmonicUpperBound.h index 84ccc73c1a..f8032ceda8 100644 --- a/modules/score_functor/include/HarmonicUpperBound.h +++ b/modules/score_functor/include/HarmonicUpperBound.h @@ -4,7 +4,7 @@ * a pair of particles. The score equals zero for * non-positive directed distances. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_HARMONIC_UPPER_BOUND_H diff --git a/modules/score_functor/include/LinearLowerBound.h b/modules/score_functor/include/LinearLowerBound.h index b1042e8690..5e273c2e1e 100644 --- a/modules/score_functor/include/LinearLowerBound.h +++ b/modules/score_functor/include/LinearLowerBound.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/LinearLowerBound.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_LINEAR_LOWER_BOUND_H diff --git a/modules/score_functor/include/LoopStatistical.h b/modules/score_functor/include/LoopStatistical.h index ba81e52e51..24a8495175 100644 --- a/modules/score_functor/include/LoopStatistical.h +++ b/modules/score_functor/include/LoopStatistical.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/LoopStatistical.h * \brief Fiser/Melo loop modeling statistical potential * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_LOOP_STATISTICAL_H diff --git a/modules/score_functor/include/OpenCubicSpline.h b/modules/score_functor/include/OpenCubicSpline.h index f8fa598480..3fb024b977 100644 --- a/modules/score_functor/include/OpenCubicSpline.h +++ b/modules/score_functor/include/OpenCubicSpline.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/OpenCubicSpline.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_OPEN_CUBIC_SPLINE_H diff --git a/modules/score_functor/include/OrientedSoap.h b/modules/score_functor/include/OrientedSoap.h index 44454325e4..5050e69477 100644 --- a/modules/score_functor/include/OrientedSoap.h +++ b/modules/score_functor/include/OrientedSoap.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/OrientedSoap.h * \brief Score a particle pair using an orientation-dependent SOAP potential. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_ORIENTED_SOAP_H diff --git a/modules/score_functor/include/PointToSphereDistance.h b/modules/score_functor/include/PointToSphereDistance.h index fc3b1ae729..d78f3e8576 100644 --- a/modules/score_functor/include/PointToSphereDistance.h +++ b/modules/score_functor/include/PointToSphereDistance.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/PointToSphereDistance.h * \brief A Score on the distance between a point and a sphere. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_POINT_TO_SPHERE_DISTANCE_H diff --git a/modules/score_functor/include/Score.h b/modules/score_functor/include/Score.h index 634cce37df..c9b32f7380 100644 --- a/modules/score_functor/include/Score.h +++ b/modules/score_functor/include/Score.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/Score.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_SCORE_H diff --git a/modules/score_functor/include/ScoreUnaryFunction.h b/modules/score_functor/include/ScoreUnaryFunction.h index dbaf35ce6c..09c20be930 100644 --- a/modules/score_functor/include/ScoreUnaryFunction.h +++ b/modules/score_functor/include/ScoreUnaryFunction.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/ScoreUnaryFunction.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_SCORE_UNARY_FUNCTION_H diff --git a/modules/score_functor/include/ScoreWithCache.h b/modules/score_functor/include/ScoreWithCache.h index e0ffa5579a..bf7dd62d35 100644 --- a/modules/score_functor/include/ScoreWithCache.h +++ b/modules/score_functor/include/ScoreWithCache.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/ScoreWithCache.h * \brief A Score on the distance between a pair of particles, with cache. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_SCORE_WITH_CACHE_H diff --git a/modules/score_functor/include/Shift.h b/modules/score_functor/include/Shift.h index 51e8b115a3..4a98f32fb9 100644 --- a/modules/score_functor/include/Shift.h +++ b/modules/score_functor/include/Shift.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/Shift.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_SHIFT_H diff --git a/modules/score_functor/include/SingletonStatistical.h b/modules/score_functor/include/SingletonStatistical.h index 25a69e1e4c..8e14ee20ba 100644 --- a/modules/score_functor/include/SingletonStatistical.h +++ b/modules/score_functor/include/SingletonStatistical.h @@ -4,7 +4,7 @@ * such as solvent accessibility * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/Soap.h b/modules/score_functor/include/Soap.h index 832c9c1d15..162512cc1a 100644 --- a/modules/score_functor/include/Soap.h +++ b/modules/score_functor/include/Soap.h @@ -3,7 +3,7 @@ * \brief A Score on the distance between a pair of particles. * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/SphereDistance.h b/modules/score_functor/include/SphereDistance.h index 5751b9b3f4..4d6045cf14 100644 --- a/modules/score_functor/include/SphereDistance.h +++ b/modules/score_functor/include/SphereDistance.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/SphereDistance.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_SPHERE_DISTANCE_H diff --git a/modules/score_functor/include/Statistical.h b/modules/score_functor/include/Statistical.h index 74a7c2740e..35e83c700c 100644 --- a/modules/score_functor/include/Statistical.h +++ b/modules/score_functor/include/Statistical.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/Statistical.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_STATISTICAL_H diff --git a/modules/score_functor/include/SurfaceDistancePairScore.h b/modules/score_functor/include/SurfaceDistancePairScore.h index 26a5926514..4869d442e7 100644 --- a/modules/score_functor/include/SurfaceDistancePairScore.h +++ b/modules/score_functor/include/SurfaceDistancePairScore.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/SurfaceDistancePairScore.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_SURFACE_DISTANCE_PAIR_SCORE_H diff --git a/modules/score_functor/include/UnaryFunctionEvaluate.h b/modules/score_functor/include/UnaryFunctionEvaluate.h index 082e25f2a5..b875e43e29 100644 --- a/modules/score_functor/include/UnaryFunctionEvaluate.h +++ b/modules/score_functor/include/UnaryFunctionEvaluate.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/UnaryFunctionEvaluate.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_UNARY_FUNCTION_EVALUATE_H diff --git a/modules/score_functor/include/WeightScore.h b/modules/score_functor/include/WeightScore.h index e938fae8db..29d9906bf1 100644 --- a/modules/score_functor/include/WeightScore.h +++ b/modules/score_functor/include/WeightScore.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/WeightScore.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_WEIGHT_SCORE_H diff --git a/modules/score_functor/include/distance_pair_score_macros.h b/modules/score_functor/include/distance_pair_score_macros.h index 6ec4a37286..42a66c1b47 100644 --- a/modules/score_functor/include/distance_pair_score_macros.h +++ b/modules/score_functor/include/distance_pair_score_macros.h @@ -3,7 +3,7 @@ * \brief Various important macros * for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/internal/PMFTable.h b/modules/score_functor/include/internal/PMFTable.h index 49ecc8081e..7a6d1ac475 100644 --- a/modules/score_functor/include/internal/PMFTable.h +++ b/modules/score_functor/include/internal/PMFTable.h @@ -2,7 +2,7 @@ * \file PMFTable.h * \brief A table for storing potentials * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/internal/RawOpenCubicSpline.h b/modules/score_functor/include/internal/RawOpenCubicSpline.h index 9340b129b9..bc76cf8b48 100644 --- a/modules/score_functor/include/internal/RawOpenCubicSpline.h +++ b/modules/score_functor/include/internal/RawOpenCubicSpline.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/OpenCubicSpline.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSCORE_FUNCTOR_RAW_OPEN_CUBIC_SPLINE_H diff --git a/modules/score_functor/include/internal/SASTable.h b/modules/score_functor/include/internal/SASTable.h index 48d7014d00..083d6b3afa 100644 --- a/modules/score_functor/include/internal/SASTable.h +++ b/modules/score_functor/include/internal/SASTable.h @@ -3,7 +3,7 @@ * \brief Storage of Solvent Accessability Statistical potential * * \authors Dina Schneidman - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/internal/direction_helpers.h b/modules/score_functor/include/internal/direction_helpers.h index 483243cfe8..455f393216 100644 --- a/modules/score_functor/include/internal/direction_helpers.h +++ b/modules/score_functor/include/internal/direction_helpers.h @@ -2,7 +2,7 @@ * \file direction_helpers.h * \brief Helper functions for directions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/internal/soap_hdf5.h b/modules/score_functor/include/internal/soap_hdf5.h index 188ac77fce..2a7f8c26fb 100644 --- a/modules/score_functor/include/internal/soap_hdf5.h +++ b/modules/score_functor/include/internal/soap_hdf5.h @@ -2,7 +2,7 @@ * \file soap_hdf5.h * \brief Handling of SOAP HDF5 files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/internal/soap_helpers.h b/modules/score_functor/include/internal/soap_helpers.h index 7900e90690..ad3917d453 100644 --- a/modules/score_functor/include/internal/soap_helpers.h +++ b/modules/score_functor/include/internal/soap_helpers.h @@ -2,7 +2,7 @@ * \file soap_helpers.h * \brief Helper functions for SOAP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/internal/surface_helpers.h b/modules/score_functor/include/internal/surface_helpers.h index c870d396a8..37fae67a17 100644 --- a/modules/score_functor/include/internal/surface_helpers.h +++ b/modules/score_functor/include/internal/surface_helpers.h @@ -2,7 +2,7 @@ * \file surface_helpers.h * \brief Helper functions for surfaces. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/include/surface_distance_pair_score_macros.h b/modules/score_functor/include/surface_distance_pair_score_macros.h index 31673a3a92..c1a4d88d2f 100644 --- a/modules/score_functor/include/surface_distance_pair_score_macros.h +++ b/modules/score_functor/include/surface_distance_pair_score_macros.h @@ -2,7 +2,7 @@ * \file IMP/score_functor/surface_distance_pair_score_macros.h * \brief Various important macros for implementing decorators. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/src/Dope.cpp b/modules/score_functor/src/Dope.cpp index 6fc0d24ae8..803fbcb152 100644 --- a/modules/score_functor/src/Dope.cpp +++ b/modules/score_functor/src/Dope.cpp @@ -2,7 +2,7 @@ * \file DopePairScore.cpp * \brief Dope score * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/src/LoopStatistical.cpp b/modules/score_functor/src/LoopStatistical.cpp index 3630453cbc..f97686e788 100644 --- a/modules/score_functor/src/LoopStatistical.cpp +++ b/modules/score_functor/src/LoopStatistical.cpp @@ -2,7 +2,7 @@ * \file LoopStatistical.cpp * \brief Fiser/Melo loop modeling statistical potential * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/src/internal/RawOpenCubicSpline.cpp b/modules/score_functor/src/internal/RawOpenCubicSpline.cpp index 137e961c46..5ebb99959b 100644 --- a/modules/score_functor/src/internal/RawOpenCubicSpline.cpp +++ b/modules/score_functor/src/internal/RawOpenCubicSpline.cpp @@ -2,7 +2,7 @@ * \file DopePairScore.cpp * \brief Dope score * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/src/internal/direction_helpers.cpp b/modules/score_functor/src/internal/direction_helpers.cpp index 819b692193..5a841182d2 100644 --- a/modules/score_functor/src/internal/direction_helpers.cpp +++ b/modules/score_functor/src/internal/direction_helpers.cpp @@ -2,7 +2,7 @@ * \file direction_helpers.cpp * \brief Helper functions for directions. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/src/internal/soap_hdf5.cpp b/modules/score_functor/src/internal/soap_hdf5.cpp index 10e18b75d2..ce34138e44 100644 --- a/modules/score_functor/src/internal/soap_hdf5.cpp +++ b/modules/score_functor/src/internal/soap_hdf5.cpp @@ -2,7 +2,7 @@ * \file soap_hdf5.cpp * \brief Handling of SOAP HDF5 files. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/src/internal/soap_helpers.cpp b/modules/score_functor/src/internal/soap_helpers.cpp index 8f380e4e42..77472d14fc 100644 --- a/modules/score_functor/src/internal/soap_helpers.cpp +++ b/modules/score_functor/src/internal/soap_helpers.cpp @@ -2,7 +2,7 @@ * \file soap_helpers.cpp * \brief Helper functions for SOAP. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/src/internal/surface_helpers.cpp b/modules/score_functor/src/internal/surface_helpers.cpp index 861c65839e..1e7147ac6d 100644 --- a/modules/score_functor/src/internal/surface_helpers.cpp +++ b/modules/score_functor/src/internal/surface_helpers.cpp @@ -2,7 +2,7 @@ * \file surface_helpers.cpp * \brief Helper functions for surfaces. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/score_functor/test/test_functor_distance_pair_scores.cpp b/modules/score_functor/test/test_functor_distance_pair_scores.cpp index 96641422b7..c64dc719e8 100644 --- a/modules/score_functor/test/test_functor_distance_pair_scores.cpp +++ b/modules/score_functor/test/test_functor_distance_pair_scores.cpp @@ -2,7 +2,7 @@ * \file test_functor_distance_pair_scores.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/bin/spb.cpp b/modules/spb/bin/spb.cpp index d713b4f703..4e65f58ecb 100644 --- a/modules/spb/bin/spb.cpp +++ b/modules/spb/bin/spb.cpp @@ -2,7 +2,7 @@ * \file spb.cpp * \brief SPB MonteCarlo * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/bin/spb_analysis.cpp b/modules/spb/bin/spb_analysis.cpp index 0feca73cad..1a9d510219 100644 --- a/modules/spb/bin/spb_analysis.cpp +++ b/modules/spb/bin/spb_analysis.cpp @@ -2,7 +2,7 @@ * \file spb_analysis.cpp * \brief SPB Analysis Tool * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/bin/spb_cluster.cpp b/modules/spb/bin/spb_cluster.cpp index 28b8ae6a89..819e47469e 100644 --- a/modules/spb/bin/spb_cluster.cpp +++ b/modules/spb/bin/spb_cluster.cpp @@ -2,7 +2,7 @@ * \file spb_cluster.cpp * \brief SPB Clustering Tool * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/bin/spb_density_perbead.cpp b/modules/spb/bin/spb_density_perbead.cpp index e3694069fe..632a3f47c8 100644 --- a/modules/spb/bin/spb_density_perbead.cpp +++ b/modules/spb/bin/spb_density_perbead.cpp @@ -2,7 +2,7 @@ * \file spb_analysis.cpp * \brief SPB Analysis Tool * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/include/AttributeDistancePairScore.h b/modules/spb/include/AttributeDistancePairScore.h index 59a52fe9ba..39cb56a6f7 100644 --- a/modules/spb/include/AttributeDistancePairScore.h +++ b/modules/spb/include/AttributeDistancePairScore.h @@ -2,7 +2,7 @@ * \file IMP/spb/AttributeDistancePairScore.h * \brief A score based on the unmodified value of an attribute. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_ATTRIBUTE_DISTANCE_PAIR_SCORE_H diff --git a/modules/spb/include/BoxedMover.h b/modules/spb/include/BoxedMover.h index 238074a6d5..7f568309f1 100644 --- a/modules/spb/include/BoxedMover.h +++ b/modules/spb/include/BoxedMover.h @@ -2,7 +2,7 @@ * \file IMP/spb/BoxedMover.h * \brief A mover that keeps a particle in a box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/CellMover.h b/modules/spb/include/CellMover.h index 502eb35daf..04fd88233c 100644 --- a/modules/spb/include/CellMover.h +++ b/modules/spb/include/CellMover.h @@ -2,7 +2,7 @@ * \file IMP/spb/CellMover.h * \brief A mover that transform a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/ChiSquareMetric.h b/modules/spb/include/ChiSquareMetric.h index fcd563ec54..161b75e6fa 100644 --- a/modules/spb/include/ChiSquareMetric.h +++ b/modules/spb/include/ChiSquareMetric.h @@ -2,7 +2,7 @@ * \file IMP/spb/ChiSquareMetric.h * \brief Contact Map Metric * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_CHI_SQUARE_METRIC_H diff --git a/modules/spb/include/ContactMapMetric.h b/modules/spb/include/ContactMapMetric.h index 05a8910e64..a95efac890 100644 --- a/modules/spb/include/ContactMapMetric.h +++ b/modules/spb/include/ContactMapMetric.h @@ -2,7 +2,7 @@ * \file IMP/spb/ContactMapMetric.h * \brief Contact Map Metric * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_CONTACT_MAP_METRIC_H diff --git a/modules/spb/include/DiameterRgyrRestraint.h b/modules/spb/include/DiameterRgyrRestraint.h index 79d4400750..f3cf8f43b2 100644 --- a/modules/spb/include/DiameterRgyrRestraint.h +++ b/modules/spb/include/DiameterRgyrRestraint.h @@ -2,7 +2,7 @@ * \file IMP/spb/DiameterRgyrRestraint.h * \brief Diameter Restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_DIAMETER_RGYR_RESTRAINT_H diff --git a/modules/spb/include/DistanceRMSDMetric.h b/modules/spb/include/DistanceRMSDMetric.h index d1d0ca1d0d..ec28ae6263 100644 --- a/modules/spb/include/DistanceRMSDMetric.h +++ b/modules/spb/include/DistanceRMSDMetric.h @@ -2,7 +2,7 @@ * \file IMP/spb/DistanceRMSDMetric.h * \brief Distance RMSD Metric * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_DISTANCE_RMSD_METRIC_H diff --git a/modules/spb/include/DistanceTerminiRestraint.h b/modules/spb/include/DistanceTerminiRestraint.h index 260fbe5dcd..2b991e7756 100644 --- a/modules/spb/include/DistanceTerminiRestraint.h +++ b/modules/spb/include/DistanceTerminiRestraint.h @@ -2,7 +2,7 @@ * \file IMP/spb/DistanceTerminiRestraint.h * \brief A distance restraint between protein termini. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_DISTANCE_TERMINI_RESTRAINT_H diff --git a/modules/spb/include/EM2DRestraint.h b/modules/spb/include/EM2DRestraint.h index 8a65b1ea4b..58c4147fb0 100644 --- a/modules/spb/include/EM2DRestraint.h +++ b/modules/spb/include/EM2DRestraint.h @@ -2,7 +2,7 @@ * \file IMP/spb/EM2DRestraint.h * \brief A restraint for using EM2D cross-corr in a Bayesian way * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/Gaussian.h b/modules/spb/include/Gaussian.h index 2e96519d1d..ab0c5d1190 100644 --- a/modules/spb/include/Gaussian.h +++ b/modules/spb/include/Gaussian.h @@ -1,7 +1,7 @@ /** * \file IMP/spb/Gaussian.h \brief Gaussian function. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_GAUSSIAN_H diff --git a/modules/spb/include/HelixDecorator.h b/modules/spb/include/HelixDecorator.h index ab1672ea27..c59e377e8e 100644 --- a/modules/spb/include/HelixDecorator.h +++ b/modules/spb/include/HelixDecorator.h @@ -2,7 +2,7 @@ * \file IMP/spb/HelixDecorator.h * \brief Add helix parameters to a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/ISDRestraint.h b/modules/spb/include/ISDRestraint.h index b519eac372..6a1e145cad 100644 --- a/modules/spb/include/ISDRestraint.h +++ b/modules/spb/include/ISDRestraint.h @@ -3,7 +3,7 @@ * \brief A lognormal restraint that uses the ISPA model to model NOE-derived * distance fit. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/KinkPairScore.h b/modules/spb/include/KinkPairScore.h index 828389dd1a..a4ca322b96 100644 --- a/modules/spb/include/KinkPairScore.h +++ b/modules/spb/include/KinkPairScore.h @@ -2,7 +2,7 @@ * \file IMP/spb/KinkPairScore.h * \brief A Score on the crossing angle between two rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_KINK_PAIR_SCORE_H diff --git a/modules/spb/include/MolecularDynamicsWithWte.h b/modules/spb/include/MolecularDynamicsWithWte.h index 13c914b0fb..e93aef3fa2 100644 --- a/modules/spb/include/MolecularDynamicsWithWte.h +++ b/modules/spb/include/MolecularDynamicsWithWte.h @@ -2,7 +2,7 @@ * \file IMP/spb/MolecularDynamicsWithWte.h * \brief Simple molecular dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/MonteCarloWithWte.h b/modules/spb/include/MonteCarloWithWte.h index 07064ce954..2df815a59b 100644 --- a/modules/spb/include/MonteCarloWithWte.h +++ b/modules/spb/include/MonteCarloWithWte.h @@ -2,7 +2,7 @@ * \file IMP/spb/MonteCarloWithWte.h * \brief An exotic version of MonteCarlo * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_MONTE_CARLO_WITH_WTE_H diff --git a/modules/spb/include/NuisanceRangeModifier.h b/modules/spb/include/NuisanceRangeModifier.h index 4a07c900e7..fa2075f312 100644 --- a/modules/spb/include/NuisanceRangeModifier.h +++ b/modules/spb/include/NuisanceRangeModifier.h @@ -2,7 +2,7 @@ * \file IMP/spb/NuisanceRangeModifier.h * \brief Ensure that a Nuisance stays within its set range. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_NUISANCE_RANGE_MODIFIER_H diff --git a/modules/spb/include/PbcBoxedMover.h b/modules/spb/include/PbcBoxedMover.h index e0da8b4e02..cc81fe361d 100644 --- a/modules/spb/include/PbcBoxedMover.h +++ b/modules/spb/include/PbcBoxedMover.h @@ -2,7 +2,7 @@ * \file IMP/spb/PbcBoxedMover.h * \brief A mover that keeps a particle in a box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/PbcBoxedRigidBodyMover.h b/modules/spb/include/PbcBoxedRigidBodyMover.h index f338ef7799..bc7a45b59f 100644 --- a/modules/spb/include/PbcBoxedRigidBodyMover.h +++ b/modules/spb/include/PbcBoxedRigidBodyMover.h @@ -2,7 +2,7 @@ * \file IMP/spb/PbcBoxedRigidBodyMover.h * \brief A mover that transform a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/RMSDMetric.h b/modules/spb/include/RMSDMetric.h index 5785ec85a0..9368232b67 100644 --- a/modules/spb/include/RMSDMetric.h +++ b/modules/spb/include/RMSDMetric.h @@ -2,7 +2,7 @@ * \file IMP/spb/RMSDMetric.h * \brief Distance RMSD Metric * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_RMSD_METRIC_H diff --git a/modules/spb/include/RigidBodyNewMover.h b/modules/spb/include/RigidBodyNewMover.h index e9206dce39..ce02c457ba 100644 --- a/modules/spb/include/RigidBodyNewMover.h +++ b/modules/spb/include/RigidBodyNewMover.h @@ -2,7 +2,7 @@ * \file IMP/spb/RigidBodyNewMover.h * \brief A mover that transform a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/RigidBodyPackingScore.h b/modules/spb/include/RigidBodyPackingScore.h index 2260b997ac..1885118c54 100644 --- a/modules/spb/include/RigidBodyPackingScore.h +++ b/modules/spb/include/RigidBodyPackingScore.h @@ -2,7 +2,7 @@ * \file IMP/spb/RigidBodyPackingScore.h * \brief A Score on the crossing angle between two rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_RIGID_BODY_PACKING_SCORE_H diff --git a/modules/spb/include/SameParticlePairFilter.h b/modules/spb/include/SameParticlePairFilter.h index cad1ad2f9d..0701c636e0 100644 --- a/modules/spb/include/SameParticlePairFilter.h +++ b/modules/spb/include/SameParticlePairFilter.h @@ -2,7 +2,7 @@ * \file IMP/spb/SameParticlePairFilter.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_SAME_PARTICLE_PAIR_FILTER_H diff --git a/modules/spb/include/SameRigidBodyPairFilter.h b/modules/spb/include/SameRigidBodyPairFilter.h index 4c33ad0306..4e060044ed 100644 --- a/modules/spb/include/SameRigidBodyPairFilter.h +++ b/modules/spb/include/SameRigidBodyPairFilter.h @@ -2,7 +2,7 @@ * \file IMP/spb/SameRigidBodyPairFilter.h * \brief A Score on the distance between a pair of particles. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_SAME_RIGID_BODY_PAIR_FILTER_H diff --git a/modules/spb/include/TiltSingletonScore.h b/modules/spb/include/TiltSingletonScore.h index 2d296ed163..f3908774ca 100644 --- a/modules/spb/include/TiltSingletonScore.h +++ b/modules/spb/include/TiltSingletonScore.h @@ -2,7 +2,7 @@ * \file IMP/spb/TiltSingletonScore.h * \brief A Score on the distance to a fixed point. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_TILT_SINGLETON_SCORE_H diff --git a/modules/spb/include/TransformationSymmetry.h b/modules/spb/include/TransformationSymmetry.h index fa86179fca..dfa759cd16 100644 --- a/modules/spb/include/TransformationSymmetry.h +++ b/modules/spb/include/TransformationSymmetry.h @@ -2,7 +2,7 @@ * \file IMP/spb/TransformationSymmetry.h * \brief Implement various types of symmetry * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/TwoStateGoModelRestraint.h b/modules/spb/include/TwoStateGoModelRestraint.h index d03bcb8699..c381e128ee 100644 --- a/modules/spb/include/TwoStateGoModelRestraint.h +++ b/modules/spb/include/TwoStateGoModelRestraint.h @@ -2,7 +2,7 @@ * \file IMP/spb/TwoStateGoModelRestraint.h * \brief Two-state Go-Model Restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSPB_TWO_STATE_GO_MODEL_RESTRAINT_H diff --git a/modules/spb/include/UniformBoundedRestraint.h b/modules/spb/include/UniformBoundedRestraint.h index 0dc15761c3..bea525abfa 100644 --- a/modules/spb/include/UniformBoundedRestraint.h +++ b/modules/spb/include/UniformBoundedRestraint.h @@ -2,7 +2,7 @@ * \file IMP/spb/UniformBoundedRestraint.h * \brief A uniform bounded restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/pt_stuff.h b/modules/spb/include/pt_stuff.h index b990356229..8d1c849262 100644 --- a/modules/spb/include/pt_stuff.h +++ b/modules/spb/include/pt_stuff.h @@ -2,7 +2,7 @@ * \file IMP/spb/pt_stuff.h * \brief Useful stuff for parallel tempering * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/spb_ISD_particles.h b/modules/spb/include/spb_ISD_particles.h index 43d57e7e32..8e21b3b776 100644 --- a/modules/spb/include/spb_ISD_particles.h +++ b/modules/spb/include/spb_ISD_particles.h @@ -2,7 +2,7 @@ * \file IMP/spb/spb_ISD_particles.h * \brief SPB ISD particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/spb_assemble_restraints.h b/modules/spb/include/spb_assemble_restraints.h index 9429557f74..b2e66620d4 100644 --- a/modules/spb/include/spb_assemble_restraints.h +++ b/modules/spb/include/spb_assemble_restraints.h @@ -2,7 +2,7 @@ * \file IMP/spb/spb_assemble_restraints.h * \brief Assemble SPB restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/spb_main.h b/modules/spb/include/spb_main.h index 10e8f49d5a..558b26271c 100644 --- a/modules/spb/include/spb_main.h +++ b/modules/spb/include/spb_main.h @@ -2,7 +2,7 @@ * \file IMP/spb/spb_main.h * \brief SPB MonteCarlo * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/spb_parser.h b/modules/spb/include/spb_parser.h index adc51a5deb..2e21451029 100644 --- a/modules/spb/include/spb_parser.h +++ b/modules/spb/include/spb_parser.h @@ -2,7 +2,7 @@ * \file IMP/spb/spb_parser.h * \brief SPB Parser * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/spb_representation.h b/modules/spb/include/spb_representation.h index ef87a1d5e0..cda695bb98 100644 --- a/modules/spb/include/spb_representation.h +++ b/modules/spb/include/spb_representation.h @@ -2,7 +2,7 @@ * \file IMP/spb/spb_representation.h * \brief SPB Representation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/spb_restraint.h b/modules/spb/include/spb_restraint.h index beef83ea6b..449bb50bfe 100644 --- a/modules/spb/include/spb_restraint.h +++ b/modules/spb/include/spb_restraint.h @@ -2,7 +2,7 @@ * \file IMP/spb/spb_restraint.h * \brief SPB Restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/include/spb_sampler.h b/modules/spb/include/spb_sampler.h index 0e3c7cf58b..5824615975 100644 --- a/modules/spb/include/spb_sampler.h +++ b/modules/spb/include/spb_sampler.h @@ -2,7 +2,7 @@ * \file IMP/spb/spb_sampler.h * \brief SPB Sampler * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/AttributeDistancePairScore.cpp b/modules/spb/src/AttributeDistancePairScore.cpp index b02bdeaced..a49397ccc6 100644 --- a/modules/spb/src/AttributeDistancePairScore.cpp +++ b/modules/spb/src/AttributeDistancePairScore.cpp @@ -2,7 +2,7 @@ * \file AttributeDistancePairScore.cpp * \brief A score based on the difference between the attributes * of two particles - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/BoxedMover.cpp b/modules/spb/src/BoxedMover.cpp index 43ebb913f5..e7ba064262 100644 --- a/modules/spb/src/BoxedMover.cpp +++ b/modules/spb/src/BoxedMover.cpp @@ -2,7 +2,7 @@ * \file BoxedMover.cpp * \brief A mover that keeps a particle in a box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/CellMover.cpp b/modules/spb/src/CellMover.cpp index 0eba946b14..f45575cb01 100644 --- a/modules/spb/src/CellMover.cpp +++ b/modules/spb/src/CellMover.cpp @@ -2,7 +2,7 @@ * \file CellMover.cpp * \brief A mover that transforms a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/ChiSquareMetric.cpp b/modules/spb/src/ChiSquareMetric.cpp index 73f2700571..1c6c8d1fe5 100644 --- a/modules/spb/src/ChiSquareMetric.cpp +++ b/modules/spb/src/ChiSquareMetric.cpp @@ -2,7 +2,7 @@ * \file ChiSquareMetric.cpp * \brief Contact Map Metric * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/ContactMapMetric.cpp b/modules/spb/src/ContactMapMetric.cpp index dc95c4c22e..28a96dc1f0 100644 --- a/modules/spb/src/ContactMapMetric.cpp +++ b/modules/spb/src/ContactMapMetric.cpp @@ -2,7 +2,7 @@ * \file ContactMapMetric.cpp * \brief Contact Map Metric * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/DiameterRgyrRestraint.cpp b/modules/spb/src/DiameterRgyrRestraint.cpp index 2941e67fdc..ce9ec8d8f4 100644 --- a/modules/spb/src/DiameterRgyrRestraint.cpp +++ b/modules/spb/src/DiameterRgyrRestraint.cpp @@ -2,7 +2,7 @@ * \file DiameterRgyrRestraint.cpp * \brief Diameter restraint based on radius of gyration * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/DistanceRMSDMetric.cpp b/modules/spb/src/DistanceRMSDMetric.cpp index 4a0bc41217..3a66823be6 100644 --- a/modules/spb/src/DistanceRMSDMetric.cpp +++ b/modules/spb/src/DistanceRMSDMetric.cpp @@ -2,7 +2,7 @@ * \file DistanceRMSDMetric.cpp * \brief Distance RMSD Metric with PBC and identical particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/DistanceTerminiRestraint.cpp b/modules/spb/src/DistanceTerminiRestraint.cpp index 10f33bd7e2..c0ef99c82c 100644 --- a/modules/spb/src/DistanceTerminiRestraint.cpp +++ b/modules/spb/src/DistanceTerminiRestraint.cpp @@ -1,7 +1,7 @@ /** * \brief A distance restraint between protein termini. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/EM2DRestraint.cpp b/modules/spb/src/EM2DRestraint.cpp index bfa3e66629..d9ccfc91f7 100644 --- a/modules/spb/src/EM2DRestraint.cpp +++ b/modules/spb/src/EM2DRestraint.cpp @@ -3,7 +3,7 @@ * \brief * Put description here * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/HelixDecorator.cpp b/modules/spb/src/HelixDecorator.cpp index c1cf7d2b07..62d38b6b52 100644 --- a/modules/spb/src/HelixDecorator.cpp +++ b/modules/spb/src/HelixDecorator.cpp @@ -2,7 +2,7 @@ * \file spb/HelixDecorator.cpp * \brief Add a name to a particle. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/KinkPairScore.cpp b/modules/spb/src/KinkPairScore.cpp index 20266a56ae..376a9009cd 100644 --- a/modules/spb/src/KinkPairScore.cpp +++ b/modules/spb/src/KinkPairScore.cpp @@ -2,7 +2,7 @@ * \file KinkPairScore.cpp * \brief A score on the kink angle between two rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/MolecularDynamicsWithWte.cpp b/modules/spb/src/MolecularDynamicsWithWte.cpp index ceca50eb8c..4f07e7229d 100644 --- a/modules/spb/src/MolecularDynamicsWithWte.cpp +++ b/modules/spb/src/MolecularDynamicsWithWte.cpp @@ -1,7 +1,7 @@ /** * \file MolecularDynamicsWithWte.cpp \brief Molecular dynamics optimizer. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/MonteCarloWithWte.cpp b/modules/spb/src/MonteCarloWithWte.cpp index d64595256f..f5d79a4257 100644 --- a/modules/spb/src/MonteCarloWithWte.cpp +++ b/modules/spb/src/MonteCarloWithWte.cpp @@ -2,7 +2,7 @@ * \file MonteCarloWithWte.cpp * \brief An exotic version of MonteCarlo * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/NuisanceRangeModifier.cpp b/modules/spb/src/NuisanceRangeModifier.cpp index a9cf112dd8..24255b1edb 100644 --- a/modules/spb/src/NuisanceRangeModifier.cpp +++ b/modules/spb/src/NuisanceRangeModifier.cpp @@ -2,7 +2,7 @@ * \file spb/NuisanceRangeModifier.cpp * \brief Ensure that a Nuisance stays within its set range. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/PbcBoxedMover.cpp b/modules/spb/src/PbcBoxedMover.cpp index cf6fd46161..1e5a38f648 100644 --- a/modules/spb/src/PbcBoxedMover.cpp +++ b/modules/spb/src/PbcBoxedMover.cpp @@ -2,7 +2,7 @@ * \file PbcBoxedMover.cpp * \brief A mover that keeps a particle in a box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/PbcBoxedRigidBodyMover.cpp b/modules/spb/src/PbcBoxedRigidBodyMover.cpp index 7b4072ed5c..c60947faf6 100644 --- a/modules/spb/src/PbcBoxedRigidBodyMover.cpp +++ b/modules/spb/src/PbcBoxedRigidBodyMover.cpp @@ -2,7 +2,7 @@ * \file PbcBoxedRigidBodyMover.cpp * \brief A mover that transforms a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/RMSDMetric.cpp b/modules/spb/src/RMSDMetric.cpp index b51b7858f4..37c96863fb 100644 --- a/modules/spb/src/RMSDMetric.cpp +++ b/modules/spb/src/RMSDMetric.cpp @@ -2,7 +2,7 @@ * \file RMSDMetric.cpp * \brief Distance RMSD Metric with PBC and identical particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/RigidBodyNewMover.cpp b/modules/spb/src/RigidBodyNewMover.cpp index f4893709f7..151d5bde90 100644 --- a/modules/spb/src/RigidBodyNewMover.cpp +++ b/modules/spb/src/RigidBodyNewMover.cpp @@ -2,7 +2,7 @@ * \file RigidBodyNewMover.cpp * \brief A mover that transforms a rigid body * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/RigidBodyPackingScore.cpp b/modules/spb/src/RigidBodyPackingScore.cpp index 6e5e2dff2c..710ef349dc 100644 --- a/modules/spb/src/RigidBodyPackingScore.cpp +++ b/modules/spb/src/RigidBodyPackingScore.cpp @@ -2,7 +2,7 @@ * \file RigidBodyPackingScore.cpp * \brief A Score on the crossing angle between two rigid bodies * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/SameParticlePairFilter.cpp b/modules/spb/src/SameParticlePairFilter.cpp index 0aac88c765..1ff25fee89 100644 --- a/modules/spb/src/SameParticlePairFilter.cpp +++ b/modules/spb/src/SameParticlePairFilter.cpp @@ -2,7 +2,7 @@ * \file BondPairFilter.cpp * \brief A fake container that returns true if a pair of particles are bonded * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/SameRigidBodyPairFilter.cpp b/modules/spb/src/SameRigidBodyPairFilter.cpp index 0ebd9d8df7..1171f3b1dc 100644 --- a/modules/spb/src/SameRigidBodyPairFilter.cpp +++ b/modules/spb/src/SameRigidBodyPairFilter.cpp @@ -2,7 +2,7 @@ * \file BondPairFilter.cpp * \brief A fake container that returns true if a pair of particles are bonded * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/TiltSingletonScore.cpp b/modules/spb/src/TiltSingletonScore.cpp index 3ed0829ec8..81502c40b5 100644 --- a/modules/spb/src/TiltSingletonScore.cpp +++ b/modules/spb/src/TiltSingletonScore.cpp @@ -2,7 +2,7 @@ * \file TiltSingletonScore.cpp * \brief A Score on the distance to a fixed point. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/spb/src/TransformationSymmetry.cpp b/modules/spb/src/TransformationSymmetry.cpp index 7b4e82582e..a7528489f7 100644 --- a/modules/spb/src/TransformationSymmetry.cpp +++ b/modules/spb/src/TransformationSymmetry.cpp @@ -2,7 +2,7 @@ * \file TransformationSymmetry.cpp * \brief Transform a particle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include "IMP/spb/TransformationSymmetry.h" diff --git a/modules/spb/src/TwoStateGoModelRestraint.cpp b/modules/spb/src/TwoStateGoModelRestraint.cpp index b07933b1bf..818f1780d1 100644 --- a/modules/spb/src/TwoStateGoModelRestraint.cpp +++ b/modules/spb/src/TwoStateGoModelRestraint.cpp @@ -1,7 +1,7 @@ /** * \file TwoStateGoModelRestraint.cpp \brief FRET_R restraint * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/UniformBoundedRestraint.cpp b/modules/spb/src/UniformBoundedRestraint.cpp index 49627037e1..f40dec95e8 100644 --- a/modules/spb/src/UniformBoundedRestraint.cpp +++ b/modules/spb/src/UniformBoundedRestraint.cpp @@ -2,7 +2,7 @@ * \file spb/ UniformBoundedRestraint.h * \brief * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/spb/src/pt_stuff.cpp b/modules/spb/src/pt_stuff.cpp index 120b395e66..f9c61c6f16 100644 --- a/modules/spb/src/pt_stuff.cpp +++ b/modules/spb/src/pt_stuff.cpp @@ -2,7 +2,7 @@ * \file pt_stuff.cpp * \brief Useful stuff for parallel tempering * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/spb_ISD_particles.cpp b/modules/spb/src/spb_ISD_particles.cpp index c5457252bc..977b6f063f 100644 --- a/modules/spb/src/spb_ISD_particles.cpp +++ b/modules/spb/src/spb_ISD_particles.cpp @@ -2,7 +2,7 @@ * \file spb_ISD_particles.cpp * \brief SPB ISD particles * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/spb_assemble_restraints.cpp b/modules/spb/src/spb_assemble_restraints.cpp index 9777771e4d..04402bce19 100644 --- a/modules/spb/src/spb_assemble_restraints.cpp +++ b/modules/spb/src/spb_assemble_restraints.cpp @@ -2,7 +2,7 @@ * \file spb_create_restraints.cpp * \brief Assemble the restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/spb_parser.cpp b/modules/spb/src/spb_parser.cpp index b5f698b830..84f4b87bde 100644 --- a/modules/spb/src/spb_parser.cpp +++ b/modules/spb/src/spb_parser.cpp @@ -2,7 +2,7 @@ * \file spb_parser.cpp * \brief SPB parser * -* Copyright 2007-2021 IMP Inventors. All rights reserved. +* Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/spb_representation.cpp b/modules/spb/src/spb_representation.cpp index 1e0047e681..377d9cea13 100644 --- a/modules/spb/src/spb_representation.cpp +++ b/modules/spb/src/spb_representation.cpp @@ -2,7 +2,7 @@ * \file spb_representation.cpp * \brief SPB Representation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/spb_restraint.cpp b/modules/spb/src/spb_restraint.cpp index 57a9ca59a4..e640bf13b0 100644 --- a/modules/spb/src/spb_restraint.cpp +++ b/modules/spb/src/spb_restraint.cpp @@ -2,7 +2,7 @@ * \file spb_restraint.cpp * \brief SPB Restraints * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/spb/src/spb_sampler.cpp b/modules/spb/src/spb_sampler.cpp index e1acd689a0..e9dd90586c 100644 --- a/modules/spb/src/spb_sampler.cpp +++ b/modules/spb/src/spb_sampler.cpp @@ -2,7 +2,7 @@ * \file spb_sampler.cpp * \brief SPB MonteCarlo * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/include/ChiSquareMetric.h b/modules/statistics/include/ChiSquareMetric.h index 3c31b8a554..19ab6ea121 100644 --- a/modules/statistics/include/ChiSquareMetric.h +++ b/modules/statistics/include/ChiSquareMetric.h @@ -2,7 +2,7 @@ * \file IMP/statistics/ChiSquareMetric.h * \brief Chi2 Metric * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPSTATISTICS_CHI_SQUARE_METRIC_H diff --git a/modules/statistics/include/Embedding.h b/modules/statistics/include/Embedding.h index 24e01143b2..65876a2fc8 100644 --- a/modules/statistics/include/Embedding.h +++ b/modules/statistics/include/Embedding.h @@ -2,7 +2,7 @@ * \file IMP/statistics/Embedding.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/HistogramD.h b/modules/statistics/include/HistogramD.h index 2b8e45c7f3..ed5681e2d0 100644 --- a/modules/statistics/include/HistogramD.h +++ b/modules/statistics/include/HistogramD.h @@ -1,7 +1,7 @@ /** * \file IMP/statistics/HistogramD.h \brief Holds a histogram * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/Metric.h b/modules/statistics/include/Metric.h index e9795f238f..e8414523c3 100644 --- a/modules/statistics/include/Metric.h +++ b/modules/statistics/include/Metric.h @@ -2,7 +2,7 @@ * \file IMP/statistics/Metric.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/PartitionalClustering.h b/modules/statistics/include/PartitionalClustering.h index d98c5bbd8f..eda437856b 100644 --- a/modules/statistics/include/PartitionalClustering.h +++ b/modules/statistics/include/PartitionalClustering.h @@ -2,7 +2,7 @@ * \file IMP/statistics/PartitionalClustering.h * \brief Compute a distance metric between two points * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/PartitionalClusteringWithCenter.h b/modules/statistics/include/PartitionalClusteringWithCenter.h index b70ce82db1..f49b7a228d 100644 --- a/modules/statistics/include/PartitionalClusteringWithCenter.h +++ b/modules/statistics/include/PartitionalClusteringWithCenter.h @@ -2,7 +2,7 @@ * \file IMP/statistics/PartitionalClusteringWithCenter.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/RecursivePartitionalClusteringEmbedding.h b/modules/statistics/include/RecursivePartitionalClusteringEmbedding.h index 361c50d20a..076a20b0ed 100644 --- a/modules/statistics/include/RecursivePartitionalClusteringEmbedding.h +++ b/modules/statistics/include/RecursivePartitionalClusteringEmbedding.h @@ -2,7 +2,7 @@ * \file IMP/statistics/RecursivePartitionalClusteringEmbedding.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/RecursivePartitionalClusteringMetric.h b/modules/statistics/include/RecursivePartitionalClusteringMetric.h index 0d37419b1b..194d9fcda5 100644 --- a/modules/statistics/include/RecursivePartitionalClusteringMetric.h +++ b/modules/statistics/include/RecursivePartitionalClusteringMetric.h @@ -2,7 +2,7 @@ * \file IMP/statistics/RecursivePartitionalClusteringMetric.h * \brief Metric for clustering data that has already been clustered once. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/embeddings.h b/modules/statistics/include/embeddings.h index 3c28f2bfbf..2d5cf3c48e 100644 --- a/modules/statistics/include/embeddings.h +++ b/modules/statistics/include/embeddings.h @@ -2,7 +2,7 @@ * \file IMP/statistics/embeddings.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/ClusteringEngine.h b/modules/statistics/include/internal/ClusteringEngine.h index dce57d73c4..0632c16d9a 100644 --- a/modules/statistics/include/internal/ClusteringEngine.h +++ b/modules/statistics/include/internal/ClusteringEngine.h @@ -2,7 +2,7 @@ * \file IMP/statistics/ClusteringEngine.h * \brief Virtual anchor points clustering engine * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/DataPoints.h b/modules/statistics/include/internal/DataPoints.h index d2ef9e3c27..c30ba95be1 100644 --- a/modules/statistics/include/internal/DataPoints.h +++ b/modules/statistics/include/internal/DataPoints.h @@ -2,7 +2,7 @@ * \file IMP/statistics/DataPoints.h * \brief Handling of data for anchor points segmentation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMCenters.h b/modules/statistics/include/internal/KMCenters.h index a42e81bb79..198ef2463b 100644 --- a/modules/statistics/include/internal/KMCenters.h +++ b/modules/statistics/include/internal/KMCenters.h @@ -1,7 +1,7 @@ /** * \file KMCenters.h \brief Holds the centers of the clusters * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMCentersNode.h b/modules/statistics/include/internal/KMCentersNode.h index 9c15fe5f22..da4562f892 100644 --- a/modules/statistics/include/internal/KMCentersNode.h +++ b/modules/statistics/include/internal/KMCentersNode.h @@ -1,7 +1,7 @@ /** * \file KMCentersNode.h \brief generic node of the kc-tree * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMCentersNodeLeaf.h b/modules/statistics/include/internal/KMCentersNodeLeaf.h index 01ea021338..effb06a713 100644 --- a/modules/statistics/include/internal/KMCentersNodeLeaf.h +++ b/modules/statistics/include/internal/KMCentersNodeLeaf.h @@ -1,7 +1,7 @@ /** * \file KMCentersNode.h \brief leaf node of the kc-tree * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMCentersNodeSplit.h b/modules/statistics/include/internal/KMCentersNodeSplit.h index a692de7cd7..5f50b34718 100644 --- a/modules/statistics/include/internal/KMCentersNodeSplit.h +++ b/modules/statistics/include/internal/KMCentersNodeSplit.h @@ -2,7 +2,7 @@ * \file KMCentersNodeSplit.h * \brief a split node in the kc-tree with two children * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMCentersTree.h b/modules/statistics/include/internal/KMCentersTree.h index 9e650b8b07..75b5ddeab0 100644 --- a/modules/statistics/include/internal/KMCentersTree.h +++ b/modules/statistics/include/internal/KMCentersTree.h @@ -1,7 +1,7 @@ /** * \file KMCentersTree.h \brief A tree that handles point partition * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMData.h b/modules/statistics/include/internal/KMData.h index ac99549c7f..0a576967c3 100644 --- a/modules/statistics/include/internal/KMData.h +++ b/modules/statistics/include/internal/KMData.h @@ -1,7 +1,7 @@ /** * \file KMData.h \brief Holds data points to cluster using k-means * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMFilterCenters.h b/modules/statistics/include/internal/KMFilterCenters.h index 36fb1cbf58..ba3bbc19da 100644 --- a/modules/statistics/include/internal/KMFilterCenters.h +++ b/modules/statistics/include/internal/KMFilterCenters.h @@ -2,7 +2,7 @@ * \file KMFilterCenters.h * \brief Provides efficient algorithm for compuing distortions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMLProxy.h b/modules/statistics/include/internal/KMLProxy.h index 57a1ba632d..2f681ad675 100644 --- a/modules/statistics/include/internal/KMLProxy.h +++ b/modules/statistics/include/internal/KMLProxy.h @@ -1,7 +1,7 @@ /** * \file KMLProxy.h \brief proxy to k-means * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMLocalSearch.h b/modules/statistics/include/internal/KMLocalSearch.h index 723142fc37..58ae6bd874 100644 --- a/modules/statistics/include/internal/KMLocalSearch.h +++ b/modules/statistics/include/internal/KMLocalSearch.h @@ -2,7 +2,7 @@ * \file KMLocalSearch.h \brief Generic algorithm from k-means * clustering by local search * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMLocalSearchLloyd.h b/modules/statistics/include/internal/KMLocalSearchLloyd.h index 839356710b..53dd6d8c46 100644 --- a/modules/statistics/include/internal/KMLocalSearchLloyd.h +++ b/modules/statistics/include/internal/KMLocalSearchLloyd.h @@ -2,7 +2,7 @@ * \file KMLocalSearchLloyd.h * \brief Lloyd's algorithm with random restarts * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMRectangle.h b/modules/statistics/include/internal/KMRectangle.h index 9d8ab3ac86..bc6e459017 100644 --- a/modules/statistics/include/internal/KMRectangle.h +++ b/modules/statistics/include/internal/KMRectangle.h @@ -1,7 +1,7 @@ /** * \file KMRectangle.h \brief Orthogonal (axis aligned) rectangle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/KMTerminationCondition.h b/modules/statistics/include/internal/KMTerminationCondition.h index f0515ef8f3..eea11a1d5f 100644 --- a/modules/statistics/include/internal/KMTerminationCondition.h +++ b/modules/statistics/include/internal/KMTerminationCondition.h @@ -2,7 +2,7 @@ * \file KMTerminationCondition.h * \brief Stores data controlling the termination and phase changes * of the kmean clustering - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/TrivialPartitionalClustering.h b/modules/statistics/include/internal/TrivialPartitionalClustering.h index 4fe365d3af..01da395c30 100644 --- a/modules/statistics/include/internal/TrivialPartitionalClustering.h +++ b/modules/statistics/include/internal/TrivialPartitionalClustering.h @@ -2,7 +2,7 @@ * \file IMP/statistics/internal/TrivialPartitionalClustering.h * \brief Partitional clustering with a static list of cluster assignments. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/VQClustering.h b/modules/statistics/include/internal/VQClustering.h index 4b62ab64fb..da1e308138 100644 --- a/modules/statistics/include/internal/VQClustering.h +++ b/modules/statistics/include/internal/VQClustering.h @@ -2,7 +2,7 @@ * \file IMP/statistics/VQClustering.h * \brief Vector quantization clustering. Based on Wriggers et at, JMB 1998 * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/centrality_clustering.h b/modules/statistics/include/internal/centrality_clustering.h index 1ebc10b117..e582bcc3d8 100644 --- a/modules/statistics/include/internal/centrality_clustering.h +++ b/modules/statistics/include/internal/centrality_clustering.h @@ -1,7 +1,7 @@ /** * \file random_generator.h \brief random number generator * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/histogram.h b/modules/statistics/include/internal/histogram.h index d535e1046c..46a6ee8a5f 100644 --- a/modules/statistics/include/internal/histogram.h +++ b/modules/statistics/include/internal/histogram.h @@ -1,7 +1,7 @@ /** * \file random_generator.h \brief random number generator * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/internal/random_generator.h b/modules/statistics/include/internal/random_generator.h index f4e898bfb1..8577136653 100644 --- a/modules/statistics/include/internal/random_generator.h +++ b/modules/statistics/include/internal/random_generator.h @@ -1,7 +1,7 @@ /** * \file random_generator.h \brief random number generator * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/metric_clustering.h b/modules/statistics/include/metric_clustering.h index 3a8da7c41b..a0bc7fa840 100644 --- a/modules/statistics/include/metric_clustering.h +++ b/modules/statistics/include/metric_clustering.h @@ -2,7 +2,7 @@ * \file IMP/statistics/metric_clustering.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/metrics.h b/modules/statistics/include/metrics.h index f93fbbb9fa..2917ffa95d 100644 --- a/modules/statistics/include/metrics.h +++ b/modules/statistics/include/metrics.h @@ -2,7 +2,7 @@ * \file IMP/statistics/metrics.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/point_clustering.h b/modules/statistics/include/point_clustering.h index 513e657968..6780a6f1bb 100644 --- a/modules/statistics/include/point_clustering.h +++ b/modules/statistics/include/point_clustering.h @@ -2,7 +2,7 @@ * \file IMP/statistics/point_clustering.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/python_only.h b/modules/statistics/include/python_only.h index 6ba4be7277..3f1c6d79a0 100644 --- a/modules/statistics/include/python_only.h +++ b/modules/statistics/include/python_only.h @@ -1,7 +1,7 @@ /** * \file IMP/statistics/python_only.h \brief Python-only functionality * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/include/utility.h b/modules/statistics/include/utility.h index 0bd8062081..63ce2aed5a 100644 --- a/modules/statistics/include/utility.h +++ b/modules/statistics/include/utility.h @@ -2,7 +2,7 @@ * \file IMP/statistics/utility.h * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/src/ChiSquareMetric.cpp b/modules/statistics/src/ChiSquareMetric.cpp index 2f6a80dd86..a897f26677 100644 --- a/modules/statistics/src/ChiSquareMetric.cpp +++ b/modules/statistics/src/ChiSquareMetric.cpp @@ -2,7 +2,7 @@ * \file ChiSquareMetric.cpp * \brief Chi2 Metric * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/statistics/src/Embedding.cpp b/modules/statistics/src/Embedding.cpp index 086418cb05..c23ef2fe3f 100644 --- a/modules/statistics/src/Embedding.cpp +++ b/modules/statistics/src/Embedding.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/HistogramD.cpp b/modules/statistics/src/HistogramD.cpp index 46b6b1fd77..f03c856ea8 100644 --- a/modules/statistics/src/HistogramD.cpp +++ b/modules/statistics/src/HistogramD.cpp @@ -1,7 +1,7 @@ /** * \file Histogram.cpp \brief simple histogram class * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/statistics/src/Metric.cpp b/modules/statistics/src/Metric.cpp index 3d5ed0530b..85cca1b37f 100644 --- a/modules/statistics/src/Metric.cpp +++ b/modules/statistics/src/Metric.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/PartitionalClustering.cpp b/modules/statistics/src/PartitionalClustering.cpp index b19de7ca2e..4de40b4b38 100644 --- a/modules/statistics/src/PartitionalClustering.cpp +++ b/modules/statistics/src/PartitionalClustering.cpp @@ -1,7 +1,7 @@ /** * \file Clustering.cpp \brief Holds data points to cluster using k-means * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/PartitionalClusteringWithCenter.cpp b/modules/statistics/src/PartitionalClusteringWithCenter.cpp index 667672dbc5..f8dc4b6333 100644 --- a/modules/statistics/src/PartitionalClusteringWithCenter.cpp +++ b/modules/statistics/src/PartitionalClusteringWithCenter.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/RecursivePartitionalClusteringEmbedding.cpp b/modules/statistics/src/RecursivePartitionalClusteringEmbedding.cpp index 393a064c17..78ad4ebce2 100644 --- a/modules/statistics/src/RecursivePartitionalClusteringEmbedding.cpp +++ b/modules/statistics/src/RecursivePartitionalClusteringEmbedding.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/RecursivePartitionalClusteringMetric.cpp b/modules/statistics/src/RecursivePartitionalClusteringMetric.cpp index e63986899a..8b43143937 100644 --- a/modules/statistics/src/RecursivePartitionalClusteringMetric.cpp +++ b/modules/statistics/src/RecursivePartitionalClusteringMetric.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/embeddings.cpp b/modules/statistics/src/embeddings.cpp index 30a819378d..c037000899 100644 --- a/modules/statistics/src/embeddings.cpp +++ b/modules/statistics/src/embeddings.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/internal/DataPoints.cpp b/modules/statistics/src/internal/DataPoints.cpp index c757e5afe4..09665352e7 100644 --- a/modules/statistics/src/internal/DataPoints.cpp +++ b/modules/statistics/src/internal/DataPoints.cpp @@ -2,7 +2,7 @@ * \file DataPoints.cpp * \brief Handling of data for anchor points segmentation * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/internal/KMCenters.cpp b/modules/statistics/src/internal/KMCenters.cpp index 41ffd5cf56..13e80ac9e4 100644 --- a/modules/statistics/src/internal/KMCenters.cpp +++ b/modules/statistics/src/internal/KMCenters.cpp @@ -2,7 +2,7 @@ * \file KMCenters.cpp * \brief Holds the centers of the clusters * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/internal/KMCentersNode.cpp b/modules/statistics/src/internal/KMCentersNode.cpp index cd07ca08cb..28a233faf1 100644 --- a/modules/statistics/src/internal/KMCentersNode.cpp +++ b/modules/statistics/src/internal/KMCentersNode.cpp @@ -2,7 +2,7 @@ * \file KMCenetersNode.cpp * \brief generic node of the kc-tree * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/internal/KMCentersNodeLeaf.cpp b/modules/statistics/src/internal/KMCentersNodeLeaf.cpp index 98b8e2674c..a46a7d6b93 100644 --- a/modules/statistics/src/internal/KMCentersNodeLeaf.cpp +++ b/modules/statistics/src/internal/KMCentersNodeLeaf.cpp @@ -2,7 +2,7 @@ * \file KMCenetersNode.cpp * \brief leaf node of the kc-tree * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/src/internal/KMCentersNodeSplit.cpp b/modules/statistics/src/internal/KMCentersNodeSplit.cpp index 2ebba741f9..3f184bf7cd 100644 --- a/modules/statistics/src/internal/KMCentersNodeSplit.cpp +++ b/modules/statistics/src/internal/KMCentersNodeSplit.cpp @@ -2,7 +2,7 @@ * \file KMCenetersNodeSplit.cpp * \brief a split node in the kc-tree with two children * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/src/internal/KMCentersTree.cpp b/modules/statistics/src/internal/KMCentersTree.cpp index 824b3214c0..2067010829 100644 --- a/modules/statistics/src/internal/KMCentersTree.cpp +++ b/modules/statistics/src/internal/KMCentersTree.cpp @@ -1,7 +1,7 @@ /** * \file KMCentersTree.cpp \brief A tree that handles point partition * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/internal/KMData.cpp b/modules/statistics/src/internal/KMData.cpp index 050a3bc212..ce2934740b 100644 --- a/modules/statistics/src/internal/KMData.cpp +++ b/modules/statistics/src/internal/KMData.cpp @@ -1,7 +1,7 @@ /** * \file KMData.cpp \brief Holds data points to cluster using k-means * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/internal/KMFilterCenters.cpp b/modules/statistics/src/internal/KMFilterCenters.cpp index fa7b7faa3b..72c4d8997d 100644 --- a/modules/statistics/src/internal/KMFilterCenters.cpp +++ b/modules/statistics/src/internal/KMFilterCenters.cpp @@ -2,7 +2,7 @@ * \file KMFilterCenters.cpp * \brief Provides efficient algorithm for compuing distortions * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/src/internal/KMLProxy.cpp b/modules/statistics/src/internal/KMLProxy.cpp index 3b4e827117..58ebd7acc1 100644 --- a/modules/statistics/src/internal/KMLProxy.cpp +++ b/modules/statistics/src/internal/KMLProxy.cpp @@ -1,7 +1,7 @@ /** * \file KMLProxy.cpp \brief proxy to k-mean algorithm * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/modules/statistics/src/internal/KMLocalSearch.cpp b/modules/statistics/src/internal/KMLocalSearch.cpp index b862acba16..0877530157 100644 --- a/modules/statistics/src/internal/KMLocalSearch.cpp +++ b/modules/statistics/src/internal/KMLocalSearch.cpp @@ -2,7 +2,7 @@ * \file KMLocalSearch.cpp \brief Generic algorithm from k-means * clustering by local search * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/src/internal/KMLocalSearchLloyd.cpp b/modules/statistics/src/internal/KMLocalSearchLloyd.cpp index 3c4ee5bd6e..2d9231d77d 100644 --- a/modules/statistics/src/internal/KMLocalSearchLloyd.cpp +++ b/modules/statistics/src/internal/KMLocalSearchLloyd.cpp @@ -2,7 +2,7 @@ * \file KMLocalSearchLloyd.cpp * \brief Lloyd's algorithm with random restarts * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/internal/KMRectangle.cpp b/modules/statistics/src/internal/KMRectangle.cpp index 9327852e75..d6c47637c7 100644 --- a/modules/statistics/src/internal/KMRectangle.cpp +++ b/modules/statistics/src/internal/KMRectangle.cpp @@ -1,7 +1,7 @@ /** * \file KMRectangle.cpp \brief Orthogonal (axis aligned) rectangle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/internal/VQClustering.cpp b/modules/statistics/src/internal/VQClustering.cpp index 231a70c09e..6b8d15ba11 100644 --- a/modules/statistics/src/internal/VQClustering.cpp +++ b/modules/statistics/src/internal/VQClustering.cpp @@ -2,7 +2,7 @@ * \file VQClustering.cpp * \brief Vector quantization clustering. Based on Wriggers et at, JMB 1998 * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/statistics/src/internal/centrality_clustering.cpp b/modules/statistics/src/internal/centrality_clustering.cpp index 94149764d7..9dffbc1d67 100644 --- a/modules/statistics/src/internal/centrality_clustering.cpp +++ b/modules/statistics/src/internal/centrality_clustering.cpp @@ -1,7 +1,7 @@ /** * \file KMRectangle.cpp \brief Orthogonal (axis aligned) rectangle * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/metric_clustering.cpp b/modules/statistics/src/metric_clustering.cpp index 935d5431f2..11a3d9f934 100644 --- a/modules/statistics/src/metric_clustering.cpp +++ b/modules/statistics/src/metric_clustering.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/metrics.cpp b/modules/statistics/src/metrics.cpp index be758b9321..c65108ddeb 100644 --- a/modules/statistics/src/metrics.cpp +++ b/modules/statistics/src/metrics.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/point_clustering.cpp b/modules/statistics/src/point_clustering.cpp index d1f5b604d6..025e8fab9b 100644 --- a/modules/statistics/src/point_clustering.cpp +++ b/modules/statistics/src/point_clustering.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/src/utility.cpp b/modules/statistics/src/utility.cpp index 6a197222eb..9cccbe0668 100644 --- a/modules/statistics/src/utility.cpp +++ b/modules/statistics/src/utility.cpp @@ -2,7 +2,7 @@ * \file point_clustering.cpp * \brief Cluster sets of points. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/statistics/test/test_histograph_1d.cpp b/modules/statistics/test/test_histograph_1d.cpp index 0f41cb9865..e8964cc8bd 100644 --- a/modules/statistics/test/test_histograph_1d.cpp +++ b/modules/statistics/test/test_histograph_1d.cpp @@ -2,7 +2,7 @@ * \file test_cache.cpp * \brief A nullptr-initialized pointer to an \imp Object. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/symmetry/include/BallMover.h b/modules/symmetry/include/BallMover.h index 32b4f05216..cc2c784d5c 100644 --- a/modules/symmetry/include/BallMover.h +++ b/modules/symmetry/include/BallMover.h @@ -2,7 +2,7 @@ * \file IMP/symmetry/BallMover.h * \brief A mover that keeps a particle in a box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/symmetry/include/RigidBodyMover.h b/modules/symmetry/include/RigidBodyMover.h index 20c31d279e..8b5ca14059 100644 --- a/modules/symmetry/include/RigidBodyMover.h +++ b/modules/symmetry/include/RigidBodyMover.h @@ -2,7 +2,7 @@ * \file IMP/symmetry/RigidBodyMover.h * \brief A mover that keeps a rigid body in a box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/symmetry/src/BallMover.cpp b/modules/symmetry/src/BallMover.cpp index bcf2bc7fcc..b4ef07fdd3 100644 --- a/modules/symmetry/src/BallMover.cpp +++ b/modules/symmetry/src/BallMover.cpp @@ -2,7 +2,7 @@ * \file BallMover.cpp * \brief A mover that keeps a particle in a box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/symmetry/src/RigidBodyMover.cpp b/modules/symmetry/src/RigidBodyMover.cpp index ebaf0b5382..aa44051630 100644 --- a/modules/symmetry/src/RigidBodyMover.cpp +++ b/modules/symmetry/src/RigidBodyMover.cpp @@ -2,7 +2,7 @@ * \file RigidBodyMover.cpp * \brief A mover that keeps a rigid body in a box * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ #include diff --git a/modules/test/include/test_macros.h b/modules/test/include/test_macros.h index bca7fd12fa..91935f25b2 100644 --- a/modules/test/include/test_macros.h +++ b/modules/test/include/test_macros.h @@ -7,7 +7,7 @@ * test suite). For runtime checks of IMP itself, see IMP_INTERNAL_CHECK * and IMP_USAGE_CHECK. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/config_templates/header.h b/tools/build/config_templates/header.h index 66af329d4f..a900dcea03 100644 --- a/tools/build/config_templates/header.h +++ b/tools/build/config_templates/header.h @@ -19,7 +19,7 @@ * There are similar macros for module code that is designed to be for * internal use only. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/config_templates/src.cpp b/tools/build/config_templates/src.cpp index 6070b1b3f9..266954d77a 100644 --- a/tools/build/config_templates/src.cpp +++ b/tools/build/config_templates/src.cpp @@ -2,7 +2,7 @@ * \file config.cpp * \brief %(name)s module version information. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/container_templates/container/ClassnameContainerSet.h b/tools/build/container_templates/container/ClassnameContainerSet.h index e7ce3b08eb..2a35de7224 100644 --- a/tools/build/container_templates/container/ClassnameContainerSet.h +++ b/tools/build/container_templates/container/ClassnameContainerSet.h @@ -2,7 +2,7 @@ * \file IMP/container/ClassnameContainerSet.h * \brief Store a set of ClassnameContainers * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CLASSNAME_CONTAINER_SET_H diff --git a/tools/build/container_templates/container/ClassnameContainerStatistics.h b/tools/build/container_templates/container/ClassnameContainerStatistics.h index ca6b7515c9..d702b7facc 100644 --- a/tools/build/container_templates/container/ClassnameContainerStatistics.h +++ b/tools/build/container_templates/container/ClassnameContainerStatistics.h @@ -2,7 +2,7 @@ * \file IMP/container/ClassnameContainerStatistics.h * \brief A container for Classnames. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CLASSNAME_CONTAINER_STATISTICS_H diff --git a/tools/build/container_templates/container/ClassnamesConstraint.h b/tools/build/container_templates/container/ClassnamesConstraint.h index f7cc056990..3894b5f3d8 100644 --- a/tools/build/container_templates/container/ClassnamesConstraint.h +++ b/tools/build/container_templates/container/ClassnamesConstraint.h @@ -3,7 +3,7 @@ * \brief Use a ClassnameModifier applied to a PLURALVARIABLETYPE to * maintain an invariant * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CLASSNAMES_CONSTRAINT_H diff --git a/tools/build/container_templates/container/ClassnamesOptimizerState.h b/tools/build/container_templates/container/ClassnamesOptimizerState.h index 7c1e2e9d08..48c4d6bd26 100644 --- a/tools/build/container_templates/container/ClassnamesOptimizerState.h +++ b/tools/build/container_templates/container/ClassnamesOptimizerState.h @@ -3,7 +3,7 @@ * \brief Use a ClassnameModifier applied to a PLURALVARIABLETYPE to * maintain an invariant * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CLASSNAMES_OPTIMIZER_STATE_H diff --git a/tools/build/container_templates/container/ClassnamesRestraint.h b/tools/build/container_templates/container/ClassnamesRestraint.h index 98a477a512..372b64554f 100644 --- a/tools/build/container_templates/container/ClassnamesRestraint.h +++ b/tools/build/container_templates/container/ClassnamesRestraint.h @@ -2,7 +2,7 @@ * \file IMP/container/ClassnamesRestraint.h * \brief Apply a ClassnameScore to each Classname in a list. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/container_templates/container/DistributeClassnamesScoreState.h b/tools/build/container_templates/container/DistributeClassnamesScoreState.h index c8d69e5d10..34ff52a730 100644 --- a/tools/build/container_templates/container/DistributeClassnamesScoreState.h +++ b/tools/build/container_templates/container/DistributeClassnamesScoreState.h @@ -2,7 +2,7 @@ * \file IMP/container/DistributeClassnamesScoreState.h * \brief Apply a ClassnameScore to each Classname in a list. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/container_templates/container/DynamicListClassnameContainer.h b/tools/build/container_templates/container/DynamicListClassnameContainer.h index 9306ef4528..adb997b09d 100644 --- a/tools/build/container_templates/container/DynamicListClassnameContainer.h +++ b/tools/build/container_templates/container/DynamicListClassnameContainer.h @@ -2,7 +2,7 @@ * \file IMP/container/DynamicListClassnameContainer.h * \brief Store a list of PLURALVARIABLETYPE * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_DYNAMIC_LIST_CLASSNAME_CONTAINER_H diff --git a/tools/build/container_templates/container/EventClassnamesOptimizerState.h b/tools/build/container_templates/container/EventClassnamesOptimizerState.h index 0a75020e5d..3a5c151c28 100644 --- a/tools/build/container_templates/container/EventClassnamesOptimizerState.h +++ b/tools/build/container_templates/container/EventClassnamesOptimizerState.h @@ -2,7 +2,7 @@ * \file IMP/container/EventClassnamesOptimizerState.h * \brief Define some predicates. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_EVENT_CLASSNAMES_OPTIMIZER_STATE_H diff --git a/tools/build/container_templates/container/InContainerClassnameFilter.h b/tools/build/container_templates/container/InContainerClassnameFilter.h index f06c42fe81..b4cf1d5cd2 100644 --- a/tools/build/container_templates/container/InContainerClassnameFilter.h +++ b/tools/build/container_templates/container/InContainerClassnameFilter.h @@ -2,7 +2,7 @@ * \file IMP/container/InContainerClassnameFilter.h * \brief A filter for Classnames. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_IN_CONTAINER_CLASSNAME_FILTER_H diff --git a/tools/build/container_templates/container/ListClassnameContainer.h b/tools/build/container_templates/container/ListClassnameContainer.h index 43e8766e27..bd46e3a3c2 100644 --- a/tools/build/container_templates/container/ListClassnameContainer.h +++ b/tools/build/container_templates/container/ListClassnameContainer.h @@ -2,7 +2,7 @@ * \file IMP/container/ListClassnameContainer.h * \brief Store a list of PLURALINDEXTYPE. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_LIST_CLASSNAME_CONTAINER_H diff --git a/tools/build/container_templates/container/MinimumClassnameRestraint.h b/tools/build/container_templates/container/MinimumClassnameRestraint.h index 77a531dc6c..79780c5d5b 100644 --- a/tools/build/container_templates/container/MinimumClassnameRestraint.h +++ b/tools/build/container_templates/container/MinimumClassnameRestraint.h @@ -2,7 +2,7 @@ * \file IMP/container/MinimumClassnameRestraint.h * \brief Score based on the minimum score over a set of Classnames * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_MINIMUM_CLASSNAME_RESTRAINT_H diff --git a/tools/build/container_templates/container/MinimumClassnameScore.h b/tools/build/container_templates/container/MinimumClassnameScore.h index b7bac6b049..2839ca760b 100644 --- a/tools/build/container_templates/container/MinimumClassnameScore.h +++ b/tools/build/container_templates/container/MinimumClassnameScore.h @@ -2,7 +2,7 @@ * \file IMP/container/MinimumClassnameScore.h * \brief Define ClassnameScore. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_MINIMUM_CLASSNAME_SCORE_H diff --git a/tools/build/container_templates/container/PredicateClassnamesRestraint.h b/tools/build/container_templates/container/PredicateClassnamesRestraint.h index 0af517bb92..303a1da099 100644 --- a/tools/build/container_templates/container/PredicateClassnamesRestraint.h +++ b/tools/build/container_templates/container/PredicateClassnamesRestraint.h @@ -2,7 +2,7 @@ * \file IMP/container/PredicateClassnamesRestraint.h * \brief Apply a ClassnameScore to each Classname in a list. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/container_templates/container/classnames.cpp b/tools/build/container_templates/container/classnames.cpp index f82ce66411..d9b93fc333 100644 --- a/tools/build/container_templates/container/classnames.cpp +++ b/tools/build/container_templates/container/classnames.cpp @@ -1,7 +1,7 @@ /** * \file ClassnameContainerStatistics.cpp \brief Container for classname. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/container_templates/container/internal/ClassnameContainerIndex.h b/tools/build/container_templates/container/internal/ClassnameContainerIndex.h index f3f5b0082e..73acdeabab 100644 --- a/tools/build/container_templates/container/internal/ClassnameContainerIndex.h +++ b/tools/build/container_templates/container/internal/ClassnameContainerIndex.h @@ -2,7 +2,7 @@ * \file IMP/container/ClassnameContainerStatistics.h * \brief A container for Classnames. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCONTAINER_CLASSNAME_CONTAINER_INDEX_H diff --git a/tools/build/container_templates/core/ClassnameConstraint.h b/tools/build/container_templates/core/ClassnameConstraint.h index 4a3e0fa4a4..2117f9dba4 100644 --- a/tools/build/container_templates/core/ClassnameConstraint.h +++ b/tools/build/container_templates/core/ClassnameConstraint.h @@ -3,7 +3,7 @@ * \brief Use a ClassnameModifier applied to a PLURALVARIABLETYPE to * maintain an invariant * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_CLASSNAME_CONSTRAINT_H diff --git a/tools/build/container_templates/core/ClassnameRestraint.h b/tools/build/container_templates/core/ClassnameRestraint.h index af7cdd6dfb..8ee9aad8ce 100644 --- a/tools/build/container_templates/core/ClassnameRestraint.h +++ b/tools/build/container_templates/core/ClassnameRestraint.h @@ -2,7 +2,7 @@ * \file IMP/core/ClassnameRestraint.h * \brief Apply a ClassnameScore to a Classname. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/container_templates/core/classname_predicates.cpp b/tools/build/container_templates/core/classname_predicates.cpp index 8dbef7a1d0..3e2d2ac752 100644 --- a/tools/build/container_templates/core/classname_predicates.cpp +++ b/tools/build/container_templates/core/classname_predicates.cpp @@ -1,7 +1,7 @@ /** * \file ClassnamePredicate.cpp \brief Define ClassnamePredicate * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/tools/build/container_templates/core/classname_predicates.h b/tools/build/container_templates/core/classname_predicates.h index 0cbe75f343..f4cad3b669 100644 --- a/tools/build/container_templates/core/classname_predicates.h +++ b/tools/build/container_templates/core/classname_predicates.h @@ -2,7 +2,7 @@ * \file IMP/core/classname_predicates.h * \brief Define some predicates. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPCORE_CLASSNAME_PREDICATES_H diff --git a/tools/build/container_templates/kernel/ClassnameContainer.h b/tools/build/container_templates/kernel/ClassnameContainer.h index 3fcc8c43b8..3bbfae06d2 100644 --- a/tools/build/container_templates/kernel/ClassnameContainer.h +++ b/tools/build/container_templates/kernel/ClassnameContainer.h @@ -2,7 +2,7 @@ * \file IMP/ClassnameContainer.h * \brief A container for Classnames. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_CLASSNAME_CONTAINER_H diff --git a/tools/build/container_templates/kernel/ClassnameDerivativeModifier.h b/tools/build/container_templates/kernel/ClassnameDerivativeModifier.h index 76f42ae861..e0a74a3d5e 100644 --- a/tools/build/container_templates/kernel/ClassnameDerivativeModifier.h +++ b/tools/build/container_templates/kernel/ClassnameDerivativeModifier.h @@ -2,7 +2,7 @@ * \file IMP/ClassnameDerivativeModifier.h * \brief A Modifier on PLURALVARIABLETYPE * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_CLASSNAME_DERIVATIVE_MODIFIER_H diff --git a/tools/build/container_templates/kernel/ClassnameModifier.h b/tools/build/container_templates/kernel/ClassnameModifier.h index 98c716dbac..c50447ade5 100644 --- a/tools/build/container_templates/kernel/ClassnameModifier.h +++ b/tools/build/container_templates/kernel/ClassnameModifier.h @@ -2,7 +2,7 @@ * \file IMP/ClassnameModifier.h * \brief A Modifier on PLURALVARIABLETYPE * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_CLASSNAME_MODIFIER_H diff --git a/tools/build/container_templates/kernel/ClassnamePredicate.h b/tools/build/container_templates/kernel/ClassnamePredicate.h index 1b332fca58..986823d356 100644 --- a/tools/build/container_templates/kernel/ClassnamePredicate.h +++ b/tools/build/container_templates/kernel/ClassnamePredicate.h @@ -2,7 +2,7 @@ * \file IMP/ClassnamePredicate.h * \brief Define ClassnamePredicate. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_CLASSNAME_PREDICATE_H diff --git a/tools/build/container_templates/kernel/ClassnameScore.h b/tools/build/container_templates/kernel/ClassnameScore.h index 5814ab3e96..5e78915753 100644 --- a/tools/build/container_templates/kernel/ClassnameScore.h +++ b/tools/build/container_templates/kernel/ClassnameScore.h @@ -2,7 +2,7 @@ * \file IMP/ClassnameScore.h * \brief Define ClassnameScore. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_CLASSNAME_SCORE_H diff --git a/tools/build/container_templates/kernel/classname_macros.h b/tools/build/container_templates/kernel/classname_macros.h index c7498e1699..824eb1259f 100644 --- a/tools/build/container_templates/kernel/classname_macros.h +++ b/tools/build/container_templates/kernel/classname_macros.h @@ -2,7 +2,7 @@ * \file IMP/classname_macros.h * \brief Macros for various classes. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #ifndef IMPKERNEL_CLASSNAME_MACROS_H diff --git a/tools/build/container_templates/kernel/classnames.cpp b/tools/build/container_templates/kernel/classnames.cpp index d79762f532..e38650eed8 100644 --- a/tools/build/container_templates/kernel/classnames.cpp +++ b/tools/build/container_templates/kernel/classnames.cpp @@ -1,7 +1,7 @@ /** * \file ClassnameContainer.cpp \brief Container for classname. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/tools/build/make_swig_wrapper.py b/tools/build/make_swig_wrapper.py index ec23c5c8a1..db8af80131 100755 --- a/tools/build/make_swig_wrapper.py +++ b/tools/build/make_swig_wrapper.py @@ -75,7 +75,7 @@ def patch_py_wrapper(infile, outfile, module): outfh = open(outfile, "w") in_initial_comment = True header = """# This wrapper is part of IMP, -# Copyright 2007-2021 IMP Inventors. All rights reserved. +# Copyright 2007-2022 IMP Inventors. All rights reserved. from __future__ import print_function, division, absolute_import """ diff --git a/tools/debian/copyright b/tools/debian/copyright index e156978c24..058b418c31 100644 --- a/tools/debian/copyright +++ b/tools/debian/copyright @@ -2,7 +2,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: imp Source: https://integrativemodeling.org/ -Copyright: 2007-2021 IMP Inventors +Copyright: 2007-2022 IMP Inventors License: LGPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by diff --git a/tools/nightly-tests/test-install/test.cpp b/tools/nightly-tests/test-install/test.cpp index 4dac9be24d..3788b7ff5a 100644 --- a/tools/nightly-tests/test-install/test.cpp +++ b/tools/nightly-tests/test-install/test.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/tools/nightly-tests/test-install/test_rmf.cpp b/tools/nightly-tests/test-install/test_rmf.cpp index 0f2aaa1d5a..98029888a8 100644 --- a/tools/nightly-tests/test-install/test_rmf.cpp +++ b/tools/nightly-tests/test-install/test_rmf.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. */ #include diff --git a/tools/w32/pyapp_wrapper.c b/tools/w32/pyapp_wrapper.c index 970ee53418..f8f2b7302b 100644 --- a/tools/w32/pyapp_wrapper.c +++ b/tools/w32/pyapp_wrapper.c @@ -1,7 +1,7 @@ /** * \file pyapp_wrapper.c \brief Windows Python application wrapper. * - * Copyright 2007-2021 IMP Inventors. All rights reserved. + * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ From 6a5fd68daa79e376bfcc8727fc23197489ef8385 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 10 Jan 2022 10:57:12 -0800 Subject: [PATCH 005/155] Squashed 'modules/core/dependency/python-ihm/' changes from a2ea144cf0..32bda4dd99 32bda4dd99 Skip validator example in GitHub Actions 83b84b8b49 Update copyright year 5224f2c2c0 Remove SystemReaderBase class 74be42df20 python-ma doesn't need the complete assembly 5d331f2fe6 Drop SystemBase class 004509b233 Document type for variant arg to read() e8008bf869 Document missing members of System, SystemReader e423dd5e18 Incorporate changes from python-ma 2f426fd5d3 Fix typo git-subtree-dir: modules/core/dependency/python-ihm git-subtree-split: 32bda4dd99c4edd5326053567c6751cf82620060 --- modules/core/dependency/python-ihm/LICENSE | 2 +- .../core/dependency/python-ihm/docs/conf.py | 2 +- .../dependency/python-ihm/docs/dumper.rst | 6 + .../dependency/python-ihm/docs/reader.rst | 7 + .../dependency/python-ihm/ihm/__init__.py | 88 +++++-- .../core/dependency/python-ihm/ihm/dumper.py | 220 +++++++++--------- .../core/dependency/python-ihm/ihm/reader.py | 199 +++++++++------- .../python-ihm/test/test_examples.py | 2 + .../dependency/python-ihm/test/test_main.py | 8 + 9 files changed, 311 insertions(+), 223 deletions(-) diff --git a/modules/core/dependency/python-ihm/LICENSE b/modules/core/dependency/python-ihm/LICENSE index 2501b9d1c9..88777eae03 100644 --- a/modules/core/dependency/python-ihm/LICENSE +++ b/modules/core/dependency/python-ihm/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2018-2021 IHM Working Group +Copyright (c) 2018-2022 IHM Working Group Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/modules/core/dependency/python-ihm/docs/conf.py b/modules/core/dependency/python-ihm/docs/conf.py index 4821f75335..d707deb374 100644 --- a/modules/core/dependency/python-ihm/docs/conf.py +++ b/modules/core/dependency/python-ihm/docs/conf.py @@ -47,7 +47,7 @@ # General information about the project. project = u'Python-IHM' -copyright = u'2018-2021, Benjamin Webb' +copyright = u'2018-2022, Benjamin Webb' author = u'Benjamin Webb' # The version info for the project you're documenting, acts as replacement for diff --git a/modules/core/dependency/python-ihm/docs/dumper.rst b/modules/core/dependency/python-ihm/docs/dumper.rst index 66c478b168..5578010749 100644 --- a/modules/core/dependency/python-ihm/docs/dumper.rst +++ b/modules/core/dependency/python-ihm/docs/dumper.rst @@ -10,4 +10,10 @@ The :mod:`ihm.dumper` Python module .. autoclass:: Dumper :members: +.. autoclass:: Variant + :members: + +.. autoclass:: IHMVariant + :members: + .. autofunction:: write diff --git a/modules/core/dependency/python-ihm/docs/reader.rst b/modules/core/dependency/python-ihm/docs/reader.rst index d5c69b4119..1c86b3fa54 100644 --- a/modules/core/dependency/python-ihm/docs/reader.rst +++ b/modules/core/dependency/python-ihm/docs/reader.rst @@ -20,9 +20,16 @@ The :mod:`ihm.reader` Python module .. autoclass:: SystemReader :members: + :inherited-members: .. autoclass:: IDMapper :members: .. autoclass:: RangeIDMapper :members: + +.. autoclass:: Variant + :members: + +.. autoclass:: IHMVariant + :members: diff --git a/modules/core/dependency/python-ihm/ihm/__init__.py b/modules/core/dependency/python-ihm/ihm/__init__.py index 858d0a599a..279f7de185 100644 --- a/modules/core/dependency/python-ihm/ihm/__init__.py +++ b/modules/core/dependency/python-ihm/ihm/__init__.py @@ -18,6 +18,7 @@ except ImportError: import urllib2 import json +from . import util __version__ = '0.25' @@ -86,7 +87,7 @@ def __init__(self, title=None, id='model'): #: List of all authors of this system, as a list of strings (last name #: followed by initials, e.g. "Smith AJ"). When writing out a file, - #: if this is list is empty, the set of all citation authors (see + #: if this list is empty, the set of all citation authors (see #: :attr:`Citation.authors`) is used instead. self.authors = [] @@ -211,6 +212,26 @@ def __init__(self, title=None, id='model'): #: See :class:`~ihm.flr.FLRData`. self.flr_data = [] + def _make_complete_assembly(self): + """Fill in the complete assembly with all asym units""" + # Clear out any existing components + self.complete_assembly[:] = [] + + # Include all asym units + for asym in self.asym_units: + self.complete_assembly.append(asym) + + def _all_models(self): + """Iterate over all Models in the system""" + # todo: raise an error if a model is present in multiple groups + for group in self._all_model_groups(): + seen_models = {} + for model in group: + if model in seen_models: + continue + seen_models[model] = None + yield group, model + def update_locations_in_repositories(self, repos): """Update all :class:`Location` objects in the system that lie within a checked-out :class:`Repository` to point to that repository. @@ -283,17 +304,6 @@ def _all_model_groups(self, only_in_states=True): yield edge.group_begin yield edge.group_end - def _all_models(self): - """Iterate over all Models in the system""" - # todo: raise an error if a model is present in multiple groups - for group in self._all_model_groups(): - seen_models = {} - for model in group: - if model in seen_models: - continue - seen_models[model] = None - yield group, model - def _all_representations(self): """Iterate over all Representations in the system. This includes all Representations referenced from other objects, @@ -529,14 +539,26 @@ def _all_entity_ranges(self): for comp in f._all_entities_or_asyms()), (d.asym_unit for d in self._all_densities()))) - def _make_complete_assembly(self): - """Fill in the complete assembly with all asym units""" - # Clear out any existing components - self.complete_assembly[:] = [] - - # Include all asym units - for asym in self.asym_units: - self.complete_assembly.append(asym) + def _before_write(self): + """Do any setup necessary before writing out to a file""" + # Here, we initialize all RestraintGroups by removing any assigned ID + for g in self.restraint_groups: + util._remove_id(g) + # Fill in complete assembly + self._make_complete_assembly() + + def _check_after_write(self): + """Make sure everything was successfully written""" + # Here, we check that all RestraintGroups were successfully dumped""" + for g in self.restraint_groups: + if len(g) > 0 and not hasattr(g, '_id'): + raise TypeError( + "RestraintGroup(%s) contains an unsupported combination " + "of Restraints. Due to limitations of the underlying " + "dictionary, all objects in a RestraintGroup must be of " + "the same type, and only certain types (currently only " + "DerivedDistanceRestraint or PredictedContactRestraint) " + "can be grouped." % g) class Software(object): @@ -1180,6 +1202,22 @@ def __hash__(self): entity = property(lambda self: self.asym.entity) +class AsymUnitSegment(object): + """An aligned part of an asymmetric unit. + + Usually these objects are created from + an :class:`AsymUnit`, e.g. to get a segment covering residues 1 through + 3 in `asym` use:: + + asym = ihm.AsymUnit(entity) + seg = asym.segment('--ACG', 1, 3) + """ + def __init__(self, asym, gapped_sequence, seq_id_begin, seq_id_end): + self.asym = asym + self.gapped_sequence = gapped_sequence + self.seq_id_range = (seq_id_begin, seq_id_end) + + class AsymUnit(object): """An asymmetric unit, i.e. a unique instance of an Entity that was modeled. @@ -1240,6 +1278,16 @@ def residue(self, seq_id): """Get a :class:`Residue` at the given sequence position""" return Residue(asym=self, seq_id=seq_id) + def segment(self, gapped_sequence, seq_id_begin, seq_id_end): + """Get an object representing the alignment of part of this sequence. + + :param str gapped_sequence: Sequence of the segment, including gaps. + :param int seq_id_begin: Start of the segment. + :param int seq_id_end: End of the segment. + """ + # todo: cache so we return the same object for same parameters + return AsymUnitSegment(self, gapped_sequence, seq_id_begin, seq_id_end) + seq_id_range = property(lambda self: self.entity.seq_id_range, doc="Sequence range") diff --git a/modules/core/dependency/python-ihm/ihm/dumper.py b/modules/core/dependency/python-ihm/ihm/dumper.py index 5889b637f4..13f48966e0 100644 --- a/modules/core/dependency/python-ihm/ihm/dumper.py +++ b/modules/core/dependency/python-ihm/ihm/dumper.py @@ -711,7 +711,7 @@ def dump(self, system, writer): details=asym.details) -class _AssemblyDumper(Dumper): +class _AssemblyDumperBase(Dumper): def finalize(self, system): # Sort each assembly by entity id/asym id/range def component_key(comp): @@ -749,6 +749,8 @@ def component_key(comp): for a in all_assemblies: a.description = description_by_id[a._id] + +class _AssemblyDumper(_AssemblyDumperBase): def dump(self, system, writer): self.dump_summary(system, writer) self.dump_details(system, writer) @@ -1405,7 +1407,7 @@ def _check_representation(self, obj, asym, type_check, seq_id_range): for x in self.repr_asym_ids[asym._id]))) -class _ModelDumper(Dumper): +class _ModelDumperBase(Dumper): def finalize(self, system): # Remove any existing ID @@ -1429,41 +1431,6 @@ def finalize(self, system): "OrderedProcess. ModelGroups should be " "stored in State objects." % g) - def dump(self, system, writer): - self.dump_model_list(system, writer) - self.dump_model_groups(system, writer) - seen_types = self.dump_atoms(system, writer) - self.dump_spheres(system, writer) - self.dump_atom_type(seen_types, system, writer) - - def dump_model_list(self, system, writer): - with writer.loop("_ihm_model_list", - ["model_id", "model_name", "assembly_id", - "protocol_id", "representation_id"]) as lp: - for group, model in system._all_models(): - lp.write(model_id=model._id, - model_name=model.name, - assembly_id=model.assembly._id, - protocol_id=model.protocol._id - if model.protocol else None, - representation_id=model.representation._id) - - def dump_model_groups(self, system, writer): - self.dump_model_group_summary(system, writer) - self.dump_model_group_link(system, writer) - - def dump_model_group_summary(self, system, writer): - with writer.loop("_ihm_model_group", ["id", "name", "details"]) as lp: - for group in system._all_model_groups(): - lp.write(id=group._id, name=group.name) - - def dump_model_group_link(self, system, writer): - with writer.loop("_ihm_model_group_link", - ["group_id", "model_id"]) as lp: - for group in system._all_model_groups(): - for model_id in sorted(set(model._id for model in group)): - lp.write(model_id=model_id, group_id=group._id) - def dump_atom_type(self, seen_types, system, writer): """Output the atom_type table with a list of elements used in atom_site. This table is needed by atom_site. Note that we output it *after* @@ -1474,18 +1441,17 @@ def dump_atom_type(self, seen_types, system, writer): for element in elements: lp.write(symbol=element) - def dump_atoms(self, system, writer): + def dump_atoms(self, system, writer, add_ihm=True): seen_types = {} ordinal = itertools.count(1) - with writer.loop("_atom_site", - ["group_PDB", "id", "type_symbol", - "label_atom_id", "label_alt_id", "label_comp_id", - "label_seq_id", "auth_seq_id", "pdbx_PDB_ins_code", - "label_asym_id", "Cartn_x", - "Cartn_y", "Cartn_z", "occupancy", "label_entity_id", - "auth_asym_id", - "B_iso_or_equiv", "pdbx_PDB_model_num", - "ihm_model_id"]) as lp: + it = ["group_PDB", "id", "type_symbol", "label_atom_id", + "label_alt_id", "label_comp_id", "label_seq_id", "auth_seq_id", + "pdbx_PDB_ins_code", "label_asym_id", "Cartn_x", "Cartn_y", + "Cartn_z", "occupancy", "label_entity_id", "auth_asym_id", + "B_iso_or_equiv", "pdbx_PDB_model_num"] + if add_ihm: + it.append("ihm_model_id") + with writer.loop("_atom_site", it) as lp: for group, model in system._all_models(): rngcheck = _RangeChecker(model) for atom in model.get_atoms(): @@ -1513,6 +1479,43 @@ def dump_atoms(self, system, writer): ihm_model_id=model._id) return seen_types + +class _ModelDumper(_ModelDumperBase): + def dump(self, system, writer): + self.dump_model_list(system, writer) + self.dump_model_groups(system, writer) + seen_types = self.dump_atoms(system, writer) + self.dump_spheres(system, writer) + self.dump_atom_type(seen_types, system, writer) + + def dump_model_groups(self, system, writer): + self.dump_model_group_summary(system, writer) + self.dump_model_group_link(system, writer) + + def dump_model_list(self, system, writer): + with writer.loop("_ihm_model_list", + ["model_id", "model_name", "assembly_id", + "protocol_id", "representation_id"]) as lp: + for group, model in system._all_models(): + lp.write(model_id=model._id, + model_name=model.name, + assembly_id=model.assembly._id, + protocol_id=model.protocol._id + if model.protocol else None, + representation_id=model.representation._id) + + def dump_model_group_summary(self, system, writer): + with writer.loop("_ihm_model_group", ["id", "name", "details"]) as lp: + for group in system._all_model_groups(): + lp.write(id=group._id, name=group.name) + + def dump_model_group_link(self, system, writer): + with writer.loop("_ihm_model_group_link", + ["group_id", "model_id"]) as lp: + for group in system._all_model_groups(): + for model_id in sorted(set(model._id for model in group)): + lp.write(model_id=model_id, group_id=group._id) + def dump_spheres(self, system, writer): ordinal = itertools.count(1) with writer.loop("_ihm_sphere_obj_site", @@ -3091,26 +3094,55 @@ def dump_mpp_modeling(self, system, writer): mpp_atom_position_group_id=x.mpp_atom_position_group._id) -def _init_restraint_groups(system): - """Initialize all RestraintGroups by removing any assigned ID""" - for g in system.restraint_groups: - util._remove_id(g) +_flr_dumpers = [_FLRExperimentDumper, _FLRInstSettingDumper, + _FLR_ExpConditionDumper, _FLRInstrumentDumper, + _FLREntityAssemblyDumper, _FLRSampleConditionDumper, + _FLRSampleDumper, _FLRProbeDumper, + _FLRSampleProbeDetailsDumper, _FLRPolyProbePositionDumper, + _FLRConjugateDumper, _FLRForsterRadiusDumper, + _FLRCalibrationParametersDumper, _FLRLifetimeFitModelDumper, + _FLRRefMeasurementDumper, _FLRAnalysisDumper, + _FLRPeakAssignmentDumper, _FLRDistanceRestraintDumper, + _FLRModelQualityDumper, _FLRModelDistanceDumper, + _FLRFPSModelingDumper, _FLRFPSAVModelingDumper, + _FLRFPSMPPModelingDumper] -def _check_restraint_groups(system): - """Check that all RestraintGroups were successfully dumped""" - for g in system.restraint_groups: - if len(g) > 0 and not hasattr(g, '_id'): - raise TypeError( - "RestraintGroup(%s) contains an unsupported combination of " - "Restraints. Due to limitations of the underlying dictionary, " - "all objects in a RestraintGroup must be of the same type, " - "and only certain types (currently only " - "DerivedDistanceRestraint or PredictedContactRestraint) " - "can be grouped." % g) +class Variant(object): + """Utility class to select the type of file to output by :func:`write`.""" + + def get_dumpers(self): + """Get the :class:`Dumper` objects to use to write output. + + :return: a list of :class:`Dumper` objects. + """ + pass -def write(fh, systems, format='mmCIF', dumpers=[]): +class IHMVariant(Variant): + """Used to select typical PDBx/IHM file output. See :func:`write`.""" + _dumpers = [ + _EntryDumper, # must be first + _StructDumper, _CommentDumper, _AuditConformDumper, _CitationDumper, + _SoftwareDumper, _AuditAuthorDumper, _GrantDumper, _ChemCompDumper, + _ChemDescriptorDumper, _EntityDumper, _EntitySrcGenDumper, + _EntitySrcNatDumper, _EntitySrcSynDumper, _StructRefDumper, + _EntityPolyDumper, _EntityNonPolyDumper, _EntityPolySeqDumper, + _EntityPolySegmentDumper, _StructAsymDumper, _PolySeqSchemeDumper, + _NonPolySchemeDumper, _AssemblyDumper, _ExternalReferenceDumper, + _DatasetDumper, _ModelRepresentationDumper, _StartingModelDumper, + _ProtocolDumper, _PostProcessDumper, _PseudoSiteDumper, + _GeometricObjectDumper, _FeatureDumper, _CrossLinkDumper, + _GeometricRestraintDumper, _DerivedDistanceRestraintDumper, + _PredictedContactRestraintDumper, _EM3DDumper, _EM2DDumper, _SASDumper, + _ModelDumper, _EnsembleDumper, _DensityDumper, _MultiStateDumper, + _OrderedDumper] + + def get_dumpers(self): + return [d() for d in self._dumpers + _flr_dumpers] + + +def write(fh, systems, format='mmCIF', dumpers=[], variant=IHMVariant): """Write out all `systems` to the file handle `fh`. Files can be written in either the text-based mmCIF format or the BinaryCIF format. The BinaryCIF writer needs the msgpack Python @@ -3130,64 +3162,26 @@ def write(fh, systems, format='mmCIF', dumpers=[]): default) for the (text-based) mmCIF format or 'BCIF' for BinaryCIF. :param list dumpers: A list of :class:`Dumper` classes (not objects). - These can be used to add extra categories to the file.""" - dumpers = [_EntryDumper(), # must be first - _StructDumper(), _CommentDumper(), - _AuditConformDumper(), _CitationDumper(), _SoftwareDumper(), - _AuditAuthorDumper(), _GrantDumper(), - _ChemCompDumper(), _ChemDescriptorDumper(), - _EntityDumper(), _EntitySrcGenDumper(), _EntitySrcNatDumper(), - _EntitySrcSynDumper(), _StructRefDumper(), - _EntityPolyDumper(), - _EntityNonPolyDumper(), - _EntityPolySeqDumper(), _EntityPolySegmentDumper(), - _StructAsymDumper(), - _PolySeqSchemeDumper(), - _NonPolySchemeDumper(), - _AssemblyDumper(), - _ExternalReferenceDumper(), - _DatasetDumper(), - _ModelRepresentationDumper(), - _StartingModelDumper(), - _ProtocolDumper(), - _PostProcessDumper(), - _PseudoSiteDumper(), - _GeometricObjectDumper(), _FeatureDumper(), - _CrossLinkDumper(), _GeometricRestraintDumper(), - _DerivedDistanceRestraintDumper(), - _PredictedContactRestraintDumper(), - _EM3DDumper(), - _EM2DDumper(), - _SASDumper(), - _ModelDumper(), - _EnsembleDumper(), - _DensityDumper(), - _MultiStateDumper(), _OrderedDumper(), - _FLRExperimentDumper(), _FLRInstSettingDumper(), - _FLR_ExpConditionDumper(), - _FLRInstrumentDumper(), _FLREntityAssemblyDumper(), - _FLRSampleConditionDumper(), _FLRSampleDumper(), - _FLRProbeDumper(), _FLRSampleProbeDetailsDumper(), - _FLRPolyProbePositionDumper(), _FLRConjugateDumper(), - _FLRForsterRadiusDumper(), _FLRCalibrationParametersDumper(), - _FLRLifetimeFitModelDumper(), _FLRRefMeasurementDumper(), - _FLRAnalysisDumper(), _FLRPeakAssignmentDumper(), - _FLRDistanceRestraintDumper(), _FLRModelQualityDumper(), - _FLRModelDistanceDumper(), _FLRFPSModelingDumper(), - _FLRFPSAVModelingDumper(), - _FLRFPSMPPModelingDumper()] + [d() for d in dumpers] + These can be used to add extra categories to the file. + :param variant: A class or object that selects the type of file to + output. This primarily controls the set of tables that are + written to the file. In most cases the default + :class:`IHMVariant` should be used. + :type variant: :class:`Variant` + """ + if isinstance(variant, type): + variant = variant() + dumpers = variant.get_dumpers() + [d() for d in dumpers] writer_map = {'mmCIF': ihm.format.CifWriter, 'BCIF': ihm.format_bcif.BinaryCifWriter} writer = writer_map[format](fh) for system in systems: - _init_restraint_groups(system) - # Fill in complete assembly - system._make_complete_assembly() + system._before_write() for d in dumpers: d.finalize(system) - _check_restraint_groups(system) + system._check_after_write() for d in dumpers: d.dump(system, writer) writer.flush() diff --git a/modules/core/dependency/python-ihm/ihm/reader.py b/modules/core/dependency/python-ihm/ihm/reader.py index 6a812bfb2f..c53d6451d2 100644 --- a/modules/core/dependency/python-ihm/ihm/reader.py +++ b/modules/core/dependency/python-ihm/ihm/reader.py @@ -417,6 +417,12 @@ def __init__(self, model_class, starting_model_class): #: Mapping from ID to :class:`ihm.source.Synthetic` objects self.src_syns = IDMapper(None, ihm.source.Synthetic) + #: Mapping from ID to :class:`ihm.AsymUnit` objects + self.asym_units = IDMapper(self.system.asym_units, ihm.AsymUnit, None) + + #: Mapping from ID to :class:`ihm.ChemComp` objects + self.chem_comps = _ChemCompIDMapper(None, ihm.ChemComp, *(None,) * 3) + #: Mapping from ID to :class:`ihm.reference.Alignment` objects self.alignments = IDMapper(None, ihm.reference.Alignment) @@ -427,12 +433,6 @@ def __init__(self, model_class, starting_model_class): self.chem_descriptors = IDMapper(self.system.orphan_chem_descriptors, ihm.ChemDescriptor, None) - #: Mapping from ID to :class:`ihm.AsymUnit` objects - self.asym_units = IDMapper(self.system.asym_units, ihm.AsymUnit, None) - - #: Mapping from ID to :class:`ihm.ChemComp` objects - self.chem_comps = _ChemCompIDMapper(None, ihm.ChemComp, *(None,) * 3) - #: Mapping from ID to :class:`ihm.Assembly` objects self.assemblies = IDMapper(self.system.orphan_assemblies, ihm.Assembly) @@ -3060,11 +3060,105 @@ def __call__(self, ordinal_id, fps_modeling_id, mpp_id, mpp_atom_position_group_id) +_flr_handlers = [_FLRChemDescriptorHandler, _FLRInstSettingHandler, + _FLRExpConditionHandler, _FLRInstrumentHandler, + _FLRSampleConditionHandler, _FLREntityAssemblyHandler, + _FLRSampleHandler, _FLRExperimentHandler, + _FLRProbeListHandler, _FLRProbeDescriptorHandler, + _FLRPolyProbePositionHandler, + _FLRPolyProbePositionModifiedHandler, + _FLRPolyProbePositionMutatedHandler, + _FLRSampleProbeDetailsHandler, _FLRPolyProbeConjugateHandler, + _FLRFretForsterRadiusHandler, + _FLRFretCalibrationParametersHandler, _FLRFretAnalysisHandler, + _FLRFretAnalysisIntensityHandler, + _FLRFretAnalysisLifetimeHandler, _FLRLifetimeFitModelHandler, + _FLRRefMeasurementHandler, _FLRRefMeasurementGroupHandler, + _FLRRefMeasurementGroupLinkHandler, + _FLRRefMeasurementLifetimeHandler, _FLRPeakAssignmentHandler, + _FLRFretDistanceRestraintHandler, _FLRFretModelQualityHandler, + _FLRFretModelDistanceHandler, _FLRFPSGlobalParameterHandler, + _FLRFPSModelingHandler, _FLRFPSAVParameterHandler, + _FLRFPSAVModelingHandler, _FLRFPSMPPHandler, + _FLRFPSMPPAtomPositionHandler, _FLRFPSMPPModelingHandler] + + +class Variant(object): + """Utility class to select the type of file to read with :func:`read`.""" + + #: Class to track global file information, e.g. :class:`SystemReader` + system_reader = None + + def get_handlers(self, sysr): + """Get the :class:`Handler` objects to use to parse input. + + :param sysr: class to track global file information. + :type sysr: :class:`SystemReader` + :return: a list of :class:`Dumper` objects. + """ + pass + + def get_audit_conform_handler(self, sysr): + """Get a :class:`Handler` to check the audit_conform table. + If :func:`read` is called with ``reject_old_file=True``, this + handler is used to check the audit_conform table and reject the + file if it is deemed to be too old. + + :param sysr: class to track global file information. + :type sysr: :class:`SystemReader` + :return: a suitable handler. + :rtype: :class:`Handler` + """ + pass + + +class IHMVariant(Variant): + """Used to select typical PDBx/IHM file input. See :func:`read`.""" + system_reader = SystemReader + + _handlers = [ + _StructHandler, _SoftwareHandler, _CitationHandler, + _AuditAuthorHandler, _GrantHandler, _CitationAuthorHandler, + _ChemCompHandler, _ChemDescriptorHandler, _EntityHandler, + _EntitySrcNatHandler, _EntitySrcGenHandler, _EntitySrcSynHandler, + _StructRefHandler, _StructRefSeqHandler, _StructRefSeqDifHandler, + _EntityPolyHandler, _EntityPolySeqHandler, _EntityNonPolyHandler, + _EntityPolySegmentHandler, _StructAsymHandler, _AssemblyDetailsHandler, + _AssemblyHandler, _ExtRefHandler, _ExtFileHandler, _DatasetListHandler, + _DatasetGroupHandler, _DatasetGroupLinkHandler, _DatasetExtRefHandler, + _DatasetDBRefHandler, _DataTransformationHandler, + _RelatedDatasetsHandler, _ModelRepresentationHandler, + _ModelRepresentationDetailsHandler, _StartingModelDetailsHandler, + _StartingComputationalModelsHandler, _StartingComparativeModelsHandler, + _ProtocolHandler, _ProtocolDetailsHandler, _PostProcessHandler, + _ModelListHandler, _ModelGroupHandler, _ModelGroupLinkHandler, + _MultiStateHandler, _MultiStateLinkHandler, _EnsembleHandler, + _DensityHandler, _SubsampleHandler, _EM3DRestraintHandler, + _EM2DRestraintHandler, _EM2DFittingHandler, _SASRestraintHandler, + _SphereObjSiteHandler, _AtomSiteHandler, _FeatureListHandler, + _PolyResidueFeatureHandler, _PolyAtomFeatureHandler, + _NonPolyFeatureHandler, _PseudoSiteFeatureHandler, _PseudoSiteHandler, + _DerivedDistanceRestraintHandler, _PredictedContactRestraintHandler, + _CenterHandler, _TransformationHandler, _GeometricObjectHandler, + _SphereHandler, _TorusHandler, _HalfTorusHandler, _AxisHandler, + _PlaneHandler, _GeometricRestraintHandler, _PolySeqSchemeHandler, + _NonPolySchemeHandler, _CrossLinkListHandler, + _CrossLinkRestraintHandler, _CrossLinkPseudoSiteHandler, + _CrossLinkResultHandler, _StartingModelSeqDifHandler, + _OrderedEnsembleHandler] + + def get_handlers(self, sysr): + return [h(sysr) for h in self._handlers + _flr_handlers] + + def get_audit_conform_handler(self, sysr): + return _AuditConformHandler(sysr) + + def read(fh, model_class=ihm.model.Model, format='mmCIF', handlers=[], warn_unknown_category=False, warn_unknown_keyword=False, read_starting_model_coord=True, starting_model_class=ihm.startmodel.StartingModel, - reject_old_file=False): + reject_old_file=False, variant=IHMVariant): """Read data from the file handle `fh`. Note that the reader currently expects to see a file compliant @@ -3132,8 +3226,15 @@ def read(fh, model_class=ihm.model.Model, format='mmCIF', handlers=[], :exc:`ihm.reader.OldFileError` if the file conforms to an older version of the dictionary than this library supports (by default the library will read what it can from the file). + :param variant: A class or object that selects the type of file to + read. This primarily controls the set of tables that are + read from the file. In most cases the default + :class:`IHMVariant` should be used. + :type variant: :class:`Variant` :return: A list of :class:`ihm.System` objects. """ + if isinstance(variant, type): + variant = variant() systems = [] reader_map = {'mmCIF': ihm.format.CifReader, 'BCIF': ihm.format_bcif.BinaryCifReader} @@ -3144,88 +3245,10 @@ def read(fh, model_class=ihm.model.Model, format='mmCIF', handlers=[], r = reader_map[format](fh, {}, unknown_category_handler=uchandler, unknown_keyword_handler=ukhandler) while True: - s = SystemReader(model_class, starting_model_class) - hs = [_StructHandler(s), _SoftwareHandler(s), _CitationHandler(s), - _AuditAuthorHandler(s), _GrantHandler(s), - _CitationAuthorHandler(s), _ChemCompHandler(s), - _ChemDescriptorHandler(s), _EntityHandler(s), - _EntitySrcNatHandler(s), _EntitySrcGenHandler(s), - _EntitySrcSynHandler(s), _StructRefHandler(s), - _StructRefSeqHandler(s), _StructRefSeqDifHandler(s), - _EntityPolyHandler(s), - _EntityPolySeqHandler(s), _EntityNonPolyHandler(s), - _EntityPolySegmentHandler(s), - _StructAsymHandler(s), _AssemblyDetailsHandler(s), - _AssemblyHandler(s), _ExtRefHandler(s), _ExtFileHandler(s), - _DatasetListHandler(s), _DatasetGroupHandler(s), - _DatasetGroupLinkHandler(s), - _DatasetExtRefHandler(s), _DatasetDBRefHandler(s), - _DataTransformationHandler(s), - _RelatedDatasetsHandler(s), _ModelRepresentationHandler(s), - _ModelRepresentationDetailsHandler(s), - _StartingModelDetailsHandler(s), - _StartingComputationalModelsHandler(s), - _StartingComparativeModelsHandler(s), - _ProtocolHandler(s), _ProtocolDetailsHandler(s), - _PostProcessHandler(s), _ModelListHandler(s), - _ModelGroupHandler(s), _ModelGroupLinkHandler(s), - _MultiStateHandler(s), _MultiStateLinkHandler(s), - _EnsembleHandler(s), _DensityHandler(s), - _SubsampleHandler(s), - _EM3DRestraintHandler(s), _EM2DRestraintHandler(s), - _EM2DFittingHandler(s), _SASRestraintHandler(s), - _SphereObjSiteHandler(s), _AtomSiteHandler(s), - _FeatureListHandler(s), - _PolyResidueFeatureHandler(s), _PolyAtomFeatureHandler(s), - _NonPolyFeatureHandler(s), _PseudoSiteFeatureHandler(s), - _PseudoSiteHandler(s), - _DerivedDistanceRestraintHandler(s), - _PredictedContactRestraintHandler(s), _CenterHandler(s), - _TransformationHandler(s), _GeometricObjectHandler(s), - _SphereHandler(s), _TorusHandler(s), _HalfTorusHandler(s), - _AxisHandler(s), _PlaneHandler(s), _GeometricRestraintHandler(s), - _PolySeqSchemeHandler(s), _NonPolySchemeHandler(s), - _CrossLinkListHandler(s), _CrossLinkRestraintHandler(s), - _CrossLinkPseudoSiteHandler(s), - _CrossLinkResultHandler(s), _StartingModelSeqDifHandler(s), - _OrderedEnsembleHandler(s), _FLRChemDescriptorHandler(s), - _FLRInstSettingHandler(s), - _FLRExpConditionHandler(s), - _FLRInstrumentHandler(s), - _FLRSampleConditionHandler(s), - _FLREntityAssemblyHandler(s), - _FLRSampleHandler(s), - _FLRExperimentHandler(s), - _FLRProbeListHandler(s), - _FLRProbeDescriptorHandler(s), - _FLRPolyProbePositionHandler(s), - _FLRPolyProbePositionModifiedHandler(s), - _FLRPolyProbePositionMutatedHandler(s), - _FLRSampleProbeDetailsHandler(s), - _FLRPolyProbeConjugateHandler(s), - _FLRFretForsterRadiusHandler(s), - _FLRFretCalibrationParametersHandler(s), - _FLRFretAnalysisHandler(s), - _FLRFretAnalysisIntensityHandler(s), - _FLRFretAnalysisLifetimeHandler(s), - _FLRLifetimeFitModelHandler(s), - _FLRRefMeasurementHandler(s), - _FLRRefMeasurementGroupHandler(s), - _FLRRefMeasurementGroupLinkHandler(s), - _FLRRefMeasurementLifetimeHandler(s), - _FLRPeakAssignmentHandler(s), - _FLRFretDistanceRestraintHandler(s), - _FLRFretModelQualityHandler(s), - _FLRFretModelDistanceHandler(s), - _FLRFPSGlobalParameterHandler(s), - _FLRFPSModelingHandler(s), - _FLRFPSAVParameterHandler(s), - _FLRFPSAVModelingHandler(s), - _FLRFPSMPPHandler(s), - _FLRFPSMPPAtomPositionHandler(s), - _FLRFPSMPPModelingHandler(s)] + [h(s) for h in handlers] + s = variant.system_reader(model_class, starting_model_class) + hs = variant.get_handlers(s) + [h(s) for h in handlers] if reject_old_file: - hs.append(_AuditConformHandler(s)) + hs.append(variant.get_audit_conform_handler(s)) if read_starting_model_coord: hs.append(_StartingModelCoordHandler(s)) if uchandler: diff --git a/modules/core/dependency/python-ihm/test/test_examples.py b/modules/core/dependency/python-ihm/test/test_examples.py index 0422873027..f0ed7a190e 100644 --- a/modules/core/dependency/python-ihm/test/test_examples.py +++ b/modules/core/dependency/python-ihm/test/test_examples.py @@ -23,6 +23,8 @@ class Tests(unittest.TestCase): @unittest.skipIf('APPVEYOR' in os.environ, "AppVeyor environments have old SSL certs") + @unittest.skipIf('GITHUB_ACTIONS' in os.environ, + "Example is slow and fails when PDB-Dev is down") def test_validator_example(self): """Test validator example""" subprocess.check_call([sys.executable, diff --git a/modules/core/dependency/python-ihm/test/test_main.py b/modules/core/dependency/python-ihm/test/test_main.py index 19375f7fc7..02c50e6c36 100644 --- a/modules/core/dependency/python-ihm/test/test_main.py +++ b/modules/core/dependency/python-ihm/test/test_main.py @@ -402,6 +402,14 @@ def test_asym_range(self): self.assertNotEqual(r, e(3, 4)) # asym_range != entity_range self.assertNotEqual(r, e) # asym_range != entity + def test_asym_segment(self): + """Test AsymUnitSegment class""" + e = ihm.Entity('AHCDAH') + a = ihm.AsymUnit(e) + seg = a.segment('AH--CD', 1, 4) + self.assertEqual(seg.gapped_sequence, 'AH--CD') + self.assertEqual(seg.seq_id_range, (1, 4)) + def test_auth_seq_id_offset(self): """Test auth_seq_id offset from seq_id""" e = ihm.Entity('AHCDAH') From 52866a9ed1b55dd18b97fa53e64f6f2b07724ee4 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 10 Jan 2022 15:13:14 -0800 Subject: [PATCH 006/155] Squashed 'modules/pmi/' changes from fa61820fad..c51f8b6e47 c51f8b6e47 Allow multi-character chains in ComponentMapper git-subtree-dir: modules/pmi git-subtree-split: c51f8b6e475b3a222aed5fd7f3d0f25d609a50ab --- modules/pmi/pyext/src/mmcif.py | 3 ++- modules/pmi/test/test_mmcif_pmi2.py | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/pmi/pyext/src/mmcif.py b/modules/pmi/pyext/src/mmcif.py index 9087e368e2..c4f955d81e 100644 --- a/modules/pmi/pyext/src/mmcif.py +++ b/modules/pmi/pyext/src/mmcif.py @@ -65,7 +65,8 @@ def __init__(self, prot): self.prot = prot self.name = 'cif-output' self.o.dictionary_pdbs[self.name] = self.prot - self.o._init_dictchain(self.name, self.prot, multichar_chain=True) + self.o._init_dictchain(self.name, self.prot, + multichar_chain=True, mmcif=True) def __getitem__(self, p): protname, is_a_bead = self.o.get_prot_name_from_particle(self.name, p) diff --git a/modules/pmi/test/test_mmcif_pmi2.py b/modules/pmi/test/test_mmcif_pmi2.py index 9e36199105..636abf627d 100644 --- a/modules/pmi/test/test_mmcif_pmi2.py +++ b/modules/pmi/test/test_mmcif_pmi2.py @@ -42,7 +42,8 @@ def test_component_mapper(self): po = IMP.pmi.mmcif.ProtocolOutput() s.add_protocol_output(po) state = s.create_state() - nup84 = state.create_molecule("Nup84", "MELS", "A") + # Should be OK with a multi-character chain ID + nup84 = state.create_molecule("Nup84", "MELS", "AA") nup84.add_representation(resolutions=[1]) hier = s.build() c = IMP.pmi.mmcif._ComponentMapper(hier) From 3238f260b3c397def71372f49386999bd685d9aa Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 10 Jan 2022 19:16:04 -0800 Subject: [PATCH 007/155] Remove CoarseCC class --- ChangeLog.md | 4 +++ modules/em/include/CoarseCC.h | 49 ---------------------------- modules/em/pyext/swig.i-in | 1 - modules/em/src/CoarseCC.cpp | 39 ---------------------- modules/em/test/standards_exceptions | 5 --- 5 files changed, 4 insertions(+), 94 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index d4421791e2..6be00edcce 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,6 +1,10 @@ ChangeLog {#changelog} ========= +# HEAD +- The IMP::em::CoarseCC class has been removed. Use similarly-named free + functions instead to calculate coarse cross correlation. + # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} - OpenCubicSpline now throws a ValueException for out-of-range values, to be consistent with ClosedCubicSpline (previously it threw ModelException). diff --git a/modules/em/include/CoarseCC.h b/modules/em/include/CoarseCC.h index a7a26369c8..9bd563d3dd 100644 --- a/modules/em/include/CoarseCC.h +++ b/modules/em/include/CoarseCC.h @@ -111,55 +111,6 @@ double get_coarse_cc_local_coefficient(const DensityMap *em_map, DensityMap *model_map, double voxel_data_threshold); - -//! Responsible for performing coarse fitting between two density objects. -/** - \note Do not use this class as an example for writing new code! - The design (a class with no storage, and only static methods) - is not ideal. A better implementation would just be a collection - of free functions, not in a class; see above. - */ -class IMPEMEXPORT CoarseCC : public IMP::Object { - - public: - IMPEM_DEPRECATED_OBJECT_DECL(2.15) - CoarseCC() : Object("CoarseCC%1%") { - IMPEM_DEPRECATED_OBJECT_DEF(2.15, "Use free functions instead"); - } - - IMPEM_DEPRECATED_METHOD_DECL(2.15) - static float calc_score(DensityMap *data, SampledDensityMap *model_map, - float scalefactor, bool recalc_rms = true, - bool resample = true, - FloatPair norm_factors = FloatPair(0., 0.)); - -#if !defined(IMP_DOXYGEN) && !defined(SWIG) - IMPEM_DEPRECATED_METHOD_DECL(2.15) - static algebra::Vector3Ds calc_derivatives(const DensityMap *em_map, - const DensityMap *model_map, - const Particles &model_ps, - const FloatKey &mass_key, - KernelParameters *kernel_params, - const float &scalefac, - const algebra::Vector3Ds &dv); -#endif - - IMPEM_DEPRECATED_METHOD_DECL(2.15) - static double cross_correlation_coefficient(const DensityMap *grid1, - const DensityMap *grid2, - float grid2_voxel_data_threshold, - bool allow_padding = false, - FloatPair norm_factors = - FloatPair(0., 0.)); - - IMPEM_DEPRECATED_METHOD_DECL(2.15) - static float local_cross_correlation_coefficient(const DensityMap *em_map, - DensityMap *model_map, - float voxel_data_threshold); - - IMP_OBJECT_METHODS(CoarseCC); -}; - IMPEM_END_NAMESPACE #endif /* IMPEM_COARSE_CC_H */ diff --git a/modules/em/pyext/swig.i-in b/modules/em/pyext/swig.i-in index 6f96f091af..87a12afb3c 100644 --- a/modules/em/pyext/swig.i-in +++ b/modules/em/pyext/swig.i-in @@ -22,7 +22,6 @@ IMP_SWIG_OBJECT(IMP::em, MRCReaderWriter, MRCReaderWriters); IMP_SWIG_OBJECT(IMP::em, SpiderMapReaderWriter, SpiderMapReaderWriters); IMP_SWIG_OBJECT(IMP::em, EMReaderWriter, EMReaderWriters); IMP_SWIG_OBJECT(IMP::em, XplorReaderWriter, XplorReaderWriters); -IMP_SWIG_OBJECT(IMP::em, CoarseCC, CoarseCCs); IMP_SWIG_OBJECT(IMP::em, CoarseCCatIntervals, CoarseCCatIntervalsList); IMP_SWIG_VALUE(IMP::em, FittingSolutions, FittingSolutionsList); IMP_SWIG_OBJECT(IMP::em, MapDistanceTransform, MapDistanceTransforms); diff --git a/modules/em/src/CoarseCC.cpp b/modules/em/src/CoarseCC.cpp index e652485747..59652d3ab4 100644 --- a/modules/em/src/CoarseCC.cpp +++ b/modules/em/src/CoarseCC.cpp @@ -416,43 +416,4 @@ algebra::Vector3Ds get_coarse_cc_derivatives(const DensityMap *em_map, return dv_out; } -float CoarseCC::calc_score(DensityMap *em_map, SampledDensityMap *model_map, - float scalefac, bool recalc_rms, bool resample, - FloatPair norm_factors) { - IMPEM_DEPRECATED_METHOD_DEF(2.15, "Use get_coarse_cc_score() instead"); - return get_coarse_cc_score(em_map, model_map, scalefac, recalc_rms, - resample, norm_factors); -} - -double CoarseCC::cross_correlation_coefficient(const DensityMap *grid1, - const DensityMap *grid2, - float grid2_voxel_data_threshold, - bool allow_padding, - FloatPair norm_factors) { - IMPEM_DEPRECATED_METHOD_DEF(2.15, "Use get_coarse_cc_coefficient() instead"); - return get_coarse_cc_coefficient(grid1, grid2, grid2_voxel_data_threshold, - allow_padding, norm_factors); -} - -float CoarseCC::local_cross_correlation_coefficient( - const DensityMap *em_map, DensityMap *model_map, - float voxel_data_threshold) { - IMPEM_DEPRECATED_METHOD_DEF(2.15, - "Use get_coarse_cc_local_coefficient() instead"); - return get_coarse_cc_local_coefficient(em_map, model_map, - voxel_data_threshold); -} - -algebra::Vector3Ds CoarseCC::calc_derivatives(const DensityMap *em_map, - const DensityMap *model_map, - const Particles &model_ps, - const FloatKey &w_key, - KernelParameters *kernel_params, - const float &scalefac, - const algebra::Vector3Ds &dv) { - IMPEM_DEPRECATED_METHOD_DEF(2.15, "Use get_coarse_cc_derivatives() instead"); - return get_coarse_cc_derivatives(em_map, model_map, model_ps, w_key, - kernel_params, scalefac, dv); -} - IMPEM_END_NAMESPACE diff --git a/modules/em/test/standards_exceptions b/modules/em/test/standards_exceptions index 6032c79818..8505dc283b 100644 --- a/modules/em/test/standards_exceptions +++ b/modules/em/test/standards_exceptions @@ -4,11 +4,6 @@ function_name_exceptions = [ 'get_coarse_cc_score', 'get_coarse_cc_coefficient', 'get_coarse_cc_local_coefficient', - 'CoarseCC.calc_derivatives', - 'CoarseCC.calc_derivatives_fast', - 'CoarseCC.calc_score', - 'CoarseCC.cross_correlation_coefficient', - 'CoarseCC.local_cross_correlation_coefficient', 'CoarseCCatIntervals.calc_derivatives', 'CoarseCCatIntervals.calc_derivatives_fast', 'CoarseCCatIntervals.calc_score', From 83d9715203f25e6dd2819c6615149912b21b921d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 12 Jan 2022 10:36:16 -0800 Subject: [PATCH 008/155] Fix Python 2 deps on Ubuntu 22.04 --- tools/debian/make-package.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/tools/debian/make-package.sh b/tools/debian/make-package.sh index 15512ed3fc..55302c45a9 100755 --- a/tools/debian/make-package.sh +++ b/tools/debian/make-package.sh @@ -26,6 +26,11 @@ cp -r tools/debian/ . || exit 1 rm debian/make-package.sh debian/make-imp-install.py || exit 1 perl -pi -e "s/\@VERSION\@/$VERSION/; s/\@DATE\@/$DATE/; s/\@CODENAME\@/$CODENAME/;" debian/changelog || exit 1 +# Newer distributions don't have Python 2 modules, and renamed libgsl0 +if [ "${CODENAME}" = "jammy" ]; then + perl -pi -e "s/, python-numpy, python-protobuf//" debian/control || exit 1 + perl -pi -e "s/libgsl0-dev/libgsl-dev/" debian/control || exit 1 +fi if [ "${CODENAME}" = "xenial" -o "${CODENAME}" = "bionic" ]; then # CGAL cmake support on Xenial or later requires Qt5 headers too perl -pi -e "s/libcgal\-dev/libcgal-dev, libcgal-qt5-dev/g" debian/control || exit 1 From 55cc59da12d607dc121bcf49e88ab4b825f0ab67 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 12 Jan 2022 10:48:11 -0800 Subject: [PATCH 009/155] Run test cases in a Python 3 environment All Ubuntu LTS releases now have a full Python 3 environment, but the latest (22.04) dropped Python 2 packages for numpy and protobuf, so many tests now fail there. Switch all builds to run tests in a Python 3 environment instead. --- tools/debian/rules | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/tools/debian/rules b/tools/debian/rules index acb1d8fcd0..90d3becf01 100755 --- a/tools/debian/rules +++ b/tools/debian/rules @@ -22,15 +22,16 @@ override_dh_auto_configure: cd build/libTAU-1.0.1/lib/debian && ln -sf libTAU.so.1 libTAU.so # Allow mpiexec to work inside a docker/podman container (as root) perl -pi -e 's#\{MPIEXEC_PREFLAGS\}#\{MPIEXEC_PREFLAGS\};--allow-run-as-root#' modules/mpi/dependency/MPI.cmake - cd build && cmake .. -DCMAKE_BUILD_TYPE=Release \ + cd build && py3_ver=`python3 -c "import sys; print('%d.%d' % sys.version_info[:2])"` \ + && cmake .. -DCMAKE_BUILD_TYPE=Release \ -DCGAL_DIR=/usr/lib/x86_64-linux-gnu/cmake/CGAL/ \ - -DCMAKE_INSTALL_PYTHONDIR=/usr/lib/python2.7/dist-packages \ + -DCMAKE_INSTALL_PYTHONDIR=/usr/lib/python$${py3_ver}/dist-packages \ -DCMAKE_INCLUDE_PATH=`pwd` \ -DCMAKE_LIBRARY_PATH=`pwd`/libTAU-1.0.1/lib/debian \ -DCMAKE_INSTALL_PREFIX=/usr \ -DIMP_TIMEOUT_FACTOR=4 \ -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/imp \ - -DIMP_DISABLED_MODULES=scratch -DUSE_PYTHON2=on + -DIMP_DISABLED_MODULES=scratch -DUSE_PYTHON2=off override_dh_auto_build: mkdir build/logs @@ -38,19 +39,18 @@ override_dh_auto_build: override_dh_install: $(MAKE) -C build DESTDIR=$(CURDIR)/debian/tmp install - # Install Python 3 extension modules + # Install Python 2 extension modules cd build \ && py2_ver=`python2 -c "import sys; print('%d.%d' % sys.version_info[:2])"` \ - && py3_ver=`python3 -c "import sys; print('%d.%d' % sys.version_info[:2])"` \ && unamem=`uname -m` \ - && py3_lib=`echo /usr/lib/$${unamem}-*/libpython3*.so` \ - && py3_inc=/usr/include/python$${py3_ver} \ + && py2_lib=`echo /usr/lib/$${unamem}-*/libpython2*.so` \ + && py2_inc=/usr/include/python$${py2_ver} \ && cmake .. \ - -DCMAKE_INSTALL_PYTHONDIR=/usr/lib/python$${py3_ver}/dist-packages \ - -DSWIG_PYTHON_LIBRARIES=$${py3_lib} \ - -DPYTHON_INCLUDE_DIRS=$${py3_inc} \ - -DPYTHON_INCLUDE_PATH=$${py3_inc} -DPYTHON_LIBRARIES=$${py3_lib} \ - -DUSE_PYTHON2=off \ + -DCMAKE_INSTALL_PYTHONDIR=/usr/lib/python2.7/dist-packages \ + -DSWIG_PYTHON_LIBRARIES=$${py2_lib} \ + -DPYTHON_INCLUDE_DIRS=$${py2_inc} \ + -DPYTHON_INCLUDE_PATH=$${py2_inc} -DPYTHON_LIBRARIES=$${py2_lib} \ + -DUSE_PYTHON2=on \ && $(MAKE) -j4 DESTDIR=$(CURDIR)/debian/tmp install # Bundle libTAU so users don't have to get it separately cp build/libTAU-1.0.1/lib/debian/libTAU.so.1 debian/tmp/usr/lib/*linux*/ From a9f0132f0a72922131ae2d56c26cf66683d5db72 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 14 Jan 2022 09:51:14 -0800 Subject: [PATCH 010/155] Don't symlink Python 2 to 3 __init__.py We used to replace all Python 2 code with symlinks to the Python 3 code, since it is the same. However, in Ubuntu 22.04 or later, each module's __init__.py might be different, since it contains configuration information (e.g. the Python 3 build uses numpy but the Python 2 build no longer does). So now we leave those copies as is. --- tools/debian/rules | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/tools/debian/rules b/tools/debian/rules index 90d3becf01..72e0d7009c 100755 --- a/tools/debian/rules +++ b/tools/debian/rules @@ -63,10 +63,13 @@ override_dh_install: rm -f debian/tmp/usr/lib/*/libimp_mpi*.so rm -f debian/tmp/usr/lib/*/libimp_spb*.so # Replace Python 2 .py files with symlinks to Python 3 files - # (since they are the same) + # (since they are the same) but not the SWIG-generated __init__.py + # files (since these contain config information which might be + # different; e.g. in Ubuntu 22.04 the Python 3 wrappers include numpy + # support but the Python 2 wrappers do not) (cd debian/tmp/usr/lib/python2* \ && py3_ver=`python3 -c "import sys; print('%d.%d' % sys.version_info[:2])"` \ - && find dist-packages -name '*.py' \ + && find dist-packages -name '*.py' -a ! -name __init__.py \ -exec ln -sf $(CURDIR)/debian/tmp/usr/lib/python$${py3_ver}/\{\} \{\} \; \ && symlinks -rc .) # Make sure all Python applications use the system Python in /usr/bin From e6c37e56edc705ccf6f3472c8be6feda786e4f27 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Sat, 15 Jan 2022 18:50:12 -0800 Subject: [PATCH 011/155] Skip Python 2 npctransport tests on Ubuntu 22.04 Ubuntu no longer ships a Python 2 protobuf package, so skip Python 2 npctransport tests there. --- tools/nightly-tests/test-install/test_mock.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/tools/nightly-tests/test-install/test_mock.py b/tools/nightly-tests/test-install/test_mock.py index ca3b247228..2fa23a1025 100644 --- a/tools/nightly-tests/test-install/test_mock.py +++ b/tools/nightly-tests/test-install/test_mock.py @@ -23,10 +23,11 @@ def test_modules_installed(self): import IMP.npctransport # Ubuntu only supports protobuf with Python 3 in 18.04 or later; # our Windows protobuf install is Python 2 only; - # for RHEL8 and Fedora we only have Python 3 protobuf wrappers. + # for RHEL8, Fedora and Ubuntu 22.04 or later we only have Python 3 + # protobuf wrappers. py2only_pb = frozenset(('ubuntu-trusty', 'ubuntu-xenial', 'w32', 'w64')) - py3only_pb = frozenset(('epel-8-x86_64',)) + py3only_pb = frozenset(('epel-8-x86_64', 'ubuntu-jammy')) if ((sys.version_info[0] == 3 and mock_config not in py2only_pb) or (sys.version_info[0] == 2 and mock_config not in py3only_pb and not mock_config.startswith('fedora'))): From f54e5f3488d24ae8cec7b01f2fd4af8f08e1fe3e Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Sun, 30 Jan 2022 17:37:32 -0800 Subject: [PATCH 012/155] Fix scipy download link --- doc/manual/installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/manual/installation.md b/doc/manual/installation.md index e43f7920c0..1ce19155fd 100644 --- a/doc/manual/installation.md +++ b/doc/manual/installation.md @@ -58,7 +58,7 @@ will not build, and some will not function optimally. - [Protobuf](https://github.com/google/protobuf): needed to use the IMP.npctransport module. - An [MPI](@ref IMP::mpi) library is needed to use the IMP.mpi module. -- The [scipy](http://www.scipy.org/scipylib/download.html), +- The [scipy](https://scipy.org/download/), [scikit-learn](http://scikit-learn.org/stable/install.html), and [matplotlib](http://matplotlib.org/downloads.html) Python libraries are also recommended. From 913a4a697ab00e9a349148060c9e102311bc848f Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 1 Feb 2022 12:47:09 -0800 Subject: [PATCH 013/155] Squashed 'modules/core/dependency/python-ihm/' changes from 32bda4dd99..60e3116cae 60e3116cae Prepare for 0.27 release 140c85d658 Link to ModelCIF validator example 99aae03140 python-ma is now python-modelcif 9ebdd3cc23 Note use of scientific notation 84fc8579f7 Don't redocument get_audit_conform_handler 0573e3ccbb Write out pdbx_structure_determination_methodology 1f34049bc0 Link to python-ma 11c93d8562 Update for 0.26 release b628a394cb Document the new Variant classes 8f1fca5c5a Fix markup d64ca19bc7 Fix markup for note d007b615c7 Fix typo 1b3780b03b Handle negative values too 91eee95035 Improve the display of very small numbers git-subtree-dir: modules/core/dependency/python-ihm git-subtree-split: 60e3116caea18a85147708f7965c2003fd24c554 --- modules/core/dependency/python-ihm/ChangeLog.rst | 13 +++++++++++++ modules/core/dependency/python-ihm/MANIFEST.in | 2 +- modules/core/dependency/python-ihm/README.md | 6 ++++++ modules/core/dependency/python-ihm/docs/dumper.rst | 1 - modules/core/dependency/python-ihm/docs/reader.rst | 1 - .../python-ihm/examples/validate_pdb_dev.py | 5 ++++- modules/core/dependency/python-ihm/ihm/__init__.py | 4 +++- modules/core/dependency/python-ihm/ihm/dumper.py | 4 +++- modules/core/dependency/python-ihm/ihm/format.py | 12 ++++++++---- .../core/dependency/python-ihm/ihm/format_bcif.py | 7 ++++++- modules/core/dependency/python-ihm/ihm/reader.py | 2 +- modules/core/dependency/python-ihm/setup.py | 2 +- .../core/dependency/python-ihm/test/test_dumper.py | 3 ++- .../dependency/python-ihm/test/test_examples.py | 8 ++++---- .../core/dependency/python-ihm/test/test_format.py | 2 ++ 15 files changed, 54 insertions(+), 18 deletions(-) diff --git a/modules/core/dependency/python-ihm/ChangeLog.rst b/modules/core/dependency/python-ihm/ChangeLog.rst index db58821023..3063b2d2c7 100644 --- a/modules/core/dependency/python-ihm/ChangeLog.rst +++ b/modules/core/dependency/python-ihm/ChangeLog.rst @@ -1,3 +1,16 @@ +0.27 - 2022-01-27 +================= + - Minor documentation improvements. + - Add support for the _struct.pdbx_structure_determination_methodology + mmCIF data item. + +0.26 - 2022-01-12 +================= + - :func:`ihm.dumper.write` and :func:`ihm.reader.read` both now take + a ``variant`` argument which can be used to control the set of tables + that are read/written. This can be used by other libraries (such as + python-ma) to support other mmCIF extensions. + 0.25 - 2021-12-03 ================= - :func:`ihm.dictionary.Dictionary.validate` will now report errors for diff --git a/modules/core/dependency/python-ihm/MANIFEST.in b/modules/core/dependency/python-ihm/MANIFEST.in index e889dfc955..235fc020ad 100644 --- a/modules/core/dependency/python-ihm/MANIFEST.in +++ b/modules/core/dependency/python-ihm/MANIFEST.in @@ -4,4 +4,4 @@ include examples/* include util/make-mmcif.py include src/ihm_format.h include src/ihm_format.i -include src/ihm_format_wrap_0.25.c +include src/ihm_format_wrap_0.27.c diff --git a/modules/core/dependency/python-ihm/README.md b/modules/core/dependency/python-ihm/README.md index e373e2487f..68433cb4f8 100644 --- a/modules/core/dependency/python-ihm/README.md +++ b/modules/core/dependency/python-ihm/README.md @@ -11,6 +11,12 @@ and [BinaryCIF](https://github.com/dsehnal/BinaryCIF) files compliant with the [integrative/hybrid modeling (IHM)](http://mmcif.wwpdb.org/dictionaries/mmcif_ihm.dic/Index/) extension. It works with Python 2.7 or Python 3. +To handle non-integrative theoretical models (for example, homology models), +see the [python-modelcif](https://github.com/ihmwg/python-modelcif) package +which supports files compliant with the +[ModelCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/) +extension. + Please [see the documentation](https://python-ihm.readthedocs.org/) or some [worked examples](https://github.com/ihmwg/python-ihm/tree/main/examples) diff --git a/modules/core/dependency/python-ihm/docs/dumper.rst b/modules/core/dependency/python-ihm/docs/dumper.rst index 5578010749..78829e0d1a 100644 --- a/modules/core/dependency/python-ihm/docs/dumper.rst +++ b/modules/core/dependency/python-ihm/docs/dumper.rst @@ -14,6 +14,5 @@ The :mod:`ihm.dumper` Python module :members: .. autoclass:: IHMVariant - :members: .. autofunction:: write diff --git a/modules/core/dependency/python-ihm/docs/reader.rst b/modules/core/dependency/python-ihm/docs/reader.rst index 1c86b3fa54..4798bed872 100644 --- a/modules/core/dependency/python-ihm/docs/reader.rst +++ b/modules/core/dependency/python-ihm/docs/reader.rst @@ -32,4 +32,3 @@ The :mod:`ihm.reader` Python module :members: .. autoclass:: IHMVariant - :members: diff --git a/modules/core/dependency/python-ihm/examples/validate_pdb_dev.py b/modules/core/dependency/python-ihm/examples/validate_pdb_dev.py index 77aecca7d0..d8740c3b8a 100644 --- a/modules/core/dependency/python-ihm/examples/validate_pdb_dev.py +++ b/modules/core/dependency/python-ihm/examples/validate_pdb_dev.py @@ -1,7 +1,10 @@ # This example demonstrates the use of the Python IHM library's validator. # A structure is downloaded from the PDB-Dev database and checked against # the PDBx and IHM dictionaries for compliance. This validator can be used -# to perform basic integrity checking against any mmCIF dictionary. +# to perform basic integrity checking against any mmCIF dictionary; for an +# example of using it to validate homology models against the ModelCIF +# dictionary, see +# https://github.com/ihmwg/python-modelcif/blob/main/examples/validate_modbase.py. import io import sys diff --git a/modules/core/dependency/python-ihm/ihm/__init__.py b/modules/core/dependency/python-ihm/ihm/__init__.py index 279f7de185..1c5075fc69 100644 --- a/modules/core/dependency/python-ihm/ihm/__init__.py +++ b/modules/core/dependency/python-ihm/ihm/__init__.py @@ -20,7 +20,7 @@ import json from . import util -__version__ = '0.25' +__version__ = '0.27' class __UnknownValue(object): @@ -74,6 +74,8 @@ class System(object): :param str id: Unique identifier for this system in the mmCIF file. """ + structure_determination_methodology = "integrative" + def __init__(self, title=None, id='model'): self.id = id self.title = title diff --git a/modules/core/dependency/python-ihm/ihm/dumper.py b/modules/core/dependency/python-ihm/ihm/dumper.py index 13f48966e0..013fae7341 100644 --- a/modules/core/dependency/python-ihm/ihm/dumper.py +++ b/modules/core/dependency/python-ihm/ihm/dumper.py @@ -90,7 +90,9 @@ def dump(self, system, writer): class _StructDumper(Dumper): def dump(self, system, writer): with writer.category("_struct") as lp: - lp.write(title=system.title, entry_id=system.id) + mth = system.structure_determination_methodology + lp.write(title=system.title, entry_id=system.id, + pdbx_structure_determination_methodology=mth) class _CommentDumper(Dumper): diff --git a/modules/core/dependency/python-ihm/ihm/format.py b/modules/core/dependency/python-ihm/ihm/format.py index 107831e48d..677677fd50 100644 --- a/modules/core/dependency/python-ihm/ihm/format.py +++ b/modules/core/dependency/python-ihm/ihm/format.py @@ -120,9 +120,10 @@ class CifWriter(_Writer): to write to - and provides methods to write Python objects to that file. Most simple Python types are supported (string, float, bool, int). The Python bool type is mapped to CIF strings - 'NO' and 'YES'. Floats are always represented with 3 decimal places; - if a different amount of precision is desired, convert the float to - a string first.""" + 'NO' and 'YES'. Floats are always represented with 3 decimal places + (or in scientific notation with 3 digits of precision if smaller + than 1e-3); if a different amount of precision is desired, convert + the float to a string first.""" def flush(self): # noop - data is written as it is encountered @@ -191,7 +192,10 @@ def _repr(self, obj): and obj not in ('save_', 'loop_', 'stop_', 'global_', '?', '.'): return obj elif isinstance(obj, float): - return "%.3f" % obj + if abs(obj) < 1e-3: + return "%.3g" % obj + else: + return "%.3f" % obj elif isinstance(obj, bool): return self._boolmap[obj] # Don't use repr(x) if type(x) == long since that adds an 'L' suffix, diff --git a/modules/core/dependency/python-ihm/ihm/format_bcif.py b/modules/core/dependency/python-ihm/ihm/format_bcif.py index 0bdcea5436..f96482e1ef 100644 --- a/modules/core/dependency/python-ihm/ihm/format_bcif.py +++ b/modules/core/dependency/python-ihm/ihm/format_bcif.py @@ -206,6 +206,7 @@ def __init__(self, fh, category_handler, unknown_category_handler=None, def read_file(self): """Read the file and extract data. + :return: True iff more data blocks are available to be read. """ self._add_category_keys() @@ -549,7 +550,11 @@ def loop(self, category, keys): def write_comment(self, comment): """See :meth:`ihm.format.CifWriter.write_comment`. - @note BinaryCIF does not support comments, so this is a noop""" + + .. note:: + + BinaryCIF does not support comments, so this is a noop. + """ pass def _encode_data(self, data): diff --git a/modules/core/dependency/python-ihm/ihm/reader.py b/modules/core/dependency/python-ihm/ihm/reader.py index c53d6451d2..fa954e8d2c 100644 --- a/modules/core/dependency/python-ihm/ihm/reader.py +++ b/modules/core/dependency/python-ihm/ihm/reader.py @@ -3094,7 +3094,7 @@ def get_handlers(self, sysr): :param sysr: class to track global file information. :type sysr: :class:`SystemReader` - :return: a list of :class:`Dumper` objects. + :return: a list of :class:`Handler` objects. """ pass diff --git a/modules/core/dependency/python-ihm/setup.py b/modules/core/dependency/python-ihm/setup.py index c717105340..efa2a8ba6a 100755 --- a/modules/core/dependency/python-ihm/setup.py +++ b/modules/core/dependency/python-ihm/setup.py @@ -7,7 +7,7 @@ import sys import os -VERSION = "0.25" +VERSION = "0.27" copy_args = sys.argv[1:] diff --git a/modules/core/dependency/python-ihm/test/test_dumper.py b/modules/core/dependency/python-ihm/test/test_dumper.py index da24652ac2..aeedb2cba5 100644 --- a/modules/core/dependency/python-ihm/test/test_dumper.py +++ b/modules/core/dependency/python-ihm/test/test_dumper.py @@ -51,7 +51,7 @@ def test_write(self): ihm.dumper.write(fh, [sys1, sys2]) lines = fh.getvalue().split('\n') self.assertEqual(lines[:2], ["data_system1", "_entry.id system1"]) - self.assertEqual(lines[14:16], + self.assertEqual(lines[15:17], ["data_system23", "_entry.id 'system 2+3'"]) def test_write_custom_dumper(self): @@ -113,6 +113,7 @@ def test_struct_dumper(self): dumper = ihm.dumper._StructDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """_struct.entry_id model +_struct.pdbx_structure_determination_methodology integrative _struct.title 'test model' """) diff --git a/modules/core/dependency/python-ihm/test/test_examples.py b/modules/core/dependency/python-ihm/test/test_examples.py index f0ed7a190e..826d3ef6aa 100644 --- a/modules/core/dependency/python-ihm/test/test_examples.py +++ b/modules/core/dependency/python-ihm/test/test_examples.py @@ -41,7 +41,7 @@ def test_simple_docking_example(self): # can read it with open(os.path.join(tmpdir, 'output.cif')) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 314) + self.assertEqual(len(contents), 315) with open(os.path.join(tmpdir, 'output.cif')) as fh: s, = ihm.reader.read(fh) @@ -55,7 +55,7 @@ def test_locations_example(self): # can read it with open(out) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 68) + self.assertEqual(len(contents), 69) with open(out) as fh: s, = ihm.reader.read(fh) os.unlink(out) @@ -70,7 +70,7 @@ def test_ligands_water_example(self): # can read it with open(out) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 160) + self.assertEqual(len(contents), 161) with open(out) as fh: s, = ihm.reader.read(fh) # Make sure that resulting Python objects are picklable @@ -92,7 +92,7 @@ def test_non_standard_residues_example(self): # can read it with open(out) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 64) + self.assertEqual(len(contents), 65) with open(out) as fh: s, = ihm.reader.read(fh) os.unlink(out) diff --git a/modules/core/dependency/python-ihm/test/test_format.py b/modules/core/dependency/python-ihm/test/test_format.py index 93f0391e2d..96075ab44a 100644 --- a/modules/core/dependency/python-ihm/test/test_format.py +++ b/modules/core/dependency/python-ihm/test/test_format.py @@ -182,6 +182,8 @@ def test_repr(self): self.assertEqual(w._repr("fo'o"), '"fo\'o"') self.assertEqual(w._repr('foo bar'), "'foo bar'") self.assertEqual(w._repr(42.123456), '42.123') + self.assertEqual(w._repr(0.000123456), '0.000123') + self.assertEqual(w._repr(0.00000123456), '1.23e-06') self.assertEqual(w._repr(False), 'NO') self.assertEqual(w._repr(True), 'YES') if sys.version_info[0] == 2: From 7b38db45f94d6ba2a274585517bd20e66691f1af Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 1 Feb 2022 13:53:10 -0800 Subject: [PATCH 014/155] Get latest IMP.sampcon --- modules/sampcon | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/sampcon b/modules/sampcon index 0a2daca4de..5ac303a195 160000 --- a/modules/sampcon +++ b/modules/sampcon @@ -1 +1 @@ -Subproject commit 0a2daca4de2d2107d3c0ee22617a4dc08e4aa5d4 +Subproject commit 5ac303a195f29dba3668a3a7393621a6799becfe From 46ae458669d68ef9b9f5c22f30f53cdeadf33fab Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 1 Feb 2022 16:37:54 -0800 Subject: [PATCH 015/155] Squashed 'modules/pmi/' changes from c51f8b6e47..86cd0b6b86 86cd0b6b86 Update to match latest python-ihm git-subtree-dir: modules/pmi git-subtree-split: 86cd0b6b86ed5f054b4da8598ba8026d37b545c4 --- modules/pmi/test/test_mmcif.py | 8 ++++---- modules/pmi/test/test_mmcif_pmi2.py | 8 +++++--- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/modules/pmi/test/test_mmcif.py b/modules/pmi/test/test_mmcif.py index f648df5623..32983dea12 100644 --- a/modules/pmi/test/test_mmcif.py +++ b/modules/pmi/test/test_mmcif.py @@ -1364,7 +1364,7 @@ class DummyProtocolStep(object): _ihm_2dem_class_average_fitting.tr_vector[2] _ihm_2dem_class_average_fitting.tr_vector[3] 1 1 9 0.873 -0.406503 -0.909500 -0.086975 0.379444 -0.254653 0.889480 -0.831131 -0.328574 0.448622 304.187 219.586 0.000 +0.328574 0.448622 304.187 219.586 0 # """) @@ -1525,13 +1525,13 @@ def test_add_membrane_surface_restraint(self): """Test add_membrane_surface_restraint method""" self._check_membrane_restraint( 'add_membrane_surface_location_restraint', - "'upper bound' 0.500 . 0.000") + "'upper bound' 0.500 . 0") def test_add_membrane_exclusion_restraint(self): """Test add_membrane_exclusion_restraint method""" self._check_membrane_restraint( 'add_membrane_exclusion_restraint', - "'lower bound' 0.500 0.000 .") + "'lower bound' 0.500 0 .") def _check_membrane_restraint(self, method_name, expected_dist_rsr): class MockObject(object): @@ -1586,7 +1586,7 @@ class MockObject(object): _ihm_geometric_object_transformation.tr_vector[2] _ihm_geometric_object_transformation.tr_vector[3] 1 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000 0.000 0.000 0.000 +1.000000 0 0 0 # # loop_ diff --git a/modules/pmi/test/test_mmcif_pmi2.py b/modules/pmi/test/test_mmcif_pmi2.py index 636abf627d..c7ddf8e67e 100644 --- a/modules/pmi/test/test_mmcif_pmi2.py +++ b/modules/pmi/test/test_mmcif_pmi2.py @@ -92,9 +92,11 @@ def test_finalize_write_mmcif(self): po.finalize() fh = StringIO() ihm.dumper.write(fh, [po.system]) - self.assertEqual(fh.getvalue().split('\n')[:4], - ['data_model', '_entry.id model', - '_struct.entry_id model', '_struct.title .']) + self.assertEqual( + fh.getvalue().split('\n')[:5], + ['data_model', '_entry.id model', '_struct.entry_id model', + '_struct.pdbx_structure_determination_methodology integrative', + '_struct.title .']) def test_finalize_write_bcif(self): """Test ProtocolOutput.finalize() and BinaryCIF output""" From 475f3c8670a638bd768d0eca15e1b9c56203d13f Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 1 Feb 2022 16:38:48 -0800 Subject: [PATCH 016/155] Get latest PMI1 --- modules/pmi1 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/pmi1 b/modules/pmi1 index a98c741f0d..3bf65bedb2 160000 --- a/modules/pmi1 +++ b/modules/pmi1 @@ -1 +1 @@ -Subproject commit a98c741f0da9ac75ee28984b641c1ca581d66841 +Subproject commit 3bf65bedb2f8db6f74e392148636cca24d071ed7 From d90607a0d9e65c341cf7aed82abb83edfdf97def Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 2 Feb 2022 11:08:23 -0800 Subject: [PATCH 017/155] Use new canonical URLs for GitHub docs GitHub reorganized their help docs and set up permanent redirects to the new URLs, so update our links to match. --- doc/manual/bugs.md | 2 +- doc/manual/devsetup.md | 4 ++-- doc/manual/scm.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/manual/bugs.md b/doc/manual/bugs.md index ed45b02f55..e182031ca7 100644 --- a/doc/manual/bugs.md +++ b/doc/manual/bugs.md @@ -5,7 +5,7 @@ To report a bug, [open an issue at GitHub](https://github.com/salilab/imp/issues You can also [email us](https://integrativemodeling.org/contact.html), but GitHub issues are preferred because we won't forget about them. -If you write code to fix a bug, [reference the issue number in the commit message](https://help.github.com/articles/closing-issues-via-commit-messages/). +If you write code to fix a bug, [reference the issue number in the commit message](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue). This makes it a lot easier to look back at old issues and figure out how they were resolved. (If the code you write does not fix the bug but only relates to it, for example if you write a test case that demonstrates the problem, diff --git a/doc/manual/devsetup.md b/doc/manual/devsetup.md index cfd5a88366..075ded3308 100644 --- a/doc/manual/devsetup.md +++ b/doc/manual/devsetup.md @@ -11,7 +11,7 @@ tasks, you will need to [work with git](@ref faq_git) and make a copy of the used to [build IMP from source](@ref installation_download). 1. Make a copy (fork) of the [IMP repository](https://github.com/salilab/imp). - There is an [excellent help page at GitHub](https://help.github.com/articles/fork-a-repo/) + There is an [excellent help page at GitHub](https://docs.github.com/en/get-started/quickstart/fork-a-repo) that explains this in detail. 2. Build %IMP [as previously described](@ref installation_download) - the only @@ -22,7 +22,7 @@ used to [build IMP from source](@ref installation_download). 3. Make your changes to %IMP (described in more detail below). 4. When you are finished with your changes, - [open a pull request](https://help.github.com/articles/using-pull-requests/) + [open a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) to get it incorporated into the main %IMP repository. \note There are other ways of working with %IMP. For %example, if you are diff --git a/doc/manual/scm.md b/doc/manual/scm.md index 4aae52a0c7..bb1f54c31e 100644 --- a/doc/manual/scm.md +++ b/doc/manual/scm.md @@ -20,7 +20,7 @@ following: - Periodically run `git pull` to get latest 'upstream' changes into your copy (if you [made a fork](@ref devsetup), you should also periodically - [sync it with the main repository](https://help.github.com/articles/syncing-a-fork/). + [sync it with the main repository](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork). `git imp update` is similar but will also show you any new entries from the changelog. From f21d984a665cfa714174526fe577cc9d922dea21 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 4 Feb 2022 16:30:39 -0800 Subject: [PATCH 018/155] Add metamodeling as a component --- .gitmodules | 3 +++ components/metamodeling | 1 + 2 files changed, 4 insertions(+) create mode 160000 components/metamodeling diff --git a/.gitmodules b/.gitmodules index b180bc32ff..c23fbf7e50 100644 --- a/.gitmodules +++ b/.gitmodules @@ -4,6 +4,9 @@ [submodule "components/pathway_mapping"] path = components/pathway_mapping url = https://github.com/salilab/pathway_mapping.git +[submodule "components/metamodeling"] + path = components/metamodeling + url = https://github.com/salilab/metamodeling.git [submodule "modules/pmi1"] path = modules/pmi1 url = https://github.com/salilab/pmi.git diff --git a/components/metamodeling b/components/metamodeling new file mode 160000 index 0000000000..0d4e523ed0 --- /dev/null +++ b/components/metamodeling @@ -0,0 +1 @@ +Subproject commit 0d4e523ed03c0cd0554c7ce93329b71ae561b547 From 820217dba363851eb5a340ab38b21ab9256568ea Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 17 Feb 2022 10:31:56 -0800 Subject: [PATCH 019/155] Minor documentation improvements --- modules/atom/include/Atom.h | 4 ++-- modules/atom/include/BondEndpointsRefiner.h | 5 ++-- modules/atom/include/BrownianDynamics.h | 22 ++++++++---------- modules/atom/include/BrownianDynamicsTAMD.h | 5 ++-- modules/atom/include/CHARMMAtom.h | 4 ++-- modules/atom/include/CenterOfMass.h | 4 ++-- modules/atom/include/Copy.h | 4 ++-- modules/atom/include/Diffusion.h | 2 +- modules/atom/include/SameResiduePairFilter.h | 2 +- .../atom/include/SecondaryStructureResidue.h | 1 + modules/atom/include/Simulator.h | 2 +- modules/atom/include/atom_macros.h | 4 ++-- modules/atom/include/constants.h | 3 ++- modules/atom/include/estimates.h | 10 ++++---- modules/atom/include/force_fields.h | 23 ++++++++----------- modules/atom/include/protein_ligand_score.h | 2 +- 16 files changed, 46 insertions(+), 51 deletions(-) diff --git a/modules/atom/include/Atom.h b/modules/atom/include/Atom.h index 73828ef9c9..1c04c6755d 100644 --- a/modules/atom/include/Atom.h +++ b/modules/atom/include/Atom.h @@ -240,10 +240,10 @@ class IMPATOMEXPORT Atom : public Hierarchy { public: IMP_DECORATOR_METHODS(Atom, Hierarchy); IMP_DECORATOR_SETUP_1(Atom, Atom, other); - /** Add the required attributes using the passed AtomType. */ + //! Add the required attributes using the passed AtomType. IMP_DECORATOR_SETUP_1(Atom, AtomType, atom_type); - /** return true if the particle has the needed attributes */ + //! return true if the particle has the needed attributes static bool get_is_setup(Model *m, ParticleIndex pi) { return m->get_has_attribute(get_atom_type_key(), pi) && Hierarchy::get_is_setup(m, pi); diff --git a/modules/atom/include/BondEndpointsRefiner.h b/modules/atom/include/BondEndpointsRefiner.h index d53dd014ea..0db2ae4053 100644 --- a/modules/atom/include/BondEndpointsRefiner.h +++ b/modules/atom/include/BondEndpointsRefiner.h @@ -14,9 +14,8 @@ IMPATOM_BEGIN_NAMESPACE //! Return the endpoints of a bond. -/** - \ingroup bond - \see Bond +/** \ingroup bond + \see Bond */ class IMPATOMEXPORT BondEndpointsRefiner : public Refiner { public: diff --git a/modules/atom/include/BrownianDynamics.h b/modules/atom/include/BrownianDynamics.h index c6d7bc2d2e..f36493d3bb 100644 --- a/modules/atom/include/BrownianDynamics.h +++ b/modules/atom/include/BrownianDynamics.h @@ -116,17 +116,16 @@ class IMPATOMEXPORT BrownianDynamics : public Simulator { IMP_OBJECT_METHODS(BrownianDynamics); protected: - /** a set of setup operations before a series of simulation steps */ + //! a set of setup operations before a series of simulation steps virtual void setup(const ParticleIndexes &ps) IMP_OVERRIDE; - /** Calls do_advance_chunk() to advance ps in chunks + //! Calls do_advance_chunk() to advance ps in chunks + /** @param sc particles to simulate in this step + @param dt_fs step size in femtoseconds - @param sc particles to simulate in this step - @param dt_fs step size in femtoseconds - - @return the time step actually simulated (for this class, - it is always equal to the input dt_fs) - */ + @return the time step actually simulated (for this class, + it is always equal to the input dt_fs) + */ virtual double do_step(const ParticleIndexes &sc, double dt_fs) IMP_OVERRIDE; @@ -134,14 +133,13 @@ class IMPATOMEXPORT BrownianDynamics : public Simulator { IMP_OVERRIDE; protected: - /** advances a chunk of ps from index begin to end - - @param dtfs time step in femtoseconds + //! advances a chunk of ps from index begin to end + /** @param dtfs time step in femtoseconds @param ikt inverse kT for current chunk step @param ps particle indexes to advance @param begin beginning index of chunk of ps @param end end index of chunk of ps - */ + */ virtual void do_advance_chunk(double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end); diff --git a/modules/atom/include/BrownianDynamicsTAMD.h b/modules/atom/include/BrownianDynamicsTAMD.h index f840b440ca..b2f298c1c9 100644 --- a/modules/atom/include/BrownianDynamicsTAMD.h +++ b/modules/atom/include/BrownianDynamicsTAMD.h @@ -89,9 +89,8 @@ class IMPATOMEXPORT BrownianDynamicsTAMD : public BrownianDynamics { double wave_factor = 1.0); protected: - /** advances a chunk of ps from index begin to end - - @param dtfs time step in femtoseconds + //! advances a chunk of ps from index begin to end + /** @param dtfs time step in femtoseconds @param ikt inverse kT for current chunk step @param ps particle indexes to advance @param begin beginning index of chunk of ps diff --git a/modules/atom/include/CHARMMAtom.h b/modules/atom/include/CHARMMAtom.h index 74abf6a967..3356d97509 100644 --- a/modules/atom/include/CHARMMAtom.h +++ b/modules/atom/include/CHARMMAtom.h @@ -31,8 +31,8 @@ class IMPATOMEXPORT CHARMMAtom : public Atom { public: IMP_DECORATOR_METHODS(CHARMMAtom, Atom); - /** Create a decorator with the passed CHARMM type. - The particle is assumed to already have all atom attributes. + //! Create a decorator with the passed CHARMM type. + /** The particle is assumed to already have all atom attributes. */ IMP_DECORATOR_SETUP_1(CHARMMAtom, String, charmm_type); diff --git a/modules/atom/include/CenterOfMass.h b/modules/atom/include/CenterOfMass.h index 91e6d19983..81e5d3378b 100644 --- a/modules/atom/include/CenterOfMass.h +++ b/modules/atom/include/CenterOfMass.h @@ -33,8 +33,8 @@ IMPATOM_BEGIN_NAMESPACE class IMPATOMEXPORT CenterOfMass : public IMP::Decorator { IMP_CONSTRAINT_DECORATOR_DECL(CenterOfMass); private: - /** Sets up CenterOfMass over particles in pis. - pi is decorated with core::XYZ and atom::Mass decorators, its + //! Sets up CenterOfMass over particles in pis. + /** pi is decorated with core::XYZ and atom::Mass decorators, its coordinates are set to the current center of mass of pis, and its mass is set to the sum of their masses. */ diff --git a/modules/atom/include/Copy.h b/modules/atom/include/Copy.h index 34a98a218b..504c993af9 100644 --- a/modules/atom/include/Copy.h +++ b/modules/atom/include/Copy.h @@ -21,7 +21,7 @@ IMPATOM_BEGIN_NAMESPACE //! A decorator for keeping track of copies of a molecule. /** This decorator is for differentiating and keeping track - of identity when there are multiple copies of + of identity when there are multiple copies of a molecule in the system. It should only be applied to Molecule particles. */ @@ -38,7 +38,7 @@ class IMPATOMEXPORT Copy : public Molecule { static IntKey get_copy_index_key(); IMP_DECORATOR_METHODS(Copy, Molecule); - /** Create a decorator for the numberth copy. */ + //! Create a decorator for the numberth copy. IMP_DECORATOR_SETUP_1(Copy, Int, number); static bool get_is_setup(Model *m, ParticleIndex pi) { diff --git a/modules/atom/include/Diffusion.h b/modules/atom/include/Diffusion.h index 1e3fed9669..c9f6d342ee 100644 --- a/modules/atom/include/Diffusion.h +++ b/modules/atom/include/Diffusion.h @@ -99,7 +99,7 @@ class IMPATOMEXPORT RigidBodyDiffusion : public Diffusion { public: IMP_DECORATOR_METHODS(RigidBodyDiffusion, Diffusion); - /** All diffusion coefficients are determined from the radius */ + //! All diffusion coefficients are determined from the radius IMP_DECORATOR_SETUP_0(RigidBodyDiffusion); //! returns the rotational diffusion coefficient in \f$radians^2/fs\f$ diff --git a/modules/atom/include/SameResiduePairFilter.h b/modules/atom/include/SameResiduePairFilter.h index e34b36658c..7a57d24a12 100644 --- a/modules/atom/include/SameResiduePairFilter.h +++ b/modules/atom/include/SameResiduePairFilter.h @@ -1,6 +1,6 @@ /** * \file IMP/atom/SameResiduePairFilter.h - * \brief A Score on the distance between a pair of particles. + * \brief Filter out atoms that belong to the same residue. * * Copyright 2007-2022 IMP Inventors. All rights reserved. */ diff --git a/modules/atom/include/SecondaryStructureResidue.h b/modules/atom/include/SecondaryStructureResidue.h index ceee890f12..b136eb405a 100644 --- a/modules/atom/include/SecondaryStructureResidue.h +++ b/modules/atom/include/SecondaryStructureResidue.h @@ -1,6 +1,7 @@ /** * \file IMP/atom/SecondaryStructureResidue.h * \brief A decorator for storing secondary structure probabilities. + * * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ diff --git a/modules/atom/include/Simulator.h b/modules/atom/include/Simulator.h index 1b0b8f13be..f8b1ae8f20 100644 --- a/modules/atom/include/Simulator.h +++ b/modules/atom/include/Simulator.h @@ -1,6 +1,6 @@ /** * \file IMP/atom/Simulator.h - * \brief Simple molecular dynamics optimizer. + * \brief Base class for "simulators", such as molecular dynamics. * * Copyright 2007-2022 IMP Inventors. All rights reserved. * diff --git a/modules/atom/include/atom_macros.h b/modules/atom/include/atom_macros.h index 55cfa8fd00..f3d83ebfcf 100644 --- a/modules/atom/include/atom_macros.h +++ b/modules/atom/include/atom_macros.h @@ -1,6 +1,6 @@ /** - * \file IMP/atom/atom_macros.h \brief Various important macros - * for implementing decorators. + * \file IMP/atom/atom_macros.h + * \brief Macros for maintaining molecular hierarchies. * * Copyright 2007-2022 IMP Inventors. All rights reserved. * diff --git a/modules/atom/include/constants.h b/modules/atom/include/constants.h index da4d1f6cd8..d5f5cce9cc 100644 --- a/modules/atom/include/constants.h +++ b/modules/atom/include/constants.h @@ -1,5 +1,6 @@ /** - * \file IMP/atom/constants.h \brief Define the elements used in \imp. + * \file IMP/atom/constants.h + * \brief Define various useful constants for atomic simulations. * * Copyright 2007-2022 IMP Inventors. All rights reserved. * diff --git a/modules/atom/include/estimates.h b/modules/atom/include/estimates.h index 3ba5a30c3d..cd0f3c4edb 100644 --- a/modules/atom/include/estimates.h +++ b/modules/atom/include/estimates.h @@ -1,9 +1,9 @@ /** - * \file IMP/atom/estimates.h - * \brief Estimates of various physical quantities. - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - */ + * \file IMP/atom/estimates.h + * \brief Estimates of various physical quantities. + * + * Copyright 2007-2022 IMP Inventors. All rights reserved. + */ #ifndef IMPATOM_ESTIMATES_H #define IMPATOM_ESTIMATES_H diff --git a/modules/atom/include/force_fields.h b/modules/atom/include/force_fields.h index 528267994e..52f99683e8 100644 --- a/modules/atom/include/force_fields.h +++ b/modules/atom/include/force_fields.h @@ -18,23 +18,20 @@ IMPATOM_BEGIN_NAMESPACE -/** - Add bonds using definitions from given force field parameters. Note - that, at the moment, all added bonds are reported as - IMP::Bond::SINGLE, whether or not they actually are. +//! Add bonds using definitions from given force field parameters. +/** Note that, at the moment, all added bonds are reported as + IMP::Bond::SINGLE, whether or not they actually are. - \see Hierarchy - \see ForceFieldParameters -*/ + \see Hierarchy + \see ForceFieldParameters + */ IMPATOMEXPORT void add_bonds(Hierarchy d, const ForceFieldParameters* ffp = get_all_atom_CHARMM_parameters()); -/** - Add vdW radius from given force field. - - \see Hierarchy - \see ForceFieldParameters -*/ +//! Add vdW radius from given force field. +/** \see Hierarchy + \see ForceFieldParameters + */ IMPATOMEXPORT void add_radii(Hierarchy d, const ForceFieldParameters* ffp = get_all_atom_CHARMM_parameters(), FloatKey radius_key = FloatKey("radius")); diff --git a/modules/atom/include/protein_ligand_score.h b/modules/atom/include/protein_ligand_score.h index d38ae298ac..b6e8106ef4 100644 --- a/modules/atom/include/protein_ligand_score.h +++ b/modules/atom/include/protein_ligand_score.h @@ -1,6 +1,6 @@ /** * \file IMP/atom/protein_ligand_score.h - * \brief Functions to read mol2s + * \brief Functions to score protein-ligand interactions * * Copyright 2007-2022 IMP Inventors. All rights reserved. * From b29500bb57434cf273ecdfd1c53021bc055bedab Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 17 Feb 2022 14:14:21 -0800 Subject: [PATCH 020/155] Update to fontawesome 6 and self-host --- doc/doxygen/header.html | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/doxygen/header.html b/doc/doxygen/header.html index 7ac63d069c..404adbf47d 100644 --- a/doc/doxygen/header.html +++ b/doc/doxygen/header.html @@ -14,7 +14,8 @@ $mathjax $extrastylesheet - + + From 37f97cc7c9f58bce663e29440d5a1a0425c96c40 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 22 Feb 2022 12:10:41 -0800 Subject: [PATCH 021/155] Don't use std::auto_ptr in SWIG wrappers Replace std::auto_ptr with std::unique_ptr (if available) when building the kernel SWIG wrappers. This fixes builds in C++17 mode, where auto_ptr has been removed from the language. --- .../kernel/pyext/include/IMP_kernel.streams.i | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/modules/kernel/pyext/include/IMP_kernel.streams.i b/modules/kernel/pyext/include/IMP_kernel.streams.i index d2b9adee39..983c34e969 100644 --- a/modules/kernel/pyext/include/IMP_kernel.streams.i +++ b/modules/kernel/pyext/include/IMP_kernel.streams.i @@ -163,7 +163,7 @@ class PyOutFileAdapter : public IMP::Object { - std::auto_ptr ostr_; + IMP_UNIQUE_PTR ostr_; struct StreamBuf:public std::streambuf { PyObject *write_method_; @@ -270,7 +270,7 @@ Py_XDECREF(write_method_); } }; - std::auto_ptr stream_buf_; + IMP_UNIQUE_PTR stream_buf_; public: PyOutFileAdapter():IMP::Object("PyOutFileAdapter") { } @@ -288,10 +288,10 @@ public: if (!wm) { return NULL; } - stream_buf_= std::auto_ptr(new StreamBuf(wm)); + stream_buf_= IMP_UNIQUE_PTR(new StreamBuf(wm)); IMP_INTERNAL_CHECK(!ostr_.get(), "Already set the stream."); - ostr_ = std::auto_ptr(new std::ostream(stream_buf_.get())); + ostr_ = IMP_UNIQUE_PTR(new std::ostream(stream_buf_.get())); ostr_->exceptions(std::ostream::badbit); return ostr_.get(); fail: @@ -479,8 +479,8 @@ protected: { virtual ~PyInFileAdapter(){ } - std::auto_ptr streambuf_; - std::auto_ptr istr_; + IMP_UNIQUE_PTR streambuf_; + IMP_UNIQUE_PTR istr_; public: PyInFileAdapter(): IMP::Object("PyInFileAdapter") {} std::string get_type_name() const {return "Python input file";} @@ -507,7 +507,7 @@ public: #if PY_VERSION_HEX < 0x03000000 if (real_file) { - streambuf_ = std::auto_ptr(new PyInCFileAdapter(PyFile_AsFile(p))); + streambuf_ = IMP_UNIQUE_PTR(new PyInCFileAdapter(PyFile_AsFile(p))); } else #endif { @@ -515,10 +515,10 @@ public: if (!(read_method = PyObject_GetAttrString(p, "read"))) { return NULL; } - streambuf_ = std::auto_ptr(new PyInFilelikeAdapter(read_method)); + streambuf_ = IMP_UNIQUE_PTR(new PyInFilelikeAdapter(read_method)); } IMP_INTERNAL_CHECK(!istr_.get(), "Already set the stream."); - istr_ = std::auto_ptr(new std::istream(streambuf_.get())); + istr_ = IMP_UNIQUE_PTR(new std::istream(streambuf_.get())); istr_->exceptions(std::istream::badbit); return istr_.get(); } From 301b43a76c7df09ea37071a8858a42d9f7d6e348 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 22 Feb 2022 12:44:21 -0800 Subject: [PATCH 022/155] Squashed 'modules/rmf/dependency/RMF/' changes from 468586c638..9ff9059b1b 9ff9059b1b Test build with log4cxx 90bb761ee8 Fix build with log4cxx 0.12 or later git-subtree-dir: modules/rmf/dependency/RMF git-subtree-split: 9ff9059b1b953f9c09453d1b8b5db903e6087569 --- modules/rmf/dependency/RMF/.github/workflows/build.yml | 2 +- modules/rmf/dependency/RMF/include/RMF/log.h | 1 - modules/rmf/dependency/RMF/src/log.cpp | 8 ++++---- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/modules/rmf/dependency/RMF/.github/workflows/build.yml b/modules/rmf/dependency/RMF/.github/workflows/build.yml index a18d42367a..09ff68d17b 100644 --- a/modules/rmf/dependency/RMF/.github/workflows/build.yml +++ b/modules/rmf/dependency/RMF/.github/workflows/build.yml @@ -56,7 +56,7 @@ jobs: - name: Install dependencies (Mac) if: matrix.os == 'macos-latest' run: | - brew install swig boost ${{ matrix.install }} + brew install swig boost log4cxx ${{ matrix.install }} pip install coverage - name: Build and test run: | diff --git a/modules/rmf/dependency/RMF/include/RMF/log.h b/modules/rmf/dependency/RMF/include/RMF/log.h index ec995468b7..6715155bf4 100644 --- a/modules/rmf/dependency/RMF/include/RMF/log.h +++ b/modules/rmf/dependency/RMF/include/RMF/log.h @@ -16,7 +16,6 @@ #include // IWYU pragma: export #include // IWYU pragma: export #include // IWYU pragma: export -#include // IWYU pragma: export #include // IWYU pragma: export #endif diff --git a/modules/rmf/dependency/RMF/src/log.cpp b/modules/rmf/dependency/RMF/src/log.cpp index e284d4970f..55a4771db2 100644 --- a/modules/rmf/dependency/RMF/src/log.cpp +++ b/modules/rmf/dependency/RMF/src/log.cpp @@ -41,10 +41,10 @@ struct Configurator { void do_init() { // "%-4r [%t] %-5p %c %x - %m%n" - static log4cxx::PatternLayoutPtr layout = - new log4cxx::PatternLayout(LOG4CXX_STR("%-6r %-5p %c- %m%n")); - static log4cxx::ConsoleAppenderPtr appender = - new log4cxx::ConsoleAppender(layout); + static log4cxx::PatternLayoutPtr layout( + new log4cxx::PatternLayout(LOG4CXX_STR("%-6r %-5p %c- %m%n"))); + static log4cxx::ConsoleAppenderPtr appender( + new log4cxx::ConsoleAppender(layout)); static Configurator config(appender); use(config); set_log_level("off"); From 5c1081f64383adbccf9e00204e3d6e5e33935e9d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 22 Feb 2022 13:13:12 -0800 Subject: [PATCH 023/155] Get latest IMP.sampcon --- modules/sampcon | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/sampcon b/modules/sampcon index 5ac303a195..d7643a4041 160000 --- a/modules/sampcon +++ b/modules/sampcon @@ -1 +1 @@ -Subproject commit 5ac303a195f29dba3668a3a7393621a6799becfe +Subproject commit d7643a404148a6d0042c0cc7210bc34bc71ed994 From 9a8e5afc5cf6655522566326a5c1aadfcbcf5f8a Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 22 Feb 2022 13:23:20 -0800 Subject: [PATCH 024/155] Squashed 'modules/rmf/dependency/RMF/' changes from 9ff9059b1b..e0424dd8ab e0424dd8ab Squashed 'tools/dev_tools/' changes from b7538367..9c0221d4 git-subtree-dir: modules/rmf/dependency/RMF git-subtree-split: e0424dd8abea2f064c115e3d0cbd95c3b69b3dd2 --- modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py b/modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py index 3dd65368a6..7b0b2507bc 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py @@ -39,7 +39,7 @@ def make_files(d): def search_start(d): for cd in [o for o in os.listdir(d) if os.path.isdir(os.path.join(d, o))]: - if cd.startswith("."): + if cd.startswith(".") or cd == 'components': continue cp = os.path.join(d, cd) if cd in ["bin", "src", "test", "examples", "benchmark", "utility"]: From 4137bed64dc6dcfe55c6f1a958fd0ba58ab16a07 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 22 Feb 2022 16:02:21 -0800 Subject: [PATCH 025/155] Don't use 'register' storage class Modern compilers ignore the 'register' storage class anyway, and this code won't compile with C++17, which has removed the class entirely. --- modules/kmeans/src/internal/KM_ANN.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/kmeans/src/internal/KM_ANN.cpp b/modules/kmeans/src/internal/KM_ANN.cpp index 3614402cef..603e044a05 100644 --- a/modules/kmeans/src/internal/KM_ANN.cpp +++ b/modules/kmeans/src/internal/KM_ANN.cpp @@ -41,9 +41,9 @@ IMPKMEANS_BEGIN_INTERNAL_NAMESPACE KMdist kmDist( // interpoint squared distance int dim, KMpoint p, KMpoint q) { - register int d; - register KMcoord diff; - register KMcoord dist; + int d; + KMcoord diff; + KMcoord dist; dist = 0; for (d = 0; d < dim; d++) { From 43f307a10eb8b79b01fa4db3af1fd84e5588c433 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 22 Feb 2022 16:25:53 -0800 Subject: [PATCH 026/155] Replace std::random_shuffle with std::shuffle std::random_shuffle has been removed in C++17, so use std::shuffle instead. As a bonus this uses the IMP random number generator, so will now respect changes to the IMP seed. --- modules/domino/src/particle_states.cpp | 15 ++------------- .../bin/interface_cross_links.cpp | 4 +++- modules/kinematics/src/RRT.cpp | 5 ++--- modules/misc/include/MetricClosePairsFinder.h | 3 ++- 4 files changed, 9 insertions(+), 18 deletions(-) diff --git a/modules/domino/src/particle_states.cpp b/modules/domino/src/particle_states.cpp index 6d3559927e..381608431a 100644 --- a/modules/domino/src/particle_states.cpp +++ b/modules/domino/src/particle_states.cpp @@ -173,17 +173,6 @@ void RecursiveStates::load_particle_state(unsigned int i, } } -namespace { -struct RandomWrapper { - int operator()(int i) { - IMP_INTERNAL_CHECK(i > 0, "Zero i"); - boost::uniform_int ri(0, i - i); - unsigned int ret = ri(random_number_generator); - return ret; - } -}; -} - PermutationStates::PermutationStates(ParticleStates *inner) : ParticleStates("PermutationStates %1%"), inner_(inner), @@ -191,8 +180,8 @@ PermutationStates::PermutationStates(ParticleStates *inner) for (unsigned int i = 0; i < permutation_.size(); ++i) { permutation_[i] = i; } - RandomWrapper rr; - std::random_shuffle(permutation_.begin(), permutation_.end(), rr); + std::shuffle(permutation_.begin(), permutation_.end(), + random_number_generator); } IMPDOMINO_END_NAMESPACE diff --git a/modules/integrative_docking/bin/interface_cross_links.cpp b/modules/integrative_docking/bin/interface_cross_links.cpp index d5c509d79b..0d8889ddda 100644 --- a/modules/integrative_docking/bin/interface_cross_links.cpp +++ b/modules/integrative_docking/bin/interface_cross_links.cpp @@ -9,6 +9,7 @@ #include #include +#include #include #include #include @@ -216,7 +217,8 @@ int main(int argc, char** argv) { } select_cross_links(cross_links, selected_cross_links); - std::random_shuffle(selected_cross_links.begin(), selected_cross_links.end()); + std::shuffle(selected_cross_links.begin(), selected_cross_links.end(), + IMP::random_number_generator); if (selected_cross_links.size() > 0) { write_cross_link_file(out_file_name, selected_cross_links); diff --git a/modules/kinematics/src/RRT.cpp b/modules/kinematics/src/RRT.cpp index f45b86b39f..a5c1768aa8 100644 --- a/modules/kinematics/src/RRT.cpp +++ b/modules/kinematics/src/RRT.cpp @@ -6,6 +6,7 @@ * */ #include +#include IMPKINEMATICS_BEGIN_NAMESPACE @@ -20,12 +21,10 @@ std::ostream& operator<<(std::ostream& s, const RRT::Parameters& p) { namespace { -int myrandom (int i) { return std::rand()%i;} - std::vector select_k_out_of_n_dofs(unsigned int k, unsigned int n) { std::vector arr(n); for(unsigned int i=0; i ret(n, false); for(unsigned int i=0; i ret(k); diff --git a/modules/misc/include/MetricClosePairsFinder.h b/modules/misc/include/MetricClosePairsFinder.h index e42c2f6d1a..84298aaf58 100644 --- a/modules/misc/include/MetricClosePairsFinder.h +++ b/modules/misc/include/MetricClosePairsFinder.h @@ -12,6 +12,7 @@ #include #include #include +#include #include #include #include @@ -50,7 +51,7 @@ class MetricClosePairsFinder : public core::ClosePairsFinder { Index get_index(Model *m, ParticleIndexes inputs) const { unsigned int index_size = std::min( 1U, std::sqrt(static_cast(inputs.size()))); - std::random_shuffle(inputs.begin(), inputs.end()); + std::shuffle(inputs.begin(), inputs.end(), random_number_generator); Index ret; ParticleIndexes indexes(inputs.begin(), inputs.begin() + index_size); From 0ba3aa34242ae1d799879b7d09acc7af19e2782b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 22 Feb 2022 22:41:29 -0800 Subject: [PATCH 027/155] Update to latest Ubuntu, drop Python 2 --- .github/workflows/ci.yml | 26 ++++++++------------------ 1 file changed, 8 insertions(+), 18 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 85542c2442..27df91541c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,38 +10,28 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: ["2.7", "3.6"] - os: [ubuntu-18.04] + python-version: ["3.8"] + os: [ubuntu-20.04] compiler: [gcc] env: CC: ${{ matrix.compiler }} - PY2: ${{ startsWith(matrix.python-version, 2) && 'on' || 'off' }} steps: - uses: actions/checkout@v2 - name: Install dependencies run: | sudo apt-get update -qq - sudo apt-get install -qq libboost-all-dev swig libhdf5-serial-dev libeigen3-dev \ + sudo apt-get install -qq libboost-all-dev swig libhdf5-dev libeigen3-dev \ cmake libcgal-dev libcgal-qt5-dev \ - libfftw3-dev libopencv-dev libgsl0-dev libann-dev \ + libfftw3-dev libopencv-dev libgsl-dev libann-dev \ libprotobuf-dev protobuf-compiler \ - libopenmpi-dev - if [ "${{ env.PY2 }}" == "on" ] - then - sudo apt-get install -qq python-dev python-numpy python-protobuf \ - python-nose python-pip python-biopython - export PIP=pip2 - else - sudo apt-get install -qq python3-dev python3-numpy python3-protobuf \ - python3-nose python3-pip python3-biopython - export PIP=pip3 - fi - $PIP install codecov + libopenmpi-dev python3-dev python3-numpy python3-protobuf \ + python3-nose python3-pip python3-biopython + pip3 install codecov - name: Set up git run: ./setup_git.py - name: Build IMP run: | mkdir build cd build - cmake .. -DUSE_PYTHON2=${{ env.PY2 }} -DCMAKE_CXX_FLAGS="${{ env.CXXFLAGS }}" -DCGAL_DIR=/usr/lib/x86_64-linux-gnu/cmake/CGAL/ + cmake .. -DUSE_PYTHON2=OFF -DCMAKE_CXX_FLAGS="${{ env.CXXFLAGS }}" -DCGAL_DIR=/usr/lib/x86_64-linux-gnu/cmake/CGAL/ make -k -j 2 From f1b873faeee361a89a393ae30aa67497b86e5c1f Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 23 Feb 2022 12:09:20 -0800 Subject: [PATCH 028/155] Use std::random_shuffle if it is available For now, only use std::shuffle if std::random_shuffle isn't provided. This should fix builds on pre-C++11 platforms (std::shuffle is a C++11 feature) and also on Ubuntu 22 (which fails because it has gcc11, which requires that min() and max() of the RNG are constexpr, but this wasn't done in Boost until 1.75 and Ubuntu 22 has 1.74). --- modules/domino/src/particle_states.cpp | 18 ++++++++++++++++++ .../bin/interface_cross_links.cpp | 4 ++++ modules/kernel/compiler/has_random_shuffle.cpp | 15 +++++++++++++++ modules/kinematics/src/RRT.cpp | 8 ++++++++ modules/misc/include/MetricClosePairsFinder.h | 4 ++++ 5 files changed, 49 insertions(+) create mode 100644 modules/kernel/compiler/has_random_shuffle.cpp diff --git a/modules/domino/src/particle_states.cpp b/modules/domino/src/particle_states.cpp index 381608431a..3e78954abc 100644 --- a/modules/domino/src/particle_states.cpp +++ b/modules/domino/src/particle_states.cpp @@ -173,6 +173,19 @@ void RecursiveStates::load_particle_state(unsigned int i, } } +#if !IMP_COMPILER_HAS_RANDOM_SHUFFLE +namespace { +struct RandomWrapper { + int operator()(int i) { + IMP_INTERNAL_CHECK(i > 0, "Zero i"); + boost::uniform_int ri(0, i - i); + unsigned int ret = ri(random_number_generator); + return ret; + } +}; +} +#endif + PermutationStates::PermutationStates(ParticleStates *inner) : ParticleStates("PermutationStates %1%"), inner_(inner), @@ -180,8 +193,13 @@ PermutationStates::PermutationStates(ParticleStates *inner) for (unsigned int i = 0; i < permutation_.size(); ++i) { permutation_[i] = i; } +#if IMP_COMPILER_HAS_RANDOM_SHUFFLE + RandomWrapper rr; + std::random_shuffle(permutation_.begin(), permutation_.end(), rr); +#else std::shuffle(permutation_.begin(), permutation_.end(), random_number_generator); +#endif } IMPDOMINO_END_NAMESPACE diff --git a/modules/integrative_docking/bin/interface_cross_links.cpp b/modules/integrative_docking/bin/interface_cross_links.cpp index 0d8889ddda..7f9c20fc5e 100644 --- a/modules/integrative_docking/bin/interface_cross_links.cpp +++ b/modules/integrative_docking/bin/interface_cross_links.cpp @@ -217,8 +217,12 @@ int main(int argc, char** argv) { } select_cross_links(cross_links, selected_cross_links); +#if IMP_COMPILER_HAS_RANDOM_SHUFFLE + std::random_shuffle(selected_cross_links.begin(), selected_cross_links.end()); +#else std::shuffle(selected_cross_links.begin(), selected_cross_links.end(), IMP::random_number_generator); +#endif if (selected_cross_links.size() > 0) { write_cross_link_file(out_file_name, selected_cross_links); diff --git a/modules/kernel/compiler/has_random_shuffle.cpp b/modules/kernel/compiler/has_random_shuffle.cpp new file mode 100644 index 0000000000..d4045eecf7 --- /dev/null +++ b/modules/kernel/compiler/has_random_shuffle.cpp @@ -0,0 +1,15 @@ +/** + * \file nothing.cpp + * \brief nothing + * + * Copyright 2007-2022 IMP Inventors. All rights reserved. + * + */ + +#include + +int main(void) { + int x[5]; + std::random_shuffle(&x[0], &x[4]); + return 0; +} diff --git a/modules/kinematics/src/RRT.cpp b/modules/kinematics/src/RRT.cpp index a5c1768aa8..430efe649f 100644 --- a/modules/kinematics/src/RRT.cpp +++ b/modules/kinematics/src/RRT.cpp @@ -21,10 +21,18 @@ std::ostream& operator<<(std::ostream& s, const RRT::Parameters& p) { namespace { +#if !IMP_COMPILER_HAS_RANDOM_SHUFFLE +int myrandom (int i) { return std::rand()%i;} +#endif + std::vector select_k_out_of_n_dofs(unsigned int k, unsigned int n) { std::vector arr(n); for(unsigned int i=0; i ret(n, false); for(unsigned int i=0; i ret(k); diff --git a/modules/misc/include/MetricClosePairsFinder.h b/modules/misc/include/MetricClosePairsFinder.h index 84298aaf58..bf3881c84c 100644 --- a/modules/misc/include/MetricClosePairsFinder.h +++ b/modules/misc/include/MetricClosePairsFinder.h @@ -51,7 +51,11 @@ class MetricClosePairsFinder : public core::ClosePairsFinder { Index get_index(Model *m, ParticleIndexes inputs) const { unsigned int index_size = std::min( 1U, std::sqrt(static_cast(inputs.size()))); +#if IMP_COMPILER_HAS_RANDOM_SHUFFLE + std::random_shuffle(inputs.begin(), inputs.end()); +#else std::shuffle(inputs.begin(), inputs.end(), random_number_generator); +#endif Index ret; ParticleIndexes indexes(inputs.begin(), inputs.begin() + index_size); From 65064eae1991d4224a1205456e97aa8c85e19e15 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 23 Feb 2022 12:49:29 -0800 Subject: [PATCH 029/155] Fix reversed test --- modules/domino/src/particle_states.cpp | 2 +- modules/kinematics/src/RRT.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/domino/src/particle_states.cpp b/modules/domino/src/particle_states.cpp index 3e78954abc..29b9ff45eb 100644 --- a/modules/domino/src/particle_states.cpp +++ b/modules/domino/src/particle_states.cpp @@ -173,7 +173,7 @@ void RecursiveStates::load_particle_state(unsigned int i, } } -#if !IMP_COMPILER_HAS_RANDOM_SHUFFLE +#if IMP_COMPILER_HAS_RANDOM_SHUFFLE namespace { struct RandomWrapper { int operator()(int i) { diff --git a/modules/kinematics/src/RRT.cpp b/modules/kinematics/src/RRT.cpp index 430efe649f..bdb2f70537 100644 --- a/modules/kinematics/src/RRT.cpp +++ b/modules/kinematics/src/RRT.cpp @@ -21,7 +21,7 @@ std::ostream& operator<<(std::ostream& s, const RRT::Parameters& p) { namespace { -#if !IMP_COMPILER_HAS_RANDOM_SHUFFLE +#if IMP_COMPILER_HAS_RANDOM_SHUFFLE int myrandom (int i) { return std::rand()%i;} #endif From 630c127a76decc807b9549a3c7e59c71de8a52cc Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 24 Feb 2022 08:55:54 -0800 Subject: [PATCH 030/155] Add support for building on macOS 10.10 --- tools/mac/make-package.sh | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tools/mac/make-package.sh b/tools/mac/make-package.sh index 73639db821..1a8013b120 100755 --- a/tools/mac/make-package.sh +++ b/tools/mac/make-package.sh @@ -33,8 +33,11 @@ case ${TARGET_OSX_VER} in 10.8): PYTHONS="2.7" ;; + 10.10): + PYTHONS="2.7" + ;; *): - echo "This script currently only works on Mac OS X 10.4, 10.6, or 10.8 machines" + echo "This script currently only works on Mac OS X 10.4, 10.6, 10.8, or 10.10 machines" exit 1 ;; esac From 93b11efa374bfc5a5f38c5cfdd0766db100ed071 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 24 Feb 2022 18:35:02 -0800 Subject: [PATCH 031/155] Add compile-type check for std::ref We can replace calls to std::ptr_fun (which has been removed in C++17) with std::ref, but only if it is available, so add a check. --- modules/kernel/compiler/has_ref.cpp | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 modules/kernel/compiler/has_ref.cpp diff --git a/modules/kernel/compiler/has_ref.cpp b/modules/kernel/compiler/has_ref.cpp new file mode 100644 index 0000000000..ce2c8d25d5 --- /dev/null +++ b/modules/kernel/compiler/has_ref.cpp @@ -0,0 +1,16 @@ +/** + * \file nothing.cpp + * \brief nothing + * + * Copyright 2007-2022 IMP Inventors. All rights reserved. + * + */ + +#include + +bool testfunc(char c) { return false; } + +int main(void) { + std::reference_wrapper x = std::ref(testfunc); + return 0; +} From 1d4d7ed276b73e547be51501a7f257dd482e9841 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 25 Feb 2022 10:47:01 -0800 Subject: [PATCH 032/155] Update jpeg package on Mac 10.10 build machine --- tools/mac/make-package.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/mac/make-package.sh b/tools/mac/make-package.sh index 1a8013b120..8d9400d057 100755 --- a/tools/mac/make-package.sh +++ b/tools/mac/make-package.sh @@ -167,7 +167,7 @@ if [ "${TARGET_OSX_VER}" != "10.4" ]; then /usr/local/lib/libopencv_core.2.4.dylib \ /usr/local/lib/libopencv_imgproc.2.4.13.dylib \ /usr/local/lib/libopencv_imgproc.2.4.dylib \ - /usr/local/lib/libjpeg.8.dylib \ + /usr/local/lib/libjpeg.9.dylib \ /usr/local/lib/libtiff.5.dylib \ /usr/local/lib/liblzma.5.dylib \ /usr/local/lib/libprotobuf.9.dylib \ From e075b1dd397f2c6f1274b5c72d7abd85fdbdad4b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 13:38:14 -0800 Subject: [PATCH 033/155] Start adding support for C++20 Add a test for the new "spaceship" or three-way comparison operator <=> introduced in C++20, and use it in Pointer comparisons, as our existing operator== and operator!= will recurse infinitely in C++20. --- modules/kernel/compiler/has_three_way.cpp | 13 +++++++++++++ modules/kernel/include/internal/PointerBase.h | 7 +++++++ 2 files changed, 20 insertions(+) create mode 100644 modules/kernel/compiler/has_three_way.cpp diff --git a/modules/kernel/compiler/has_three_way.cpp b/modules/kernel/compiler/has_three_way.cpp new file mode 100644 index 0000000000..aee30d6182 --- /dev/null +++ b/modules/kernel/compiler/has_three_way.cpp @@ -0,0 +1,13 @@ +/** + * \file nothing.cpp + * \brief nothing + * + * Copyright 2007-2022 IMP Inventors. All rights reserved. + * + */ + +#include +int main(void) { + int A = 1, B = 2; + return (A <=> B) < 0; +} diff --git a/modules/kernel/include/internal/PointerBase.h b/modules/kernel/include/internal/PointerBase.h index 796838b727..469dfb00b0 100644 --- a/modules/kernel/include/internal/PointerBase.h +++ b/modules/kernel/include/internal/PointerBase.h @@ -285,6 +285,12 @@ inline void swap(PointerBase& a, PointerBase& b) { a.swap_with(b); } +#if IMP_COMPILER_HAS_THREE_WAY +template +inline std::strong_ordering operator<=>(OT* o, const PointerBase& p) { + return p <=> o; +} +#else template inline bool operator==(OT* o, const PointerBase& p) { return p == o; @@ -310,6 +316,7 @@ inline bool operator<=(OT* o, const PointerBase& p) { return p >= o; } #endif +#endif IMPKERNEL_END_INTERNAL_NAMESPACE From 42a0153be86a03579bee64139fd784845ec92cc1 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 13:44:41 -0800 Subject: [PATCH 034/155] Require a C++11 compiler to build --- ChangeLog.md | 3 +++ doc/manual/installation.md | 2 ++ 2 files changed, 5 insertions(+) diff --git a/ChangeLog.md b/ChangeLog.md index 6be00edcce..d97f95d946 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -4,6 +4,9 @@ ChangeLog {#changelog} # HEAD - The IMP::em::CoarseCC class has been removed. Use similarly-named free functions instead to calculate coarse cross correlation. +- IMP now requires a C++11 compiler to build. Most compilers less than + 10 years old should support C++11, such as gcc, clang or MS Visual + Studio 2010 or later. # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} - OpenCubicSpline now throws a ValueException for out-of-range values, to diff --git a/doc/manual/installation.md b/doc/manual/installation.md index 1ce19155fd..391fae19c2 100644 --- a/doc/manual/installation.md +++ b/doc/manual/installation.md @@ -22,6 +22,8 @@ to see if the code is currently stable enough for your purposes. In order to build %IMP from source, you will need: +- A C++ compiler that supports the C++11 standard, such as gcc, clang, + or Microsoft Visual Studio 2010 or later. - [CMake](https://cmake.org) (2.8.12 or later; 3.14 or later is recommended) - [Boost](https://www.boost.org) (1.53 or later; Boost.Iostreams must be built with its [zlib filter enabled](https://www.boost.org/doc/libs/1_67_0/libs/iostreams/doc/installation.html)) From 5cb79baf1dfb544c56ae09102c28a9adf6e4e049 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 14:05:34 -0800 Subject: [PATCH 035/155] Assume std::unique_ptr is always available Since we now require C++11 on all our build platforms, we no longer need a macro to choose between std::unique_ptr and std::auto_ptr - the former should always be available. --- modules/em2d/src/internal/Projection.cpp | 8 ++++---- modules/em2d/src/internal/Projector.cpp | 12 ++++++------ modules/kernel/compiler/has_unique_ptr.cpp | 13 ------------- modules/kernel/include/utility_macros.h | 8 +++----- .../kernel/pyext/include/IMP_kernel.streams.i | 18 +++++++++--------- 5 files changed, 22 insertions(+), 37 deletions(-) delete mode 100644 modules/kernel/compiler/has_unique_ptr.cpp diff --git a/modules/em2d/src/internal/Projection.cpp b/modules/em2d/src/internal/Projection.cpp index 9d113b54d8..861317536f 100644 --- a/modules/em2d/src/internal/Projection.cpp +++ b/modules/em2d/src/internal/Projection.cpp @@ -235,9 +235,9 @@ void compute_projections(const Particles& particles, rotated_points[point_index] = r * points[point_index]; } // project - IMP_UNIQUE_PTR p(new Projection(rotated_points, mass, - pixel_size, resolution, - axis_size)); + std::unique_ptr p(new Projection(rotated_points, mass, + pixel_size, resolution, + axis_size)); p->set_rotation(r); p->set_axis(IMP::algebra::Vector3D(v.get_cartesian_coordinates())); p->set_id(i); @@ -313,7 +313,7 @@ void compute_projections(const Particles& all_particles, rotated_ligand_points[p_index] = r * lig_points[p_index]; // project - IMP_UNIQUE_PTR p( + std::unique_ptr p( new Projection(rotated_points, rotated_ligand_points, lig_mass, pixel_size, resolution, axis_size)); p->set_rotation(r); diff --git a/modules/em2d/src/internal/Projector.cpp b/modules/em2d/src/internal/Projector.cpp index 5d18853ccb..e874b32288 100644 --- a/modules/em2d/src/internal/Projector.cpp +++ b/modules/em2d/src/internal/Projector.cpp @@ -70,9 +70,9 @@ void Projector::compute_projections(boost::ptr_vector& projections, rotated_points[point_index] = rotations[i] * points[point_index]; } // project - IMP_UNIQUE_PTR p(new Projection(rotated_points, mass_, - pixel_size_, resolution_, - axis_size)); + std::unique_ptr p(new Projection(rotated_points, mass_, + pixel_size_, resolution_, + axis_size)); p->set_rotation(rotations[i]); p->set_axis(axes[i]); p->set_id(i); @@ -107,9 +107,9 @@ void Projector::compute_projections(const algebra::Vector3Ds& axis, rotated_points[point_index] = rotations[i] * points[point_index]; } // project - IMP_UNIQUE_PTR p(new Projection(rotated_points, mass_, - pixel_size_, resolution_, - axis_size)); + std::unique_ptr p(new Projection(rotated_points, mass_, + pixel_size_, resolution_, + axis_size)); p->set_rotation(rotations[i]); p->set_axis(axes[i]); p->set_id(i); diff --git a/modules/kernel/compiler/has_unique_ptr.cpp b/modules/kernel/compiler/has_unique_ptr.cpp deleted file mode 100644 index 7b375ef4db..0000000000 --- a/modules/kernel/compiler/has_unique_ptr.cpp +++ /dev/null @@ -1,13 +0,0 @@ -/** - * \file nothing.cpp - * \brief nothing - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - * - */ - -#include -int main(void) { - std::unique_ptr a(new int); - return 0; -} diff --git a/modules/kernel/include/utility_macros.h b/modules/kernel/include/utility_macros.h index 008f68edbe..1f89fe1e29 100644 --- a/modules/kernel/include/utility_macros.h +++ b/modules/kernel/include/utility_macros.h @@ -42,11 +42,9 @@ */ #define IMP_UNIQUE_PTR #else -#if IMP_COMPILER_HAS_UNIQUE_PTR -#define IMP_UNIQUE_PTR std::unique_ptr -#else -#define IMP_UNIQUE_PTR std::auto_ptr -#endif +#define IMP_UNIQUE_PTR \ + IMPKERNEL_DEPRECATED_MACRO(2.17, "Use std::unique_ptr instead."); \ + std::unique_ptr #endif #endif /* IMPKERNEL_UTILITY_MACROS_H */ diff --git a/modules/kernel/pyext/include/IMP_kernel.streams.i b/modules/kernel/pyext/include/IMP_kernel.streams.i index 983c34e969..50b7a5a1f9 100644 --- a/modules/kernel/pyext/include/IMP_kernel.streams.i +++ b/modules/kernel/pyext/include/IMP_kernel.streams.i @@ -163,7 +163,7 @@ class PyOutFileAdapter : public IMP::Object { - IMP_UNIQUE_PTR ostr_; + std::unique_ptr ostr_; struct StreamBuf:public std::streambuf { PyObject *write_method_; @@ -270,7 +270,7 @@ Py_XDECREF(write_method_); } }; - IMP_UNIQUE_PTR stream_buf_; + std::unique_ptr stream_buf_; public: PyOutFileAdapter():IMP::Object("PyOutFileAdapter") { } @@ -288,10 +288,10 @@ public: if (!wm) { return NULL; } - stream_buf_= IMP_UNIQUE_PTR(new StreamBuf(wm)); + stream_buf_= std::unique_ptr(new StreamBuf(wm)); IMP_INTERNAL_CHECK(!ostr_.get(), "Already set the stream."); - ostr_ = IMP_UNIQUE_PTR(new std::ostream(stream_buf_.get())); + ostr_ = std::unique_ptr(new std::ostream(stream_buf_.get())); ostr_->exceptions(std::ostream::badbit); return ostr_.get(); fail: @@ -479,8 +479,8 @@ protected: { virtual ~PyInFileAdapter(){ } - IMP_UNIQUE_PTR streambuf_; - IMP_UNIQUE_PTR istr_; + std::unique_ptr streambuf_; + std::unique_ptr istr_; public: PyInFileAdapter(): IMP::Object("PyInFileAdapter") {} std::string get_type_name() const {return "Python input file";} @@ -507,7 +507,7 @@ public: #if PY_VERSION_HEX < 0x03000000 if (real_file) { - streambuf_ = IMP_UNIQUE_PTR(new PyInCFileAdapter(PyFile_AsFile(p))); + streambuf_ = std::unique_ptr(new PyInCFileAdapter(PyFile_AsFile(p))); } else #endif { @@ -515,10 +515,10 @@ public: if (!(read_method = PyObject_GetAttrString(p, "read"))) { return NULL; } - streambuf_ = IMP_UNIQUE_PTR(new PyInFilelikeAdapter(read_method)); + streambuf_ = std::unique_ptr(new PyInFilelikeAdapter(read_method)); } IMP_INTERNAL_CHECK(!istr_.get(), "Already set the stream."); - istr_ = IMP_UNIQUE_PTR(new std::istream(streambuf_.get())); + istr_ = std::unique_ptr(new std::istream(streambuf_.get())); istr_->exceptions(std::istream::badbit); return istr_.get(); } From 02e5655b4bb48a06b26712b12afa47b4466f4167 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 14:14:09 -0800 Subject: [PATCH 036/155] Remove test for 'auto' keyword 'auto' should always be available now since we require C++11. --- modules/kernel/compiler/has_auto.cpp | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 modules/kernel/compiler/has_auto.cpp diff --git a/modules/kernel/compiler/has_auto.cpp b/modules/kernel/compiler/has_auto.cpp deleted file mode 100644 index ef9c0cbf82..0000000000 --- a/modules/kernel/compiler/has_auto.cpp +++ /dev/null @@ -1,12 +0,0 @@ -/** - * \file nothing.cpp - * \brief nothing - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - * - */ - -int main() { - auto a = 6; - return 0; -} From 500b5f63778fd785d8f42a8dcdb516a4e571f5bd Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 14:38:49 -0800 Subject: [PATCH 037/155] Assume 'override' keyword is always available Now that we require C++11 we can use the 'override' keyword, so use it rather than the IMP_OVERRIDE macro, but keep the macro for now for backwards compatibility. --- modules/algebra/include/UnitSimplexD.h | 4 +- modules/algebra/include/vector_metrics.h | 8 +- modules/atom/include/AngleSingletonScore.h | 4 +- .../BerendsenThermostatOptimizerState.h | 2 +- modules/atom/include/BondEndpointsRefiner.h | 6 +- modules/atom/include/BondPairContainer.h | 10 +-- modules/atom/include/BondSingletonScore.h | 4 +- modules/atom/include/BondedPairFilter.h | 4 +- modules/atom/include/BrownianDynamics.h | 6 +- modules/atom/include/BrownianDynamicsTAMD.h | 2 +- modules/atom/include/CAAngleRestraint.h | 4 +- modules/atom/include/CADihedralRestraint.h | 4 +- modules/atom/include/CHARMMParameters.h | 2 +- .../include/CHARMMStereochemistryRestraint.h | 4 +- modules/atom/include/CoulombPairScore.h | 4 +- modules/atom/include/CoverBond.h | 6 +- modules/atom/include/DihedralSingletonScore.h | 4 +- modules/atom/include/EzRestraint.h | 4 +- modules/atom/include/HelixRestraint.h | 4 +- modules/atom/include/ImproperSingletonScore.h | 4 +- .../LangevinThermostatOptimizerState.h | 2 +- modules/atom/include/LennardJonesPairScore.h | 4 +- modules/atom/include/MolecularDynamics.h | 6 +- .../include/RemoveRigidMotionOptimizerState.h | 2 +- .../include/RemoveTranslationOptimizerState.h | 2 +- modules/atom/include/SameResiduePairFilter.h | 4 +- modules/atom/include/Selection.h | 2 +- modules/atom/include/Simulator.h | 2 +- modules/atom/include/SoapPairFilter.h | 4 +- .../atom/include/StereochemistryPairFilter.h | 4 +- .../include/VelocityScalingOptimizerState.h | 2 +- modules/atom/include/hierarchy_tools.h | 4 +- modules/atom/include/internal/Gaussian.h | 4 +- .../include/internal/SelectionPredicate.h | 8 +- modules/atom/include/internal/Sigmoid.h | 4 +- modules/atom/include/mol2.h | 4 +- modules/atom/include/pdb.h | 46 +++++------ modules/atom/include/smoothing_functions.h | 4 +- modules/atom/src/Selection.cpp | 29 ++++--- .../include/AllBipartitePairContainer.h | 10 +-- modules/container/include/AllPairContainer.h | 10 +-- .../include/CloseBipartitePairContainer.h | 2 +- .../container/include/ClosePairContainer.h | 2 +- .../include/ConnectingPairContainer.h | 10 +-- .../include/ConsecutivePairContainer.h | 30 ++++---- .../internal/CloseBipartitePairContainer.h | 8 +- .../include/internal/ClosePairContainer.h | 8 +- modules/core/include/AngleTripletScore.h | 4 +- modules/core/include/BallMover.h | 6 +- .../include/BoundingBox3DSingletonScore.h | 4 +- .../include/BoundingSphere3DSingletonScore.h | 4 +- .../core/include/BoxSweepClosePairsFinder.h | 10 +-- modules/core/include/CentroidOfRefined.h | 6 +- modules/core/include/ChecksScoreState.h | 8 +- modules/core/include/ChildrenRefiner.h | 6 +- modules/core/include/ClosePairsPairScore.h | 12 +-- modules/core/include/ClosedCubicSpline.h | 4 +- modules/core/include/ConjugateGradients.h | 2 +- modules/core/include/ConnectivityRestraint.h | 6 +- modules/core/include/ConstantRestraint.h | 4 +- modules/core/include/Cosine.h | 4 +- modules/core/include/CoverRefined.h | 6 +- modules/core/include/DerivativesFromRefined.h | 6 +- modules/core/include/DerivativesToRefined.h | 6 +- modules/core/include/DiameterRestraint.h | 8 +- modules/core/include/DihedralRestraint.h | 4 +- modules/core/include/DirectionMover.h | 6 +- .../core/include/DistanceToSingletonScore.h | 8 +- .../core/include/ExcludedVolumeRestraint.h | 12 +-- modules/core/include/FixedRefiner.h | 10 +-- .../include/GenericAttributeSingletonScore.h | 4 +- modules/core/include/GridClosePairsFinder.h | 10 +-- modules/core/include/Harmonic.h | 4 +- modules/core/include/HarmonicLowerBound.h | 4 +- modules/core/include/HarmonicUpperBound.h | 4 +- modules/core/include/HarmonicWell.h | 4 +- modules/core/include/Hierarchy.h | 4 +- .../core/include/IncrementalScoringFunction.h | 8 +- modules/core/include/LeavesRefiner.h | 6 +- modules/core/include/Linear.h | 4 +- modules/core/include/LogNormalMover.h | 6 +- modules/core/include/MCCGSampler.h | 2 +- .../core/include/MSConnectivityRestraint.h | 6 +- modules/core/include/MinimumRestraint.h | 6 +- modules/core/include/MonteCarlo.h | 6 +- modules/core/include/MonteCarloMover.h | 2 +- .../core/include/MoveStatisticsScoreState.h | 8 +- .../core/include/MultipleBinormalRestraint.h | 4 +- .../NearestNeighborsClosePairsFinder.h | 10 +-- modules/core/include/NeighborsTable.h | 8 +- modules/core/include/NormalMover.h | 6 +- .../core/include/QuadraticClosePairsFinder.h | 10 +-- modules/core/include/RefinedPairsPairScore.h | 4 +- .../core/include/RestraintsScoringFunction.h | 8 +- .../core/include/RigidBodyAnglePairScore.h | 4 +- modules/core/include/RigidBodyMover.h | 6 +- modules/core/include/RigidBodyTunneler.h | 6 +- modules/core/include/RigidBodyUmbrella.h | 4 +- modules/core/include/RigidClosePairsFinder.h | 14 ++-- modules/core/include/SerialMover.h | 8 +- .../core/include/SphereDistancePairScore.h | 12 +-- modules/core/include/SteepestDescent.h | 2 +- modules/core/include/SubsetMover.h | 8 +- modules/core/include/Surface.h | 26 +++---- modules/core/include/SurfaceMover.h | 6 +- .../core/include/SurfaceSymmetryConstraint.h | 8 +- modules/core/include/SurfaceTetheredChain.h | 4 +- modules/core/include/TableRefiner.h | 6 +- modules/core/include/Transform.h | 6 +- .../include/TransformedDistancePairScore.h | 4 +- modules/core/include/TruncatedHarmonic.h | 4 +- modules/core/include/TypedPairScore.h | 4 +- modules/core/include/VolumeRestraint.h | 4 +- .../include/WeightedDerivativesToRefined.h | 6 +- modules/core/include/WeightedSum.h | 4 +- .../core/include/WeightedSumOfExponential.h | 4 +- modules/core/include/direction.h | 16 ++-- .../internal/MovedSingletonContainer.h | 30 ++++---- modules/core/include/model_statistics.h | 2 +- modules/core/include/predicates.h | 16 ++-- modules/core/include/rigid_bodies.h | 6 +- modules/core/include/rigid_body_geometries.h | 4 +- modules/core/include/symmetry.h | 18 ++--- .../core/src/IncrementalScoringFunction.cpp | 2 +- modules/core/src/MCCGSampler.cpp | 6 +- .../internal/incremental_scoring_function.cpp | 6 +- modules/core/src/rigid_bodies.cpp | 26 +++---- modules/display/include/FilterGeometry.h | 10 +-- modules/display/include/GeometrySet.h | 2 +- modules/display/include/LogOptimizerState.h | 2 +- modules/display/include/PymolWriter.h | 16 ++-- modules/display/include/Writer.h | 2 +- modules/display/include/geometry_macros.h | 14 ++-- modules/display/include/internal/writers.h | 2 +- modules/display/include/particle_geometry.h | 8 +- .../display/include/primitive_geometries.h | 6 +- modules/display/include/restraint_geometry.h | 4 +- modules/display/include/writer_macros.h | 8 +- .../domino/include/BranchAndBoundSampler.h | 2 +- modules/domino/include/DependencyScoreState.h | 8 +- modules/domino/include/DiscreteSampler.h | 2 +- modules/domino/include/DominoSampler.h | 2 +- .../domino/include/assignment_containers.h | 66 ++++++++-------- modules/domino/include/assignment_tables.h | 8 +- modules/domino/include/domino_macros.h | 12 +-- modules/domino/include/particle_states.h | 40 +++++----- modules/domino/include/subset_filters.h | 20 ++--- modules/domino/src/analysis.cpp | 6 +- modules/domino/src/particle_states.cpp | 8 +- modules/domino/src/subset_filters.cpp | 16 ++-- modules/em/include/DensityFillingRestraint.h | 4 +- modules/em/include/EMReaderWriter.h | 4 +- modules/em/include/EnvelopeFitRestraint.h | 4 +- .../em/include/EnvelopePenetrationRestraint.h | 4 +- modules/em/include/EnvelopeScore.h | 2 +- modules/em/include/FitRestraint.h | 4 +- modules/em/include/FitRestraintBayesEM3D.h | 4 +- modules/em/include/MRCReaderWriter.h | 4 +- modules/em/include/PCAAligner.h | 2 +- modules/em/include/PCAFitRestraint.h | 4 +- modules/em/include/SpiderReaderWriter.h | 4 +- modules/em/include/SurfaceShellDensityMap.h | 2 +- modules/em/include/XplorReaderWriter.h | 4 +- modules/em/include/embedding.h | 4 +- modules/em2d/include/DummyRestraint.h | 8 +- modules/em2d/include/Em2DRestraint.h | 4 +- .../include/Fine2DRegistrationRestraint.h | 4 +- modules/em2d/include/JPGImageReaderWriter.h | 12 +-- modules/em2d/include/PCAFitRestraint.h | 8 +- modules/em2d/include/ProjectionParameters.h | 8 +- modules/em2d/include/RelativePositionMover.h | 4 +- .../include/RigidBodiesImageFitRestraint.h | 4 +- .../em2d/include/SpiderImageReaderWriter.h | 12 +-- modules/em2d/include/TIFFImageReaderWriter.h | 12 +-- modules/em2d/include/domino_filter_tables.h | 4 +- modules/em2d/include/domino_filters.h | 2 +- modules/em2d/include/domino_particle_states.h | 8 +- modules/em2d/include/scores2D.h | 6 +- .../example/include/ExampleComplexRestraint.h | 4 +- modules/example/include/ExampleConstraint.h | 8 +- modules/example/include/ExamplePairScore.h | 4 +- modules/example/include/ExampleRestraint.h | 4 +- .../include/ExampleSingletonModifier.h | 6 +- .../include/ExampleSubsetFilterTable.h | 4 +- .../example/include/ExampleUnaryFunction.h | 4 +- .../example/src/ExampleSubsetFilterTable.cpp | 2 +- modules/gsl/include/ConjugateGradients.h | 2 +- modules/gsl/include/QuasiNewton.h | 2 +- modules/gsl/include/Simplex.h | 2 +- modules/isd/include/AmbiguousNOERestraint.h | 4 +- modules/isd/include/AmbiguousRestraint.h | 4 +- .../isd/include/AtomicCrossLinkMSRestraint.h | 4 +- modules/isd/include/CrossLinkMSRestraint.h | 4 +- .../isd/include/CysteineCrossLinkRestraint.h | 4 +- modules/isd/include/FNormal.h | 8 +- modules/isd/include/FStudentT.h | 6 +- modules/isd/include/FretRestraint.h | 4 +- modules/isd/include/GammaPrior.h | 4 +- .../isd/include/GaussianAnchorEMRestraint.h | 6 +- modules/isd/include/GaussianEMRestraint.h | 8 +- .../GaussianProcessInterpolationRestraint.h | 12 +-- modules/isd/include/GaussianRestraint.h | 4 +- modules/isd/include/HybridMonteCarlo.h | 4 +- modules/isd/include/ISDRestraint.h | 4 +- modules/isd/include/JeffreysRestraint.h | 4 +- modules/isd/include/LogWrapper.h | 8 +- .../isd/include/LognormalAmbiguousRestraint.h | 4 +- modules/isd/include/LognormalRestraint.h | 4 +- modules/isd/include/MarginalHBondRestraint.h | 4 +- modules/isd/include/MarginalNOERestraint.h | 4 +- modules/isd/include/MolecularDynamics.h | 12 +-- modules/isd/include/MolecularDynamicsMover.h | 6 +- modules/isd/include/NOERestraint.h | 4 +- modules/isd/include/NormalSigmaPCRestraint.h | 4 +- modules/isd/include/Nuisance.h | 8 +- .../isd/include/PenalizedComplexityPrior.h | 6 +- .../isd/include/RepulsiveDistancePairScore.h | 4 +- modules/isd/include/StudentTRestraint.h | 4 +- modules/isd/include/TALOSRestraint.h | 4 +- modules/isd/include/UniformPrior.h | 8 +- modules/isd/include/Weight.h | 8 +- modules/isd/include/WeightMover.h | 6 +- modules/isd/include/WeightRestraint.h | 4 +- modules/isd/include/bivariate_functions.h | 36 ++++----- modules/isd/include/univariate_functions.h | 68 ++++++++--------- .../include/vonMisesKappaConjugateRestraint.h | 4 +- .../include/vonMisesKappaJeffreysRestraint.h | 4 +- modules/kernel/include/ConfigurationSet.h | 2 +- modules/kernel/include/Constraint.h | 4 +- modules/kernel/include/Model.h | 2 +- modules/kernel/include/ModelObject.h | 2 +- modules/kernel/include/Optimizer.h | 4 +- modules/kernel/include/OptimizerState.h | 4 +- modules/kernel/include/Particle.h | 6 +- modules/kernel/include/Restraint.h | 2 +- modules/kernel/include/RestraintSet.h | 18 ++--- modules/kernel/include/ScoreState.h | 2 +- modules/kernel/include/ScoringFunction.h | 2 +- modules/kernel/include/compiler_macros.h | 18 +---- modules/kernel/include/container_base.h | 2 +- modules/kernel/include/doxygen_macros.h | 10 +-- .../internal/AccumulatorScoreModifier.h | 10 +-- .../include/internal/ContainerConstraint.h | 10 +-- .../include/internal/ContainerRestraint.h | 12 +-- .../include/internal/ContainerScoreState.h | 8 +- .../include/internal/DynamicListContainer.h | 6 +- .../include/internal/ListLikeContainer.h | 12 +-- .../internal/RestraintsScoringFunction.h | 8 +- .../include/internal/StaticListContainer.h | 6 +- .../kernel/include/internal/TupleConstraint.h | 8 +- .../kernel/include/internal/TupleRestraint.h | 6 +- .../include/internal/scoring_functions.h | 14 ++-- modules/kernel/include/internal/swig.h | 20 ++--- modules/kernel/include/object_macros.h | 4 +- modules/kernel/src/ScoringFunction.cpp | 6 +- modules/kernel/src/file.cpp | 6 +- modules/kinematics/include/CompositeJoint.h | 4 +- modules/kinematics/include/DihedralMover.h | 6 +- modules/kinematics/include/FibrilSampler.h | 4 +- .../include/KinematicForestScoreState.h | 8 +- modules/kinematics/include/PrismaticJoint.h | 2 +- modules/kinematics/include/RRT.h | 2 +- .../kinematics/include/RevoluteJointMover.h | 6 +- .../include/UniformBackboneSampler.h | 4 +- modules/kinematics/include/local_planners.h | 2 +- modules/kinematics/include/revolute_joints.h | 12 +-- modules/kmeans/include/internal/KCtree.h | 20 ++--- .../kmeans/include/internal/KMfilterCenters.h | 2 +- modules/kmeans/include/internal/KMlocal.h | 58 +++++++------- .../misc/include/CommonEndpointPairFilter.h | 4 +- .../DecayPairContainerOptimizerState.h | 2 +- modules/misc/include/LogPairScore.h | 4 +- modules/misc/include/LowestRefinedPairScore.h | 4 +- modules/misc/include/MetricClosePairsFinder.h | 10 +-- modules/misc/include/SoftCylinderPairScore.h | 4 +- modules/misc/include/StateAdaptor.h | 8 +- .../include/SAXSMultiStateModelScore.h | 14 ++-- .../include/ComplementarityRestraint.h | 6 +- modules/multifit/include/DensityDataPoints.h | 2 +- .../include/RadiusOfGyrationRestraint.h | 4 +- modules/multifit/include/RigidLeavesRefiner.h | 6 +- .../include/WeightedExcludedVolumeRestraint.h | 4 +- modules/multifit/include/fitting_states.h | 4 +- modules/multifit/include/merge_tree_utils.h | 4 +- .../src/internal/GeometricComplementarity.cpp | 2 +- modules/npc/include/CompositeRestraint.h | 4 +- .../include/MinimumSphereDistancePairScore.h | 4 +- .../include/ProteinLocalizationRestraint.h | 76 +++++++++---------- modules/rmf/include/HierarchyLoadLink.h | 8 +- modules/rmf/include/HierarchySaveLink.h | 6 +- modules/rmf/include/SaveOptimizerState.h | 2 +- modules/rmf/include/simple_links.h | 4 +- modules/rmf/src/geometry_io.cpp | 26 +++---- modules/rmf/src/particle_io.cpp | 10 +-- modules/rmf/src/restraint_io.cpp | 24 +++--- .../saxs/include/RadiusOfGyrationRestraint.h | 4 +- modules/saxs/include/Restraint.h | 6 +- .../score_functor/include/DistancePairScore.h | 4 +- .../include/DistancePairScoreWithCache.h | 10 +-- .../include/ScoreUnaryFunction.h | 4 +- .../include/SurfaceDistancePairScore.h | 8 +- .../spb/include/AttributeDistancePairScore.h | 4 +- modules/spb/include/BoxedMover.h | 6 +- modules/spb/include/CellMover.h | 6 +- modules/spb/include/ChiSquareMetric.h | 4 +- modules/spb/include/ContactMapMetric.h | 4 +- modules/spb/include/DiameterRgyrRestraint.h | 4 +- modules/spb/include/DistanceRMSDMetric.h | 4 +- .../spb/include/DistanceTerminiRestraint.h | 4 +- modules/spb/include/EM2DRestraint.h | 6 +- modules/spb/include/Gaussian.h | 4 +- modules/spb/include/KinkPairScore.h | 4 +- .../spb/include/MolecularDynamicsWithWte.h | 6 +- modules/spb/include/MonteCarloWithWte.h | 4 +- modules/spb/include/NuisanceRangeModifier.h | 6 +- modules/spb/include/PbcBoxedMover.h | 6 +- modules/spb/include/PbcBoxedRigidBodyMover.h | 6 +- modules/spb/include/RMSDMetric.h | 4 +- modules/spb/include/RigidBodyNewMover.h | 6 +- modules/spb/include/RigidBodyPackingScore.h | 4 +- modules/spb/include/SameParticlePairFilter.h | 4 +- modules/spb/include/SameRigidBodyPairFilter.h | 4 +- modules/spb/include/TiltSingletonScore.h | 4 +- modules/spb/include/TransformationSymmetry.h | 6 +- .../spb/include/TwoStateGoModelRestraint.h | 4 +- modules/spb/include/UniformBoundedRestraint.h | 6 +- modules/statistics/include/ChiSquareMetric.h | 6 +- .../include/PartitionalClusteringWithCenter.h | 6 +- .../RecursivePartitionalClusteringEmbedding.h | 4 +- .../RecursivePartitionalClusteringMetric.h | 4 +- modules/statistics/include/embeddings.h | 12 +-- .../include/internal/KMCentersNodeLeaf.h | 10 +-- .../include/internal/KMCentersNodeSplit.h | 10 +-- .../include/internal/KMFilterCenters.h | 4 +- .../include/internal/KMLocalSearchLloyd.h | 12 +-- .../internal/TrivialPartitionalClustering.h | 6 +- .../include/internal/VQClustering.h | 6 +- modules/statistics/include/metrics.h | 8 +- modules/symmetry/include/BallMover.h | 6 +- modules/symmetry/include/RigidBodyMover.h | 6 +- 340 files changed, 1226 insertions(+), 1243 deletions(-) diff --git a/modules/algebra/include/UnitSimplexD.h b/modules/algebra/include/UnitSimplexD.h index fcdf0fadb8..bdd5ff5ab1 100644 --- a/modules/algebra/include/UnitSimplexD.h +++ b/modules/algebra/include/UnitSimplexD.h @@ -71,7 +71,7 @@ class UnitSimplexD : public UnitSimplexBaseD { UnitSimplexD() { IMP_USAGE_CHECK(D > 0, "Dimension must be positive."); } //! Get dimension D of embedded real space. - int get_dimension() const IMP_OVERRIDE { return D; } + int get_dimension() const override { return D; } IMP_SHOWABLE_INLINE(UnitSimplexD, { out << "UnitSimplex" << D << "D"; }); }; @@ -89,7 +89,7 @@ class UnitSimplexD<-1> : public UnitSimplexBaseD<-1> { } //! Get dimension of embedded real space. - int get_dimension() const IMP_OVERRIDE { return d_; } + int get_dimension() const override { return d_; } // FIXME: SWIG doesn't seem to use this. IMP_SHOWABLE_INLINE(UnitSimplexD<-1>, diff --git a/modules/algebra/include/vector_metrics.h b/modules/algebra/include/vector_metrics.h index 5b22853bbb..d916b89202 100644 --- a/modules/algebra/include/vector_metrics.h +++ b/modules/algebra/include/vector_metrics.h @@ -34,10 +34,10 @@ IMP_OBJECTS(VectorKDMetric, VectorKDMetrics); class IMPALGEBRAEXPORT EuclideanVectorKDMetric : public VectorKDMetric { public: EuclideanVectorKDMetric(std::string name = "EuclideanVectorKDMetric%1%"); - double get_distance(const VectorKD &a, const VectorKD &b) const IMP_OVERRIDE { + double get_distance(const VectorKD &a, const VectorKD &b) const override { return get_l2_norm(a - b); } - VectorKD get_centroid(const VectorKDs &vs) const IMP_OVERRIDE { + VectorKD get_centroid(const VectorKDs &vs) const override { IMP_USAGE_CHECK(!vs.empty(), "Needs things to have a centroid"); VectorKD sum = std::accumulate(vs.begin(), vs.end(), get_zero_vector_kd(vs[0].get_dimension())); @@ -52,10 +52,10 @@ class IMPALGEBRAEXPORT EuclideanVectorKDMetric : public VectorKDMetric { class IMPALGEBRAEXPORT MaxVectorKDMetric : public VectorKDMetric { public: MaxVectorKDMetric(std::string name = "MaxVectorKDMetric%1%"); - double get_distance(const VectorKD &a, const VectorKD &b) const IMP_OVERRIDE { + double get_distance(const VectorKD &a, const VectorKD &b) const override { return get_linf_norm(a - b); } - VectorKD get_centroid(const VectorKDs &vs) const IMP_OVERRIDE { + VectorKD get_centroid(const VectorKDs &vs) const override { IMP_USAGE_CHECK(!vs.empty(), "Needs things to have a centroid"); BoundingBoxKD bb = std::accumulate(vs.begin(), vs.end(), BoundingBoxKD(vs[0].get_dimension())); diff --git a/modules/atom/include/AngleSingletonScore.h b/modules/atom/include/AngleSingletonScore.h index 8bd6eaf66c..e38b34e50d 100644 --- a/modules/atom/include/AngleSingletonScore.h +++ b/modules/atom/include/AngleSingletonScore.h @@ -34,9 +34,9 @@ class IMPATOMEXPORT AngleSingletonScore : public SingletonScore { //! Use f to penalize deviations in angle AngleSingletonScore(UnaryFunction *f); virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_SCORE_METHODS(AngleSingletonScore); IMP_OBJECT_METHODS(AngleSingletonScore); ; diff --git a/modules/atom/include/BerendsenThermostatOptimizerState.h b/modules/atom/include/BerendsenThermostatOptimizerState.h index cf72adb272..e1bc45bab4 100644 --- a/modules/atom/include/BerendsenThermostatOptimizerState.h +++ b/modules/atom/include/BerendsenThermostatOptimizerState.h @@ -55,7 +55,7 @@ class IMPATOMEXPORT BerendsenThermostatOptimizerState : public OptimizerState { IMP_OBJECT_METHODS(BerendsenThermostatOptimizerState); protected: - virtual void do_update(unsigned int) IMP_OVERRIDE; + virtual void do_update(unsigned int) override; private: Particles pis_; diff --git a/modules/atom/include/BondEndpointsRefiner.h b/modules/atom/include/BondEndpointsRefiner.h index 0db2ae4053..d5c6190788 100644 --- a/modules/atom/include/BondEndpointsRefiner.h +++ b/modules/atom/include/BondEndpointsRefiner.h @@ -22,14 +22,14 @@ class IMPATOMEXPORT BondEndpointsRefiner : public Refiner { //! no arguments BondEndpointsRefiner(); - virtual bool get_can_refine(Particle *) const IMP_OVERRIDE; + virtual bool get_can_refine(Particle *) const override; virtual const ParticlesTemp get_refined(Particle *) const - IMP_OVERRIDE; + override; #ifndef SWIG using Refiner::get_refined; #endif virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(BondEndpointsRefiner); }; diff --git a/modules/atom/include/BondPairContainer.h b/modules/atom/include/BondPairContainer.h index 9708b40329..f50c515417 100644 --- a/modules/atom/include/BondPairContainer.h +++ b/modules/atom/include/BondPairContainer.h @@ -30,7 +30,7 @@ IMPATOM_BEGIN_NAMESPACE class IMPATOMEXPORT BondPairContainer : public PairContainer { IMP::PointerMember sc_; - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE { + virtual std::size_t do_get_contents_hash() const override { return sc_->get_contents_hash(); } @@ -48,12 +48,12 @@ class IMPATOMEXPORT BondPairContainer : public PairContainer { //! The container containing the bonds BondPairContainer(SingletonContainer* sc); - virtual ParticleIndexPairs get_indexes() const IMP_OVERRIDE; - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ParticleIndexPairs get_indexes() const override; + virtual ParticleIndexPairs get_range_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override { return ModelObjects(1, sc_); } - ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; + ParticleIndexes get_all_possible_indexes() const override; IMP_PAIR_CONTAINER_METHODS(BondPairContainer); IMP_OBJECT_METHODS(BondPairContainer); }; diff --git a/modules/atom/include/BondSingletonScore.h b/modules/atom/include/BondSingletonScore.h index 7ef5c82975..57db8a1061 100644 --- a/modules/atom/include/BondSingletonScore.h +++ b/modules/atom/include/BondSingletonScore.h @@ -32,9 +32,9 @@ class IMPATOMEXPORT BondSingletonScore : public SingletonScore { BondSingletonScore(UnaryFunction *f); UnaryFunction *get_unary_function() const { return f_; } virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_SCORE_METHODS(BondSingletonScore); IMP_OBJECT_METHODS(BondSingletonScore); }; diff --git a/modules/atom/include/BondedPairFilter.h b/modules/atom/include/BondedPairFilter.h index 56142c594c..26cdb5be9b 100644 --- a/modules/atom/include/BondedPairFilter.h +++ b/modules/atom/include/BondedPairFilter.h @@ -27,9 +27,9 @@ class IMPATOMEXPORT BondedPairFilter : public PairPredicate { virtual int get_value_index(Model *m, const ParticleIndexPair &p) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_PREDICATE_METHODS(BondedPairFilter); IMP_OBJECT_METHODS(BondedPairFilter); ; diff --git a/modules/atom/include/BrownianDynamics.h b/modules/atom/include/BrownianDynamics.h index f36493d3bb..11c324a3c9 100644 --- a/modules/atom/include/BrownianDynamics.h +++ b/modules/atom/include/BrownianDynamics.h @@ -117,7 +117,7 @@ class IMPATOMEXPORT BrownianDynamics : public Simulator { protected: //! a set of setup operations before a series of simulation steps - virtual void setup(const ParticleIndexes &ps) IMP_OVERRIDE; + virtual void setup(const ParticleIndexes &ps) override; //! Calls do_advance_chunk() to advance ps in chunks /** @param sc particles to simulate in this step @@ -127,10 +127,10 @@ class IMPATOMEXPORT BrownianDynamics : public Simulator { it is always equal to the input dt_fs) */ virtual double do_step(const ParticleIndexes &sc, - double dt_fs) IMP_OVERRIDE; + double dt_fs) override; virtual bool get_is_simulation_particle(ParticleIndex p) const - IMP_OVERRIDE; + override; protected: //! advances a chunk of ps from index begin to end diff --git a/modules/atom/include/BrownianDynamicsTAMD.h b/modules/atom/include/BrownianDynamicsTAMD.h index b2f298c1c9..1d850a4323 100644 --- a/modules/atom/include/BrownianDynamicsTAMD.h +++ b/modules/atom/include/BrownianDynamicsTAMD.h @@ -99,7 +99,7 @@ class IMPATOMEXPORT BrownianDynamicsTAMD : public BrownianDynamics { void do_advance_chunk(double dtfs, double ikt, const ParticleIndexes &ps, unsigned int begin, unsigned int end) - IMP_OVERRIDE; + override; private: void advance_coordinates_1(ParticleIndex pi, unsigned int i, diff --git a/modules/atom/include/CAAngleRestraint.h b/modules/atom/include/CAAngleRestraint.h index bd965e98f1..5720f07a21 100644 --- a/modules/atom/include/CAAngleRestraint.h +++ b/modules/atom/include/CAAngleRestraint.h @@ -44,8 +44,8 @@ class IMPATOMEXPORT CAAngleRestraint : public Restraint virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(CAAngleRestraint); private: diff --git a/modules/atom/include/CADihedralRestraint.h b/modules/atom/include/CADihedralRestraint.h index 3b73ba6681..0900e97536 100644 --- a/modules/atom/include/CADihedralRestraint.h +++ b/modules/atom/include/CADihedralRestraint.h @@ -52,8 +52,8 @@ class IMPATOMEXPORT CADihedralRestraint : public Restraint virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(CADihedralRestraint); private: diff --git a/modules/atom/include/CHARMMParameters.h b/modules/atom/include/CHARMMParameters.h index c451849cc3..a14c8a97af 100644 --- a/modules/atom/include/CHARMMParameters.h +++ b/modules/atom/include/CHARMMParameters.h @@ -324,7 +324,7 @@ class IMPATOMEXPORT CHARMMParameters : public ForceFieldParameters { IMP_OBJECT_METHODS(CHARMMParameters); private: - virtual String get_force_field_atom_type(Atom atom) const IMP_OVERRIDE; + virtual String get_force_field_atom_type(Atom atom) const override; void read_parameter_file(TextInput input_file); // read topology file diff --git a/modules/atom/include/CHARMMStereochemistryRestraint.h b/modules/atom/include/CHARMMStereochemistryRestraint.h index 121277af17..1ff01eaffa 100644 --- a/modules/atom/include/CHARMMStereochemistryRestraint.h +++ b/modules/atom/include/CHARMMStereochemistryRestraint.h @@ -70,8 +70,8 @@ class IMPATOMEXPORT CHARMMStereochemistryRestraint : public Restraint { StereochemistryPairFilter *get_full_pair_filter(); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(CHARMMStereochemistryRestraint); }; diff --git a/modules/atom/include/CoulombPairScore.h b/modules/atom/include/CoulombPairScore.h index 2d1cf57451..b9895c93ad 100644 --- a/modules/atom/include/CoulombPairScore.h +++ b/modules/atom/include/CoulombPairScore.h @@ -47,9 +47,9 @@ class IMPATOMEXPORT CoulombPairScore : public PairScore { virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(CoulombPairScore); IMP_OBJECT_METHODS(CoulombPairScore); ; diff --git a/modules/atom/include/CoverBond.h b/modules/atom/include/CoverBond.h index ef5ca9f6a4..ac1033407b 100644 --- a/modules/atom/include/CoverBond.h +++ b/modules/atom/include/CoverBond.h @@ -26,11 +26,11 @@ class IMPATOMEXPORT CoverBond : public SingletonModifier { CoverBond(); virtual void apply_index(Model *m, ParticleIndex p) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(CoverBond); IMP_OBJECT_METHODS(CoverBond); ; diff --git a/modules/atom/include/DihedralSingletonScore.h b/modules/atom/include/DihedralSingletonScore.h index ac6eca7619..87a5927fad 100644 --- a/modules/atom/include/DihedralSingletonScore.h +++ b/modules/atom/include/DihedralSingletonScore.h @@ -31,9 +31,9 @@ class IMPATOMEXPORT DihedralSingletonScore : public SingletonScore { public: DihedralSingletonScore(); virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_SCORE_METHODS(DihedralSingletonScore); IMP_OBJECT_METHODS(DihedralSingletonScore); ; diff --git a/modules/atom/include/EzRestraint.h b/modules/atom/include/EzRestraint.h index f2db065ffc..7a27251827 100644 --- a/modules/atom/include/EzRestraint.h +++ b/modules/atom/include/EzRestraint.h @@ -31,8 +31,8 @@ class IMPATOMEXPORT EzRestraint : public Restraint { protected: virtual double unprotected_evaluate(DerivativeAccumulator *da) const - IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + virtual ModelObjectsTemp do_get_inputs() const override; public: EzRestraint(Model *m, ParticleIndexesAdaptor ps); diff --git a/modules/atom/include/HelixRestraint.h b/modules/atom/include/HelixRestraint.h index 4dfdbd4fc7..3f6b2a92b2 100644 --- a/modules/atom/include/HelixRestraint.h +++ b/modules/atom/include/HelixRestraint.h @@ -35,8 +35,8 @@ class IMPATOMEXPORT HelixRestraint : public Restraint { int get_number_of_dihedrals(){return dihedral_rs_.size();} virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(HelixRestraint); }; diff --git a/modules/atom/include/ImproperSingletonScore.h b/modules/atom/include/ImproperSingletonScore.h index 02b94ff00f..a5f5839c39 100644 --- a/modules/atom/include/ImproperSingletonScore.h +++ b/modules/atom/include/ImproperSingletonScore.h @@ -39,9 +39,9 @@ class IMPATOMEXPORT ImproperSingletonScore : public SingletonScore { //! Use f to penalize deviations in angle ImproperSingletonScore(UnaryFunction *f); virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_SCORE_METHODS(ImproperSingletonScore); IMP_OBJECT_METHODS(ImproperSingletonScore); ; diff --git a/modules/atom/include/LangevinThermostatOptimizerState.h b/modules/atom/include/LangevinThermostatOptimizerState.h index 7f8a3815c1..775939d31b 100644 --- a/modules/atom/include/LangevinThermostatOptimizerState.h +++ b/modules/atom/include/LangevinThermostatOptimizerState.h @@ -44,7 +44,7 @@ class IMPATOMEXPORT LangevinThermostatOptimizerState : public OptimizerState { IMP_OBJECT_METHODS(LangevinThermostatOptimizerState); protected: - virtual void do_update(unsigned int) IMP_OVERRIDE; + virtual void do_update(unsigned int) override; private: Particles pis_; diff --git a/modules/atom/include/LennardJonesPairScore.h b/modules/atom/include/LennardJonesPairScore.h index afc4e639f4..3c64b90745 100644 --- a/modules/atom/include/LennardJonesPairScore.h +++ b/modules/atom/include/LennardJonesPairScore.h @@ -78,9 +78,9 @@ class IMPATOMEXPORT LennardJonesPairScore : public PairScore { virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(LennardJonesPairScore); IMP_OBJECT_METHODS(LennardJonesPairScore); ; diff --git a/modules/atom/include/MolecularDynamics.h b/modules/atom/include/MolecularDynamics.h index 0430f82958..71fc82e731 100644 --- a/modules/atom/include/MolecularDynamics.h +++ b/modules/atom/include/MolecularDynamics.h @@ -131,11 +131,11 @@ class IMPATOMEXPORT MolecularDynamics : public Simulator { //! Assign velocities representative of the given temperature virtual void assign_velocities(Float temperature); - virtual void setup(const ParticleIndexes &ps) IMP_OVERRIDE; + virtual void setup(const ParticleIndexes &ps) override; virtual double do_step(const ParticleIndexes &sc, - double dt) IMP_OVERRIDE; + double dt) override; virtual bool get_is_simulation_particle(ParticleIndex p) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(MolecularDynamics); diff --git a/modules/atom/include/RemoveRigidMotionOptimizerState.h b/modules/atom/include/RemoveRigidMotionOptimizerState.h index 99e3b170aa..5de9cd99ef 100644 --- a/modules/atom/include/RemoveRigidMotionOptimizerState.h +++ b/modules/atom/include/RemoveRigidMotionOptimizerState.h @@ -31,7 +31,7 @@ class IMPATOMEXPORT RemoveRigidMotionOptimizerState : public OptimizerState { IMP_OBJECT_METHODS(RemoveRigidMotionOptimizerState); protected: - virtual void do_update(unsigned int call) IMP_OVERRIDE; + virtual void do_update(unsigned int call) override; private: void remove_linear() const; diff --git a/modules/atom/include/RemoveTranslationOptimizerState.h b/modules/atom/include/RemoveTranslationOptimizerState.h index 3b6d844f8b..06019c9988 100644 --- a/modules/atom/include/RemoveTranslationOptimizerState.h +++ b/modules/atom/include/RemoveTranslationOptimizerState.h @@ -34,7 +34,7 @@ class IMPATOMEXPORT RemoveTranslationOptimizerState : public OptimizerState { IMP_OBJECT_METHODS(RemoveTranslationOptimizerState); protected: - virtual void do_update(unsigned int call) IMP_OVERRIDE; + virtual void do_update(unsigned int call) override; private: Particles pis_; diff --git a/modules/atom/include/SameResiduePairFilter.h b/modules/atom/include/SameResiduePairFilter.h index 7a57d24a12..3c5a0d0d9c 100644 --- a/modules/atom/include/SameResiduePairFilter.h +++ b/modules/atom/include/SameResiduePairFilter.h @@ -24,9 +24,9 @@ class IMPATOMEXPORT SameResiduePairFilter : public PairPredicate { SameResiduePairFilter(); virtual int get_value_index(Model *m, const ParticleIndexPair &p) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_PREDICATE_METHODS(SameResiduePairFilter); IMP_OBJECT_METHODS(SameResiduePairFilter); ; diff --git a/modules/atom/include/Selection.h b/modules/atom/include/Selection.h index 884f767df1..9c1483a480 100644 --- a/modules/atom/include/Selection.h +++ b/modules/atom/include/Selection.h @@ -353,7 +353,7 @@ class IMPATOMEXPORT SelectionGeometry : public display::Geometry { public: SelectionGeometry(atom::Selection d, std::string name = "Selection") : display::Geometry(name), res_(d) {} - display::Geometries get_components() const IMP_OVERRIDE; + display::Geometries get_components() const override; IMP_OBJECT_METHODS(SelectionGeometry); }; diff --git a/modules/atom/include/Simulator.h b/modules/atom/include/Simulator.h index f8b1ae8f20..8b6133b001 100644 --- a/modules/atom/include/Simulator.h +++ b/modules/atom/include/Simulator.h @@ -167,7 +167,7 @@ class IMPATOMEXPORT Simulator : public Optimizer { protected: /** @} */ - virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE IMP_FINAL; + virtual Float do_optimize(unsigned int max_steps) override IMP_FINAL; /** Perform any setup operations needed before running a series of simulation steps diff --git a/modules/atom/include/SoapPairFilter.h b/modules/atom/include/SoapPairFilter.h index db33d16ea2..a7a14a10af 100644 --- a/modules/atom/include/SoapPairFilter.h +++ b/modules/atom/include/SoapPairFilter.h @@ -42,7 +42,7 @@ class SoapPairFilter : public PairPredicate { virtual int get_value_index(Model *m, const ParticleIndexPair &p) const - IMP_OVERRIDE { + override { #ifdef IMP_SCORE_FUNCTOR_USE_HDF5 return !chainsep_.get_separation_ok(m, p) || !bondsep_.get_separation_ok(m, p); @@ -52,7 +52,7 @@ class SoapPairFilter : public PairPredicate { } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { ModelObjectsTemp ret = IMP::get_particles(m, pis); #ifdef IMP_SCORE_FUNCTOR_USE_HDF5 if (chainsep_.enabled() || bondsep_.enabled()) { diff --git a/modules/atom/include/StereochemistryPairFilter.h b/modules/atom/include/StereochemistryPairFilter.h index cd500f3948..ceaf92e22b 100644 --- a/modules/atom/include/StereochemistryPairFilter.h +++ b/modules/atom/include/StereochemistryPairFilter.h @@ -49,9 +49,9 @@ class IMPATOMEXPORT StereochemistryPairFilter : public PairPredicate { virtual int get_value_index(Model *m, const ParticleIndexPair &p) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_PREDICATE_METHODS(StereochemistryPairFilter); IMP_OBJECT_METHODS(StereochemistryPairFilter); ; diff --git a/modules/atom/include/VelocityScalingOptimizerState.h b/modules/atom/include/VelocityScalingOptimizerState.h index 9a872ece95..339b9b8c85 100644 --- a/modules/atom/include/VelocityScalingOptimizerState.h +++ b/modules/atom/include/VelocityScalingOptimizerState.h @@ -40,7 +40,7 @@ class IMPATOMEXPORT VelocityScalingOptimizerState : public OptimizerState { IMP_OBJECT_METHODS(VelocityScalingOptimizerState); protected: - virtual void do_update(unsigned int call) IMP_OVERRIDE; + virtual void do_update(unsigned int call) override; private: Particles pis_; diff --git a/modules/atom/include/hierarchy_tools.h b/modules/atom/include/hierarchy_tools.h index 09b9f36e90..c3175fd39c 100644 --- a/modules/atom/include/hierarchy_tools.h +++ b/modules/atom/include/hierarchy_tools.h @@ -185,7 +185,7 @@ class HierarchyGeometry : public display::SingletonGeometry { public: HierarchyGeometry(core::Hierarchy d, double resolution = 0) : SingletonGeometry(d), res_(resolution) {} - display::Geometries get_components() const IMP_OVERRIDE { + display::Geometries get_components() const override { display::Geometries ret; atom::Hierarchy d(get_particle()); atom::Selection sel(d); @@ -210,7 +210,7 @@ class HierarchiesGeometry : public display::SingletonsGeometry { public: HierarchiesGeometry(SingletonContainer *sc, double resolution = -1) : SingletonsGeometry(sc), res_(resolution) {} - display::Geometries get_components() const IMP_OVERRIDE { + display::Geometries get_components() const override { display::Geometries ret; IMP_FOREACH(ParticleIndex pi, get_container()->get_contents()) { Model *m = get_container()->get_model(); diff --git a/modules/atom/include/internal/Gaussian.h b/modules/atom/include/internal/Gaussian.h index dc854573ad..90f5713e97 100644 --- a/modules/atom/include/internal/Gaussian.h +++ b/modules/atom/include/internal/Gaussian.h @@ -21,13 +21,13 @@ class Gaussian : public UnaryFunction { : Emin_(Emin), Zmin_(Zmin), sigma_(sigma) {} virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return DerivativePair(evaluate(feature), -Emin_* exp(-(feature - Zmin_) * (feature - Zmin_) / sigma_ / sigma_ / 2.0) * (feature - Zmin_) / sigma_ / sigma_); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return Emin_* exp(-(feature - Zmin_) * (feature - Zmin_) / sigma_ / sigma_ / 2.0); } diff --git a/modules/atom/include/internal/SelectionPredicate.h b/modules/atom/include/internal/SelectionPredicate.h index 07815da418..a045ce92e0 100644 --- a/modules/atom/include/internal/SelectionPredicate.h +++ b/modules/atom/include/internal/SelectionPredicate.h @@ -114,10 +114,10 @@ class ListSelectionPredicate : public SelectionPredicate { public: ListSelectionPredicate(std::string name) : SelectionPredicate(name) {} - virtual unsigned get_number_of_children() const IMP_OVERRIDE { + virtual unsigned get_number_of_children() const override { return predicates_.size(); } - virtual SelectionPredicate *get_child(unsigned i) const IMP_OVERRIDE { + virtual SelectionPredicate *get_child(unsigned i) const override { return predicates_[i]; } @@ -126,7 +126,7 @@ class ListSelectionPredicate : public SelectionPredicate { predicates_.push_back(p); } - virtual int setup_bitset(int index) IMP_OVERRIDE { + virtual int setup_bitset(int index) override { index = SelectionPredicate::setup_bitset(index); /* Set indexes for subpredicates */ IMP_FOREACH(SelectionPredicate *p, predicates_) { @@ -137,7 +137,7 @@ class ListSelectionPredicate : public SelectionPredicate { virtual ModelObjectsTemp do_get_inputs( Model *m, const ParticleIndexes &pis) const - IMP_OVERRIDE { + override { return IMP::get_particles(m, pis); } }; diff --git a/modules/atom/include/internal/Sigmoid.h b/modules/atom/include/internal/Sigmoid.h index c87a2452a0..4f7a88ef3b 100644 --- a/modules/atom/include/internal/Sigmoid.h +++ b/modules/atom/include/internal/Sigmoid.h @@ -24,13 +24,13 @@ class Sigmoid : public UnaryFunction { Sigmoid(Float E0, Float Zmid, Float n) : E0_(E0), Zmid_(Zmid), n_(n) {} virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return DerivativePair(evaluate(feature), -E0_ * n_ * pow(feature / Zmid_, n_) / (feature * (1.0 + pow(feature / Zmid_, n_)) * (1.0 + pow(feature / Zmid_, n_)))); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return E0_ / (1.0 + std::pow(feature / Zmid_, n_)); } IMP_OBJECT_METHODS(Sigmoid); diff --git a/modules/atom/include/mol2.h b/modules/atom/include/mol2.h index 2068080dab..709814fc59 100644 --- a/modules/atom/include/mol2.h +++ b/modules/atom/include/mol2.h @@ -33,7 +33,7 @@ class IMPATOMEXPORT Mol2Selector : public IMP::Object { //! Read all atoms class AllMol2Selector : public Mol2Selector { public: - bool get_is_selected(const std::string& mol2_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string& mol2_line) const override { return (true || mol2_line.empty()); } }; @@ -41,7 +41,7 @@ class AllMol2Selector : public Mol2Selector { //! Defines a selector that will pick only non-hydrogen atoms class IMPATOMEXPORT NonHydrogenMol2Selector : public Mol2Selector { public: - bool get_is_selected(const std::string& mol2_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string& mol2_line) const override { String atom_type = internal::pick_mol2atom_type(mol2_line); return (atom_type[0] != 'H'); } diff --git a/modules/atom/include/pdb.h b/modules/atom/include/pdb.h index 648a287076..f7225ba1fe 100644 --- a/modules/atom/include/pdb.h +++ b/modules/atom/include/pdb.h @@ -53,7 +53,7 @@ class NonAlternativePDBSelector : public PDBSelector { NonAlternativePDBSelector(std::string name = "NonAlternativePDBSelector%1%") : PDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { return (internal::atom_alt_loc_indicator(pdb_line) == ' ' || internal::atom_alt_loc_indicator(pdb_line) == 'A'); } @@ -66,7 +66,7 @@ class ATOMPDBSelector : public NonAlternativePDBSelector { ATOMPDBSelector(std::string name = "ATOMPDBSelector%1%") : NonAlternativePDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { return (NonAlternativePDBSelector::get_is_selected(pdb_line) && internal::is_ATOM_rec(pdb_line)); } @@ -79,7 +79,7 @@ class CAlphaPDBSelector : public NonAlternativePDBSelector { CAlphaPDBSelector(std::string name = "CAlphaPDBSelector%1%") : NonAlternativePDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) return false; const std::string type = internal::atom_type(pdb_line); return (type[1] == 'C' && type[2] == 'A' && type[3] == ' '); @@ -93,7 +93,7 @@ class CBetaPDBSelector : public NonAlternativePDBSelector { CBetaPDBSelector(std::string name = "CBetaPDBSelector%1%") : NonAlternativePDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) return false; const std::string type = internal::atom_type(pdb_line); return (type[1] == 'C' && type[2] == 'B' && type[3] == ' '); @@ -115,7 +115,7 @@ class AtomTypePDBSelector : public PDBSelector { std::sort(atom_types_.begin(), atom_types_.end()); } - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { std::string type = internal::atom_type(pdb_line); boost::trim(type); return std::binary_search(atom_types_.begin(), atom_types_.end(), type); @@ -137,7 +137,7 @@ class ResidueTypePDBSelector : public PDBSelector { std::sort(residue_types_.begin(), residue_types_.end()); } - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { std::string type = internal::atom_residue_name(pdb_line); boost::trim(type); return std::binary_search(residue_types_.begin(), residue_types_.end(), @@ -152,7 +152,7 @@ class CPDBSelector : public NonAlternativePDBSelector { CPDBSelector(std::string name = "CPDBSelector%1%") : NonAlternativePDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) return false; const std::string type = internal::atom_type(pdb_line); return (type[1] == 'C' && type[2] == ' ' && type[3] == ' '); @@ -166,7 +166,7 @@ class NPDBSelector : public NonAlternativePDBSelector { NPDBSelector(std::string name = "NPDBSelector%1%") : NonAlternativePDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) return false; const std::string type = internal::atom_type(pdb_line); return (type[1] == 'N' && type[2] == ' ' && type[3] == ' '); @@ -179,7 +179,7 @@ class AllPDBSelector : public PDBSelector { public: AllPDBSelector(std::string name = "AllPDBSelector%1%") : PDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { return (true || pdb_line.empty()); } IMP_OBJECT_METHODS(AllPDBSelector); @@ -188,7 +188,7 @@ class AllPDBSelector : public PDBSelector { //! Select all ATOM and HETATM records with the given chain ids class ChainPDBSelector : public NonAlternativePDBSelector { public: - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) { return false; } @@ -215,7 +215,7 @@ class WaterPDBSelector : public NonAlternativePDBSelector { WaterPDBSelector(std::string name = "WaterPDBSelector%1%") : NonAlternativePDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) { return false; } @@ -234,7 +234,7 @@ class IMPATOMEXPORT HydrogenPDBSelector : public NonAlternativePDBSelector { HydrogenPDBSelector(std::string name = "HydrogenPDBSelector%1%") : NonAlternativePDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) return false; return is_hydrogen(pdb_line); } @@ -246,7 +246,7 @@ class NonWaterNonHydrogenPDBSelector : public NonAlternativePDBSelector { IMP::PointerMember ws_, hs_; public: - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) { return false; } @@ -268,7 +268,7 @@ class NonHydrogenPDBSelector : public NonAlternativePDBSelector { IMP::PointerMember hs_; public: - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) { return false; } @@ -288,7 +288,7 @@ class NonWaterPDBSelector : public NonAlternativePDBSelector { IMP::PointerMember ws_; public: - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) { return false; } @@ -308,7 +308,7 @@ class BackbonePDBSelector : public NonWaterNonHydrogenPDBSelector { BackbonePDBSelector(std::string name = "BackbonePDBSelector%1%") : NonWaterNonHydrogenPDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonWaterNonHydrogenPDBSelector::get_is_selected(pdb_line)) return false; const std::string type = internal::atom_type(pdb_line); @@ -326,7 +326,7 @@ class PPDBSelector : public NonAlternativePDBSelector { PPDBSelector(std::string name = "PPDBSelector%1%") : NonAlternativePDBSelector(name) {} - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { if (!NonAlternativePDBSelector::get_is_selected(pdb_line)) return false; const std::string type = internal::atom_type(pdb_line); return (type[1] == 'P' && type[2] == ' ' && type[3] == ' '); @@ -349,7 +349,7 @@ class AndPDBSelector : public PDBSelector { const IMP::PointerMember a_, b_; public: - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { return a_->get_is_selected(pdb_line) && b_->get_is_selected(pdb_line); } IMP_OBJECT_METHODS(AndPDBSelector); @@ -372,7 +372,7 @@ class OrPDBSelector : public PDBSelector { const IMP::PointerMember a_, b_; public: - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { return a_->get_is_selected(pdb_line) || b_->get_is_selected(pdb_line); } IMP_OBJECT_METHODS(OrPDBSelector); @@ -396,7 +396,7 @@ class XorPDBSelector : public PDBSelector { const IMP::PointerMember a_, b_; public: - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { return a_->get_is_selected(pdb_line) != b_->get_is_selected(pdb_line); } IMP_OBJECT_METHODS(XorPDBSelector); @@ -419,7 +419,7 @@ class NotPDBSelector : public PDBSelector { const IMP::PointerMember a_; public: - bool get_is_selected(const std::string &pdb_line) const IMP_OVERRIDE { + bool get_is_selected(const std::string &pdb_line) const override { return !a_->get_is_selected(pdb_line); } IMP_OBJECT_METHODS(NotPDBSelector); @@ -601,8 +601,8 @@ class IMPATOMEXPORT WritePDBOptimizerState : public OptimizerState { WritePDBOptimizerState(const atom::Hierarchies mh, std::string filename); protected: - virtual void do_update(unsigned int call) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual void do_update(unsigned int call) override; + virtual ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(WritePDBOptimizerState); }; diff --git a/modules/atom/include/smoothing_functions.h b/modules/atom/include/smoothing_functions.h index c7e66698ca..608f9cd88c 100644 --- a/modules/atom/include/smoothing_functions.h +++ b/modules/atom/include/smoothing_functions.h @@ -104,13 +104,13 @@ class IMPATOMEXPORT ForceSwitch : public SmoothingFunction { deriv_prefactor_ = 6.0 * value_prefactor_; } - double operator()(double score, double distance) const IMP_OVERRIDE { + double operator()(double score, double distance) const override { double factor = get_value(distance); return score * factor; } DerivativePair operator()(double score, double deriv, - double distance) const IMP_OVERRIDE { + double distance) const override { double factor = get_value(distance); double deriv_factor = get_deriv(distance); return std::make_pair(score * factor, diff --git a/modules/atom/src/Selection.cpp b/modules/atom/src/Selection.cpp index 133ba7923d..383fc113c0 100644 --- a/modules/atom/src/Selection.cpp +++ b/modules/atom/src/Selection.cpp @@ -62,19 +62,19 @@ namespace { std::string name = "NotSelectionPredicate%1%") : internal::SelectionPredicate(name), predicate_(predicate) {} - virtual unsigned get_number_of_children() const IMP_OVERRIDE { + virtual unsigned get_number_of_children() const override { return 1; } - virtual SelectionPredicate *get_child(unsigned) const IMP_OVERRIDE { + virtual SelectionPredicate *get_child(unsigned) const override { return predicate_; } - virtual SelectionPredicate *clone(bool) IMP_OVERRIDE { + virtual SelectionPredicate *clone(bool) override { set_was_used(true); return new NotSelectionPredicate(predicate_->clone(false)); } - virtual int setup_bitset(int index) IMP_OVERRIDE { + virtual int setup_bitset(int index) override { index = internal::SelectionPredicate::setup_bitset(index); /* Set index for subpredicate */ index = predicate_->setup_bitset(index); @@ -83,13 +83,13 @@ namespace { virtual ModelObjectsTemp do_get_inputs( Model *m, const ParticleIndexes &pis) const - IMP_OVERRIDE { + override { return IMP::get_particles(m, pis); } virtual MatchType do_get_value_index(Model *m, ParticleIndex pi, boost::dynamic_bitset<> &bs) - const IMP_OVERRIDE { + const override { MatchType v = predicate_->get_value_index(m, pi, bs); switch(v) { case NO_MATCH: @@ -116,7 +116,7 @@ namespace { AndSelectionPredicate(std::string name = "AndSelectionPredicate%1%") : internal::ListSelectionPredicate(name) {} - virtual SelectionPredicate *clone(bool toplevel) IMP_OVERRIDE { + virtual SelectionPredicate *clone(bool toplevel) override { set_was_used(true); // If only one predicate and we're not the top level, // no need to keep ourself around @@ -131,7 +131,7 @@ namespace { virtual MatchType do_get_value_index(Model *m, ParticleIndex pi, boost::dynamic_bitset<> &bs) - const IMP_OVERRIDE { + const override { // Empty list matches everything if (predicates_.size() == 0) { return MATCH_WITH_CHILDREN; @@ -165,7 +165,7 @@ namespace { OrSelectionPredicate(std::string name = "OrSelectionPredicate%1%") : internal::ListSelectionPredicate(name) {} - virtual SelectionPredicate *clone(bool) IMP_OVERRIDE { + virtual SelectionPredicate *clone(bool) override { set_was_used(true); Pointer a = new OrSelectionPredicate(); clone_predicates(a); @@ -174,7 +174,7 @@ namespace { virtual MatchType do_get_value_index(Model *m, ParticleIndex pi, boost::dynamic_bitset<> &bs) - const IMP_OVERRIDE { + const override { // Empty list matches everything if (predicates_.size() == 0) { return MATCH_WITH_CHILDREN; @@ -208,7 +208,7 @@ namespace { XorSelectionPredicate(std::string name = "XorSelectionPredicate%1%") : internal::ListSelectionPredicate(name) {} - virtual SelectionPredicate *clone(bool) IMP_OVERRIDE { + virtual SelectionPredicate *clone(bool) override { set_was_used(true); Pointer a = new XorSelectionPredicate(); clone_predicates(a); @@ -217,7 +217,7 @@ namespace { virtual MatchType do_get_value_index(Model *m, ParticleIndex pi, boost::dynamic_bitset<> &bs) - const IMP_OVERRIDE { + const override { // Empty list matches everything if (predicates_.size() == 0) { return MATCH_WITH_CHILDREN; @@ -339,12 +339,11 @@ namespace { virtual MatchType do_get_value_index(Model *m, \ ParticleIndex pi, \ boost::dynamic_bitset<> &) \ - const IMP_OVERRIDE { \ + const override { \ check; \ } \ virtual ModelObjectsTemp do_get_inputs( \ - Model *m, const ParticleIndexes &pis) const \ - IMP_OVERRIDE { \ + Model *m, const ParticleIndexes &pis) const override { \ return IMP::get_particles(m, pis); \ } \ IMP_OBJECT_METHODS(Name##SelectionPredicate); \ diff --git a/modules/container/include/AllBipartitePairContainer.h b/modules/container/include/AllBipartitePairContainer.h index 714e7ae059..ce466a1ba4 100644 --- a/modules/container/include/AllBipartitePairContainer.h +++ b/modules/container/include/AllBipartitePairContainer.h @@ -29,7 +29,7 @@ class IMPCONTAINEREXPORT AllBipartitePairContainer : public PairContainer { IMP::PointerMember a_, b_; protected: - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE { + virtual std::size_t do_get_contents_hash() const override { std::size_t ret = a_->get_contents_hash(); boost::hash_combine(ret, b_->get_contents_hash()); return ret; @@ -54,10 +54,10 @@ class IMPCONTAINEREXPORT AllBipartitePairContainer : public PairContainer { AllBipartitePairContainer(SingletonContainerAdaptor a, SingletonContainerAdaptor b, std::string name = "AllBipartitePairContainer%1%"); - virtual ParticleIndexPairs get_indexes() const IMP_OVERRIDE; - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; + virtual ParticleIndexPairs get_indexes() const override; + virtual ParticleIndexPairs get_range_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ParticleIndexes get_all_possible_indexes() const override; IMP_PAIR_CONTAINER_METHODS(AllBipartitePairContainer); IMP_OBJECT_METHODS(AllBipartitePairContainer); }; diff --git a/modules/container/include/AllPairContainer.h b/modules/container/include/AllPairContainer.h index f9544b3782..f2448fe162 100644 --- a/modules/container/include/AllPairContainer.h +++ b/modules/container/include/AllPairContainer.h @@ -25,7 +25,7 @@ class IMPCONTAINEREXPORT AllPairContainer : public PairContainer { IMP::PointerMember c_; protected: - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE { + virtual std::size_t do_get_contents_hash() const override { return c_->get_contents_hash(); } @@ -43,10 +43,10 @@ class IMPCONTAINEREXPORT AllPairContainer : public PairContainer { //! Get the individual particles from the passed SingletonContainer AllPairContainer(SingletonContainerAdaptor c, std::string name = "AllPairContainer%1%"); - virtual ParticleIndexPairs get_indexes() const IMP_OVERRIDE; - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; + virtual ParticleIndexPairs get_indexes() const override; + virtual ParticleIndexPairs get_range_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ParticleIndexes get_all_possible_indexes() const override; IMP_PAIR_CONTAINER_METHODS(AllPairContainer); IMP_OBJECT_METHODS(AllPairContainer); }; diff --git a/modules/container/include/CloseBipartitePairContainer.h b/modules/container/include/CloseBipartitePairContainer.h index ffcff80d8a..4a544789ac 100644 --- a/modules/container/include/CloseBipartitePairContainer.h +++ b/modules/container/include/CloseBipartitePairContainer.h @@ -77,7 +77,7 @@ class IMPCONTAINEREXPORT CloseBipartitePairContainer : ParticleIndexes get_all_possible_indexes() const; private: - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE; + virtual std::size_t do_get_contents_hash() const override; #endif IMP_OBJECT_METHODS(CloseBipartitePairContainer); }; diff --git a/modules/container/include/ClosePairContainer.h b/modules/container/include/ClosePairContainer.h index 7f67d26200..d59afb61e0 100644 --- a/modules/container/include/ClosePairContainer.h +++ b/modules/container/include/ClosePairContainer.h @@ -120,7 +120,7 @@ class IMPCONTAINEREXPORT ClosePairContainer : unsigned int get_number_of_partial_rebuilds() const; private: - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE; + virtual std::size_t do_get_contents_hash() const override; #endif IMP_OBJECT_METHODS(ClosePairContainer); }; diff --git a/modules/container/include/ConnectingPairContainer.h b/modules/container/include/ConnectingPairContainer.h index 420677955b..1dc200c790 100644 --- a/modules/container/include/ConnectingPairContainer.h +++ b/modules/container/include/ConnectingPairContainer.h @@ -67,16 +67,16 @@ class IMPCONTAINEREXPORT ConnectingPairContainer : IMP_OBJECT_METHODS(ConnectingPairContainer); private: - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE; + virtual std::size_t do_get_contents_hash() const override; #else - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual ParticleIndexes get_all_possible_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override; ModelObjectsTemp get_score_state_inputs() const; void do_score_state_before_evaluate(); void do_score_state_after_evaluate() {} - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; + virtual ParticleIndexPairs get_range_indexes() const override; IMP_OBJECT_METHODS(ConnectingPairContainer); - bool get_is_decomposable() const IMP_OVERRIDE { return false; } + bool get_is_decomposable() const override { return false; } #endif }; diff --git a/modules/container/include/ConsecutivePairContainer.h b/modules/container/include/ConsecutivePairContainer.h index 792c1f7431..b3abae4ecd 100644 --- a/modules/container/include/ConsecutivePairContainer.h +++ b/modules/container/include/ConsecutivePairContainer.h @@ -45,7 +45,7 @@ class IMPCONTAINEREXPORT ConsecutivePairContainer : public PairContainer { } protected: - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE { return 0; } + virtual std::size_t do_get_contents_hash() const override { return 0; } public: //! apply to each item in container @@ -60,10 +60,10 @@ class IMPCONTAINEREXPORT ConsecutivePairContainer : public PairContainer { ConsecutivePairContainer(Model *m, const ParticleIndexes &ps, std::string name = "ConsecutivePairContainer%1%"); - virtual ParticleIndexPairs get_indexes() const IMP_OVERRIDE; - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; + virtual ParticleIndexPairs get_indexes() const override; + virtual ParticleIndexPairs get_range_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ParticleIndexes get_all_possible_indexes() const override; IMP_PAIR_CONTAINER_METHODS(ConsecutivePairContainer); IMP_OBJECT_METHODS(ConsecutivePairContainer); }; @@ -83,11 +83,11 @@ class IMPCONTAINEREXPORT ConsecutivePairFilter : public PairPredicate { virtual int get_value_index(Model *, const ParticleIndexPair &pip) const - IMP_OVERRIDE { + override { return cpc_->get_contains(pip); } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pi) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pi) const override { ModelObjectsTemp ret; ret += IMP::get_particles(m, pi); return ret; @@ -132,14 +132,14 @@ class IMPCONTAINEREXPORT ExclusiveConsecutivePairContainer void init(); protected: - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE { return 0; } + virtual std::size_t do_get_contents_hash() const override { return 0; } /** Called by Object destructor - removes all keys associated with the exclusive consecutive pair container, so it can be now added to another exclusive consecutive pair container */ - virtual void do_destroy() IMP_OVERRIDE; + virtual void do_destroy() override; public: @@ -156,10 +156,10 @@ class IMPCONTAINEREXPORT ExclusiveConsecutivePairContainer std::string name = "ExclusiveConsecutivePairContainer%1%"); - virtual ParticleIndexPairs get_indexes() const IMP_OVERRIDE; - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; + virtual ParticleIndexPairs get_indexes() const override; + virtual ParticleIndexPairs get_range_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ParticleIndexes get_all_possible_indexes() const override; IMP_PAIR_CONTAINER_METHODS(ExclusiveConsecutivePairContainer); IMP_OBJECT_METHODS(ExclusiveConsecutivePairContainer); }; @@ -173,11 +173,11 @@ class IMPCONTAINEREXPORT ExclusiveConsecutivePairFilter : public PairPredicate { virtual int get_value_index(Model *m, const ParticleIndexPair &pip) const - IMP_OVERRIDE { + override { return ExclusiveConsecutivePairContainer::get_contains(m, pip); } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pi) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pi) const override { ModelObjectsTemp ret; ret += IMP::get_particles(m, pi); return ret; diff --git a/modules/container/include/internal/CloseBipartitePairContainer.h b/modules/container/include/internal/CloseBipartitePairContainer.h index d5f31c3376..988a62e680 100644 --- a/modules/container/include/internal/CloseBipartitePairContainer.h +++ b/modules/container/include/internal/CloseBipartitePairContainer.h @@ -89,12 +89,12 @@ class IMPCONTAINEREXPORT CloseBipartitePairContainer set_has_dependencies(false); }, ); /**@}*/ - void clear_caches() IMP_OVERRIDE { reset_ = true; } - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + void clear_caches() override { reset_ = true; } + virtual ParticleIndexes get_all_possible_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override; void do_score_state_before_evaluate(); void do_score_state_after_evaluate() {} - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; + virtual ParticleIndexPairs get_range_indexes() const override; IMP_OBJECT_METHODS(CloseBipartitePairContainer); }; diff --git a/modules/container/include/internal/ClosePairContainer.h b/modules/container/include/internal/ClosePairContainer.h index 1b4df4da77..1412e2c507 100644 --- a/modules/container/include/internal/ClosePairContainer.h +++ b/modules/container/include/internal/ClosePairContainer.h @@ -45,9 +45,9 @@ class IMPCONTAINEREXPORT ClosePairContainer public: ModelObjectsTemp get_score_state_inputs() const; - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual ParticleIndexes get_all_possible_indexes() const override; + virtual ParticleIndexPairs get_range_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override; void do_score_state_before_evaluate(); void do_score_state_after_evaluate() {} @@ -63,7 +63,7 @@ class IMPCONTAINEREXPORT ClosePairContainer }, { set_has_dependencies(false); }, ); - void clear_caches() IMP_OVERRIDE { first_call_ = true; } + void clear_caches() override { first_call_ = true; } double get_slack() const { return slack_; } double get_distance() const { return distance_; } void update() { do_score_state_before_evaluate(); } diff --git a/modules/core/include/AngleTripletScore.h b/modules/core/include/AngleTripletScore.h index de309fd944..d25054dd43 100644 --- a/modules/core/include/AngleTripletScore.h +++ b/modules/core/include/AngleTripletScore.h @@ -27,9 +27,9 @@ class IMPCOREEXPORT AngleTripletScore : public TripletScore { AngleTripletScore(UnaryFunction *f); virtual double evaluate_index(Model *m, const ParticleIndexTriplet &pi, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_TRIPLET_SCORE_METHODS(AngleTripletScore); IMP_OBJECT_METHODS(AngleTripletScore); }; diff --git a/modules/core/include/BallMover.h b/modules/core/include/BallMover.h index 337be4a646..fcb7c1b136 100644 --- a/modules/core/include/BallMover.h +++ b/modules/core/include/BallMover.h @@ -65,13 +65,13 @@ class IMPCOREEXPORT BallMover : public MonteCarloMover { Float get_radius() const { return radius_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; //! Move particle attributes within a ball, as specified in constructor - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; + virtual MonteCarloMoverResult do_propose() override; //! Restore original attributes from before do_propose() - virtual void do_reject() IMP_OVERRIDE; + virtual void do_reject() override; IMP_OBJECT_METHODS(BallMover); }; diff --git a/modules/core/include/BoundingBox3DSingletonScore.h b/modules/core/include/BoundingBox3DSingletonScore.h index 96c9b3cd82..5d4cf17b63 100644 --- a/modules/core/include/BoundingBox3DSingletonScore.h +++ b/modules/core/include/BoundingBox3DSingletonScore.h @@ -35,9 +35,9 @@ class GenericBoundingBox3DSingletonScore : public SingletonScore { GenericBoundingBox3DSingletonScore(UF *f, const algebra::BoundingBoxD<3> &bb); virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { return IMP::get_particles(m, pis); } IMP_SINGLETON_SCORE_METHODS(GenericBoundingBox3DSingletonScore); diff --git a/modules/core/include/BoundingSphere3DSingletonScore.h b/modules/core/include/BoundingSphere3DSingletonScore.h index 454c93eef9..481e03edc0 100644 --- a/modules/core/include/BoundingSphere3DSingletonScore.h +++ b/modules/core/include/BoundingSphere3DSingletonScore.h @@ -36,9 +36,9 @@ class GenericBoundingSphere3DSingletonScore : public SingletonScore { GenericBoundingSphere3DSingletonScore(UF *f, const algebra::Sphere3D &sphere); virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { return IMP::get_particles(m, pis); } IMP_SINGLETON_SCORE_METHODS(GenericBoundingSphere3DSingletonScore); diff --git a/modules/core/include/BoxSweepClosePairsFinder.h b/modules/core/include/BoxSweepClosePairsFinder.h index 2e404afbaf..60fe13f269 100644 --- a/modules/core/include/BoxSweepClosePairsFinder.h +++ b/modules/core/include/BoxSweepClosePairsFinder.h @@ -26,17 +26,17 @@ class IMPCOREEXPORT BoxSweepClosePairsFinder : public ClosePairsFinder { BoxSweepClosePairsFinder(); virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual ParticleIndexPairs get_close_pairs( - Model *m, const ParticleIndexes &pc) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pc) const override; virtual ParticleIndexPairs get_close_pairs( Model *m, const ParticleIndexes &pca, - const ParticleIndexes &pcb) const IMP_OVERRIDE; + const ParticleIndexes &pcb) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(BoxSweepClosePairsFinder); }; #endif /* IMP_USE_CGAL */ diff --git a/modules/core/include/CentroidOfRefined.h b/modules/core/include/CentroidOfRefined.h index f9a69451a5..efb61ddcf2 100644 --- a/modules/core/include/CentroidOfRefined.h +++ b/modules/core/include/CentroidOfRefined.h @@ -59,13 +59,13 @@ class IMPCOREEXPORT CentroidOfRefined : public SingletonModifier { @param pi the centroid particle */ virtual void apply_index(Model *m, ParticleIndex pi) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(CentroidOfRefined); diff --git a/modules/core/include/ChecksScoreState.h b/modules/core/include/ChecksScoreState.h index 5f92a476b4..14d1fa3d41 100644 --- a/modules/core/include/ChecksScoreState.h +++ b/modules/core/include/ChecksScoreState.h @@ -25,10 +25,10 @@ class IMPCOREEXPORT ChecksScoreState : public ScoreState { unsigned int get_number_of_checked() const { return num_checked_; } - virtual void do_before_evaluate() IMP_OVERRIDE; - virtual void do_after_evaluate(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual void do_before_evaluate() override; + virtual void do_after_evaluate(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_outputs() const override; + virtual ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ChecksScoreState); }; diff --git a/modules/core/include/ChildrenRefiner.h b/modules/core/include/ChildrenRefiner.h index 4e76d103a6..a8b75c90bd 100644 --- a/modules/core/include/ChildrenRefiner.h +++ b/modules/core/include/ChildrenRefiner.h @@ -32,14 +32,14 @@ class IMPCOREEXPORT ChildrenRefiner : public Refiner { //! Create a refiner for a particular type of hierarchy ChildrenRefiner(HierarchyTraits tr); - virtual bool get_can_refine(Particle *) const IMP_OVERRIDE; + virtual bool get_can_refine(Particle *) const override; virtual const ParticlesTemp get_refined(Particle *) const - IMP_OVERRIDE; + override; #ifndef SWIG using Refiner::get_refined; #endif virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(ChildrenRefiner); }; diff --git a/modules/core/include/ClosePairsPairScore.h b/modules/core/include/ClosePairsPairScore.h index 6a26f06a84..18dc3f93b4 100644 --- a/modules/core/include/ClosePairsPairScore.h +++ b/modules/core/include/ClosePairsPairScore.h @@ -52,13 +52,13 @@ class IMPCOREEXPORT KClosePairsPairScore : public PairScore { virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual double evaluate_if_good_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, - double max) const IMP_OVERRIDE; + double max) const override; IMP_PAIR_SCORE_METHODS(KClosePairsPairScore); IMP_OBJECT_METHODS(KClosePairsPairScore); }; @@ -96,13 +96,13 @@ class IMPCOREEXPORT ClosePairsPairScore : public PairScore { virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual double evaluate_if_good_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, - double max) const IMP_OVERRIDE; + double max) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(KClosePairsPairScore); IMP_OBJECT_METHODS(ClosePairsPairScore); }; diff --git a/modules/core/include/ClosedCubicSpline.h b/modules/core/include/ClosedCubicSpline.h index 3cc264b342..4945997551 100644 --- a/modules/core/include/ClosedCubicSpline.h +++ b/modules/core/include/ClosedCubicSpline.h @@ -28,9 +28,9 @@ class IMPCOREEXPORT ClosedCubicSpline : public UnaryFunction { ClosedCubicSpline(const Floats &values, double minrange, double spacing); virtual DerivativePair evaluate_with_derivative( - double feature) const IMP_OVERRIDE; + double feature) const override; - virtual double evaluate(double feature) const IMP_OVERRIDE; + virtual double evaluate(double feature) const override; IMP_OBJECT_METHODS(ClosedCubicSpline); diff --git a/modules/core/include/ConjugateGradients.h b/modules/core/include/ConjugateGradients.h index 1a06229e3c..9492f4a829 100644 --- a/modules/core/include/ConjugateGradients.h +++ b/modules/core/include/ConjugateGradients.h @@ -46,7 +46,7 @@ class IMPCOREEXPORT ConjugateGradients : public AttributeOptimizer { //! Limit how far anything can change each time step void set_max_change(Float t) { max_change_ = t; } - virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE; + virtual Float do_optimize(unsigned int max_steps) override; IMP_OBJECT_METHODS(ConjugateGradients); private: diff --git a/modules/core/include/ConnectivityRestraint.h b/modules/core/include/ConnectivityRestraint.h index 8657aefa4c..f9f9ecab3a 100644 --- a/modules/core/include/ConnectivityRestraint.h +++ b/modules/core/include/ConnectivityRestraint.h @@ -54,12 +54,12 @@ class IMPCOREEXPORT ConnectivityRestraint : public Restraint { //! Return the pair score used for scoring PairScore *get_pair_score() const { return ps_; } - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + Restraints do_create_current_decomposition() const override; public: double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ConnectivityRestraint); ; }; diff --git a/modules/core/include/ConstantRestraint.h b/modules/core/include/ConstantRestraint.h index c0b39697f9..fc94de1039 100644 --- a/modules/core/include/ConstantRestraint.h +++ b/modules/core/include/ConstantRestraint.h @@ -29,8 +29,8 @@ class IMPCOREEXPORT ConstantRestraint : public Restraint { ConstantRestraint(Model *m, Float v); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ConstantRestraint); }; diff --git a/modules/core/include/Cosine.h b/modules/core/include/Cosine.h index 6ea83123fa..79c9aa30dc 100644 --- a/modules/core/include/Cosine.h +++ b/modules/core/include/Cosine.h @@ -32,9 +32,9 @@ class IMPCOREEXPORT Cosine : public UnaryFunction { phase_(phase) {} virtual DerivativePair evaluate_with_derivative( - double feature) const IMP_OVERRIDE; + double feature) const override; - virtual double evaluate(double feature) const IMP_OVERRIDE; + virtual double evaluate(double feature) const override; IMP_OBJECT_METHODS(Cosine); diff --git a/modules/core/include/CoverRefined.h b/modules/core/include/CoverRefined.h index 96fbd21fce..a30a9375e3 100644 --- a/modules/core/include/CoverRefined.h +++ b/modules/core/include/CoverRefined.h @@ -52,11 +52,11 @@ class IMPCOREEXPORT CoverRefined : public SingletonModifier { void set_slack(Float slack) { slack_ = slack; } virtual void apply_index(Model *m, ParticleIndex a) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(CoverRefined); IMP_OBJECT_METHODS(CoverRefined); }; diff --git a/modules/core/include/DerivativesFromRefined.h b/modules/core/include/DerivativesFromRefined.h index 6f2ec76ce7..eec490f187 100644 --- a/modules/core/include/DerivativesFromRefined.h +++ b/modules/core/include/DerivativesFromRefined.h @@ -36,11 +36,11 @@ class IMPCOREEXPORT DerivativesFromRefined DerivativesFromRefined(Refiner *r, FloatKeys ks = XYZ::get_xyz_keys()); virtual void apply_index(Model *m, ParticleIndex a) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(DerivativesFromRefined); IMP_OBJECT_METHODS(DerivativesFromRefined); }; diff --git a/modules/core/include/DerivativesToRefined.h b/modules/core/include/DerivativesToRefined.h index 1537c5df43..4c199302b0 100644 --- a/modules/core/include/DerivativesToRefined.h +++ b/modules/core/include/DerivativesToRefined.h @@ -35,11 +35,11 @@ class IMPCOREEXPORT DerivativesToRefined : public SingletonDerivativeModifier { DerivativesToRefined(Refiner *r, FloatKeys ks = XYZ::get_xyz_keys()); virtual void apply_index(Model *m, ParticleIndex a) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(DerivativesToRefined); IMP_OBJECT_METHODS(DerivativesToRefined); }; diff --git a/modules/core/include/DiameterRestraint.h b/modules/core/include/DiameterRestraint.h index dc65b3f6dc..479eabf474 100644 --- a/modules/core/include/DiameterRestraint.h +++ b/modules/core/include/DiameterRestraint.h @@ -45,12 +45,12 @@ class IMPCOREEXPORT DiameterRestraint : public Restraint { DiameterRestraint(UnaryFunction *f, SingletonContainer *sc, Float diameter); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(DiameterRestraint); #ifndef IMP_DOXYGEN - Restraints do_create_decomposition() const IMP_OVERRIDE; - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + Restraints do_create_decomposition() const override; + Restraints do_create_current_decomposition() const override; #endif }; diff --git a/modules/core/include/DihedralRestraint.h b/modules/core/include/DihedralRestraint.h index 50e3fe23d7..e740a7ce2e 100644 --- a/modules/core/include/DihedralRestraint.h +++ b/modules/core/include/DihedralRestraint.h @@ -36,8 +36,8 @@ class IMPCOREEXPORT DihedralRestraint : public Restraint { ParticleIndexAdaptor p4); virtual double unprotected_evaluate(IMP::DerivativeAccumulator* accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(DihedralRestraint); private: diff --git a/modules/core/include/DirectionMover.h b/modules/core/include/DirectionMover.h index 4b13b958be..a1fcc365b5 100644 --- a/modules/core/include/DirectionMover.h +++ b/modules/core/include/DirectionMover.h @@ -59,9 +59,9 @@ class IMPCOREEXPORT DirectionMover : public MonteCarloMover { Direction get_direction() const { return Direction(get_model(), pi_); } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(DirectionMover); }; diff --git a/modules/core/include/DistanceToSingletonScore.h b/modules/core/include/DistanceToSingletonScore.h index d94b375ec7..c6e985dd55 100644 --- a/modules/core/include/DistanceToSingletonScore.h +++ b/modules/core/include/DistanceToSingletonScore.h @@ -47,9 +47,9 @@ class GenericDistanceToSingletonScore : public SingletonScore { public: GenericDistanceToSingletonScore(UF *f, const algebra::Vector3D &pt); virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { return IMP::get_particles(m, pis); } IMP_SINGLETON_SCORE_METHODS(GenericDistanceToSingletonScore); @@ -106,9 +106,9 @@ class IMPCOREEXPORT SphereDistanceToSingletonScore : public SingletonScore { public: SphereDistanceToSingletonScore(UnaryFunction *f, const algebra::Vector3D &pt); virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { return IMP::get_particles(m, pis); } IMP_SINGLETON_SCORE_METHODS(SphereDistanceToSingletonScore); diff --git a/modules/core/include/ExcludedVolumeRestraint.h b/modules/core/include/ExcludedVolumeRestraint.h index 6e7688fd57..f874f0730f 100644 --- a/modules/core/include/ExcludedVolumeRestraint.h +++ b/modules/core/include/ExcludedVolumeRestraint.h @@ -85,20 +85,20 @@ class IMPCOREEXPORT ExcludedVolumeRestraint : public Restraint { double slack = 10, std::string name = "ExcludedVolumeRestraint%1%"); - void clear_caches() IMP_OVERRIDE; + void clear_caches() override; #if !defined(IMP_DOXYGEN) && !defined(SWIG) double unprotected_evaluate_if_good(DerivativeAccumulator *da, - double max) const IMP_OVERRIDE; + double max) const override; #endif public: double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ExcludedVolumeRestraint); ; - Restraints do_create_decomposition() const IMP_OVERRIDE; - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + Restraints do_create_decomposition() const override; + Restraints do_create_current_decomposition() const override; #ifndef IMP_DOXYGEN const ParticleIndexPairs &get_indexes() const { return cur_list_; } #endif diff --git a/modules/core/include/FixedRefiner.h b/modules/core/include/FixedRefiner.h index 0eadb36e74..b5ddc3d5bf 100644 --- a/modules/core/include/FixedRefiner.h +++ b/modules/core/include/FixedRefiner.h @@ -30,14 +30,14 @@ class IMPCOREEXPORT FixedRefiner : public Refiner { //! Store the set of particle indexes from passed model FixedRefiner(Model* m, const ParticleIndexes &pis); - virtual bool get_can_refine(Particle *) const IMP_OVERRIDE + virtual bool get_can_refine(Particle *) const override { return true; } //! Returns the fixed set of particles. /** \note the passed Particle is ignored. */ virtual const ParticlesTemp get_refined(Particle *p) const - IMP_OVERRIDE; + override; //! Returns the fixed set of particles, as indexes. /** @note the passed ParticleIndex is ignored. @@ -49,7 +49,7 @@ class IMPCOREEXPORT FixedRefiner : public Refiner { */ virtual ParticleIndexes get_refined_indexes - (Model* m, ParticleIndex) const IMP_OVERRIDE + (Model* m, ParticleIndex) const override { IMP_USAGE_CHECK(m == m_, "mismatching models for refined and coarse particles"); @@ -58,7 +58,7 @@ class IMPCOREEXPORT FixedRefiner : public Refiner { } virtual ParticleIndexes const& get_refined_indexes_by_ref - (Model *m, ParticleIndex pi) const IMP_OVERRIDE + (Model *m, ParticleIndex pi) const override { IMP_USAGE_CHECK(m == m_, "mismatching models for refined and coarse particles"); @@ -72,7 +72,7 @@ class IMPCOREEXPORT FixedRefiner : public Refiner { using Refiner::get_refined; #endif virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(FixedRefiner); }; diff --git a/modules/core/include/GenericAttributeSingletonScore.h b/modules/core/include/GenericAttributeSingletonScore.h index a8496416b0..04a834e2ac 100644 --- a/modules/core/include/GenericAttributeSingletonScore.h +++ b/modules/core/include/GenericAttributeSingletonScore.h @@ -29,9 +29,9 @@ class GenericAttributeSingletonScore : public SingletonScore { //! Apply function f to attribute k GenericAttributeSingletonScore(UF *f, FloatKey k); virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { return IMP::get_particles(m, pis); } //! get access to the unary function object used for scoring the attribute diff --git a/modules/core/include/GridClosePairsFinder.h b/modules/core/include/GridClosePairsFinder.h index a91ef2a908..7fc7c82f98 100644 --- a/modules/core/include/GridClosePairsFinder.h +++ b/modules/core/include/GridClosePairsFinder.h @@ -22,17 +22,17 @@ class IMPCOREEXPORT GridClosePairsFinder : public ClosePairsFinder { public: GridClosePairsFinder(); virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual ParticleIndexPairs get_close_pairs( - Model *m, const ParticleIndexes &pc) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pc) const override; virtual ParticleIndexPairs get_close_pairs( Model *m, const ParticleIndexes &pca, - const ParticleIndexes &pcb) const IMP_OVERRIDE; + const ParticleIndexes &pcb) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(GridClosePairsFinder); }; diff --git a/modules/core/include/Harmonic.h b/modules/core/include/Harmonic.h index 3d2e4808b5..958bc39800 100644 --- a/modules/core/include/Harmonic.h +++ b/modules/core/include/Harmonic.h @@ -27,12 +27,12 @@ class Harmonic : public UnaryFunction { Harmonic(Float mean, Float k) : mean_(mean), k_(k) {} virtual DerivativePair evaluate_with_derivative( - double feature) const IMP_OVERRIDE { + double feature) const override { return DerivativePair(0.5 * k_ * square(feature - mean_), k_ * (feature - mean_)); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return 0.5 * k_ * square(feature - mean_); } diff --git a/modules/core/include/HarmonicLowerBound.h b/modules/core/include/HarmonicLowerBound.h index 2a0973e2d9..bffd52790c 100644 --- a/modules/core/include/HarmonicLowerBound.h +++ b/modules/core/include/HarmonicLowerBound.h @@ -21,11 +21,11 @@ class HarmonicLowerBound : public Harmonic { public: /** Create with the given mean and the spring constant k */ HarmonicLowerBound(Float mean, Float k) : Harmonic(mean, k) {} - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return feature >= Harmonic::get_mean() ? 0.0 : Harmonic::evaluate(feature); } virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return feature >= Harmonic::get_mean() ? DerivativePair(0.0, 0.0) : Harmonic::evaluate_with_derivative(feature); diff --git a/modules/core/include/HarmonicUpperBound.h b/modules/core/include/HarmonicUpperBound.h index 041e8d0da2..644f763d27 100644 --- a/modules/core/include/HarmonicUpperBound.h +++ b/modules/core/include/HarmonicUpperBound.h @@ -21,11 +21,11 @@ class HarmonicUpperBound : public Harmonic { public: /** Create with the given mean and the spring constant k */ HarmonicUpperBound(Float mean, Float k) : Harmonic(mean, k) {} - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return feature <= Harmonic::get_mean() ? 0.0 : Harmonic::evaluate(feature); } virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return feature <= Harmonic::get_mean() ? DerivativePair(0.0, 0.0) : Harmonic::evaluate_with_derivative(feature); diff --git a/modules/core/include/HarmonicWell.h b/modules/core/include/HarmonicWell.h index bd29f5d0e7..eaac7718a1 100644 --- a/modules/core/include/HarmonicWell.h +++ b/modules/core/include/HarmonicWell.h @@ -50,11 +50,11 @@ class HarmonicWell : public UnaryFunction { } virtual DerivativePair evaluate_with_derivative( - double feature) const IMP_OVERRIDE { + double feature) const override { return DerivativePair(get_score(feature), get_derivative(feature)); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return get_score(feature); } diff --git a/modules/core/include/Hierarchy.h b/modules/core/include/Hierarchy.h index a696f8af16..4d7e176b83 100644 --- a/modules/core/include/Hierarchy.h +++ b/modules/core/include/Hierarchy.h @@ -256,7 +256,7 @@ class IMPCOREEXPORT ModifierVisitor : public HierarchyVisitor { public: ModifierVisitor(SingletonModifier *sm) : sm_(sm) {} - virtual bool operator()(Hierarchy p) IMP_OVERRIDE { + virtual bool operator()(Hierarchy p) override { sm_->apply_index(p.get_model(), p.get_particle_index()); return true; } @@ -422,7 +422,7 @@ struct HierarchyCounter : public HierarchyVisitor { HierarchyCounter() : ct_(0) {} //! Increment the counter - bool operator()(Hierarchy) IMP_OVERRIDE { + bool operator()(Hierarchy) override { ++ct_; return true; } diff --git a/modules/core/include/IncrementalScoringFunction.h b/modules/core/include/IncrementalScoringFunction.h index ead845262c..caf20b7d8d 100644 --- a/modules/core/include/IncrementalScoringFunction.h +++ b/modules/core/include/IncrementalScoringFunction.h @@ -114,10 +114,10 @@ class IMPCOREEXPORT IncrementalScoringFunction : public ScoringFunction { void clear_close_pair_scores(); ParticleIndexes get_movable_indexes() const; void do_add_score_and_derivatives(IMP::ScoreAccumulator sa, - const ScoreStatesTemp &ss) IMP_OVERRIDE; - virtual Restraints create_restraints() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual void handle_set_has_required_score_states(bool) IMP_OVERRIDE; + const ScoreStatesTemp &ss) override; + virtual Restraints create_restraints() const override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual void handle_set_has_required_score_states(bool) override; IMP_OBJECT_METHODS(IncrementalScoringFunction); }; diff --git a/modules/core/include/LeavesRefiner.h b/modules/core/include/LeavesRefiner.h index 03746aae6e..4f98d49481 100644 --- a/modules/core/include/LeavesRefiner.h +++ b/modules/core/include/LeavesRefiner.h @@ -29,11 +29,11 @@ class IMPCOREEXPORT LeavesRefiner : public Refiner { //! Create a refiner for a particular type of hierarchy LeavesRefiner(HierarchyTraits tr); - virtual bool get_can_refine(Particle *) const IMP_OVERRIDE; + virtual bool get_can_refine(Particle *) const override; virtual const ParticlesTemp get_refined(Particle *) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; #ifndef SWIG using Refiner::get_refined; #endif diff --git a/modules/core/include/Linear.h b/modules/core/include/Linear.h index 58600160de..bbc5589d53 100644 --- a/modules/core/include/Linear.h +++ b/modules/core/include/Linear.h @@ -25,12 +25,12 @@ class Linear : public UnaryFunction { void set_offset(double f) { offset_ = f; } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return (feature - offset_) * slope_; } virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return DerivativePair(evaluate(feature), slope_); } diff --git a/modules/core/include/LogNormalMover.h b/modules/core/include/LogNormalMover.h index 73c328c5c6..ddaccc33b1 100644 --- a/modules/core/include/LogNormalMover.h +++ b/modules/core/include/LogNormalMover.h @@ -54,9 +54,9 @@ class IMPCOREEXPORT LogNormalMover : public MonteCarloMover { Float get_sigma() const { return stddev_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(LogNormalMover); }; diff --git a/modules/core/include/MCCGSampler.h b/modules/core/include/MCCGSampler.h index b982497842..2fa2099830 100644 --- a/modules/core/include/MCCGSampler.h +++ b/modules/core/include/MCCGSampler.h @@ -116,7 +116,7 @@ class IMPCOREEXPORT MCCGSampler : public Sampler { IMP_LIST(public, OptimizerState, optimizer_state, OptimizerState *, OptimizerStates); - virtual ConfigurationSet *do_sample() const IMP_OVERRIDE; + virtual ConfigurationSet *do_sample() const override; IMP_OBJECT_METHODS(MCCGSampler); }; diff --git a/modules/core/include/MSConnectivityRestraint.h b/modules/core/include/MSConnectivityRestraint.h index e5005d4504..dc674de2ed 100644 --- a/modules/core/include/MSConnectivityRestraint.h +++ b/modules/core/include/MSConnectivityRestraint.h @@ -90,12 +90,12 @@ class IMPCOREEXPORT MSConnectivityRestraint : public Restraint { //! Return the pair score used for scoring PairScore *get_pair_score() const { return ps_; } - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + Restraints do_create_current_decomposition() const override; double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(MSConnectivityRestraint); diff --git a/modules/core/include/MinimumRestraint.h b/modules/core/include/MinimumRestraint.h index 452aad0a00..a17c98b814 100644 --- a/modules/core/include/MinimumRestraint.h +++ b/modules/core/include/MinimumRestraint.h @@ -30,12 +30,12 @@ class IMPCOREEXPORT MinimumRestraint : public Restraint { const Restraints &rs = Restraints(), std::string name = "MinimumRestraint %1%"); - void clear_caches() IMP_OVERRIDE; + void clear_caches() override; public: double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(MinimumRestraint); ; diff --git a/modules/core/include/MonteCarlo.h b/modules/core/include/MonteCarlo.h index 6ca07dc19f..f2ddc27730 100644 --- a/modules/core/include/MonteCarlo.h +++ b/modules/core/include/MonteCarlo.h @@ -48,7 +48,7 @@ class IMPCOREEXPORT MonteCarlo : public Optimizer { protected: ParticleIndexes reset_pis_; - virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE; + virtual Float do_optimize(unsigned int max_steps) override; IMP_OBJECT_METHODS(MonteCarlo) public: /** By default, the optimizer returns the lowest scoring state @@ -244,7 +244,7 @@ class IMPCOREEXPORT MonteCarloWithLocalOptimization : public MonteCarlo { Optimizer *get_local_optimizer() const { return opt_; } protected: - virtual void do_step() IMP_OVERRIDE; + virtual void do_step() override; IMP_OBJECT_METHODS(MonteCarloWithLocalOptimization); }; @@ -262,7 +262,7 @@ class IMPCOREEXPORT MonteCarloWithBasinHopping MonteCarloWithBasinHopping(Optimizer *opt, unsigned int ns); protected: - virtual void do_step() IMP_OVERRIDE; + virtual void do_step() override; IMP_OBJECT_METHODS(MonteCarloWithBasinHopping); }; diff --git a/modules/core/include/MonteCarloMover.h b/modules/core/include/MonteCarloMover.h index 087061db70..6924ef33b0 100644 --- a/modules/core/include/MonteCarloMover.h +++ b/modules/core/include/MonteCarloMover.h @@ -101,7 +101,7 @@ class IMPCOREEXPORT MonteCarloMover : public ModelObject { //! Implement accept_proposed_move(); default implementation is empty virtual void do_accept() {} - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_outputs() const override { return get_inputs(); } }; diff --git a/modules/core/include/MoveStatisticsScoreState.h b/modules/core/include/MoveStatisticsScoreState.h index 8459aade24..0bf9f517b6 100644 --- a/modules/core/include/MoveStatisticsScoreState.h +++ b/modules/core/include/MoveStatisticsScoreState.h @@ -34,10 +34,10 @@ class IMPCOREEXPORT MoveStatisticsScoreState : public ScoreState { MoveStatisticsScoreState(const ParticlesTemp& ps); void show_statistics(std::ostream& out = std::cout) const; void reset(); - virtual void do_before_evaluate() IMP_OVERRIDE; - virtual void do_after_evaluate(DerivativeAccumulator* da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_before_evaluate() override; + virtual void do_after_evaluate(DerivativeAccumulator* da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(MoveStatisticsScoreState); }; diff --git a/modules/core/include/MultipleBinormalRestraint.h b/modules/core/include/MultipleBinormalRestraint.h index 413f968acf..0adb1e2222 100644 --- a/modules/core/include/MultipleBinormalRestraint.h +++ b/modules/core/include/MultipleBinormalRestraint.h @@ -46,8 +46,8 @@ class IMPCOREEXPORT MultipleBinormalRestraint : public Restraint { void add_term(const BinormalTerm &term) { terms_.push_back(term); } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(MultipleBinormalRestraint); }; diff --git a/modules/core/include/NearestNeighborsClosePairsFinder.h b/modules/core/include/NearestNeighborsClosePairsFinder.h index d40d75369f..419c7afa2e 100644 --- a/modules/core/include/NearestNeighborsClosePairsFinder.h +++ b/modules/core/include/NearestNeighborsClosePairsFinder.h @@ -22,17 +22,17 @@ class IMPCOREEXPORT NearestNeighborsClosePairsFinder : public ClosePairsFinder { NearestNeighborsClosePairsFinder(); virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual ParticleIndexPairs get_close_pairs( - Model *m, const ParticleIndexes &pc) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pc) const override; virtual ParticleIndexPairs get_close_pairs( Model *m, const ParticleIndexes &pca, - const ParticleIndexes &pcb) const IMP_OVERRIDE; + const ParticleIndexes &pcb) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(NearestNeighborsClosePairsFinder); }; diff --git a/modules/core/include/NeighborsTable.h b/modules/core/include/NeighborsTable.h index 16fbf10988..49b2393d6b 100644 --- a/modules/core/include/NeighborsTable.h +++ b/modules/core/include/NeighborsTable.h @@ -31,14 +31,14 @@ class IMPCOREEXPORT NeighborsTable : public ScoreState { boost::unordered_map data_; protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { return ModelObjectsTemp(1, input_); } - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_outputs() const override { return ModelObjectsTemp(); } - virtual void do_before_evaluate() IMP_OVERRIDE; - virtual void do_after_evaluate(DerivativeAccumulator *) IMP_OVERRIDE {} + virtual void do_before_evaluate() override; + virtual void do_after_evaluate(DerivativeAccumulator *) override {} public: NeighborsTable(PairContainer *input, diff --git a/modules/core/include/NormalMover.h b/modules/core/include/NormalMover.h index 5a5a525428..2eca62157d 100644 --- a/modules/core/include/NormalMover.h +++ b/modules/core/include/NormalMover.h @@ -49,9 +49,9 @@ class IMPCOREEXPORT NormalMover : public MonteCarloMover { Float get_sigma() const { return stddev_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(NormalMover); }; diff --git a/modules/core/include/QuadraticClosePairsFinder.h b/modules/core/include/QuadraticClosePairsFinder.h index 06d2868734..039ab00e1b 100644 --- a/modules/core/include/QuadraticClosePairsFinder.h +++ b/modules/core/include/QuadraticClosePairsFinder.h @@ -32,17 +32,17 @@ class IMPCOREEXPORT QuadraticClosePairsFinder : public ClosePairsFinder { bool get_are_close_and_filtered(Model *m, ParticleIndex a, ParticleIndex b) const; virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual ParticleIndexPairs get_close_pairs( - Model *m, const ParticleIndexes &pc) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pc) const override; virtual ParticleIndexPairs get_close_pairs( Model *m, const ParticleIndexes &pca, - const ParticleIndexes &pcb) const IMP_OVERRIDE; + const ParticleIndexes &pcb) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(QuadraticClosePairsFinder); }; diff --git a/modules/core/include/RefinedPairsPairScore.h b/modules/core/include/RefinedPairsPairScore.h index f8a3e0ac79..886b85cd24 100644 --- a/modules/core/include/RefinedPairsPairScore.h +++ b/modules/core/include/RefinedPairsPairScore.h @@ -31,9 +31,9 @@ class IMPCOREEXPORT RefinedPairsPairScore : public PairScore { */ RefinedPairsPairScore(Refiner *r, PairScore *f); double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(RefinedPairsPairScore); IMP_OBJECT_METHODS(RefinedPairsPairScore); ; diff --git a/modules/core/include/RestraintsScoringFunction.h b/modules/core/include/RestraintsScoringFunction.h index a9a0bded91..97004b8cdf 100644 --- a/modules/core/include/RestraintsScoringFunction.h +++ b/modules/core/include/RestraintsScoringFunction.h @@ -34,15 +34,15 @@ class RestraintsScoringFunction : : IMP::internal::RestraintsScoringFunction(rs, 1.0, NO_MAX, name) {} #if defined(SWIG) void do_add_score_and_derivatives( - ScoreAccumulator sa, const ScoreStatesTemp &ss) IMP_OVERRIDE; + ScoreAccumulator sa, const ScoreStatesTemp &ss) override; void do_add_score_and_derivatives_moved( ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, - const ScoreStatesTemp &ss) IMP_OVERRIDE; + const ScoreStatesTemp &ss) override; - virtual Restraints create_restraints() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual Restraints create_restraints() const override; + virtual ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(RestraintsScoringFunction); #endif }; diff --git a/modules/core/include/RigidBodyAnglePairScore.h b/modules/core/include/RigidBodyAnglePairScore.h index 9b12c302ee..c638a5656d 100644 --- a/modules/core/include/RigidBodyAnglePairScore.h +++ b/modules/core/include/RigidBodyAnglePairScore.h @@ -26,9 +26,9 @@ class IMPCOREEXPORT RigidBodyAnglePairScore : public PairScore virtual double evaluate_index(Model *m, const ParticleIndexPair &pi, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(RigidBodyAnglePairScore); IMP_OBJECT_METHODS(RigidBodyAnglePairScore); }; diff --git a/modules/core/include/RigidBodyMover.h b/modules/core/include/RigidBodyMover.h index 8064df4f2d..d04a428b42 100644 --- a/modules/core/include/RigidBodyMover.h +++ b/modules/core/include/RigidBodyMover.h @@ -56,9 +56,9 @@ class IMPCOREEXPORT RigidBodyMover : public MonteCarloMover { Float get_maximum_rotation() const { return max_angle_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(RigidBodyMover); }; diff --git a/modules/core/include/RigidBodyTunneler.h b/modules/core/include/RigidBodyTunneler.h index c6a432ea22..dfa78f684d 100644 --- a/modules/core/include/RigidBodyTunneler.h +++ b/modules/core/include/RigidBodyTunneler.h @@ -100,9 +100,9 @@ class IMPCOREEXPORT RigidBodyTunneler : public MonteCarloMover { Floats coords); protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(RigidBodyTunneler); private: diff --git a/modules/core/include/RigidBodyUmbrella.h b/modules/core/include/RigidBodyUmbrella.h index 13bd332398..eba5247952 100644 --- a/modules/core/include/RigidBodyUmbrella.h +++ b/modules/core/include/RigidBodyUmbrella.h @@ -91,8 +91,8 @@ class IMPCOREEXPORT RigidBodyUmbrella : public Restraint { protected: double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(RigidBodyUmbrella); private: diff --git a/modules/core/include/RigidClosePairsFinder.h b/modules/core/include/RigidClosePairsFinder.h index a0e1afb7de..538522bacb 100644 --- a/modules/core/include/RigidClosePairsFinder.h +++ b/modules/core/include/RigidClosePairsFinder.h @@ -68,28 +68,28 @@ class IMPCOREEXPORT RigidClosePairsFinder : public ClosePairsFinder { const ParticleIndexes &pa, const ParticleIndexes &pb) const; - void set_distance(double d) IMP_OVERRIDE { + void set_distance(double d) override { cpf_->set_distance(d); ClosePairsFinder::set_distance(d); } #if !defined(SWIG) && !defined(IMP_DOXYGEN) internal::MovedSingletonContainer *get_moved_singleton_container( - SingletonContainer *c, double thresold) const IMP_OVERRIDE; + SingletonContainer *c, double thresold) const override; #endif virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual IntPairs get_close_pairs(const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ParticleIndexPairs get_close_pairs( - Model *m, const ParticleIndexes &pc) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pc) const override; virtual ParticleIndexPairs get_close_pairs( Model *m, const ParticleIndexes &pca, - const ParticleIndexes &pcb) const IMP_OVERRIDE; + const ParticleIndexes &pcb) const override; IMP_OBJECT_METHODS(RigidClosePairsFinder); }; diff --git a/modules/core/include/SerialMover.h b/modules/core/include/SerialMover.h index bb2bfe6ee4..75d5f8647b 100644 --- a/modules/core/include/SerialMover.h +++ b/modules/core/include/SerialMover.h @@ -33,10 +33,10 @@ class IMPCOREEXPORT SerialMover : public MonteCarloMover { const MonteCarloMovers& get_movers() const { return movers_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; - virtual void do_accept() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; + virtual void do_accept() override; IMP_OBJECT_METHODS(SerialMover); }; diff --git a/modules/core/include/SphereDistancePairScore.h b/modules/core/include/SphereDistancePairScore.h index 31574e3445..beaaef68b8 100644 --- a/modules/core/include/SphereDistancePairScore.h +++ b/modules/core/include/SphereDistancePairScore.h @@ -75,9 +75,9 @@ class IMPCOREEXPORT HarmonicUpperBoundSphereDiameterPairScore double get_rest_length() const { return x0_; } double get_stiffness() const { return k_; } double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(HarmonicUpperBoundSphereDiameterPairScore); IMP_OBJECT_METHODS(HarmonicUpperBoundSphereDiameterPairScore); }; @@ -142,9 +142,9 @@ class IMPCOREEXPORT NormalizedSphereDistancePairScore : public PairScore { FloatKey radius = FloatKey("radius")); virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(NormalizedSphereDistancePairScore); IMP_OBJECT_METHODS(NormalizedSphereDistancePairScore); ; @@ -167,9 +167,9 @@ class IMPCOREEXPORT WeightedSphereDistancePairScore : public PairScore { FloatKey radius = FloatKey("radius")); virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(WeightedSphereDistancePairScore); IMP_OBJECT_METHODS(WeightedSphereDistancePairScore); ; diff --git a/modules/core/include/SteepestDescent.h b/modules/core/include/SteepestDescent.h index 510b235eea..e0a256b719 100644 --- a/modules/core/include/SteepestDescent.h +++ b/modules/core/include/SteepestDescent.h @@ -24,7 +24,7 @@ class IMPCOREEXPORT SteepestDescent : public AttributeOptimizer { public: SteepestDescent(Model *m, std::string name = "SteepestDescent%1%"); - virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE; + virtual Float do_optimize(unsigned int max_steps) override; IMP_OBJECT_METHODS(SteepestDescent); //! Set the minimum gradient threshold diff --git a/modules/core/include/SubsetMover.h b/modules/core/include/SubsetMover.h index a2b15496c0..6805d86099 100644 --- a/modules/core/include/SubsetMover.h +++ b/modules/core/include/SubsetMover.h @@ -38,10 +38,10 @@ class IMPCOREEXPORT SubsetMover : public MonteCarloMover { unsigned int get_subset_size() const { return n_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; - virtual void do_accept() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; + virtual void do_accept() override; IMP_OBJECT_METHODS(SubsetMover); }; diff --git a/modules/core/include/Surface.h b/modules/core/include/Surface.h index 523931fe26..3ebf0bce00 100644 --- a/modules/core/include/Surface.h +++ b/modules/core/include/Surface.h @@ -184,7 +184,7 @@ class IMPCOREEXPORT SurfaceGeometry : public display::Geometry { SurfaceGeometry(Surface s, const display::Color &c, std::string n="SurfaceGeometry"); virtual const Surface get_geometry() const { return s_; } void set_geometry(Surface s); - virtual display::Geometries get_components() const IMP_OVERRIDE; + virtual display::Geometries get_components() const override; IMP_OBJECT_METHODS(SurfaceGeometry); }; //! Create a geometry from a Surface @@ -211,20 +211,20 @@ class IMPCOREEXPORT SurfaceGeometryConstraint : public IMP::Constraint { SurfaceGeometry* get_geometry() const { return g_; } - virtual void do_update_attributes() IMP_OVERRIDE {}; - virtual void do_update_derivatives(DerivativeAccumulator *) IMP_OVERRIDE {}; - virtual void do_before_evaluate() IMP_OVERRIDE { g_->set_geometry(get_surface());} - virtual void do_after_evaluate(DerivativeAccumulator *) IMP_OVERRIDE { + virtual void do_update_attributes() override {}; + virtual void do_update_derivatives(DerivativeAccumulator *) override {}; + virtual void do_before_evaluate() override { g_->set_geometry(get_surface());} + virtual void do_after_evaluate(DerivativeAccumulator *) override { g_->set_geometry(get_surface()); }; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { ParticlesTemp ps = ParticlesTemp(1, get_surface().get_particle()); return ps; } - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_outputs() const override { ParticlesTemp ps = ParticlesTemp(1, get_surface().get_particle()); return ps; } @@ -256,23 +256,23 @@ class IMPCOREEXPORT LateralSurfaceConstraint : public IMP::Constraint { : IMP::Constraint(s.get_model(), "LateralSurfaceConstraint%1%") , spi_(s.get_particle_index()), dpi_(d.get_particle_index()) {} - virtual void do_update_attributes() IMP_OVERRIDE {} - virtual void do_update_derivatives(DerivativeAccumulator *) IMP_OVERRIDE {} - virtual void do_before_evaluate() IMP_OVERRIDE { + virtual void do_update_attributes() override {} + virtual void do_update_derivatives(DerivativeAccumulator *) override {} + virtual void do_before_evaluate() override { algebra::Vector3D d = XYZ(get_model(), dpi_).get_coordinates(); Surface s = Surface(get_model(), spi_); s.set_coordinates(s.get_plane().get_projected(d)); } - virtual void do_after_evaluate(DerivativeAccumulator *) IMP_OVERRIDE {} + virtual void do_after_evaluate(DerivativeAccumulator *) override {} - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { ParticlesTemp ps; ps.push_back(get_model()->get_particle(dpi_)); ps.push_back(get_model()->get_particle(spi_)); return ps; } - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_outputs() const override { ParticlesTemp ps = ParticlesTemp(1, get_model()->get_particle(spi_)); return ps; } diff --git a/modules/core/include/SurfaceMover.h b/modules/core/include/SurfaceMover.h index 0df4230b5e..6aa6638363 100644 --- a/modules/core/include/SurfaceMover.h +++ b/modules/core/include/SurfaceMover.h @@ -71,9 +71,9 @@ class IMPCOREEXPORT SurfaceMover : public MonteCarloMover { Surface get_surface() const { return Surface(get_model(), pi_); } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(SurfaceMover); }; diff --git a/modules/core/include/SurfaceSymmetryConstraint.h b/modules/core/include/SurfaceSymmetryConstraint.h index ad22b91d23..b42a502a54 100644 --- a/modules/core/include/SurfaceSymmetryConstraint.h +++ b/modules/core/include/SurfaceSymmetryConstraint.h @@ -50,13 +50,13 @@ class IMPCOREEXPORT SurfaceSymmetryConstraint : public IMP::Constraint { const ParticleIndexPair &ss, const ParticleIndexPair &rbs); - virtual void do_update_attributes() IMP_OVERRIDE; + virtual void do_update_attributes() override; - virtual void do_update_derivatives(DerivativeAccumulator *da) IMP_OVERRIDE; + virtual void do_update_derivatives(DerivativeAccumulator *da) override; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(SurfaceSymmetryConstraint); }; diff --git a/modules/core/include/SurfaceTetheredChain.h b/modules/core/include/SurfaceTetheredChain.h index 38ef040e82..b9487548bb 100644 --- a/modules/core/include/SurfaceTetheredChain.h +++ b/modules/core/include/SurfaceTetheredChain.h @@ -60,7 +60,7 @@ class SurfaceTetheredChain : public UnaryFunction { } virtual DerivativePair evaluate_with_derivative( - double feature) const IMP_OVERRIDE { + double feature) const override { if (feature < z_min_) { return DerivativePair(z_min_deriv_ * feature + z_min_int_, z_min_deriv_); @@ -71,7 +71,7 @@ class SurfaceTetheredChain : public UnaryFunction { } } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return evaluate_with_derivative(feature).first; } diff --git a/modules/core/include/TableRefiner.h b/modules/core/include/TableRefiner.h index 86eb61d443..637c7853b3 100644 --- a/modules/core/include/TableRefiner.h +++ b/modules/core/include/TableRefiner.h @@ -34,14 +34,14 @@ class IMPCOREEXPORT TableRefiner : public Refiner { //! Set the mapping for a particular particle void set_particle(Particle *p, const ParticlesTemp &ps); - virtual bool get_can_refine(Particle *) const IMP_OVERRIDE; + virtual bool get_can_refine(Particle *) const override; virtual const ParticlesTemp get_refined(Particle *) const - IMP_OVERRIDE; + override; #ifndef SWIG using Refiner::get_refined; #endif virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(TableRefiner); }; diff --git a/modules/core/include/Transform.h b/modules/core/include/Transform.h index 3bd1305c1c..bc9685497e 100644 --- a/modules/core/include/Transform.h +++ b/modules/core/include/Transform.h @@ -28,11 +28,11 @@ class IMPCOREEXPORT Transform : public SingletonModifier { Transform(const algebra::Transformation3D &t, bool ignore_non_xyz = false); virtual void apply_index(Model *m, ParticleIndex p) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(Transform); IMP_OBJECT_METHODS(Transform); ; diff --git a/modules/core/include/TransformedDistancePairScore.h b/modules/core/include/TransformedDistancePairScore.h index 39f61d130b..fb8b7108d5 100644 --- a/modules/core/include/TransformedDistancePairScore.h +++ b/modules/core/include/TransformedDistancePairScore.h @@ -40,9 +40,9 @@ class IMPCOREEXPORT TransformedDistancePairScore : public PairScore { void set_transformation(const algebra::Transformation3D &rot); virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(TransformedDistancePairScore); IMP_OBJECT_METHODS(TransformedDistancePairScore); ; diff --git a/modules/core/include/TruncatedHarmonic.h b/modules/core/include/TruncatedHarmonic.h index dca53b85be..fc39ef9e48 100644 --- a/modules/core/include/TruncatedHarmonic.h +++ b/modules/core/include/TruncatedHarmonic.h @@ -58,14 +58,14 @@ class TruncatedHarmonic : public UnaryFunction { TruncatedHarmonic(Float center, Float k, Float threshold) : d_(center, k, threshold, k * square(threshold)) {} virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return DerivativePair(evaluate(feature), ((DIRECTION == LOWER && (feature > d_.c_)) || (DIRECTION == UPPER && (feature < d_.c_))) ? 0 : d_.evaluate_with_derivative(feature).second); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return ((DIRECTION == LOWER && (feature > d_.c_)) || (DIRECTION == UPPER && (feature < d_.c_))) ? 0 diff --git a/modules/core/include/TypedPairScore.h b/modules/core/include/TypedPairScore.h index 9eb7f2c7a1..482ec20823 100644 --- a/modules/core/include/TypedPairScore.h +++ b/modules/core/include/TypedPairScore.h @@ -67,9 +67,9 @@ class IMPCOREEXPORT TypedPairScore : public PairScore { virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(TypedPairScore); IMP_OBJECT_METHODS(TypedPairScore); ; diff --git a/modules/core/include/VolumeRestraint.h b/modules/core/include/VolumeRestraint.h index 7785cd3b8c..48c3824e40 100644 --- a/modules/core/include/VolumeRestraint.h +++ b/modules/core/include/VolumeRestraint.h @@ -27,8 +27,8 @@ class IMPCOREEXPORT VolumeRestraint : public Restraint { VolumeRestraint(UnaryFunction *f, SingletonContainer *sc, double volume); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(VolumeRestraint); }; #endif diff --git a/modules/core/include/WeightedDerivativesToRefined.h b/modules/core/include/WeightedDerivativesToRefined.h index 28d69ec243..75df51cdb0 100644 --- a/modules/core/include/WeightedDerivativesToRefined.h +++ b/modules/core/include/WeightedDerivativesToRefined.h @@ -62,13 +62,13 @@ public SingletonDerivativeModifier { @param pi the coarse grained particle */ virtual void apply_index(Model *m, ParticleIndex pi) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(WeightedDerivativesToRefined); diff --git a/modules/core/include/WeightedSum.h b/modules/core/include/WeightedSum.h index 05cc39ba33..dcbb7b8309 100644 --- a/modules/core/include/WeightedSum.h +++ b/modules/core/include/WeightedSum.h @@ -26,7 +26,7 @@ class WeightedSum : public UnaryFunction { } virtual DerivativePair evaluate_with_derivative( - double feature) const IMP_OVERRIDE { + double feature) const override { double eval = 0; double derv = 0; DerivativePair fout; @@ -38,7 +38,7 @@ class WeightedSum : public UnaryFunction { return DerivativePair(eval, derv); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { double ret = 0; for (unsigned int i = 0; i < funcs_.size(); ++i) { ret += weights_[i] * funcs_[i]->evaluate(feature); diff --git a/modules/core/include/WeightedSumOfExponential.h b/modules/core/include/WeightedSumOfExponential.h index ff7a8a9e76..fe6f03eb59 100644 --- a/modules/core/include/WeightedSumOfExponential.h +++ b/modules/core/include/WeightedSumOfExponential.h @@ -39,7 +39,7 @@ class WeightedSumOfExponential : public UnaryFunction { } virtual DerivativePair evaluate_with_derivative( - double feature) const IMP_OVERRIDE { + double feature) const override { double exp_sum = 0; double derv_num = 0; double weight_exp; @@ -53,7 +53,7 @@ class WeightedSumOfExponential : public UnaryFunction { return DerivativePair(-std::log(exp_sum) * denom_, derv_num / exp_sum); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { double exp_sum = 0; for (unsigned int i = 0; i < funcs_.size(); ++i) { exp_sum += weights_[i] * std::exp(-funcs_[i]->evaluate(feature) / denom_); diff --git a/modules/core/include/direction.h b/modules/core/include/direction.h index 5eb363b13e..61203afa06 100644 --- a/modules/core/include/direction.h +++ b/modules/core/include/direction.h @@ -151,10 +151,10 @@ class IMPCOREEXPORT DirectionUnitConstraint : public IMP::Constraint { public: friend class Direction; - virtual void do_update_attributes() IMP_OVERRIDE; - virtual void do_update_derivatives(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_update_attributes() override; + virtual void do_update_derivatives(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(DirectionUnitConstraint); }; @@ -170,10 +170,10 @@ class IMPCOREEXPORT DirectionAngleConstraint : public IMP::Constraint { public: friend class DirectionAngle; - virtual void do_update_attributes() IMP_OVERRIDE; - virtual void do_update_derivatives(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_update_attributes() override; + virtual void do_update_derivatives(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(DirectionAngleConstraint); }; diff --git a/modules/core/include/internal/MovedSingletonContainer.h b/modules/core/include/internal/MovedSingletonContainer.h index 0e81899fbe..49b0a27f09 100644 --- a/modules/core/include/internal/MovedSingletonContainer.h +++ b/modules/core/include/internal/MovedSingletonContainer.h @@ -35,11 +35,11 @@ class IMPCOREEXPORT MovedSingletonContainer std::size_t pc_version_; PointerMember score_state_; - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; + virtual ParticleIndexes get_all_possible_indexes() const override; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; - virtual ParticleIndexes get_range_indexes() const IMP_OVERRIDE; + virtual ParticleIndexes get_range_indexes() const override; IMP_OBJECT_METHODS(MovedSingletonContainer); @@ -105,20 +105,20 @@ class IMPCOREEXPORT XYZRMovedSingletonContainer //! return any particles whose center //! may have moved by more than get_threshold() - virtual ParticleIndexes do_get_moved() IMP_OVERRIDE; + virtual ParticleIndexes do_get_moved() override; - virtual void do_reset_all() IMP_OVERRIDE; + virtual void do_reset_all() override; - virtual void do_reset_moved() IMP_OVERRIDE; + virtual void do_reset_moved() override; - virtual ParticleIndexes do_initialize() IMP_OVERRIDE; + virtual ParticleIndexes do_initialize() override; - ModelObjectsTemp get_extra_inputs() const IMP_OVERRIDE { + ModelObjectsTemp get_extra_inputs() const override { return ModelObjectsTemp(); } public: - virtual void validate() const IMP_OVERRIDE; + virtual void validate() const override; //! Track the changes of contained particles, such that at least all //! particles that moved by threshold are tracked @@ -146,18 +146,18 @@ class IMPCOREEXPORT RigidMovedSingletonContainer //! return all rigid body members that may have moved //! by more than get_threshold() (since last reset?) - virtual ParticleIndexes do_get_moved() IMP_OVERRIDE; + virtual ParticleIndexes do_get_moved() override; //! update backup_ with the current reference frames of all //! bodies_, clear moved_ - virtual void do_reset_all() IMP_OVERRIDE; + virtual void do_reset_all() override; //! update backup_ only for moved_ bodies, clear moved_ - virtual void do_reset_moved() IMP_OVERRIDE; + virtual void do_reset_moved() override; - virtual ParticleIndexes do_initialize() IMP_OVERRIDE; + virtual ParticleIndexes do_initialize() override; void do_initialize_particle(ParticleIndex pi); - virtual void validate() const IMP_OVERRIDE; + virtual void validate() const override; /** If internal checks are on, compare the global cartesian coordinates of all members of @@ -191,7 +191,7 @@ class IMPCOREEXPORT RigidMovedSingletonContainer .get_rotation()); } } - ModelObjectsTemp get_extra_inputs() const IMP_OVERRIDE; + ModelObjectsTemp get_extra_inputs() const override; public: //! Track the changes with the specified keys. diff --git a/modules/core/include/model_statistics.h b/modules/core/include/model_statistics.h index ba9c8a020c..a2b347e0db 100644 --- a/modules/core/include/model_statistics.h +++ b/modules/core/include/model_statistics.h @@ -31,7 +31,7 @@ class IMPCOREEXPORT WriteRestraintScoresOptimizerState TextOutput out); protected: - virtual void do_update(unsigned int call_num) IMP_OVERRIDE; + virtual void do_update(unsigned int call_num) override; IMP_OBJECT_METHODS(WriteRestraintScoresOptimizerState); }; diff --git a/modules/core/include/predicates.h b/modules/core/include/predicates.h index 1f2b82a20f..94a266e779 100644 --- a/modules/core/include/predicates.h +++ b/modules/core/include/predicates.h @@ -24,11 +24,11 @@ class InBoundingBox3DSingletonPredicate : public SingletonPredicate { "InBoundingBox3DSingletonPredicate%1%") : SingletonPredicate(name), bb_(bb) {} virtual int get_value_index(Model *m, ParticleIndex pi) const - IMP_OVERRIDE { + override { return bb_.get_contains(XYZ(m, pi).get_coordinates()) ? 1 : 0; } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pi) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pi) const override { ModelObjectsTemp ret; ret += IMP::get_particles(m, pi); return ret; @@ -46,11 +46,11 @@ class AttributeSingletonPredicate : public SingletonPredicate { "AttributeSingletonPredicate%1%") : SingletonPredicate(name), bb_(bb) {} virtual int get_value_index(Model *m, ParticleIndex pi) const - IMP_OVERRIDE { + override { return m->get_attribute(bb_, pi); } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pi) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pi) const override { ModelObjectsTemp ret; ret += IMP::get_particles(m, pi); return ret; @@ -66,7 +66,7 @@ class IsCollisionPairPredicate : public PairPredicate { : PairPredicate(name) {} virtual int get_value_index(Model *m, const ParticleIndexPair &pi) const - IMP_OVERRIDE { + override { Float sr = m->get_sphere(pi[0]).get_radius() + m->get_sphere(pi[1]).get_radius(); #if IMP_HAS_CHECKS > 1 @@ -89,7 +89,7 @@ class IsCollisionPairPredicate : public PairPredicate { } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pi) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pi) const override { ModelObjectsTemp ret; ret += IMP::get_particles(m, pi); return ret; @@ -124,9 +124,9 @@ class PredicateSingletonScore : public SingletonScore { scores_[val] = score; } virtual double evaluate_index(Model *m, ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_SCORE_METHODS(PredicateSingletonScore); IMP_OBJECT_METHODS(PredicateSingletonScore); }; diff --git a/modules/core/include/rigid_bodies.h b/modules/core/include/rigid_bodies.h index 87466b10df..fd1cfea79d 100644 --- a/modules/core/include/rigid_bodies.h +++ b/modules/core/include/rigid_bodies.h @@ -837,14 +837,14 @@ class IMPCOREEXPORT RigidMembersRefiner : public Refiner { public: RigidMembersRefiner(std::string name = "RigidMembersRefiner%d") : Refiner(name) {} - virtual bool get_can_refine(Particle *) const IMP_OVERRIDE; + virtual bool get_can_refine(Particle *) const override; #ifndef SWIG using Refiner::get_refined; #endif virtual const ParticlesTemp get_refined(Particle *) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(RigidMembersRefiner); }; diff --git a/modules/core/include/rigid_body_geometries.h b/modules/core/include/rigid_body_geometries.h index bec69a6b55..25da896d28 100644 --- a/modules/core/include/rigid_body_geometries.h +++ b/modules/core/include/rigid_body_geometries.h @@ -26,7 +26,7 @@ class IMPCOREEXPORT RigidBodyHierarchyGeometry public: RigidBodyHierarchyGeometry(RigidBody rb, const ParticlesTemp &constituents); - display::Geometries get_components() const IMP_OVERRIDE; + display::Geometries get_components() const override; IMP_OBJECT_METHODS(RigidBodyHierarchyGeometry); }; @@ -47,7 +47,7 @@ class IMPCOREEXPORT RigidBodyTorque : public display::SegmentGeometry { public: RigidBodyTorque(Particle *p); - const algebra::Segment3D &get_geometry() const IMP_OVERRIDE; + const algebra::Segment3D &get_geometry() const override; }; IMPCORE_END_NAMESPACE diff --git a/modules/core/include/symmetry.h b/modules/core/include/symmetry.h index 0c481ce79c..77d5a92dd1 100644 --- a/modules/core/include/symmetry.h +++ b/modules/core/include/symmetry.h @@ -59,11 +59,11 @@ class IMPCOREEXPORT TransformationAndReflectionSymmetry const algebra::Reflection3D &r); virtual void apply_index(Model *m, ParticleIndex p) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(TransformationAndReflectionSymmetry); IMP_OBJECT_METHODS(TransformationAndReflectionSymmetry); }; @@ -103,11 +103,11 @@ class IMPCOREEXPORT TransformationSymmetry : public SingletonModifier { } virtual void apply_index(Model *m, ParticleIndex p) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(TransformationSymmetry); IMP_OBJECT_METHODS(TransformationSymmetry); }; @@ -151,9 +151,9 @@ class IMPCOREEXPORT TransformationSymmetryMover : public MonteCarloMover { Float get_maximum_rotation() const { return max_angle_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(TransformationSymmetryMover); }; diff --git a/modules/core/src/IncrementalScoringFunction.cpp b/modules/core/src/IncrementalScoringFunction.cpp index 9371ba2a3c..587f8c698d 100644 --- a/modules/core/src/IncrementalScoringFunction.cpp +++ b/modules/core/src/IncrementalScoringFunction.cpp @@ -48,7 +48,7 @@ class IncrementalRestraintsScoringFunction std::string name = "IncrementalRestraintsScoringFunction%1%") : IMP::internal::RestraintsScoringFunction(rs, weight, max, name) {} // don't depend on optimized particles - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { return get_restraints(); } }; diff --git a/modules/core/src/MCCGSampler.cpp b/modules/core/src/MCCGSampler.cpp index 2f74ee584f..b7251261d1 100644 --- a/modules/core/src/MCCGSampler.cpp +++ b/modules/core/src/MCCGSampler.cpp @@ -62,9 +62,9 @@ class ScoreWeightedIncrementalBallMover : public MonteCarloMover { public: ScoreWeightedIncrementalBallMover(const ParticlesTemp &ps, unsigned int n, Float radius); - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(ScoreWeightedIncrementalBallMover); private: diff --git a/modules/core/src/internal/incremental_scoring_function.cpp b/modules/core/src/internal/incremental_scoring_function.cpp index 269888afcc..22c0404140 100644 --- a/modules/core/src/internal/incremental_scoring_function.cpp +++ b/modules/core/src/internal/incremental_scoring_function.cpp @@ -30,10 +30,10 @@ class DummyPairContainer public: DummyPairContainer(SingletonContainer *c, ClosePairsFinder *cpf); - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual ParticleIndexes get_all_possible_indexes() const override; + virtual ModelObjectsTemp do_get_inputs() const override; void do_score_state_before_evaluate() {} - virtual ParticleIndexPairs get_range_indexes() const IMP_OVERRIDE; + virtual ParticleIndexPairs get_range_indexes() const override; IMP_CLANG_PRAGMA(diagnostic push) IMP_CLANG_PRAGMA(diagnostic ignored "-Wunused-member-function") diff --git a/modules/core/src/rigid_bodies.cpp b/modules/core/src/rigid_bodies.cpp index f39e8f41f7..f8363f6e8c 100644 --- a/modules/core/src/rigid_bodies.cpp +++ b/modules/core/src/rigid_bodies.cpp @@ -100,11 +100,11 @@ class AccumulateRigidBodyDerivatives : public SingletonDerivativeModifier { "AccumulateRigidBodyDerivatives%1%") : SingletonDerivativeModifier(name) {} virtual void apply_index(Model *m, ParticleIndex pi) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(AccumulateRigidBodyDerivatives); IMP_OBJECT_METHODS(AccumulateRigidBodyDerivatives); }; @@ -125,11 +125,11 @@ class UpdateRigidBodyMembers : public SingletonModifier { UpdateRigidBodyMembers(std::string name = "UpdateRigidBodyMembers%1%") : SingletonModifier(name) {} virtual void apply_index(Model *m, ParticleIndex pi) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(UpdateRigidBodyMembers); IMP_OBJECT_METHODS(UpdateRigidBodyMembers); }; @@ -140,14 +140,14 @@ class NormalizeRotation : public SingletonModifier { NormalizeRotation(std::string name = "NormalizeRotation%1%") : SingletonModifier(name) {} virtual void apply_index(Model *m, ParticleIndex pi) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual void apply_indexes( Model *m, const ParticleIndexes &pis, unsigned int lower_bound, - unsigned int upper_bound) const IMP_OVERRIDE IMP_FINAL; + unsigned int upper_bound) const override IMP_FINAL; // IMP_SINGLETON_MODIFIER_METHODS(NormalizeRotation); IMP_OBJECT_METHODS(NormalizeRotation); }; @@ -158,11 +158,11 @@ class NullSDM : public SingletonDerivativeModifier { NullSDM(std::string name = "NullModifier%1%") : SingletonDerivativeModifier(name) {} virtual void apply_index(Model *m, ParticleIndex pi) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(NullSDM); IMP_OBJECT_METHODS(NullSDM); }; diff --git a/modules/display/include/FilterGeometry.h b/modules/display/include/FilterGeometry.h index d40d25a424..c273d3622d 100644 --- a/modules/display/include/FilterGeometry.h +++ b/modules/display/include/FilterGeometry.h @@ -29,13 +29,13 @@ class IMPDISPLAYEXPORT FilterGeometry : public GeometryProcessor, Geometries gdata_; mutable Geometries filtered_; bool handle_sphere(SphereGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_cylinder(CylinderGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_point(PointGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_segment(SegmentGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; public: //! Pay attention to the orientation of the plane. @@ -45,7 +45,7 @@ class IMPDISPLAYEXPORT FilterGeometry : public GeometryProcessor, void add_geometry(const Geometries &g); - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; + virtual IMP::display::Geometries get_components() const override; IMP_OBJECT_METHODS(FilterGeometry); }; diff --git a/modules/display/include/GeometrySet.h b/modules/display/include/GeometrySet.h index e2742ff15a..5bea71df37 100644 --- a/modules/display/include/GeometrySet.h +++ b/modules/display/include/GeometrySet.h @@ -25,7 +25,7 @@ class IMPDISPLAYEXPORT GeometrySet : public Geometry { GeometrySet(const Geometries &v, const std::string n); GeometrySet(const Geometries &v, const Color &c, std::string n); Geometries get_geometry() const { return v_; } - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; + virtual IMP::display::Geometries get_components() const override; IMP_OBJECT_METHODS(GeometrySet); }; diff --git a/modules/display/include/LogOptimizerState.h b/modules/display/include/LogOptimizerState.h index ffad7d7304..45e5d56384 100644 --- a/modules/display/include/LogOptimizerState.h +++ b/modules/display/include/LogOptimizerState.h @@ -31,7 +31,7 @@ class IMPDISPLAYEXPORT WriteOptimizerState : public OptimizerState { Geometry *, Geometries, , , ); protected: - virtual void do_update(unsigned int) IMP_OVERRIDE; + virtual void do_update(unsigned int) override; IMP_OBJECT_METHODS(WriteOptimizerState); }; diff --git a/modules/display/include/PymolWriter.h b/modules/display/include/PymolWriter.h index d27267db47..6646297b84 100644 --- a/modules/display/include/PymolWriter.h +++ b/modules/display/include/PymolWriter.h @@ -45,22 +45,22 @@ class IMPDISPLAYEXPORT PymolWriter : public TextWriter { void setup(std::string name, Type type, bool opendata = true); void cleanup(std::string name, bool close = true); bool handle_sphere(SphereGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_cylinder(CylinderGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_point(PointGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_segment(SegmentGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_polygon(PolygonGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_triangle(TriangleGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_label(LabelGeometry *g, Color color, - std::string name) IMP_OVERRIDE; + std::string name) override; bool handle_surface(SurfaceMeshGeometry *g, Color color, std::string name); - void do_set_frame() IMP_OVERRIDE; + void do_set_frame() override; public: IMP_TEXT_WRITER(PymolWriter); diff --git a/modules/display/include/Writer.h b/modules/display/include/Writer.h index e352527b85..58e6f7e485 100644 --- a/modules/display/include/Writer.h +++ b/modules/display/include/Writer.h @@ -98,7 +98,7 @@ class IMPDISPLAYEXPORT TextWriter : public Writer { //! Get the stream for inheriting classes to write to std::ostream& get_stream() { return out_; } - virtual void do_set_frame() IMP_OVERRIDE; + virtual void do_set_frame() override; public: //! Create a writer opening the file with the passed sink diff --git a/modules/display/include/geometry_macros.h b/modules/display/include/geometry_macros.h index 3b348d585b..03b801bcf1 100644 --- a/modules/display/include/geometry_macros.h +++ b/modules/display/include/geometry_macros.h @@ -38,7 +38,7 @@ Name(const Type &v, const display::Color &c, std::string n); \ virtual const Type &get_geometry() const { return v_; } \ void set_geometry(const Type &v) { v_ = v; } \ - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; \ + virtual IMP::display::Geometries get_components() const override; \ IMP_OBJECT_METHODS(Name); \ }; \ /** Create a Geometry with the passed primitive.*/ \ @@ -56,7 +56,7 @@ Name(const Type &v, const display::Color &c, std::string n); \ virtual const Type &get_geometry() const { return v_; } \ void set_geometry(const Type &v) { v_ = v; } \ - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; \ + virtual IMP::display::Geometries get_components() const override; \ IMP_OBJECT_METHODS(Name); \ }; \ /** Create a Geometry with the passed primitive.*/ \ @@ -80,7 +80,7 @@ Name(const Type &v, const display::Color &c, std::string n); \ virtual const Type &get_geometry() const { return v_; } \ void set_geometry(const Type &v) { v_ = v; } \ - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; \ + virtual IMP::display::Geometries get_components() const override; \ IMP_OBJECT_METHODS(Name); \ }; \ inline Name *create_geometry( \ @@ -102,7 +102,7 @@ Name(const Type &v, const display::Color &c, std::string n); \ virtual const Type &get_geometry() const { return v_; } \ void set_geometry(const Type &v) { v_ = v; } \ - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; \ + virtual IMP::display::Geometries get_components() const override; \ IMP_OBJECT_METHODS(Name); \ }; \ inline Name *create_geometry( \ @@ -147,7 +147,7 @@ public: \ Name##sGeometry(SingletonContainer *sc) \ : display::SingletonsGeometry(sc) {} \ - display::Geometries get_components() const IMP_OVERRIDE { \ + display::Geometries get_components() const override { \ display::Geometries ret; \ IMP_FOREACH(ParticleIndex pi, get_container()->get_contents()) { \ Decorator d(get_container()->get_model(), pi); \ @@ -164,7 +164,7 @@ public: \ Name##Geometry(const ParticlePair &pp) \ : display::PairGeometry(pp) {} \ - display::Geometries get_components() const IMP_OVERRIDE { \ + display::Geometries get_components() const override { \ display::Geometries ret; \ Decorator d0(get_particle_pair()[0]); \ Decorator d1(get_particle_pair()[1]); \ @@ -177,7 +177,7 @@ class Name##sGeometry : public display::PairsGeometry { \ public: \ Name##sGeometry(PairContainer *sc) : display::PairsGeometry(sc) {} \ - display::Geometries get_components() const IMP_OVERRIDE { \ + display::Geometries get_components() const override { \ display::Geometries ret; \ IMP_FOREACH(ParticleIndexPair pip, \ get_container()->get_contents()) { \ diff --git a/modules/display/include/internal/writers.h b/modules/display/include/internal/writers.h index ea0caa7ca0..0fd80b59a8 100644 --- a/modules/display/include/internal/writers.h +++ b/modules/display/include/internal/writers.h @@ -28,7 +28,7 @@ template class WriterFactoryHelper : public WriterFactory { public: WriterFactoryHelper() {} - Writer *create(std::string name) const IMP_OVERRIDE { + Writer *create(std::string name) const override { return new Wr(TextOutput(name)); } }; diff --git a/modules/display/include/particle_geometry.h b/modules/display/include/particle_geometry.h index 689138afb6..3a89b88651 100644 --- a/modules/display/include/particle_geometry.h +++ b/modules/display/include/particle_geometry.h @@ -27,11 +27,11 @@ class IMPDISPLAYEXPORT SingletonGeometry : public Geometry { public: SingletonGeometry(Particle *p); - bool get_has_color() const IMP_OVERRIDE { + bool get_has_color() const override { return Geometry::get_has_color() || Colored::get_is_setup(p_); } - Color get_color() const IMP_OVERRIDE { + Color get_color() const override { if (Geometry::get_has_color()) { return Geometry::get_color(); } else { @@ -67,12 +67,12 @@ class IMPDISPLAYEXPORT PairGeometry : public Geometry { public: PairGeometry(const ParticlePair &pp); - bool get_has_color() const IMP_OVERRIDE { + bool get_has_color() const override { return Geometry::get_has_color() || Colored::get_is_setup(p0_) || Colored::get_is_setup(p1_); } - Color get_color() const IMP_OVERRIDE { + Color get_color() const override { if (Geometry::get_has_color()) { return Geometry::get_color(); } else if (Colored::get_is_setup(p0_)) diff --git a/modules/display/include/primitive_geometries.h b/modules/display/include/primitive_geometries.h index 91011000ad..770d963f02 100644 --- a/modules/display/include/primitive_geometries.h +++ b/modules/display/include/primitive_geometries.h @@ -77,7 +77,7 @@ class IMPDISPLAYEXPORT LabelGeometry : public Geometry { LabelGeometry(const algebra::Vector3D &loc, std::string text); std::string get_text() const { return text_; } const algebra::Sphere3D &get_location() const { return loc_; } - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; + virtual IMP::display::Geometries get_components() const override; IMP_OBJECT_METHODS(LabelGeometry); }; @@ -96,7 +96,7 @@ class IMPDISPLAYEXPORT SurfaceMeshGeometry : public Geometry { SurfaceMeshGeometry(const algebra::Vector3Ds &vertices, const Ints &faces); const algebra::Vector3Ds &get_vertexes() const { return vertices_; } const Ints &get_faces() const { return faces_; } - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; + virtual IMP::display::Geometries get_components() const override; IMP_OBJECT_METHODS(SurfaceMeshGeometry); }; @@ -110,7 +110,7 @@ class IMPDISPLAYEXPORT PlaneGeometry : public Geometry { public: PlaneGeometry(const algebra::Plane3D &loc, const algebra::BoundingBox3D &box); - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; + virtual IMP::display::Geometries get_components() const override; IMP_OBJECT_METHODS(PlaneGeometry); }; diff --git a/modules/display/include/restraint_geometry.h b/modules/display/include/restraint_geometry.h index d62b322374..6ff5c568d9 100644 --- a/modules/display/include/restraint_geometry.h +++ b/modules/display/include/restraint_geometry.h @@ -33,7 +33,7 @@ class IMPDISPLAYEXPORT RestraintGeometry : public Geometry { public: RestraintGeometry(Restraint *p); Restraint *get_restraint() const { return r_; } - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; + virtual IMP::display::Geometries get_components() const override; IMP_OBJECT_METHODS(RestraintGeometry); }; @@ -44,7 +44,7 @@ class IMPDISPLAYEXPORT RestraintSetGeometry : public Geometry { public: RestraintSetGeometry(RestraintSet *p); RestraintSet *get_restraint_set() const { return r_; } - virtual IMP::display::Geometries get_components() const IMP_OVERRIDE; + virtual IMP::display::Geometries get_components() const override; IMP_OBJECT_METHODS(RestraintSetGeometry); }; diff --git a/modules/display/include/writer_macros.h b/modules/display/include/writer_macros.h index 447e057441..8fdaf9df01 100644 --- a/modules/display/include/writer_macros.h +++ b/modules/display/include/writer_macros.h @@ -30,15 +30,15 @@ IMP_OBJECT_METHODS(Name); \ \ protected: \ - virtual void do_destroy() IMP_OVERRIDE { do_close(); } \ - virtual void do_open() IMP_OVERRIDE; \ - virtual void do_close() IMP_OVERRIDE + virtual void do_destroy() override { do_close(); } \ + virtual void do_open() override; \ + virtual void do_close() override #define IMP_WRITER(Name) \ IMP_OBJECT_METHODS(Name); \ \ protected: \ - virtual void do_destroy() IMP_OVERRIDE { do_close(); } \ + virtual void do_destroy() override { do_close(); } \ virtual void do_open(); \ virtual void do_close() diff --git a/modules/domino/include/BranchAndBoundSampler.h b/modules/domino/include/BranchAndBoundSampler.h index bbfe5c4acd..8be40eb127 100644 --- a/modules/domino/include/BranchAndBoundSampler.h +++ b/modules/domino/include/BranchAndBoundSampler.h @@ -31,7 +31,7 @@ class IMPDOMINOEXPORT BranchAndBoundSampler : public DiscreteSampler { BranchAndBoundSampler(Model *m, ParticleStatesTable *pst, std::string name = "BranchAndBoundSampler %1%"); Assignments do_get_sample_assignments(const IMP::domino::Subset &known) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(BranchAndBoundSampler); }; diff --git a/modules/domino/include/DependencyScoreState.h b/modules/domino/include/DependencyScoreState.h index e1f4239689..7d74bd81e6 100644 --- a/modules/domino/include/DependencyScoreState.h +++ b/modules/domino/include/DependencyScoreState.h @@ -49,10 +49,10 @@ class IMPDOMINOEXPORT DependencyScoreState : public ScoreState { } protected: - virtual void do_before_evaluate() IMP_OVERRIDE; - virtual void do_after_evaluate(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_before_evaluate() override; + virtual void do_after_evaluate(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(DependencyScoreState); ; }; diff --git a/modules/domino/include/DiscreteSampler.h b/modules/domino/include/DiscreteSampler.h index d5aa37e763..ff3abdca03 100644 --- a/modules/domino/include/DiscreteSampler.h +++ b/modules/domino/include/DiscreteSampler.h @@ -60,7 +60,7 @@ class IMPDOMINOEXPORT DiscreteSampler : public Sampler { AssignmentsTable *get_assignments_table_to_use( const SubsetFilterTables &sfts, unsigned int max = std::numeric_limits::max()) const; - virtual ConfigurationSet *do_sample() const IMP_OVERRIDE; + virtual ConfigurationSet *do_sample() const override; virtual Assignments do_get_sample_assignments(const Subset &all) const = 0; RestraintsTemp get_restraints() const { diff --git a/modules/domino/include/DominoSampler.h b/modules/domino/include/DominoSampler.h index c8e0c373fd..d8e05d2267 100644 --- a/modules/domino/include/DominoSampler.h +++ b/modules/domino/include/DominoSampler.h @@ -42,7 +42,7 @@ class IMPDOMINOEXPORT DominoSampler : public DiscreteSampler { DominoSampler(Model *m, ParticleStatesTable *pst, std::string name = "DominoSampler %1%"); Assignments do_get_sample_assignments(const IMP::domino::Subset &known) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(DominoSampler); public: diff --git a/modules/domino/include/assignment_containers.h b/modules/domino/include/assignment_containers.h index cc45a50d28..ca730e19cd 100644 --- a/modules/domino/include/assignment_containers.h +++ b/modules/domino/include/assignment_containers.h @@ -69,9 +69,9 @@ class IMPDOMINOEXPORT PackedAssignmentContainer : public AssignmentContainer { public: PackedAssignmentContainer(std::string name = "PackedAssignmentContainer %1%"); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(PackedAssignmentContainer); IMP_OBJECT_METHODS(PackedAssignmentContainer); }; @@ -118,9 +118,9 @@ class IMPDOMINOEXPORT ListAssignmentContainer : public AssignmentContainer { public: ListAssignmentContainer(std::string name = "ListAssignmentContainer %1%"); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(ListAssignmentContainer); IMP_OBJECT_METHODS(ListAssignmentContainer); }; @@ -156,9 +156,9 @@ class IMPDOMINOEXPORT SampleAssignmentContainer : public AssignmentContainer { SampleAssignmentContainer(unsigned int k, std::string name = "SampleAssignmentContainer %1%"); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(SampleAssignmentContainer); IMP_OBJECT_METHODS(SampleAssignmentContainer); }; @@ -190,7 +190,7 @@ class IMPDOMINOEXPORT WriteHDF5AssignmentContainer Ints cache_; unsigned int max_cache_; void flush(); - virtual void do_destroy() IMP_OVERRIDE { flush(); } + virtual void do_destroy() override { flush(); } public: WriteHDF5AssignmentContainer(RMF::HDF5::Group parent, const Subset &s, @@ -202,9 +202,9 @@ class IMPDOMINOEXPORT WriteHDF5AssignmentContainer const ParticlesTemp &all_particles, std::string name); void set_cache_size(unsigned int words); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(WriteHDF5AssignmentContainer); IMP_OBJECT_METHODS(WriteHDF5AssignmentContainer); }; @@ -225,9 +225,9 @@ class IMPDOMINOEXPORT ReadHDF5AssignmentContainer : public AssignmentContainer { const ParticlesTemp &all_particles, std::string name); void set_cache_size(unsigned int words); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(ReadHDF5AssignmentContainer); IMP_OBJECT_METHODS(ReadHDF5AssignmentContainer); }; @@ -246,7 +246,7 @@ class IMPDOMINOEXPORT WriteAssignmentContainer : public AssignmentContainer { int number_; void flush(); - virtual void do_destroy() IMP_OVERRIDE { + virtual void do_destroy() override { flush(); #ifdef _MSC_VER _close(f_); @@ -260,9 +260,9 @@ class IMPDOMINOEXPORT WriteAssignmentContainer : public AssignmentContainer { const ParticlesTemp &all_particles, std::string name); void set_cache_size(unsigned int words); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(WriteAssignmentContainer); IMP_OBJECT_METHODS(WriteAssignmentContainer); }; @@ -278,7 +278,7 @@ class IMPDOMINOEXPORT ReadAssignmentContainer : public AssignmentContainer { unsigned int max_cache_; mutable int offset_; int size_; - virtual void do_destroy() IMP_OVERRIDE { + virtual void do_destroy() override { #ifdef _MSC_VER _close(f_); #else @@ -291,9 +291,9 @@ class IMPDOMINOEXPORT ReadAssignmentContainer : public AssignmentContainer { const ParticlesTemp &all_particles, std::string name); void set_cache_size(unsigned int words); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(ReadAssignmentContainer); IMP_OBJECT_METHODS(ReadAssignmentContainer); }; @@ -309,9 +309,9 @@ class IMPDOMINOEXPORT RangeViewAssignmentContainer public: RangeViewAssignmentContainer(AssignmentContainer *inner, unsigned int begin, unsigned int end); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(RangeViewAssignmentContainer); IMP_OBJECT_METHODS(RangeViewAssignmentContainer); }; @@ -332,9 +332,9 @@ class IMPDOMINOEXPORT HeapAssignmentContainer : public AssignmentContainer { public: HeapAssignmentContainer(Subset subset, unsigned int k, RestraintCache *rssf, std::string name = "HeapAssignmentContainer %1%"); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(HeapAssignmentContainer); IMP_OBJECT_METHODS(HeapAssignmentContainer); }; @@ -352,9 +352,9 @@ class IMPDOMINOEXPORT CappedAssignmentContainer : public AssignmentContainer { public: CappedAssignmentContainer(AssignmentContainer *contained, int max_states, std::string name); - virtual unsigned int get_number_of_assignments() const IMP_OVERRIDE; - virtual Assignment get_assignment(unsigned int i) const IMP_OVERRIDE; - virtual void add_assignment(const Assignment &a) IMP_OVERRIDE; + virtual unsigned int get_number_of_assignments() const override; + virtual Assignment get_assignment(unsigned int i) const override; + virtual void add_assignment(const Assignment &a) override; IMP_ASSIGNMENT_CONTAINER_METHODS(CappedAssignmentContainer); IMP_OBJECT_METHODS(CappedAssignmentContainer); }; diff --git a/modules/domino/include/assignment_tables.h b/modules/domino/include/assignment_tables.h index 6ddf7916db..28e8002018 100644 --- a/modules/domino/include/assignment_tables.h +++ b/modules/domino/include/assignment_tables.h @@ -54,7 +54,7 @@ class IMPDOMINOEXPORT SimpleAssignmentsTable : public AssignmentsTable { unsigned int max = std::numeric_limits::max()); virtual void load_assignments(const IMP::domino::Subset &s, - AssignmentContainer *ac) const IMP_OVERRIDE; + AssignmentContainer *ac) const override; IMP_OBJECT_METHODS(SimpleAssignmentsTable); }; @@ -74,7 +74,7 @@ class IMPDOMINOEXPORT RecursiveAssignmentsTable : public AssignmentsTable { unsigned int max = std::numeric_limits::max()); virtual void load_assignments(const IMP::domino::Subset &s, - AssignmentContainer *ac) const IMP_OVERRIDE; + AssignmentContainer *ac) const override; IMP_OBJECT_METHODS(RecursiveAssignmentsTable); }; @@ -107,7 +107,7 @@ class IMPDOMINOEXPORT BranchAndBoundAssignmentsTable : public AssignmentsTable { unsigned int max = std::numeric_limits::max()); virtual void load_assignments(const IMP::domino::Subset &s, - AssignmentContainer *ac) const IMP_OVERRIDE; + AssignmentContainer *ac) const override; IMP_OBJECT_METHODS(BranchAndBoundAssignmentsTable); }; @@ -127,7 +127,7 @@ class IMPDOMINOEXPORT ListAssignmentsTable : public AssignmentsTable { states_[s] = lsc; } virtual void load_assignments(const IMP::domino::Subset &s, - AssignmentContainer *ac) const IMP_OVERRIDE; + AssignmentContainer *ac) const override; IMP_OBJECT_METHODS(ListAssignmentsTable); }; diff --git a/modules/domino/include/domino_macros.h b/modules/domino/include/domino_macros.h index 2a9767282c..68e368260e 100644 --- a/modules/domino/include/domino_macros.h +++ b/modules/domino/include/domino_macros.h @@ -27,10 +27,10 @@ Name##SubsetFilterTable() : P(std::string(#Name) + std::string(" %1%")) {} \ virtual IMP::domino::SubsetFilter *get_subset_filter( \ const IMP::domino::Subset &s, \ - const IMP::domino::Subsets &excluded) const IMP_OVERRIDE; \ + const IMP::domino::Subsets &excluded) const override; \ virtual double get_strength(const IMP::domino::Subset &s, \ const IMP::domino::Subsets &excluded) const \ - IMP_OVERRIDE; \ + override; \ IMP_OBJECT_METHODS(Name##SubsetFilterTable); \ }; \ IMP_OBJECTS(Name##SubsetFilterTable, Name##SubsetFilterTables) @@ -81,23 +81,23 @@ */ #define IMP_ASSIGNMENT_CONTAINER_METHODS(Name) \ public: \ - virtual Assignments get_assignments(IntRange r) const IMP_OVERRIDE { \ + virtual Assignments get_assignments(IntRange r) const override { \ Assignments ret(r.second - r.first); \ for (unsigned int i = 0; i != ret.size(); ++i) { \ ret[i] = Name::get_assignment(r.first + i); \ } \ return ret; \ } \ - virtual Assignments get_assignments() const IMP_OVERRIDE { \ + virtual Assignments get_assignments() const override { \ return get_assignments(IntRange(0, get_number_of_assignments())); \ }; \ - virtual void add_assignments(const Assignments &asgn) IMP_OVERRIDE { \ + virtual void add_assignments(const Assignments &asgn) override { \ for (unsigned int i = 0; i < asgn.size(); ++i) { \ Name::add_assignment(asgn[i]); \ } \ } \ virtual Ints get_particle_assignments(unsigned int index) const \ - IMP_OVERRIDE { \ + override { \ Ints ret(Name::get_number_of_assignments()); \ for (unsigned int i = 0; i < Name::get_number_of_assignments(); ++i) { \ ret[i] = get_assignment(i)[index]; \ diff --git a/modules/domino/include/particle_states.h b/modules/domino/include/particle_states.h index 8902156d47..04b7bfcf2e 100644 --- a/modules/domino/include/particle_states.h +++ b/modules/domino/include/particle_states.h @@ -125,9 +125,9 @@ class IMPDOMINOEXPORT IndexStates : public ParticleStates { to use.*/ IndexStates(unsigned int n, IntKey k = IntKey("state")) : ParticleStates("IndexStates %1%"), n_(n), k_(k) {} - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(IndexStates); }; @@ -147,17 +147,17 @@ class IMPDOMINOEXPORT XYZStates : public ParticleStates { IMP_USAGE_CHECK(i < states_.size(), "Out of range"); return states_[i]; } - algebra::VectorKD get_embedding(unsigned int i) const IMP_OVERRIDE { + algebra::VectorKD get_embedding(unsigned int i) const override { IMP_USAGE_CHECK(i < states_.size(), "Out of range"); return states_[i]; } unsigned int get_nearest_state( - const algebra::VectorKD &v) const IMP_OVERRIDE { + const algebra::VectorKD &v) const override { return nn_->get_nearest_neighbors(v, 1)[0]; } - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(XYZStates); }; @@ -175,11 +175,11 @@ class IMPDOMINOEXPORT RigidBodyStates : public ParticleStates { IMP_USAGE_CHECK(i < states_.size(), "Out of range"); return states_[i]; } - algebra::VectorKD get_embedding(unsigned int i) const IMP_OVERRIDE; - unsigned int get_nearest_state(const algebra::VectorKD &v) const IMP_OVERRIDE; - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + algebra::VectorKD get_embedding(unsigned int i) const override; + unsigned int get_nearest_state(const algebra::VectorKD &v) const override; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(RigidBodyStates); }; @@ -204,11 +204,11 @@ class IMPDOMINOEXPORT NestedRigidBodyStates : public ParticleStates { IMP_USAGE_CHECK(i < states_.size(), "Out of range"); return states_[i]; } - algebra::VectorKD get_embedding(unsigned int i) const IMP_OVERRIDE; - unsigned int get_nearest_state(const algebra::VectorKD &v) const IMP_OVERRIDE; - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + algebra::VectorKD get_embedding(unsigned int i) const override; + unsigned int get_nearest_state(const algebra::VectorKD &v) const override; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(NestedRigidBodyStates); }; @@ -221,9 +221,9 @@ class IMPDOMINOEXPORT CompoundStates : public ParticleStates { public: CompoundStates(ParticleStates *a, ParticleStates *b) : ParticleStates("CompoundStates %1%"), a_(a), b_(b) {} - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(CompoundStates); }; @@ -242,9 +242,9 @@ class IMPDOMINOEXPORT RecursiveStates : public ParticleStates { public: RecursiveStates(Particle *p, Subset s, const Assignments &ss, ParticleStatesTable *pst); - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(RecursiveStates); }; @@ -268,9 +268,9 @@ class IMPDOMINOEXPORT PermutationStates : public ParticleStates { "Out of range state returned. This is perplexing."); return cur; } - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(PermutationStates); }; diff --git a/modules/domino/include/subset_filters.h b/modules/domino/include/subset_filters.h index e6c83259e3..c397a0e01b 100644 --- a/modules/domino/include/subset_filters.h +++ b/modules/domino/include/subset_filters.h @@ -113,10 +113,10 @@ class IMPDOMINOEXPORT RestraintScoreSubsetFilterTable ParticleStatesTable *pst); virtual IMP::domino::SubsetFilter *get_subset_filter( const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(RestraintScoreSubsetFilterTable); }; @@ -143,10 +143,10 @@ class IMPDOMINOEXPORT MinimumRestraintScoreSubsetFilterTable } virtual IMP::domino::SubsetFilter *get_subset_filter( const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(MinimumRestraintScoreSubsetFilterTable); }; @@ -279,10 +279,10 @@ class IMPDOMINOEXPORT ListSubsetFilterTable : public SubsetFilterTable { void set_allowed_states(Particle *p, const Ints &states); virtual IMP::domino::SubsetFilter *get_subset_filter( const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(ListSubsetFilterTable); }; @@ -305,10 +305,10 @@ class IMPDOMINOEXPORT PairListSubsetFilterTable : public SubsetFilterTable { void set_allowed_states(ParticlePair p, const IntPairs &states); virtual IMP::domino::SubsetFilter *get_subset_filter( const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(PairListSubsetFilterTable); }; @@ -331,10 +331,10 @@ class IMPDOMINOEXPORT ProbabilisticSubsetFilterTable ProbabilisticSubsetFilterTable(double p, bool leaves_only = false); virtual IMP::domino::SubsetFilter *get_subset_filter( const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(ProbabilisticSubsetFilterTable); }; diff --git a/modules/domino/src/analysis.cpp b/modules/domino/src/analysis.cpp index da1f143d1e..feaef1e4a0 100644 --- a/modules/domino/src/analysis.cpp +++ b/modules/domino/src/analysis.cpp @@ -25,15 +25,15 @@ class ParticleStatesEmbedding : public statistics::Embedding { ParticleStatesEmbedding(Particle *p, ParticleStates *ps, const Ints &allowed, std::string name) : Embedding(name), p_(p), ps_(ps), allowed_(allowed) {} - algebra::VectorKD get_point(unsigned int i) const IMP_OVERRIDE; - algebra::VectorKDs get_points() const IMP_OVERRIDE { + algebra::VectorKD get_point(unsigned int i) const override; + algebra::VectorKDs get_points() const override { algebra::VectorKDs ret(get_number_of_items()); for (unsigned int i = 0; i < ret.size(); ++i) { ret[i] = ParticleStatesEmbedding::get_point(i); } return ret; } - unsigned int get_number_of_items() const IMP_OVERRIDE; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(ParticleStatesEmbedding); }; diff --git a/modules/domino/src/particle_states.cpp b/modules/domino/src/particle_states.cpp index 29b9ff45eb..3f506bc390 100644 --- a/modules/domino/src/particle_states.cpp +++ b/modules/domino/src/particle_states.cpp @@ -135,10 +135,10 @@ class DummyConstraint : public Constraint { public: DummyConstraint(Particle *in, const ParticlesTemp &out) : Constraint(in->get_model(), "DummyConstraint%1%"), in_(in), out_(out) {} - virtual void do_update_attributes() IMP_OVERRIDE; - virtual void do_update_derivatives(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_update_attributes() override; + virtual void do_update_derivatives(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(DummyConstraint); }; void DummyConstraint::do_update_attributes() {} diff --git a/modules/domino/src/subset_filters.cpp b/modules/domino/src/subset_filters.cpp index 816afd51f2..edba97690e 100644 --- a/modules/domino/src/subset_filters.cpp +++ b/modules/domino/src/subset_filters.cpp @@ -44,7 +44,7 @@ class MinimumRestraintScoreSubsetFilter : public SubsetFilter { public: virtual bool get_is_ok(const IMP::domino::Assignment &assignment) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(MinimumRestraintScoreSubsetFilter); }; @@ -144,7 +144,7 @@ class DisjointSetsSubsetFilter : public SubsetFilter { } } IMP_OBJECT_METHODS(DisjointSetsSubsetFilter); - bool get_is_ok(const Assignment &state) const IMP_OVERRIDE { + bool get_is_ok(const Assignment &state) const override { IMP_OBJECT_LOG; set_was_used(true); Filter f; @@ -153,7 +153,7 @@ class DisjointSetsSubsetFilter : public SubsetFilter { } return true; } - int get_next_state(int pos, const Assignment &state) const IMP_OVERRIDE { + int get_next_state(int pos, const Assignment &state) const override { for (unsigned int i = 0; i < sets_.size(); ++i) { for (unsigned int j = 0; j < sets_[i].size(); ++j) { if (sets_[i][j] == pos) { @@ -473,9 +473,9 @@ class ListSubsetFilter : public SubsetFilter { public: ListSubsetFilter(const ListSubsetFilterTable *ka, const Ints indexes) : SubsetFilter("List score filter"), keepalive_(ka), indexes_(indexes) {} - int get_next_state(int pos, const Assignment &state) const IMP_OVERRIDE; + int get_next_state(int pos, const Assignment &state) const override; virtual bool get_is_ok(const IMP::domino::Assignment &assignment) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(ListSubsetFilter); }; @@ -600,7 +600,7 @@ class PairListSubsetFilter : public SubsetFilter { PairListSubsetFilter(const IntPairs &i, const Vector &a) : SubsetFilter("Pair list score filter"), indexes_(i), allowed_(a) {} virtual bool get_is_ok(const IMP::domino::Assignment &assignment) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(PairListSubsetFilter); }; @@ -688,7 +688,7 @@ class ProbabilisticSubsetFilter : public SubsetFilter { ProbabilisticSubsetFilter(double p) : SubsetFilter("ProbabilisticSubsetFilter %1%"), p_(p), r_(0, 1) {} virtual bool get_is_ok(const IMP::domino::Assignment &assignment) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(ProbabilisticSubsetFilter); }; @@ -741,7 +741,7 @@ class RestraintScoreSubsetFilter : public SubsetFilter { } } virtual bool get_is_ok(const IMP::domino::Assignment &assignment) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(RestraintScoreSubsetFilter); }; diff --git a/modules/em/include/DensityFillingRestraint.h b/modules/em/include/DensityFillingRestraint.h index c7e6720a68..2583a4ab39 100644 --- a/modules/em/include/DensityFillingRestraint.h +++ b/modules/em/include/DensityFillingRestraint.h @@ -42,8 +42,8 @@ class IMPEMEXPORT DensityFillingRestraint : public Restraint { Float threshold); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(DensityFillingRestraint); IMP_LIST(private, Particle, particle, Particle *, Particles); diff --git a/modules/em/include/EMReaderWriter.h b/modules/em/include/EMReaderWriter.h index 750e08aadb..ddb6aa3ba6 100644 --- a/modules/em/include/EMReaderWriter.h +++ b/modules/em/include/EMReaderWriter.h @@ -28,7 +28,7 @@ class IMPEMEXPORT EMReaderWriter : public MapReaderWriter { \exception IOException in case that the filename was not found */ void read(const char *filename, float **data, - DensityHeader &header) IMP_OVERRIDE; + DensityHeader &header) override; //! Writes a density file in EM format with the header information /** @@ -37,7 +37,7 @@ class IMPEMEXPORT EMReaderWriter : public MapReaderWriter { \param[in] header DensityHeader() with the header information */ void write(const char *filename, const float *data, - const DensityHeader &header) IMP_OVERRIDE; + const DensityHeader &header) override; #endif protected: //! Reads the header diff --git a/modules/em/include/EnvelopeFitRestraint.h b/modules/em/include/EnvelopeFitRestraint.h index adfb2c3b7a..95b620ca17 100644 --- a/modules/em/include/EnvelopeFitRestraint.h +++ b/modules/em/include/EnvelopeFitRestraint.h @@ -46,7 +46,7 @@ class IMPEMEXPORT EnvelopeFitRestraint : public IMP::Restraint { double density_threshold, double penetration_threshold); double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; // compute and return best scoring transformation algebra::Transformation3D get_transformation() const { @@ -57,7 +57,7 @@ class IMPEMEXPORT EnvelopeFitRestraint : public IMP::Restraint { // compute best scoring transformation and apply it on the particles void apply_transformation(); - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { return ps_; } + IMP::ModelObjectsTemp do_get_inputs() const override { return ps_; } IMP_OBJECT_METHODS(EnvelopeFitRestraint); private: diff --git a/modules/em/include/EnvelopePenetrationRestraint.h b/modules/em/include/EnvelopePenetrationRestraint.h index b3afa9ff7f..6a9a2d23b9 100644 --- a/modules/em/include/EnvelopePenetrationRestraint.h +++ b/modules/em/include/EnvelopePenetrationRestraint.h @@ -44,8 +44,8 @@ class IMPEMEXPORT EnvelopePenetrationRestraint : public Restraint { Float threshold); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(EnvelopePenetrationRestraint); #ifndef SWIG diff --git a/modules/em/include/EnvelopeScore.h b/modules/em/include/EnvelopeScore.h index cce6f8891e..5838b9b5b9 100644 --- a/modules/em/include/EnvelopeScore.h +++ b/modules/em/include/EnvelopeScore.h @@ -60,7 +60,7 @@ class IMPEMEXPORT EnvelopeScore : public IMP::Object { const IMP::algebra::Transformation3D& trans) const; // methods required by Object - IMP::VersionInfo get_version_info() const IMP_OVERRIDE { + IMP::VersionInfo get_version_info() const override { return IMP::VersionInfo(get_module_name(), get_module_version()); } diff --git a/modules/em/include/FitRestraint.h b/modules/em/include/FitRestraint.h index c6914bce32..681649cc66 100644 --- a/modules/em/include/FitRestraint.h +++ b/modules/em/include/FitRestraint.h @@ -68,8 +68,8 @@ class IMPEMEXPORT FitRestraint : public Restraint { void set_scale_factor(float scale) { scalefac_ = scale; } float get_scale_factor() const { return scalefac_; } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(FitRestraint); #ifndef SWIG diff --git a/modules/em/include/FitRestraintBayesEM3D.h b/modules/em/include/FitRestraintBayesEM3D.h index dd9b0a741e..2e356999a6 100644 --- a/modules/em/include/FitRestraintBayesEM3D.h +++ b/modules/em/include/FitRestraintBayesEM3D.h @@ -47,8 +47,8 @@ class IMPEMEXPORT FitRestraintBayesEM3D : public Restraint { double window_size = 1.0); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const - IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(FitRestraintBayesEM3D); private: diff --git a/modules/em/include/MRCReaderWriter.h b/modules/em/include/MRCReaderWriter.h index e8002dc383..fa5d0eb0ec 100644 --- a/modules/em/include/MRCReaderWriter.h +++ b/modules/em/include/MRCReaderWriter.h @@ -28,11 +28,11 @@ class IMPEMEXPORT MRCReaderWriter : public MapReaderWriter { MRCReaderWriter(std::string fn) { filename = fn; } #if !defined(DOXYGEN) && !defined(SWIG) //! Reads an MRC file and translates the header to the general DensityHeader - void read(const char *fn_in, float **data, DensityHeader &head) IMP_OVERRIDE; + void read(const char *fn_in, float **data, DensityHeader &head) override; //! Writes an MRC file from the data and the general DensityHeader void write(const char *fn_out, const float *data, - const DensityHeader &head) IMP_OVERRIDE; + const DensityHeader &head) override; #endif private: diff --git a/modules/em/include/PCAAligner.h b/modules/em/include/PCAAligner.h index af12048249..65cf5bf929 100644 --- a/modules/em/include/PCAAligner.h +++ b/modules/em/include/PCAAligner.h @@ -46,7 +46,7 @@ class IMPEMEXPORT PCAAligner : public IMP::Object { algebra::Transformation3Ds align(const algebra::Vector3Ds& points) const; // methods required by Object - IMP::VersionInfo get_version_info() const IMP_OVERRIDE { + IMP::VersionInfo get_version_info() const override { return IMP::VersionInfo(get_module_name(), get_module_version()); } diff --git a/modules/em/include/PCAFitRestraint.h b/modules/em/include/PCAFitRestraint.h index 5c4ade3955..dfbda3816a 100644 --- a/modules/em/include/PCAFitRestraint.h +++ b/modules/em/include/PCAFitRestraint.h @@ -48,8 +48,8 @@ class IMPEMEXPORT PCAFitRestraint : public Restraint { FloatKey weight_key = atom::Mass::get_mass_key()); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(PCAFitRestraint); #ifndef SWIG diff --git a/modules/em/include/SpiderReaderWriter.h b/modules/em/include/SpiderReaderWriter.h index 3b95698a9e..dc622f492b 100644 --- a/modules/em/include/SpiderReaderWriter.h +++ b/modules/em/include/SpiderReaderWriter.h @@ -72,7 +72,7 @@ class IMPEMEXPORT SpiderMapReaderWriter : public MapReaderWriter { * from the header. */ void read(const char *filename, float **data, - DensityHeader &header) IMP_OVERRIDE; + DensityHeader &header) override; //! Writes a map in Spider format from data and header. /** @@ -82,7 +82,7 @@ class IMPEMEXPORT SpiderMapReaderWriter : public MapReaderWriter { * data from the header. */ void write(const char *filename, const float *data, - const DensityHeader &header) IMP_OVERRIDE; + const DensityHeader &header) override; #endif IMP_OBJECT_METHODS(SpiderMapReaderWriter); }; diff --git a/modules/em/include/SurfaceShellDensityMap.h b/modules/em/include/SurfaceShellDensityMap.h index 8666dea385..87bdd5b61e 100644 --- a/modules/em/include/SurfaceShellDensityMap.h +++ b/modules/em/include/SurfaceShellDensityMap.h @@ -60,7 +60,7 @@ class IMPEMEXPORT SurfaceShellDensityMap : public SampledDensityMap { corresponding shell ( the value increases as the voxel is further away from the surface). */ - void resample() IMP_OVERRIDE; + void resample() override; //! Set the value of the map voxels as either scene or background /** \param[in] scene_val all voxels corresponding to particles will diff --git a/modules/em/include/XplorReaderWriter.h b/modules/em/include/XplorReaderWriter.h index de58118cc7..1b1c4356a4 100644 --- a/modules/em/include/XplorReaderWriter.h +++ b/modules/em/include/XplorReaderWriter.h @@ -24,10 +24,10 @@ class IMPEMEXPORT XplorReaderWriter : public MapReaderWriter { #if !defined(DOXYGEN) && !defined(SWIG) public: void read(const char *filename, float **data, - DensityHeader &header) IMP_OVERRIDE; + DensityHeader &header) override; void write(const char *filename, const float *data, - const DensityHeader &header) IMP_OVERRIDE; + const DensityHeader &header) override; protected: int read_header(std::ifstream &XPLORstream, internal::XplorHeader &header); diff --git a/modules/em/include/embedding.h b/modules/em/include/embedding.h index b62afab104..e8163369ef 100644 --- a/modules/em/include/embedding.h +++ b/modules/em/include/embedding.h @@ -23,8 +23,8 @@ class IMPEMEXPORT HighDensityEmbedding : public statistics::Embedding { public: HighDensityEmbedding(DensityMap *dm, double threshold); - algebra::VectorKD get_point(unsigned int i) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + algebra::VectorKD get_point(unsigned int i) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(HighDensityEmbedding); }; diff --git a/modules/em2d/include/DummyRestraint.h b/modules/em2d/include/DummyRestraint.h index 724a877777..92412ba305 100644 --- a/modules/em2d/include/DummyRestraint.h +++ b/modules/em2d/include/DummyRestraint.h @@ -55,8 +55,8 @@ class IMPEM2DEXPORT DummyRestraint : public Restraint { } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(DummyRestraint); }; IMP_OBJECTS(DummyRestraint, DummyRestraints); @@ -84,8 +84,8 @@ class IMPEM2DEXPORT ParticlesDummyRestraint : public Restraint { } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ParticlesDummyRestraint); }; IMP_OBJECTS(ParticlesDummyRestraint, ParticlesDummyRestraints); diff --git a/modules/em2d/include/Em2DRestraint.h b/modules/em2d/include/Em2DRestraint.h index 8a30048e77..65c1cc6e8d 100644 --- a/modules/em2d/include/Em2DRestraint.h +++ b/modules/em2d/include/Em2DRestraint.h @@ -133,8 +133,8 @@ class IMPEM2DEXPORT Em2DRestraint : public Restraint { } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(Em2DRestraint); }; diff --git a/modules/em2d/include/Fine2DRegistrationRestraint.h b/modules/em2d/include/Fine2DRegistrationRestraint.h index 281366110c..42ef7878c3 100644 --- a/modules/em2d/include/Fine2DRegistrationRestraint.h +++ b/modules/em2d/include/Fine2DRegistrationRestraint.h @@ -59,8 +59,8 @@ class IMPEM2DEXPORT Fine2DRegistrationRestraint : public Restraint { RegistrationResult get_final_registration() const; virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(Fine2DRegistrationRestraint); /** diff --git a/modules/em2d/include/JPGImageReaderWriter.h b/modules/em2d/include/JPGImageReaderWriter.h index 0a2511718a..8ffc60f7d0 100644 --- a/modules/em2d/include/JPGImageReaderWriter.h +++ b/modules/em2d/include/JPGImageReaderWriter.h @@ -20,12 +20,12 @@ class JPGImageReaderWriter : public ImageReaderWriter { JPGImageReaderWriter() {} void read(const String &filename, em::ImageHeader &header, - cv::Mat &data) const IMP_OVERRIDE { + cv::Mat &data) const override { this->read_from_ints(filename, header, data); } void write(const String &filename, em::ImageHeader &header, - const cv::Mat &data) const IMP_OVERRIDE { + const cv::Mat &data) const override { this->write_to_ints(filename, header, data); } @@ -39,7 +39,7 @@ class JPGImageReaderWriter : public ImageReaderWriter { format. Eg, Spider. */ void read_from_ints(const String &filename, em::ImageHeader &header, - cv::Mat &data) const IMP_OVERRIDE { + cv::Mat &data) const override { IMP_LOG_VERBOSE("reading with JPGImageReaderWriter" << std::endl); // read cv::Mat temp = cv::imread(filename, 0); @@ -52,10 +52,10 @@ class JPGImageReaderWriter : public ImageReaderWriter { } void write_to_floats(const String &, em::ImageHeader &, - const cv::Mat &) const IMP_OVERRIDE {} + const cv::Mat &) const override {} void read_from_floats(const String &, em::ImageHeader &, - cv::Mat &) const IMP_OVERRIDE {} + cv::Mat &) const override {} //! Writes an EM image in JPG format /*! @@ -66,7 +66,7 @@ class JPGImageReaderWriter : public ImageReaderWriter { You might be discarding float information. */ void write_to_ints(const String &filename, em::ImageHeader &header, - const cv::Mat &data) const IMP_OVERRIDE { + const cv::Mat &data) const override { IMP_UNUSED(header); // discard header IMP_LOG(IMP::WARNING, diff --git a/modules/em2d/include/PCAFitRestraint.h b/modules/em2d/include/PCAFitRestraint.h index bca92f77e8..08e450c69a 100644 --- a/modules/em2d/include/PCAFitRestraint.h +++ b/modules/em2d/include/PCAFitRestraint.h @@ -53,7 +53,7 @@ class IMPEM2DEXPORT PCAFitRestraint : public IMP::Restraint { unsigned int n_components = 1); double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; unsigned int get_projection_number() const { return projection_number_; } @@ -81,12 +81,12 @@ class IMPEM2DEXPORT PCAFitRestraint : public IMP::Restraint { void write_best_projections(std::string file_name, bool evaluate=false); //! \return Information for writing to RMF files - RestraintInfo *get_static_info() const IMP_OVERRIDE; + RestraintInfo *get_static_info() const override; //! \return Information for writing to RMF files - RestraintInfo *get_dynamic_info() const IMP_OVERRIDE; + RestraintInfo *get_dynamic_info() const override; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { return ps_; } + IMP::ModelObjectsTemp do_get_inputs() const override { return ps_; } IMP_OBJECT_METHODS(PCAFitRestraint); private: diff --git a/modules/em2d/include/ProjectionParameters.h b/modules/em2d/include/ProjectionParameters.h index 24d2ffbe07..9b9cc27874 100644 --- a/modules/em2d/include/ProjectionParameters.h +++ b/modules/em2d/include/ProjectionParameters.h @@ -110,10 +110,10 @@ class IMPEM2DEXPORT ProjectionParametersScoreState : public ScoreState { : ScoreState(p->get_model(), "ProjectionParametersScoreState%1%") { proj_params_ = p; } - virtual void do_before_evaluate() IMP_OVERRIDE; - virtual void do_after_evaluate(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_before_evaluate() override; + virtual void do_after_evaluate(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(ProjectionParametersScoreState); private: diff --git a/modules/em2d/include/RelativePositionMover.h b/modules/em2d/include/RelativePositionMover.h index fb00ca8c63..3cd1b90d81 100644 --- a/modules/em2d/include/RelativePositionMover.h +++ b/modules/em2d/include/RelativePositionMover.h @@ -58,8 +58,8 @@ class IMPEM2DEXPORT RelativePositionMover : public core::RigidBodyMover { void set_random_move_probability(Float p) { probability_of_random_move_ = p; } protected: - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(RelativePositionMover); }; diff --git a/modules/em2d/include/RigidBodiesImageFitRestraint.h b/modules/em2d/include/RigidBodiesImageFitRestraint.h index adbbe3bcaf..c7a888791b 100644 --- a/modules/em2d/include/RigidBodiesImageFitRestraint.h +++ b/modules/em2d/include/RigidBodiesImageFitRestraint.h @@ -42,8 +42,8 @@ typedef std::vector KeyIndexMaps; //! Fit rigid bodies to an image. class IMPEM2DEXPORT RigidBodiesImageFitRestraint : public Restraint { virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(RigidBodiesImageFitRestraint); protected: diff --git a/modules/em2d/include/SpiderImageReaderWriter.h b/modules/em2d/include/SpiderImageReaderWriter.h index 6ec46f1f02..0d7d494fe3 100644 --- a/modules/em2d/include/SpiderImageReaderWriter.h +++ b/modules/em2d/include/SpiderImageReaderWriter.h @@ -65,20 +65,20 @@ class SpiderImageReaderWriter : public ImageReaderWriter { } void read(const String &filename, em::ImageHeader &header, - cv::Mat &data) const IMP_OVERRIDE { + cv::Mat &data) const override { this->read_from_floats(filename, header, data); } void write(const String &filename, em::ImageHeader &header, - const cv::Mat &data) const IMP_OVERRIDE { + const cv::Mat &data) const override { this->write_to_floats(filename, header, data); } void read_from_ints(const String &, em::ImageHeader &, - cv::Mat &) const IMP_OVERRIDE {} + cv::Mat &) const override {} void write_to_ints(const String &, em::ImageHeader &, - const cv::Mat &) const IMP_OVERRIDE {} + const cv::Mat &) const override {} //! Reads an image file in Spider format and stores the content //! int the header and data parameters @@ -88,7 +88,7 @@ class SpiderImageReaderWriter : public ImageReaderWriter { \param[in] data a matrix to store the grid of data of the image */ void read_from_floats(const String &filename, em::ImageHeader &header, - cv::Mat &data) const IMP_OVERRIDE { + cv::Mat &data) const override { IMP_LOG_VERBOSE("reading with SpiderImageReaderWriter" << std::endl); std::ifstream in; in.open(filename.c_str(), std::ios::in | std::ios::binary); @@ -130,7 +130,7 @@ class SpiderImageReaderWriter : public ImageReaderWriter { * \param[in] data a matrix with the grid of data of the image */ void write_to_floats(const String &filename, em::ImageHeader &header, - const cv::Mat &data) const IMP_OVERRIDE { + const cv::Mat &data) const override { std::ofstream out; out.open(filename.c_str(), std::ios::out | std::ios::binary); //! The image header is already in Spider format, just write it diff --git a/modules/em2d/include/TIFFImageReaderWriter.h b/modules/em2d/include/TIFFImageReaderWriter.h index fe18ddae8d..05ffc9a778 100644 --- a/modules/em2d/include/TIFFImageReaderWriter.h +++ b/modules/em2d/include/TIFFImageReaderWriter.h @@ -22,20 +22,20 @@ class TIFFImageReaderWriter : public ImageReaderWriter { TIFFImageReaderWriter() {} void read(const String &filename, em::ImageHeader &header, - cv::Mat &data) const IMP_OVERRIDE { + cv::Mat &data) const override { this->read_from_ints(filename, header, data); } void write(const String &filename, em::ImageHeader &header, - const cv::Mat &data) const IMP_OVERRIDE { + const cv::Mat &data) const override { this->write_to_ints(filename, header, data); } void write_to_floats(const String &, em::ImageHeader &, - const cv::Mat &) const IMP_OVERRIDE {} + const cv::Mat &) const override {} void read_from_floats(const String &, em::ImageHeader &, - cv::Mat &) const IMP_OVERRIDE {} + cv::Mat &) const override {} //! Reads an image file in TIFF format /*! @@ -47,7 +47,7 @@ class TIFFImageReaderWriter : public ImageReaderWriter { format. Eg, Spider. */ void read_from_ints(const String &filename, em::ImageHeader &header, - cv::Mat &data) const IMP_OVERRIDE { + cv::Mat &data) const override { IMP_LOG_VERBOSE("reading with TIFFImageReaderWriter" << std::endl); // read cv::Mat temp = cv::imread(filename, 0); @@ -68,7 +68,7 @@ class TIFFImageReaderWriter : public ImageReaderWriter { You might be discarding float information. */ void write_to_ints(const String &filename, em::ImageHeader &header, - const cv::Mat &data) const IMP_OVERRIDE { + const cv::Mat &data) const override { IMP_UNUSED(header); // discard header IMP_LOG(IMP::WARNING, diff --git a/modules/em2d/include/domino_filter_tables.h b/modules/em2d/include/domino_filter_tables.h index 0b8e469bf9..c2524232eb 100644 --- a/modules/em2d/include/domino_filter_tables.h +++ b/modules/em2d/include/domino_filter_tables.h @@ -40,11 +40,11 @@ class IMPEM2DEXPORT DistanceFilterTable : public domino::SubsetFilterTable { virtual IMP::domino::SubsetFilter * get_subset_filter(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(DistanceFilterTable); }; diff --git a/modules/em2d/include/domino_filters.h b/modules/em2d/include/domino_filters.h index be383279d6..fc7f3c9692 100644 --- a/modules/em2d/include/domino_filters.h +++ b/modules/em2d/include/domino_filters.h @@ -55,7 +55,7 @@ class IMPEM2DEXPORT DistanceFilter : public domino::SubsetFilter { } virtual bool get_is_ok(const IMP::domino::Assignment &assignment) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(DistanceFilter); }; diff --git a/modules/em2d/include/domino_particle_states.h b/modules/em2d/include/domino_particle_states.h index cbdbfccaa5..fc46e56a31 100644 --- a/modules/em2d/include/domino_particle_states.h +++ b/modules/em2d/include/domino_particle_states.h @@ -58,9 +58,9 @@ class IMPEM2DEXPORT GridStates : public domino::ParticleStates { //! Returns the orientation corresponding to the state i algebra::Rotation3D get_orientation(unsigned int i) const; - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(GridStates); }; @@ -99,9 +99,9 @@ class IMPEM2DEXPORT ProjectionStates : public GridStates { //! Returns the projection corresponding to the state i; Image *get_projection(unsigned int i) const; - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(ProjectionStates); }; diff --git a/modules/em2d/include/scores2D.h b/modules/em2d/include/scores2D.h index 8b63eddc73..d07c5abb6c 100644 --- a/modules/em2d/include/scores2D.h +++ b/modules/em2d/include/scores2D.h @@ -85,7 +85,7 @@ class IMPEM2DEXPORT ChiSquaredScore : public ScoreFunction { private: mutable Pointer variance_; - double get_private_score(Image *, Image *) const IMP_OVERRIDE; + double get_private_score(Image *, Image *) const override; void set_variance_imag_private(Image *var) { variance_ = var; } }; IMP_OBJECTS(ChiSquaredScore, ChiSquaredScores); @@ -97,7 +97,7 @@ class IMPEM2DEXPORT EM2DScore : public ScoreFunction { EM2DScore() : ScoreFunction() {} private: - double get_private_score(Image *image, Image *projection) const IMP_OVERRIDE { + double get_private_score(Image *image, Image *projection) const override { return 1 - get_cross_correlation_coefficient(image->get_data(), projection->get_data()); } @@ -110,7 +110,7 @@ class IMPEM2DEXPORT MeanAbsoluteDifference : public ScoreFunction { MeanAbsoluteDifference() : ScoreFunction() {} private: - double get_private_score(Image *image, Image *projection) const IMP_OVERRIDE; + double get_private_score(Image *image, Image *projection) const override; }; IMP_OBJECTS(MeanAbsoluteDifference, MeanAbsoluteDifferences); diff --git a/modules/example/include/ExampleComplexRestraint.h b/modules/example/include/ExampleComplexRestraint.h index 7d6013edcf..5681528108 100644 --- a/modules/example/include/ExampleComplexRestraint.h +++ b/modules/example/include/ExampleComplexRestraint.h @@ -47,8 +47,8 @@ class IMPEXAMPLEEXPORT ExampleComplexRestraint : public Restraint { std::string name = "ExampleComplexRestraint%1%"); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ExampleComplexRestraint); }; diff --git a/modules/example/include/ExampleConstraint.h b/modules/example/include/ExampleConstraint.h index c1c2ba0dc4..d442608e09 100644 --- a/modules/example/include/ExampleConstraint.h +++ b/modules/example/include/ExampleConstraint.h @@ -27,10 +27,10 @@ class IMPEXAMPLEEXPORT ExampleConstraint : public Constraint { public: ExampleConstraint(Particle *p); - virtual void do_update_attributes() IMP_OVERRIDE; - virtual void do_update_derivatives(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_update_attributes() override; + virtual void do_update_derivatives(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; static IntKey get_key(); IMP_OBJECT_METHODS(ExampleConstraint); diff --git a/modules/example/include/ExamplePairScore.h b/modules/example/include/ExamplePairScore.h index 8702bd0ed2..fa74cea4da 100644 --- a/modules/example/include/ExamplePairScore.h +++ b/modules/example/include/ExamplePairScore.h @@ -29,9 +29,9 @@ class IMPEXAMPLEEXPORT ExamplePairScore : public PairScore { ExamplePairScore(double x0, double k); virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(ExamplePairScore); IMP_OBJECT_METHODS(ExamplePairScore); ; diff --git a/modules/example/include/ExampleRestraint.h b/modules/example/include/ExampleRestraint.h index 72490f2230..6c3d0b9418 100644 --- a/modules/example/include/ExampleRestraint.h +++ b/modules/example/include/ExampleRestraint.h @@ -33,8 +33,8 @@ class IMPEXAMPLEEXPORT ExampleRestraint : public Restraint { */ ExampleRestraint(Model *m, ParticleIndex p, double k); void do_add_score_and_derivatives(ScoreAccumulator sa) const - IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ExampleRestraint); }; diff --git a/modules/example/include/ExampleSingletonModifier.h b/modules/example/include/ExampleSingletonModifier.h index 9d71653cbc..862cf7312e 100644 --- a/modules/example/include/ExampleSingletonModifier.h +++ b/modules/example/include/ExampleSingletonModifier.h @@ -38,11 +38,11 @@ class IMPEXAMPLEEXPORT ExampleSingletonModifier : public SingletonModifier { // note, Doxygen wants a semicolon at the end of macro lines virtual void apply_index(Model *m, ParticleIndex p) const - IMP_OVERRIDE; + override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; virtual ModelObjectsTemp do_get_outputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(ExampleSingletonModifier); IMP_OBJECT_METHODS(ExampleSingletonModifier); }; diff --git a/modules/example/include/ExampleSubsetFilterTable.h b/modules/example/include/ExampleSubsetFilterTable.h index 78c1cd5150..b57c07f8b5 100644 --- a/modules/example/include/ExampleSubsetFilterTable.h +++ b/modules/example/include/ExampleSubsetFilterTable.h @@ -34,10 +34,10 @@ class IMPEXAMPLEEXPORT ExampleSubsetFilterTable virtual IMP::domino::SubsetFilter *get_subset_filter( const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; virtual double get_strength(const IMP::domino::Subset &s, const IMP::domino::Subsets &excluded) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(ExampleSubsetFilterTable); }; diff --git a/modules/example/include/ExampleUnaryFunction.h b/modules/example/include/ExampleUnaryFunction.h index 06148edc5c..a21abcce3e 100644 --- a/modules/example/include/ExampleUnaryFunction.h +++ b/modules/example/include/ExampleUnaryFunction.h @@ -36,10 +36,10 @@ class ExampleUnaryFunction : public UnaryFunction { } virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return DerivativePair(evaluate(feature), k_ * (feature - center_)); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return .5 * k_ * algebra::get_squared(feature - center_); } IMP_OBJECT_METHODS(ExampleUnaryFunction); diff --git a/modules/example/src/ExampleSubsetFilterTable.cpp b/modules/example/src/ExampleSubsetFilterTable.cpp index d1d9d97d0c..98ecf3f510 100644 --- a/modules/example/src/ExampleSubsetFilterTable.cpp +++ b/modules/example/src/ExampleSubsetFilterTable.cpp @@ -21,7 +21,7 @@ class ExampleSubsetFilter : public domino::SubsetFilter { indices_(indices), max_(max) {} virtual bool get_is_ok(const IMP::domino::Assignment& assignment) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(ExampleSubsetFilter); }; diff --git a/modules/gsl/include/ConjugateGradients.h b/modules/gsl/include/ConjugateGradients.h index 470c820d21..0d8ea05c28 100644 --- a/modules/gsl/include/ConjugateGradients.h +++ b/modules/gsl/include/ConjugateGradients.h @@ -26,7 +26,7 @@ class IMPGSLEXPORT ConjugateGradients : public GSLOptimizer { //! Set the gradient threshold void set_threshold(double mg) { min_gradient_ = mg; } - virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE; + virtual Float do_optimize(unsigned int max_steps) override; IMP_OBJECT_METHODS(ConjugateGradients); }; diff --git a/modules/gsl/include/QuasiNewton.h b/modules/gsl/include/QuasiNewton.h index 5007d2371e..089bbb90e3 100644 --- a/modules/gsl/include/QuasiNewton.h +++ b/modules/gsl/include/QuasiNewton.h @@ -45,7 +45,7 @@ class IMPGSLEXPORT QuasiNewton : public GSLOptimizer { IMP_USAGE_CHECK(d > 0 && d <= 1, "The minimum gradient is relative."); min_gradient_ = d; } - virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE; + virtual Float do_optimize(unsigned int max_steps) override; IMP_OBJECT_METHODS(QuasiNewton); }; diff --git a/modules/gsl/include/Simplex.h b/modules/gsl/include/Simplex.h index da477d5bdd..0a332c9e4d 100644 --- a/modules/gsl/include/Simplex.h +++ b/modules/gsl/include/Simplex.h @@ -63,7 +63,7 @@ class IMPGSLEXPORT Simplex : public GSLOptimizer { min_length_ = d; } /** @} */ - virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE; + virtual Float do_optimize(unsigned int max_steps) override; IMP_OBJECT_METHODS(Simplex); }; diff --git a/modules/isd/include/AmbiguousNOERestraint.h b/modules/isd/include/AmbiguousNOERestraint.h index 873615c26d..9e483d5ace 100644 --- a/modules/isd/include/AmbiguousNOERestraint.h +++ b/modules/isd/include/AmbiguousNOERestraint.h @@ -40,8 +40,8 @@ class IMPISDEXPORT AmbiguousNOERestraint : public Restraint { double get_chi() const { return chi_; } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(AmbiguousNOERestraint); }; diff --git a/modules/isd/include/AmbiguousRestraint.h b/modules/isd/include/AmbiguousRestraint.h index 1e8c8c9e30..8d92013f9d 100644 --- a/modules/isd/include/AmbiguousRestraint.h +++ b/modules/isd/include/AmbiguousRestraint.h @@ -41,8 +41,8 @@ class IMPISDEXPORT AmbiguousRestraint : public Restraint { double get_probability() const { return exp(-unprotected_evaluate(nullptr)); } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(AmbiguousRestraint); }; diff --git a/modules/isd/include/AtomicCrossLinkMSRestraint.h b/modules/isd/include/AtomicCrossLinkMSRestraint.h index 2cf8a2d15c..7db0717557 100644 --- a/modules/isd/include/AtomicCrossLinkMSRestraint.h +++ b/modules/isd/include/AtomicCrossLinkMSRestraint.h @@ -62,8 +62,8 @@ class IMPISDEXPORT AtomicCrossLinkMSRestraint : public Restraint { ParticleIndex get_psi() const { return psi_; } virtual double unprotected_evaluate( - IMP::DerivativeAccumulator* accum) const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator* accum) const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; void show(std::ostream &out) const { out << "Atomic XL restraint with " <get_chiexp(); } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(TALOSRestraint); private: diff --git a/modules/isd/include/UniformPrior.h b/modules/isd/include/UniformPrior.h index 6bb05d061c..85ff1b5c7d 100644 --- a/modules/isd/include/UniformPrior.h +++ b/modules/isd/include/UniformPrior.h @@ -31,8 +31,8 @@ class IMPISDEXPORT UniformPrior : public Restraint virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(UniformPrior); /* call for probability */ @@ -42,10 +42,10 @@ class IMPISDEXPORT UniformPrior : public Restraint } //! \return Information for writing to RMF files - RestraintInfo *get_static_info() const IMP_OVERRIDE; + RestraintInfo *get_static_info() const override; //! \return Information for writing to RMF files - RestraintInfo *get_dynamic_info() const IMP_OVERRIDE; + RestraintInfo *get_dynamic_info() const override; }; diff --git a/modules/isd/include/Weight.h b/modules/isd/include/Weight.h index 3458de36a2..27ac39fd0c 100755 --- a/modules/isd/include/Weight.h +++ b/modules/isd/include/Weight.h @@ -156,10 +156,10 @@ class IMPISDEXPORT WeightSimplexConstraint : public IMP::Constraint { public: friend class Weight; - virtual void do_update_attributes() IMP_OVERRIDE; - virtual void do_update_derivatives(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_update_attributes() override; + virtual void do_update_derivatives(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(WeightSimplexConstraint); }; #endif diff --git a/modules/isd/include/WeightMover.h b/modules/isd/include/WeightMover.h index 7a2de229b4..484ba73334 100644 --- a/modules/isd/include/WeightMover.h +++ b/modules/isd/include/WeightMover.h @@ -28,9 +28,9 @@ class IMPISDEXPORT WeightMover : public core::MonteCarloMover { Float get_radius() { return radius_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(WeightMover); private: diff --git a/modules/isd/include/WeightRestraint.h b/modules/isd/include/WeightRestraint.h index ea2c783e67..546957f5fe 100644 --- a/modules/isd/include/WeightRestraint.h +++ b/modules/isd/include/WeightRestraint.h @@ -27,8 +27,8 @@ class IMPISDEXPORT WeightRestraint : public Restraint { WeightRestraint(Particle *w, Float wmin, Float wmax, Float kappa); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(WeightRestraint); }; diff --git a/modules/isd/include/bivariate_functions.h b/modules/isd/include/bivariate_functions.h index 1c1bbaa2bd..3d5def5012 100644 --- a/modules/isd/include/bivariate_functions.h +++ b/modules/isd/include/bivariate_functions.h @@ -134,7 +134,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { update(); } - bool has_changed() const IMP_OVERRIDE { + bool has_changed() const override { double tmpt = Scale(tau_).get_nuisance(); double tmpl = Scale(lambda_).get_nuisance(); IMP_LOG_VERBOSE("Covariance1DFunction: has_changed(): "); @@ -150,7 +150,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { } } - void update() IMP_OVERRIDE { + void update() override { lambda_val_ = Scale(lambda_).get_nuisance(); tau_val_ = Scale(tau_).get_nuisance(); IMP_LOG_TERSE("Covariance1DFunction: update() tau:= " @@ -162,14 +162,14 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { IMP_INTERNAL_CHECK(lambda_val_ != 0, "lambda is zero."); } - Floats operator()(const Floats& x1, const Floats& x2) const IMP_OVERRIDE { + Floats operator()(const Floats& x1, const Floats& x2) const override { IMP_USAGE_CHECK(x1.size() == 1, "expecting a 1-D vector"); IMP_USAGE_CHECK(x2.size() == 1, "expecting a 1-D vector"); Floats ret(1, get_value(x1[0], x2[0])); return ret; } - Eigen::MatrixXd operator()(const IMP::FloatsList& xlist) const IMP_OVERRIDE { + Eigen::MatrixXd operator()(const IMP::FloatsList& xlist) const override { const unsigned M = xlist.size(); Eigen::MatrixXd Mret(M, M); for (unsigned i = 0; i < M; i++) { @@ -186,7 +186,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { return Mret; } - FloatsList operator()(const IMP::FloatsList& xlist, bool) const IMP_OVERRIDE { + FloatsList operator()(const IMP::FloatsList& xlist, bool) const override { Eigen::MatrixXd mat((*this)(xlist)); FloatsList ret; for (unsigned i = 0; i < xlist.size(); i++) @@ -196,7 +196,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { } void add_to_derivatives(const Floats& x1, const Floats& x2, - DerivativeAccumulator& accum) const IMP_OVERRIDE { + DerivativeAccumulator& accum) const override { // d[w(x1,x2)]/dtau = 2/tau*(w(x1,x2)) double val = get_value(x1[0], x2[0]); double tauderiv = 2. / tau_val_ * val; @@ -213,7 +213,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { } void add_to_particle_derivative(unsigned particle_no, double value, - DerivativeAccumulator& accum) const IMP_OVERRIDE { + DerivativeAccumulator& accum) const override { switch (particle_no) { case 0: // tau IMP_INTERNAL_CHECK(!IMP::isnan(value), "tau derivative is nan."); @@ -229,7 +229,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { } Eigen::MatrixXd get_derivative_matrix(unsigned particle_no, - const FloatsList& xlist) const IMP_OVERRIDE { + const FloatsList& xlist) const override { // Strategy: fill in the main diagonal, then fill with zeros // if the value of the function falls below cutoff. // assumes data points are ordered! @@ -315,7 +315,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { } FloatsList get_derivative_matrix(unsigned particle_no, - const FloatsList& xlist, bool) const IMP_OVERRIDE { + const FloatsList& xlist, bool) const override { Eigen::MatrixXd mat(get_derivative_matrix(particle_no, xlist)); FloatsList ret; for (int i = 0; i < mat.rows(); i++) { @@ -328,7 +328,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { Eigen::MatrixXd get_second_derivative_matrix( unsigned particle_a, unsigned particle_b, - const FloatsList& xlist) const IMP_OVERRIDE { + const FloatsList& xlist) const override { unsigned N(xlist.size()); Eigen::MatrixXd ret(N, N); if (particle_a > 1) IMP_THROW("Invalid particle 1 number", ModelException); @@ -372,7 +372,7 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { FloatsList get_second_derivative_matrix( unsigned particle_a, unsigned particle_b, - const FloatsList& xlist, bool) const IMP_OVERRIDE { + const FloatsList& xlist, bool) const override { Eigen::MatrixXd mat( get_second_derivative_matrix(particle_a, particle_b, xlist)); FloatsList ret; @@ -384,13 +384,13 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { return ret; } - unsigned get_ndims_x1() const IMP_OVERRIDE { return 1; } - unsigned get_ndims_x2() const IMP_OVERRIDE { return 1; } - unsigned get_ndims_y() const IMP_OVERRIDE { return 1; } + unsigned get_ndims_x1() const override { return 1; } + unsigned get_ndims_x2() const override { return 1; } + unsigned get_ndims_y() const override { return 1; } - unsigned get_number_of_particles() const IMP_OVERRIDE { return 2; } + unsigned get_number_of_particles() const override { return 2; } - bool get_particle_is_optimized(unsigned particle_no) const IMP_OVERRIDE { + bool get_particle_is_optimized(unsigned particle_no) const override { switch (particle_no) { case 0: // tau return Scale(tau_).get_nuisance_is_optimized(); @@ -401,14 +401,14 @@ class IMPISDEXPORT Covariance1DFunction : public BivariateFunction { } } - unsigned get_number_of_optimized_particles() const IMP_OVERRIDE { + unsigned get_number_of_optimized_particles() const override { unsigned count = 0; if (Scale(tau_).get_nuisance_is_optimized()) count++; if (Scale(lambda_).get_nuisance_is_optimized()) count++; return count; } - ModelObjectsTemp get_inputs() const IMP_OVERRIDE { + ModelObjectsTemp get_inputs() const override { ModelObjectsTemp ret; ret.push_back(tau_); ret.push_back(lambda_); diff --git a/modules/isd/include/univariate_functions.h b/modules/isd/include/univariate_functions.h index 56f9b79932..d38f56164a 100644 --- a/modules/isd/include/univariate_functions.h +++ b/modules/isd/include/univariate_functions.h @@ -117,7 +117,7 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { update(); } - bool has_changed() const IMP_OVERRIDE { + bool has_changed() const override { double tmpa = Nuisance(a_).get_nuisance(); double tmpb = Nuisance(b_).get_nuisance(); if ((std::abs(tmpa - a_val_) > IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM) || @@ -130,20 +130,20 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { } } - void update() IMP_OVERRIDE { + void update() override { a_val_ = Nuisance(a_).get_nuisance(); b_val_ = Nuisance(b_).get_nuisance(); IMP_LOG_TERSE("Linear1DFunction: update() a:= " << a_val_ << " b:=" << b_val_ << std::endl); } - Floats operator()(const Floats& x) const IMP_OVERRIDE { + Floats operator()(const Floats& x) const override { IMP_USAGE_CHECK(x.size() == 1, "expecting a 1-D vector"); Floats ret(1, a_val_ * x[0] + b_val_); return ret; } - Eigen::VectorXd operator()(const FloatsList& xlist) const IMP_OVERRIDE { + Eigen::VectorXd operator()(const FloatsList& xlist) const override { unsigned M = xlist.size(); Eigen::VectorXd retlist(M); for (unsigned i = 0; i < M; i++) { @@ -153,7 +153,7 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { return retlist; } - FloatsList operator()(const FloatsList& xlist, bool) const IMP_OVERRIDE { + FloatsList operator()(const FloatsList& xlist, bool) const override { Eigen::VectorXd vec((*this)(xlist)); FloatsList ret; for (unsigned i = 0; i < xlist.size(); i++) @@ -162,7 +162,7 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { } void add_to_derivatives(const Floats& x, - DerivativeAccumulator& accum) const IMP_OVERRIDE { + DerivativeAccumulator& accum) const override { // d[f(x)]/da = x Nuisance(a_).add_to_nuisance_derivative(x[0], accum); // d[f(x)]/db = 1 @@ -170,7 +170,7 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { } void add_to_particle_derivative(unsigned particle_no, double value, - DerivativeAccumulator& accum) const IMP_OVERRIDE { + DerivativeAccumulator& accum) const override { switch (particle_no) { case 0: Nuisance(a_).add_to_nuisance_derivative(value, accum); @@ -184,7 +184,7 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { } Eigen::VectorXd get_derivative_vector(unsigned particle_no, - const FloatsList& xlist) const IMP_OVERRIDE { + const FloatsList& xlist) const override { unsigned N = xlist.size(); Eigen::VectorXd ret(N); switch (particle_no) { @@ -201,7 +201,7 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { } FloatsList get_derivative_matrix( - const FloatsList& xlist, bool) const IMP_OVERRIDE { + const FloatsList& xlist, bool) const override { Eigen::MatrixXd mat(xlist.size(), 2); mat.col(0) = get_derivative_vector(0, xlist); mat.col(1) = get_derivative_vector(1, xlist); @@ -215,7 +215,7 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { } Eigen::VectorXd get_second_derivative_vector( - unsigned, unsigned, const FloatsList& xlist) const IMP_OVERRIDE { + unsigned, unsigned, const FloatsList& xlist) const override { // The Hessian is zero for all particles. unsigned N = xlist.size(); Eigen::VectorXd H(Eigen::VectorXd::Zero(N)); @@ -224,7 +224,7 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { FloatsList get_second_derivative_vector( unsigned particle_a, unsigned particle_b, - const FloatsList& xlist, bool) const IMP_OVERRIDE { + const FloatsList& xlist, bool) const override { Eigen::VectorXd mat( get_second_derivative_vector(particle_a, particle_b, xlist)); FloatsList ret; @@ -236,12 +236,12 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { return ret; } - unsigned get_ndims_x() const IMP_OVERRIDE { return 1; } - unsigned get_ndims_y() const IMP_OVERRIDE { return 1; } + unsigned get_ndims_x() const override { return 1; } + unsigned get_ndims_y() const override { return 1; } - unsigned get_number_of_particles() const IMP_OVERRIDE { return 2; } + unsigned get_number_of_particles() const override { return 2; } - bool get_particle_is_optimized(unsigned particle_no) const IMP_OVERRIDE { + bool get_particle_is_optimized(unsigned particle_no) const override { switch (particle_no) { case 0: // a return Nuisance(a_).get_nuisance_is_optimized(); @@ -252,14 +252,14 @@ class IMPISDEXPORT Linear1DFunction : public UnivariateFunction { } } - unsigned get_number_of_optimized_particles() const IMP_OVERRIDE { + unsigned get_number_of_optimized_particles() const override { unsigned count = 0; if (Nuisance(a_).get_nuisance_is_optimized()) count++; if (Nuisance(b_).get_nuisance_is_optimized()) count++; return count; } - ModelObjectsTemp get_inputs() const IMP_OVERRIDE { + ModelObjectsTemp get_inputs() const override { ModelObjectsTemp ret; ret.push_back(a_); ret.push_back(b_); @@ -301,7 +301,7 @@ class IMPISDEXPORT GeneralizedGuinierPorodFunction : public UnivariateFunction { update(); } - bool has_changed() const IMP_OVERRIDE { + bool has_changed() const override { double tmpG = Scale(G_).get_scale(); double tmpRg = Scale(Rg_).get_scale(); double tmpd = Scale(d_).get_scale(); @@ -320,7 +320,7 @@ class IMPISDEXPORT GeneralizedGuinierPorodFunction : public UnivariateFunction { } } - void update() IMP_OVERRIDE { + void update() override { G_val_ = Scale(G_).get_scale(); Rg_val_ = Scale(Rg_).get_scale(); d_val_ = Scale(d_).get_scale(); @@ -354,13 +354,13 @@ class IMPISDEXPORT GeneralizedGuinierPorodFunction : public UnivariateFunction { <= 5) IMP_THROW("Invalid particle 1 number", ModelException); if (particle_b >= 5) IMP_THROW("Invalid particle 2 number", ModelException); unsigned N = xlist.size(); @@ -717,7 +717,7 @@ class IMPISDEXPORT GeneralizedGuinierPorodFunction : public UnivariateFunction { FloatsList get_second_derivative_vector( unsigned particle_a, unsigned particle_b, - const FloatsList& xlist, bool) const IMP_OVERRIDE { + const FloatsList& xlist, bool) const override { Eigen::VectorXd mat( get_second_derivative_vector(particle_a, particle_b, xlist)); FloatsList ret; @@ -729,12 +729,12 @@ class IMPISDEXPORT GeneralizedGuinierPorodFunction : public UnivariateFunction { return ret; } - unsigned get_ndims_x() const IMP_OVERRIDE { return 1; } - unsigned get_ndims_y() const IMP_OVERRIDE { return 1; } + unsigned get_ndims_x() const override { return 1; } + unsigned get_ndims_y() const override { return 1; } - unsigned get_number_of_particles() const IMP_OVERRIDE { return 5; } + unsigned get_number_of_particles() const override { return 5; } - bool get_particle_is_optimized(unsigned particle_no) const IMP_OVERRIDE { + bool get_particle_is_optimized(unsigned particle_no) const override { switch (particle_no) { case 0: // G return Scale(G_).get_scale_is_optimized(); @@ -751,7 +751,7 @@ class IMPISDEXPORT GeneralizedGuinierPorodFunction : public UnivariateFunction { } } - unsigned get_number_of_optimized_particles() const IMP_OVERRIDE { + unsigned get_number_of_optimized_particles() const override { unsigned count = 0; if (Scale(G_).get_scale_is_optimized()) count++; if (Scale(Rg_).get_scale_is_optimized()) count++; @@ -761,7 +761,7 @@ class IMPISDEXPORT GeneralizedGuinierPorodFunction : public UnivariateFunction { return count; } - ModelObjectsTemp get_inputs() const IMP_OVERRIDE { + ModelObjectsTemp get_inputs() const override { ModelObjectsTemp ret; ret.push_back(G_); ret.push_back(Rg_); diff --git a/modules/isd/include/vonMisesKappaConjugateRestraint.h b/modules/isd/include/vonMisesKappaConjugateRestraint.h index f6e5201042..ebbcebd341 100644 --- a/modules/isd/include/vonMisesKappaConjugateRestraint.h +++ b/modules/isd/include/vonMisesKappaConjugateRestraint.h @@ -33,8 +33,8 @@ class IMPISDEXPORT vonMisesKappaConjugateRestraint : public Restraint { double c = 10.0, double R0 = 0.0); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(vonMisesKappaConjugateRestraint); virtual double get_probability() const; diff --git a/modules/isd/include/vonMisesKappaJeffreysRestraint.h b/modules/isd/include/vonMisesKappaJeffreysRestraint.h index 2c24566f56..95664cf35e 100644 --- a/modules/isd/include/vonMisesKappaJeffreysRestraint.h +++ b/modules/isd/include/vonMisesKappaJeffreysRestraint.h @@ -34,8 +34,8 @@ class IMPISDEXPORT vonMisesKappaJeffreysRestraint : public Restraint { vonMisesKappaJeffreysRestraint(Model *m, Particle *kappa); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(vonMisesKappaJeffreysRestraint); virtual double get_probability() const; diff --git a/modules/kernel/include/ConfigurationSet.h b/modules/kernel/include/ConfigurationSet.h index 26787e6285..f3deed257c 100644 --- a/modules/kernel/include/ConfigurationSet.h +++ b/modules/kernel/include/ConfigurationSet.h @@ -54,7 +54,7 @@ class IMPKERNELEXPORT SaveToConfigurationSetOptimizerState SaveToConfigurationSetOptimizerState(ConfigurationSet *cs); protected: - virtual void do_update(unsigned int update_number) IMP_OVERRIDE; + virtual void do_update(unsigned int update_number) override; IMP_OBJECT_METHODS(SaveToConfigurationSetOptimizerState); }; diff --git a/modules/kernel/include/Constraint.h b/modules/kernel/include/Constraint.h index 5933fc54bf..61c5e12ad0 100644 --- a/modules/kernel/include/Constraint.h +++ b/modules/kernel/include/Constraint.h @@ -52,8 +52,8 @@ class IMPKERNELEXPORT Constraint : public ScoreState { virtual void do_update_attributes() = 0; virtual void do_update_derivatives(DerivativeAccumulator *da) = 0; - virtual void do_before_evaluate() IMP_OVERRIDE { do_update_attributes(); } - virtual void do_after_evaluate(DerivativeAccumulator *da) IMP_OVERRIDE { + virtual void do_before_evaluate() override { do_update_attributes(); } + virtual void do_after_evaluate(DerivativeAccumulator *da) override { if (da) do_update_derivatives(da); } IMP_REF_COUNTED_DESTRUCTOR(Constraint); diff --git a/modules/kernel/include/Model.h b/modules/kernel/include/Model.h index 1c4b65a213..600fbd4011 100644 --- a/modules/kernel/include/Model.h +++ b/modules/kernel/include/Model.h @@ -426,7 +426,7 @@ class IMPKERNELEXPORT Model : public Object public: #if !defined(IMP_DOXYGEN) - virtual void do_destroy() IMP_OVERRIDE; + virtual void do_destroy() override; #endif }; diff --git a/modules/kernel/include/ModelObject.h b/modules/kernel/include/ModelObject.h index 6db7b332c8..634bc99aea 100644 --- a/modules/kernel/include/ModelObject.h +++ b/modules/kernel/include/ModelObject.h @@ -66,7 +66,7 @@ class IMPKERNELEXPORT ModelObject : public Object { const ScoreStatesTemp &get_required_score_states() const; protected: - // virtual void do_destroy() IMP_OVERRIDE {set_has_dependencies(false);} + // virtual void do_destroy() override {set_has_dependencies(false);} /** Called when set_has_required_score_states() is called.*/ virtual void handle_set_has_required_score_states(bool) {} /** Get any Particle, Container or other ModelObjects read by diff --git a/modules/kernel/include/Optimizer.h b/modules/kernel/include/Optimizer.h index 53f8a3e9cd..13a7cacd37 100644 --- a/modules/kernel/include/Optimizer.h +++ b/modules/kernel/include/Optimizer.h @@ -56,12 +56,12 @@ class IMPKERNELEXPORT Optimizer : public ModelObject { void set_is_optimizing_states(bool tf) const; #endif ModelObjectsTemp get_optimizer_state_inputs() const; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { return get_optimizer_state_inputs(); } //! don't return anything here to avoid pointless dependencies - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_outputs() const override { return ModelObjectsTemp(); } diff --git a/modules/kernel/include/OptimizerState.h b/modules/kernel/include/OptimizerState.h index d36bf0f72e..cfeded58b0 100644 --- a/modules/kernel/include/OptimizerState.h +++ b/modules/kernel/include/OptimizerState.h @@ -121,10 +121,10 @@ class IMPKERNELEXPORT OptimizerState : public ModelObject { virtual void do_set_is_optimizing(bool) {} - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { return ModelObjectsTemp(); } - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE IMP_FINAL { + virtual ModelObjectsTemp do_get_outputs() const override IMP_FINAL { return ModelObjectsTemp(); } diff --git a/modules/kernel/include/Particle.h b/modules/kernel/include/Particle.h index b64ba64340..ae2655eb87 100644 --- a/modules/kernel/include/Particle.h +++ b/modules/kernel/include/Particle.h @@ -136,13 +136,13 @@ class IMPKERNELEXPORT Particle : public ModelObject { ParticleIndex get_index() const; #if !defined(IMP_DOXYGEN) - void clear_caches() IMP_OVERRIDE; + void clear_caches() override; #endif protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE IMP_FINAL { + virtual ModelObjectsTemp do_get_inputs() const override IMP_FINAL { return ModelObjectsTemp(); } - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE IMP_FINAL { + virtual ModelObjectsTemp do_get_outputs() const override IMP_FINAL { return ModelObjectsTemp(); } }; diff --git a/modules/kernel/include/Restraint.h b/modules/kernel/include/Restraint.h index 3c6fdb2525..0ebcd07f95 100644 --- a/modules/kernel/include/Restraint.h +++ b/modules/kernel/include/Restraint.h @@ -315,7 +315,7 @@ class IMPKERNELEXPORT Restraint : public ModelObject { const ParticleIndexes &reset_pis) const; /** No outputs. */ - ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + ModelObjectsTemp do_get_outputs() const override { return ModelObjectsTemp(); } diff --git a/modules/kernel/include/RestraintSet.h b/modules/kernel/include/RestraintSet.h index 93b55f7f0e..041a29640e 100644 --- a/modules/kernel/include/RestraintSet.h +++ b/modules/kernel/include/RestraintSet.h @@ -50,7 +50,7 @@ class IMPKERNELEXPORT RestraintSet : public Restraint { RestraintSet(const RestraintsTemp &rs, double weight, const std::string &name = "RestraintSet %1%"); - double unprotected_evaluate(DerivativeAccumulator *da) const IMP_OVERRIDE; + double unprotected_evaluate(DerivativeAccumulator *da) const override; IMP_OBJECT_METHODS(RestraintSet); /** @name Methods to control the nested Restraint objects @@ -72,22 +72,22 @@ class IMPKERNELEXPORT RestraintSet : public Restraint { public: #ifndef IMP_DOXYGEN - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + ModelObjectsTemp do_get_inputs() const override; ScoringFunction *create_scoring_function( double weight = 1.0, - double max = std::numeric_limits::max()) const IMP_OVERRIDE; + double max = std::numeric_limits::max()) const override; #endif - double get_last_score() const IMP_OVERRIDE; - double get_last_last_score() const IMP_OVERRIDE; + double get_last_score() const override; + double get_last_last_score() const override; #if !defined(IMP_DOXYGEN) && !defined(SWIG) protected: - Restraints do_create_decomposition() const IMP_OVERRIDE; - Restraints do_create_current_decomposition() const IMP_OVERRIDE; - void do_add_score_and_derivatives(ScoreAccumulator sa) const IMP_OVERRIDE; + Restraints do_create_decomposition() const override; + Restraints do_create_current_decomposition() const override; + void do_add_score_and_derivatives(ScoreAccumulator sa) const override; void do_add_score_and_derivatives_moved( ScoreAccumulator sa, const ParticleIndexes &moved_pis, - const ParticleIndexes &reset_pis) const IMP_OVERRIDE; + const ParticleIndexes &reset_pis) const override; #endif }; diff --git a/modules/kernel/include/ScoreState.h b/modules/kernel/include/ScoreState.h index 37ee2ef749..e1bfbc63fc 100644 --- a/modules/kernel/include/ScoreState.h +++ b/modules/kernel/include/ScoreState.h @@ -84,7 +84,7 @@ class IMPKERNELEXPORT ScoreState : public ModelObject { #ifndef IMP_DOXYGEN bool get_has_update_order() const { return update_order_ != -1; } unsigned int get_update_order() const { return update_order_; } - virtual void handle_set_has_required_score_states(bool tf) IMP_OVERRIDE; + virtual void handle_set_has_required_score_states(bool tf) override; #endif diff --git a/modules/kernel/include/ScoringFunction.h b/modules/kernel/include/ScoringFunction.h index e9f6964022..91d2adde1f 100644 --- a/modules/kernel/include/ScoringFunction.h +++ b/modules/kernel/include/ScoringFunction.h @@ -86,7 +86,7 @@ class IMPKERNELEXPORT ScoringFunction : public ModelObject { public: ScoringFunction(Model *m, std::string name); - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_outputs() const override { return ModelObjectsTemp(); } diff --git a/modules/kernel/include/compiler_macros.h b/modules/kernel/include/compiler_macros.h index 27dfe212cc..3e9e3fb004 100644 --- a/modules/kernel/include/compiler_macros.h +++ b/modules/kernel/include/compiler_macros.h @@ -60,28 +60,12 @@ #define IMP_RESTRICT #endif -#if defined(__clang__) && __clang_major__ >= 5 -#define IMP_COMPILER_HAS_OVERRIDE 1 -#elif !defined(__clang__) && defined(__GNUC__) && __cplusplus >= 201103L -// probably should be finer here -#define IMP_COMPILER_HAS_OVERRIDE 1 -#else -#define IMP_COMPILER_HAS_OVERRIDE 0 -#endif +// Deprecated: just use the 'override' keyword directly #ifdef IMP_DOXYGEN -//! Cause a compile error if this method does not override a parent method -/** This is helpful to catch accidental mismatches of call signatures between - the method and the parent method, which would cause the method to be - overloaded rather than overridden. Usually this macro should be used - whenever implementing a method that is declared virtual in the parent. */ #define IMP_OVERRIDE #else -#if IMP_COMPILER_HAS_OVERRIDE #define IMP_OVERRIDE override -#else -#define IMP_OVERRIDE -#endif #endif #if defined(IMP_SWIG_WRAPPER) diff --git a/modules/kernel/include/container_base.h b/modules/kernel/include/container_base.h index eae19a4485..40b2d771af 100644 --- a/modules/kernel/include/container_base.h +++ b/modules/kernel/include/container_base.h @@ -64,7 +64,7 @@ class IMPKERNELEXPORT Container : public ModelObject { std::size_t get_contents_hash() const { return do_get_contents_hash(); } //! containers don't have outputs - ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + ModelObjectsTemp do_get_outputs() const override { return ModelObjectsTemp(); } diff --git a/modules/kernel/include/doxygen_macros.h b/modules/kernel/include/doxygen_macros.h index f9689b91c8..6ee19d46a3 100644 --- a/modules/kernel/include/doxygen_macros.h +++ b/modules/kernel/include/doxygen_macros.h @@ -9,7 +9,7 @@ #ifndef IMPKERNEL_DOXYGEN_MACROS_H #define IMPKERNEL_DOXYGEN_MACROS_H #include -// for IMP_OVERRIDE +// for override #include "swig_macros.h" #ifdef IMP_DOXYGEN @@ -48,11 +48,11 @@ #define IMP_IMPLEMENT(signature) signature #define IMP_IMPLEMENT_INLINE(signature, body) \ - signature IMP_OVERRIDE { body; } + signature override { body; } #ifndef SWIG #define IMP_IMPLEMENT_INLINE_NO_SWIG(signature, body) \ - signature IMP_OVERRIDE { body; } + signature override { body; } #else #define IMP_IMPLEMENT_INLINE_NO_SWIG(signature, body) @@ -60,13 +60,13 @@ #define IMP_IMPLEMENTATION_TEMPLATE_1(arg0, signature, body) \ template \ - signature IMP_OVERRIDE { \ + signature override { \ body \ } #define IMP_IMPLEMENTATION_TEMPLATE_2(arg0, arg1, signature, body) \ template \ - signature IMP_OVERRIDE { \ + signature override { \ body \ } diff --git a/modules/kernel/include/internal/AccumulatorScoreModifier.h b/modules/kernel/include/internal/AccumulatorScoreModifier.h index 47412e2a1f..be2d58c176 100644 --- a/modules/kernel/include/internal/AccumulatorScoreModifier.h +++ b/modules/kernel/include/internal/AccumulatorScoreModifier.h @@ -157,7 +157,7 @@ class AccumulatorScoreModifier : public Score::Modifier { } virtual void apply_index(Model *m, typename Score::PassIndexArgument a) const - IMP_OVERRIDE { + override { double score = (ss_->evaluate_index(m, a, sa_.get_derivative_accumulator())); IMP_OMP_PRAGMA(atomic) @@ -167,7 +167,7 @@ class AccumulatorScoreModifier : public Score::Modifier { virtual void apply_indexes( Model *m, const Vector &a, - unsigned int lower_bound, unsigned int upper_bound) const IMP_OVERRIDE { + unsigned int lower_bound, unsigned int upper_bound) const override { double score = ss_->evaluate_indexes(m, a, sa_.get_derivative_accumulator(), lower_bound, upper_bound); IMP_OMP_PRAGMA(atomic) @@ -179,7 +179,7 @@ class AccumulatorScoreModifier : public Score::Modifier { Model *m, const Vector &a, unsigned int lower_bound, unsigned int upper_bound, const ParticleIndexes &moved_pis, - const ParticleIndexes &reset_pis) const IMP_OVERRIDE { + const ParticleIndexes &reset_pis) const override { // Only support moved speedups when evaluating the entire container, // and without derivatives, for now if (lower_bound != 0 || upper_bound != a.size() @@ -271,13 +271,13 @@ class AccumulatorScoreModifier : public Score::Modifier { virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const - IMP_OVERRIDE { + override { return ss_->get_inputs(m, pis); } virtual ModelObjectsTemp do_get_outputs(Model *, const ParticleIndexes &) const - IMP_OVERRIDE { + override { return ModelObjectsTemp(); } diff --git a/modules/kernel/include/internal/ContainerConstraint.h b/modules/kernel/include/internal/ContainerConstraint.h index 66ab6146f7..6d01be97f6 100644 --- a/modules/kernel/include/internal/ContainerConstraint.h +++ b/modules/kernel/include/internal/ContainerConstraint.h @@ -37,7 +37,7 @@ class ContainerConstraint : public Constraint { void set_before_evaluate_modifier(Before *f) { f_ = f; } // only report actual interactions - ModelObjectsTemps do_get_interactions() const IMP_OVERRIDE { + ModelObjectsTemps do_get_interactions() const override { ModelObjectsTemps ret; typename Container::ContainedIndexTypes ps = c_->get_range_indexes(); for (unsigned int i = 0; i < ps.size(); ++i) { @@ -64,10 +64,10 @@ class ContainerConstraint : public Constraint { } protected: - virtual void do_update_attributes() IMP_OVERRIDE; - virtual void do_update_derivatives(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_update_attributes() override; + virtual void do_update_derivatives(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(ContainerConstraint); ; }; diff --git a/modules/kernel/include/internal/ContainerRestraint.h b/modules/kernel/include/internal/ContainerRestraint.h index d67d867bf1..6aae3c34a4 100644 --- a/modules/kernel/include/internal/ContainerRestraint.h +++ b/modules/kernel/include/internal/ContainerRestraint.h @@ -32,13 +32,13 @@ class ContainerRestraint : public Restraint { public: void do_add_score_and_derivatives(IMP::ScoreAccumulator sa) const - IMP_OVERRIDE; + override; void do_add_score_and_derivatives_moved(IMP::ScoreAccumulator sa, const ParticleIndexes &moved_pis, - const ParticleIndexes &reset_pis) const IMP_OVERRIDE; + const ParticleIndexes &reset_pis) const override; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ContainerRestraint); ; @@ -49,10 +49,10 @@ class ContainerRestraint : public Restraint { Score *get_score() const { return acc_->get_score_object(); } - Restraints do_create_decomposition() const IMP_OVERRIDE; - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + Restraints do_create_decomposition() const override; + Restraints do_create_current_decomposition() const override; - IMP_IMPLEMENT(double get_last_score() const IMP_OVERRIDE;); + IMP_IMPLEMENT(double get_last_score() const override;); }; /** Helper to create a ContainerRestraint without specifying the types. Make diff --git a/modules/kernel/include/internal/ContainerScoreState.h b/modules/kernel/include/internal/ContainerScoreState.h index 60cf36aef5..907199fa2a 100644 --- a/modules/kernel/include/internal/ContainerScoreState.h +++ b/modules/kernel/include/internal/ContainerScoreState.h @@ -25,21 +25,21 @@ class ContainerScoreState : public ScoreState { ContainerScoreState(Container *back) : ScoreState(back->get_model(), back->get_name() + "State"), back_(back) {} - virtual void do_before_evaluate() IMP_OVERRIDE { + virtual void do_before_evaluate() override { IMP_CHECK_OBJECT(back_); return back_->do_score_state_before_evaluate(); } - virtual void do_after_evaluate(DerivativeAccumulator *) IMP_OVERRIDE { + virtual void do_after_evaluate(DerivativeAccumulator *) override { back_->do_score_state_after_evaluate(); } - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { IMP_CHECK_OBJECT(back_); return back_->get_score_state_inputs(); } - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_outputs() const override { IMP_CHECK_OBJECT(back_); return ModelObjectsTemp(1, back_); } diff --git a/modules/kernel/include/internal/DynamicListContainer.h b/modules/kernel/include/internal/DynamicListContainer.h index 38c62b2090..9ba72cebb2 100644 --- a/modules/kernel/include/internal/DynamicListContainer.h +++ b/modules/kernel/include/internal/DynamicListContainer.h @@ -58,14 +58,14 @@ class DynamicListContainer : public ListLikeContainer { typename Base::ContainedIndexTypes t; P::swap(t); } - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE { + virtual ParticleIndexes get_all_possible_indexes() const override { return scope_->get_all_possible_indexes(); } - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { return ModelObjectsTemp(1, scope_); } virtual typename Base::ContainedIndexTypes get_range_indexes() const - IMP_OVERRIDE { + override { return P::get_indexes(); } IMP_OBJECT_METHODS(DynamicListContainer); diff --git a/modules/kernel/include/internal/ListLikeContainer.h b/modules/kernel/include/internal/ListLikeContainer.h index a62fecb5f7..2b23393272 100644 --- a/modules/kernel/include/internal/ListLikeContainer.h +++ b/modules/kernel/include/internal/ListLikeContainer.h @@ -25,7 +25,7 @@ class ListLikeContainer : public Base { private: std::size_t version_; typename Base::ContainedIndexTypes data_; - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE { + virtual std::size_t do_get_contents_hash() const override { return version_; } @@ -88,24 +88,24 @@ class ListLikeContainer : public Base { //! apply sm->apply_indexes to data. Use parallel mode using IMP_TASK //! if get_number_of_threads()>=2 - void do_apply(const typename Base::Modifier *sm) const IMP_OVERRIDE { + void do_apply(const typename Base::Modifier *sm) const override { apply_generic(sm); } void do_apply_moved(const typename Base::Modifier *sm, const ParticleIndexes &moved_pis, - const ParticleIndexes &reset_pis) const IMP_OVERRIDE { + const ParticleIndexes &reset_pis) const override { apply_generic_moved(sm, moved_pis, reset_pis); } //! returns a copy of list indexes of appropriate type - typename Base::ContainedIndexTypes get_indexes() const IMP_OVERRIDE { + typename Base::ContainedIndexTypes get_indexes() const override { return data_; } - bool do_get_provides_access() const IMP_OVERRIDE { return true; } + bool do_get_provides_access() const override { return true; } //! direct access to contained data (which may or may not be properly updated) - const typename Base::ContainedIndexTypes &get_access() const IMP_OVERRIDE { + const typename Base::ContainedIndexTypes &get_access() const override { return data_; } diff --git a/modules/kernel/include/internal/RestraintsScoringFunction.h b/modules/kernel/include/internal/RestraintsScoringFunction.h index 7f4fbb9071..5bf57d4cb0 100644 --- a/modules/kernel/include/internal/RestraintsScoringFunction.h +++ b/modules/kernel/include/internal/RestraintsScoringFunction.h @@ -46,7 +46,7 @@ class GenericRestraintsScoringFunction : public ScoringFunction { restraints_(rs.begin(), rs.end()) {} void do_add_score_and_derivatives(IMP::ScoreAccumulator sa, - const ScoreStatesTemp &ss) IMP_OVERRIDE { + const ScoreStatesTemp &ss) override { IMP_OBJECT_LOG; protected_evaluate(sa, restraints_, ss, get_model()); } @@ -54,20 +54,20 @@ class GenericRestraintsScoringFunction : public ScoringFunction { void do_add_score_and_derivatives_moved(IMP::ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, - const ScoreStatesTemp &ss) IMP_OVERRIDE { + const ScoreStatesTemp &ss) override { IMP_OBJECT_LOG; protected_evaluate_moved(sa, restraints_, moved_pis, reset_pis, ss, get_model()); } - Restraints create_restraints() const IMP_OVERRIDE { + Restraints create_restraints() const override { IMP_OBJECT_LOG; IMP_NEW(RestraintSet, rs, (get_model(), weight_, get_name() + " wrapper")); rs->set_maximum_score(max_); rs->add_restraints(restraints_); return Restraints(1, rs); } - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { return restraints_; } + ModelObjectsTemp do_get_inputs() const override { return restraints_; } const Storage &get_restraints() const { return restraints_; } void set_restraints(const RestraintsTemp &s) { set_has_dependencies(false); diff --git a/modules/kernel/include/internal/StaticListContainer.h b/modules/kernel/include/internal/StaticListContainer.h index bda4949398..05a397f2df 100644 --- a/modules/kernel/include/internal/StaticListContainer.h +++ b/modules/kernel/include/internal/StaticListContainer.h @@ -53,14 +53,14 @@ class StaticListContainer : public ListLikeContainer { typename Base::ContainedIndexTypes t; P::swap(t); } - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE { + virtual ParticleIndexes get_all_possible_indexes() const override { return flatten(P::get_indexes()); } - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + virtual ModelObjectsTemp do_get_inputs() const override { return ModelObjectsTemp(); } virtual typename Base::ContainedIndexTypes get_range_indexes() const - IMP_OVERRIDE { + override { return P::get_indexes(); } IMP_OBJECT_METHODS(StaticListContainer); diff --git a/modules/kernel/include/internal/TupleConstraint.h b/modules/kernel/include/internal/TupleConstraint.h index 3635da9e5d..014bf4fe1f 100644 --- a/modules/kernel/include/internal/TupleConstraint.h +++ b/modules/kernel/include/internal/TupleConstraint.h @@ -43,10 +43,10 @@ class TupleConstraint : public Constraint { } protected: - virtual void do_update_attributes() IMP_OVERRIDE; - virtual void do_update_derivatives(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_update_attributes() override; + virtual void do_update_derivatives(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(TupleConstraint); ; }; diff --git a/modules/kernel/include/internal/TupleRestraint.h b/modules/kernel/include/internal/TupleRestraint.h index b0e2f2988b..b8515be971 100644 --- a/modules/kernel/include/internal/TupleRestraint.h +++ b/modules/kernel/include/internal/TupleRestraint.h @@ -36,11 +36,11 @@ class TupleRestraint : public Restraint { } public: - double unprotected_evaluate(DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + double unprotected_evaluate(DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(TupleRestraint); ; - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + Restraints do_create_current_decomposition() const override; }; template diff --git a/modules/kernel/include/internal/scoring_functions.h b/modules/kernel/include/internal/scoring_functions.h index 5238122e3d..2b4a008ffb 100644 --- a/modules/kernel/include/internal/scoring_functions.h +++ b/modules/kernel/include/internal/scoring_functions.h @@ -51,13 +51,13 @@ class RestraintScoringFunction : public ScoringFunction { RestraintScoringFunction(RestraintType *r, std::string name) : ScoringFunction(IMP::internal::get_model(r), name), r_(r) {} void do_add_score_and_derivatives(IMP::ScoreAccumulator sa, - const ScoreStatesTemp &ss) IMP_OVERRIDE; + const ScoreStatesTemp &ss) override; void do_add_score_and_derivatives_moved(IMP::ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, - const ScoreStatesTemp &ss) IMP_OVERRIDE; - Restraints create_restraints() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const ScoreStatesTemp &ss) override; + Restraints create_restraints() const override; + virtual ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(RestraintScoringFunction); }; @@ -108,9 +108,9 @@ class WrappedRestraintScoringFunction : public ScoringFunction { weight_(weight), max_(max) {} void do_add_score_and_derivatives(IMP::ScoreAccumulator sa, - const ScoreStatesTemp &ss) IMP_OVERRIDE; - Restraints create_restraints() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const ScoreStatesTemp &ss) override; + Restraints create_restraints() const override; + virtual ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(WrappedRestraintScoringFunction); }; diff --git a/modules/kernel/include/internal/swig.h b/modules/kernel/include/internal/swig.h index 2467dcfeef..029eaa8c0b 100644 --- a/modules/kernel/include/internal/swig.h +++ b/modules/kernel/include/internal/swig.h @@ -38,10 +38,10 @@ class IMPKERNELEXPORT _ConstRestraint : public Restraint { _ConstRestraint(Model *m, const ParticleIndexes &pis, double v) : Restraint(m, "ConstRestraint%1%"), v_(v), ps_(get_particles(m, pis)) {} double get_value() const { return v_; } - Restraints do_create_decomposition() const IMP_OVERRIDE; + Restraints do_create_decomposition() const override; double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const - IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(_ConstRestraint); }; @@ -53,11 +53,11 @@ class _ConstSingletonScore : public SingletonScore { public: _ConstSingletonScore(double v) : v_(v) {} virtual double evaluate_index(Model *, ParticleIndex, - DerivativeAccumulator *) const IMP_OVERRIDE { + DerivativeAccumulator *) const override { return v_; } virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const - IMP_OVERRIDE { + override { return ModelObjectsTemp(); } IMP_SINGLETON_SCORE_METHODS(_ConstSingletonScore); @@ -71,11 +71,11 @@ class IMPKERNELEXPORT _ConstPairScore : public PairScore { public: _ConstPairScore(double v) : v_(v) {} virtual double evaluate_index(Model *, const ParticleIndexPair &, - DerivativeAccumulator *) const IMP_OVERRIDE { + DerivativeAccumulator *) const override { return v_; } virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const - IMP_OVERRIDE { + override { return ModelObjectsTemp(); } IMP_PAIR_SCORE_METHODS(_ConstPairScore); @@ -129,7 +129,7 @@ IMP_DECORATORS_WITH_TRAITS(_TrivialTraitsDecorator, _TrivialTraitsDecorators, class IMPKERNELEXPORT _ConstOptimizer : public Optimizer { public: _ConstOptimizer(Model *m) : Optimizer(m, "ConstOptimizer%1%") {} - virtual Float do_optimize(unsigned int max_steps) IMP_OVERRIDE; + virtual Float do_optimize(unsigned int max_steps) override; IMP_OBJECT_METHODS(_ConstOptimizer); }; @@ -198,9 +198,9 @@ class IMPKERNELEXPORT _LogPairScore : public PairScore { //! create with an empty map _LogPairScore() {} virtual double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs(Model *, const ParticleIndexes &) const - IMP_OVERRIDE { + override { return ModelObjectsTemp(); } IMP_PAIR_SCORE_METHODS(_LogPairScore); diff --git a/modules/kernel/include/object_macros.h b/modules/kernel/include/object_macros.h index bac3751e87..1c8726ecc0 100644 --- a/modules/kernel/include/object_macros.h +++ b/modules/kernel/include/object_macros.h @@ -24,8 +24,8 @@ */ #define IMP_OBJECT_METHODS(Name) \ public: \ - virtual std::string get_type_name() const IMP_OVERRIDE { return #Name; } \ - virtual ::IMP::VersionInfo get_version_info() const IMP_OVERRIDE { \ + virtual std::string get_type_name() const override { return #Name; } \ + virtual ::IMP::VersionInfo get_version_info() const override { \ return ::IMP::VersionInfo(get_module_name(), get_module_version()); \ } \ \ diff --git a/modules/kernel/src/ScoringFunction.cpp b/modules/kernel/src/ScoringFunction.cpp index 23c5ae365d..6ccb7b9654 100644 --- a/modules/kernel/src/ScoringFunction.cpp +++ b/modules/kernel/src/ScoringFunction.cpp @@ -25,9 +25,9 @@ class NullScoringFunction : public ScoringFunction { std::string name = "NullScoringFunction%1%") : ScoringFunction(m, name) {} void do_add_score_and_derivatives(IMP::ScoreAccumulator, - const ScoreStatesTemp &) IMP_OVERRIDE {} - Restraints create_restraints() const IMP_OVERRIDE { return Restraints(); } - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + const ScoreStatesTemp &) override {} + Restraints create_restraints() const override { return Restraints(); } + virtual ModelObjectsTemp do_get_inputs() const override { return ModelObjectsTemp(); } IMP_OBJECT_METHODS(NullScoringFunction); diff --git a/modules/kernel/src/file.cpp b/modules/kernel/src/file.cpp index 4e1466c061..6d97fda85c 100644 --- a/modules/kernel/src/file.cpp +++ b/modules/kernel/src/file.cpp @@ -33,7 +33,7 @@ struct LazyFileStorage : public internal::IOStorage { FileStream stream_; LazyFileStorage(std::string name, bool append = false) : P(name), open_(false), append_(append) {} - BaseStream &get_stream() IMP_OVERRIDE { + BaseStream &get_stream() override { if (!open_) { if (append_) { stream_.open(P::get_name().c_str(), std::fstream::app); @@ -67,7 +67,7 @@ struct StreamStorage : public internal::IOStorage { BaseStream &stream_; StreamStorage(BaseStream &stream, std::string name) : P(name), stream_(stream) {} - BaseStream &get_stream() IMP_OVERRIDE { return stream_; } + BaseStream &get_stream() override { return stream_; } }; template @@ -77,7 +77,7 @@ struct OwnedStreamStorage : public internal::IOStorage { PointerMember ref_; OwnedStreamStorage(BaseStream &stream, Object *o) : P("python stream"), stream_(stream), ref_(o) {} - BaseStream &get_stream() IMP_OVERRIDE { return stream_; } + BaseStream &get_stream() override { return stream_; } }; } diff --git a/modules/kinematics/include/CompositeJoint.h b/modules/kinematics/include/CompositeJoint.h index 0bc7288bfb..5a493b992d 100644 --- a/modules/kinematics/include/CompositeJoint.h +++ b/modules/kinematics/include/CompositeJoint.h @@ -97,7 +97,7 @@ class IMPKINEMATICSEXPORT CompositeJoint : public Joint { protected: //! Update the child node reference frame by applying all the inner joints - virtual void update_child_node_reference_frame() const IMP_OVERRIDE; + virtual void update_child_node_reference_frame() const override; /** Updates all inner joints value, and the overall transformation @@ -108,7 +108,7 @@ class IMPKINEMATICSEXPORT CompositeJoint : public Joint { calling this function. */ - virtual void update_joint_from_cartesian_witnesses() IMP_OVERRIDE; + virtual void update_joint_from_cartesian_witnesses() override; private: Joints joints_; // list of inner joints diff --git a/modules/kinematics/include/DihedralMover.h b/modules/kinematics/include/DihedralMover.h index 5b5ce178d0..451059fe87 100644 --- a/modules/kinematics/include/DihedralMover.h +++ b/modules/kinematics/include/DihedralMover.h @@ -30,9 +30,9 @@ class IMPKINEMATICSEXPORT DihedralMover : public core::MonteCarloMover { const double max_rot=0.1); protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(DihedralMover); }; diff --git a/modules/kinematics/include/FibrilSampler.h b/modules/kinematics/include/FibrilSampler.h index 0f0f0dcaa6..e6d6c47b79 100644 --- a/modules/kinematics/include/FibrilSampler.h +++ b/modules/kinematics/include/FibrilSampler.h @@ -36,14 +36,14 @@ class IMPKINEMATICSEXPORT FibrilSampler : public DOFsSampler { */ FibrilSampler(TransformationJoints trans_joint, DihedralAngleRevoluteJoints dihedral_joints, DOFs dofs); - virtual void apply(const DOFValues& values) IMP_OVERRIDE; + virtual void apply(const DOFValues& values) override; virtual void apply_floats(const Floats& values); DihedralAngleRevoluteJoints get_dihedral_joints() { return dihedral_joints_; } TransformationJoints get_transformation_joint() { return trans_joint_; } protected: - virtual DOFValues do_get_sample() const IMP_OVERRIDE; + virtual DOFValues do_get_sample() const override; private: // boost::mt19937 rng_; // init random number generator diff --git a/modules/kinematics/include/KinematicForestScoreState.h b/modules/kinematics/include/KinematicForestScoreState.h index 2fef8ea99d..90aee29731 100644 --- a/modules/kinematics/include/KinematicForestScoreState.h +++ b/modules/kinematics/include/KinematicForestScoreState.h @@ -50,17 +50,17 @@ class IMPKINEMATICSEXPORT KinematicForestScoreState : public IMP::ScoreState { atoms_(atoms) {} // functions that ScoreState requires - void do_before_evaluate() IMP_OVERRIDE { + void do_before_evaluate() override { kf_->update_all_external_coordinates(); } - void do_after_evaluate(DerivativeAccumulator *da) IMP_OVERRIDE { + void do_after_evaluate(DerivativeAccumulator *da) override { IMP_UNUSED(da); } - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + ModelObjectsTemp do_get_inputs() const override; - ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + ModelObjectsTemp do_get_outputs() const override; private: KinematicForest *kf_; diff --git a/modules/kinematics/include/PrismaticJoint.h b/modules/kinematics/include/PrismaticJoint.h index 926d757f0f..66e9eb24e6 100644 --- a/modules/kinematics/include/PrismaticJoint.h +++ b/modules/kinematics/include/PrismaticJoint.h @@ -69,7 +69,7 @@ class IMPKINEMATICSEXPORT PrismaticJoint : public Joint { @note It is assumed that external coordinates are updated before calling this function. */ - virtual void update_joint_from_cartesian_witnesses() IMP_OVERRIDE; + virtual void update_joint_from_cartesian_witnesses() override; private: IMP::core::XYZ a_; // prismatic joint from point, associated with parent diff --git a/modules/kinematics/include/RRT.h b/modules/kinematics/include/RRT.h index 149b1df38c..c055c55526 100644 --- a/modules/kinematics/include/RRT.h +++ b/modules/kinematics/include/RRT.h @@ -119,7 +119,7 @@ class IMPKINEMATICSEXPORT RRT : public IMP::Sampler { // function required by Sampler // TODO: think how to save configurations in internal coords // to be more memory efficient - IMP::ConfigurationSet* do_sample() const IMP_OVERRIDE { + IMP::ConfigurationSet* do_sample() const override { const_cast(this)->run(); return nullptr; } diff --git a/modules/kinematics/include/RevoluteJointMover.h b/modules/kinematics/include/RevoluteJointMover.h index f2bd3c6b0c..55772f4a0c 100644 --- a/modules/kinematics/include/RevoluteJointMover.h +++ b/modules/kinematics/include/RevoluteJointMover.h @@ -37,9 +37,9 @@ class IMPKINEMATICSEXPORT RevoluteJointMover : public core::MonteCarloMover { Float get_sigma() const { return stddev_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(RevoluteJointMover); }; diff --git a/modules/kinematics/include/UniformBackboneSampler.h b/modules/kinematics/include/UniformBackboneSampler.h index d04d5ef1c7..5e765f9846 100644 --- a/modules/kinematics/include/UniformBackboneSampler.h +++ b/modules/kinematics/include/UniformBackboneSampler.h @@ -32,13 +32,13 @@ class IMPKINEMATICSEXPORT UniformBackboneSampler : public DOFsSampler { */ UniformBackboneSampler(DihedralAngleRevoluteJoints joints, DOFs dofs); - virtual void apply(const DOFValues& values) IMP_OVERRIDE; + virtual void apply(const DOFValues& values) override; virtual void apply_floats(const Floats& values); DihedralAngleRevoluteJoints get_joints() { return joints_; } protected: - virtual DOFValues do_get_sample() const IMP_OVERRIDE; + virtual DOFValues do_get_sample() const override; private: // boost::mt19937 rng_; // init random number generator diff --git a/modules/kinematics/include/local_planners.h b/modules/kinematics/include/local_planners.h index 9b522c135d..08bd832530 100644 --- a/modules/kinematics/include/local_planners.h +++ b/modules/kinematics/include/local_planners.h @@ -70,7 +70,7 @@ class IMPKINEMATICSEXPORT PathLocalPlanner : public LocalPlanner { found closest to q_rand (inclusive) */ virtual std::vector plan(DOFValues q_from, DOFValues q_rand, - ScoringFunction *sf) IMP_OVERRIDE; + ScoringFunction *sf) override; private: PointerMember d_; diff --git a/modules/kinematics/include/revolute_joints.h b/modules/kinematics/include/revolute_joints.h index f229b6106e..9cbce30178 100644 --- a/modules/kinematics/include/revolute_joints.h +++ b/modules/kinematics/include/revolute_joints.h @@ -92,7 +92,7 @@ class IMPKINEMATICSEXPORT RevoluteJoint : public Joint { that affect update_axis_of_rotation_from_cartesian_witnesses() are all updated already */ - virtual void update_child_node_reference_frame() const IMP_OVERRIDE; + virtual void update_child_node_reference_frame() const override; /** this protected method updates the rot_axis_unit_vector_ @@ -116,7 +116,7 @@ class IMPKINEMATICSEXPORT RevoluteJoint : public Joint { Update the joint internal parameters based on external reference frames of witnesses and rigid bodies, assuming external parameters are updated */ - virtual void update_joint_from_cartesian_witnesses() IMP_OVERRIDE { + virtual void update_joint_from_cartesian_witnesses() override { update_axis_of_rotation_from_cartesian_witnesses(); angle_ = get_current_angle_from_cartesian_witnesses(); last_updated_angle_ = angle_; @@ -200,7 +200,7 @@ class IMPKINEMATICSEXPORT DihedralAngleRevoluteJoint : public RevoluteJoint { using b_-c_ as the axis of rotation @note it is assumed b_ and c_ have update Cartesian coordinates */ - virtual void update_axis_of_rotation_from_cartesian_witnesses() IMP_OVERRIDE { + virtual void update_axis_of_rotation_from_cartesian_witnesses() override { using namespace IMP::algebra; IMP_USAGE_CHECK( get_distance(b_.get_coordinates(), c_.get_coordinates()) > 1e-12, @@ -227,7 +227,7 @@ class IMPKINEMATICSEXPORT DihedralAngleRevoluteJoint : public RevoluteJoint { date) */ virtual double get_current_angle_from_cartesian_witnesses() - const IMP_OVERRIDE; + const override; private: IMP::core::XYZ a_; @@ -267,7 +267,7 @@ class IMPKINEMATICSEXPORT BondAngleRevoluteJoint : public RevoluteJoint { coordinates of required Cartesian witnesses are up to date) */ virtual double get_current_angle_from_cartesian_witnesses() - const IMP_OVERRIDE; + const override; /** updates the rot_axis_unit_vector_ and rot_axis_origin_ variables @@ -275,7 +275,7 @@ class IMPKINEMATICSEXPORT BondAngleRevoluteJoint : public RevoluteJoint { plane containing a_,b_,c_ as axis of rotation, in global coordinates */ - virtual void update_axis_of_rotation_from_cartesian_witnesses() IMP_OVERRIDE { + virtual void update_axis_of_rotation_from_cartesian_witnesses() override { using namespace IMP::algebra; IMP_USAGE_CHECK( diff --git a/modules/kmeans/include/internal/KCtree.h b/modules/kmeans/include/internal/KCtree.h index f1d922cf73..388845ac59 100644 --- a/modules/kmeans/include/internal/KCtree.h +++ b/modules/kmeans/include/internal/KCtree.h @@ -225,23 +225,23 @@ class IMPKMEANSEXPORT KCleaf : public KCnode { virtual void makeSums( // compute sums int &n, // number of points (returned) KMpoint &theSum, // sum (returned) - double &theSumSq) IMP_OVERRIDE; // sum of squares (returned) + double &theSumSq) override; // sum of squares (returned) virtual void getNeighbors( // compute neighbors for centers KMctrIdxArray cands, // candidate centers - int kCands) IMP_OVERRIDE; // number of centers + int kCands) override; // number of centers virtual void getAssignments( // get assignments for leaf node KMctrIdxArray cands, // candidate centers int kCands, // number of centers KMctrIdxArray closeCtr, // closest center per point - double *sqDist) IMP_OVERRIDE; // sq'd distance to center + double *sqDist) override; // sq'd distance to center // sample a center point c - virtual void sampleCtr(KMpoint c, KMorthRect &bb) IMP_OVERRIDE; + virtual void sampleCtr(KMpoint c, KMorthRect &bb) override; // print node - virtual void print(int level) IMP_OVERRIDE; + virtual void print(int level) override; }; //---------------------------------------------------------------------- @@ -288,23 +288,23 @@ class IMPKMEANSEXPORT KCsplit : public KCnode { virtual void makeSums( // compute sums int &n, // number of points (returned) KMpoint &theSum, // sum (returned) - double &theSumSq) IMP_OVERRIDE; // sum of squares (returned) + double &theSumSq) override; // sum of squares (returned) virtual void getNeighbors( // compute neighbors for centers KMctrIdxArray cands, // candidate centers - int kCands) IMP_OVERRIDE; // number of centers + int kCands) override; // number of centers virtual void getAssignments( // get assignments for leaf node KMctrIdxArray cands, // candidate centers int kCands, // number of centers KMctrIdxArray closeCtr, // closest center per point - double *sqDist) IMP_OVERRIDE; // sq'd distance to center + double *sqDist) override; // sq'd distance to center // sample a center point c - virtual void sampleCtr(KMpoint c, KMorthRect &bb) IMP_OVERRIDE; + virtual void sampleCtr(KMpoint c, KMorthRect &bb) override; // print node - virtual void print(int level) IMP_OVERRIDE; + virtual void print(int level) override; }; //---------------------------------------------------------------------- diff --git a/modules/kmeans/include/internal/KMfilterCenters.h b/modules/kmeans/include/internal/KMfilterCenters.h index fc6bb1d914..c19f53909c 100644 --- a/modules/kmeans/include/internal/KMfilterCenters.h +++ b/modules/kmeans/include/internal/KMfilterCenters.h @@ -197,7 +197,7 @@ class IMPKMEANSEXPORT KMfilterCenters : public KMcenters { @param[in] fancy Dummy variable to support fancy printing in child classes */ - virtual void print(bool fancy = true) IMP_OVERRIDE; + virtual void print(bool fancy = true) override; /** print centers to specified output stream diff --git a/modules/kmeans/include/internal/KMlocal.h b/modules/kmeans/include/internal/KMlocal.h index a33cb0ca3c..407f9bfcef 100644 --- a/modules/kmeans/include/internal/KMlocal.h +++ b/modules/kmeans/include/internal/KMlocal.h @@ -276,7 +276,7 @@ class IMPKMEANSEXPORT KMlocalLloyds : public KMlocal { double accumRDL() { // relative RDL for run return (initRunDist - curr.getDist()) / initRunDist; } - virtual void printStageStats() IMP_OVERRIDE { // print end of stage info + virtual void printStageStats() override { // print end of stage info if (kmStatLev >= STAGE) { *kmOut << "\t= term.getMaxRunStage()) { return true; // too many stages @@ -323,7 +323,7 @@ class IMPKMEANSEXPORT KMlocalLloyds : public KMlocal { return accumRDL() >= term.getMinAccumRDL(); } } - virtual void endRun() IMP_OVERRIDE { // end of run processing + virtual void endRun() override { // end of run processing if (accumRDL() < term.getMinAccumRDL()) { // unsuccessful run? isNewPhase = true; // start a new phase } else { @@ -376,29 +376,29 @@ class IMPKMEANSEXPORT KMlocalSwap : public KMlocal { : KMlocal(sol, t), maxSwaps(p) {} protected: // overridden methods - virtual void reset() IMP_OVERRIDE { + virtual void reset() override { KMlocal::reset(); // reset base class printStageStats(); } - virtual void beginRun() IMP_OVERRIDE { // start of run processing + virtual void beginRun() override { // start of run processing KMlocal::beginRun(); // base class processing swapNo = 0; // init number of swaps } - virtual KMalg selectMethod() IMP_OVERRIDE { // method = Swap + virtual KMalg selectMethod() override { // method = Swap return SWAP; } - virtual void endStage() IMP_OVERRIDE {} // do nothing - virtual bool isRunDone() IMP_OVERRIDE { // run is done + virtual void endStage() override {} // do nothing + virtual bool isRunDone() override { // run is done return KMlocal::isRunDone() || // base class say's done ++swapNo >= maxSwaps; // or enough swaps done } - virtual void endRun() IMP_OVERRIDE { // end of run processing + virtual void endRun() override { // end of run processing curr.getDist(); stageNo++; printStageStats(); // print stage info } - virtual void tryAcceptance() IMP_OVERRIDE { // test acceptance + virtual void tryAcceptance() override { // test acceptance if (curr.getDist() < best.getDist()) { // current distortion lower? best = curr; // then save the current } else { // current distortion worse @@ -616,7 +616,7 @@ class IMPKMEANSEXPORT KMlocalHybrid : public KMlocal { return (prevDist - curr.getDist()) / prevDist; } - virtual void printStageStats() IMP_OVERRIDE { // print end of stage info + virtual void printStageStats() override { // print end of stage info if (kmStatLev >= STAGE) { *kmOut << " 0) { // improvement over saved? save = curr; // save this one if (save.getDist() < best.getDist()) { // new best? @@ -795,7 +795,7 @@ class IMPKMEANSEXPORT KMlocalEZ_Hybrid : public KMlocal { return (prevDist - curr.getDist()) / prevDist; } - virtual void printStageStats() IMP_OVERRIDE { // print end of stage info + virtual void printStageStats() override { // print end of stage info if (kmStatLev >= STAGE) { *kmOut << " & weights) const IMP_OVERRIDE; + Vector& weights) const override; saxs::WeightedFitParameters get_fit_parameters( - MultiStateModel& m) const IMP_OVERRIDE; + MultiStateModel& m) const override; - saxs::WeightedFitParameters get_fit_parameters() const IMP_OVERRIDE; + saxs::WeightedFitParameters get_fit_parameters() const override; void write_fit_file(MultiStateModel& m, const saxs::WeightedFitParameters& fp, - const std::string fit_file_name) const IMP_OVERRIDE; + const std::string fit_file_name) const override; - std::string get_state_name(unsigned int id) const IMP_OVERRIDE { + std::string get_state_name(unsigned int id) const override { return profiles_[id]->get_name(); } - std::string get_dataset_name() const IMP_OVERRIDE { + std::string get_dataset_name() const override { return exp_profile_->get_name(); } diff --git a/modules/multifit/include/ComplementarityRestraint.h b/modules/multifit/include/ComplementarityRestraint.h index ec683cb5cf..497252e398 100644 --- a/modules/multifit/include/ComplementarityRestraint.h +++ b/modules/multifit/include/ComplementarityRestraint.h @@ -79,12 +79,12 @@ class IMPMULTIFITEXPORT ComplementarityRestraint : public Restraint { void set_boundary_coefficient(double bc) { boundary_coef_ = bc; } float get_voxel_size() const { return voxel_size_; } virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ComplementarityRestraint); #ifndef IMP_DOXYGEN double unprotected_evaluate_if_good(DerivativeAccumulator *accum, - double max) const IMP_OVERRIDE; + double max) const override; #endif private: typedef std::pair > diff --git a/modules/multifit/include/DensityDataPoints.h b/modules/multifit/include/DensityDataPoints.h index 8a1940ece2..10ebd5000a 100644 --- a/modules/multifit/include/DensityDataPoints.h +++ b/modules/multifit/include/DensityDataPoints.h @@ -37,7 +37,7 @@ class IMPMULTIFITEXPORT DensityDataPoints public: DensityDataPoints(em::DensityMap *dens, float density_threshold); DensityDataPoints(const DensGrid &dens, float density_threshold); - IMP::statistics::internal::Array1DD sample() const IMP_OVERRIDE; + IMP::statistics::internal::Array1DD sample() const override; // em::DensityMap* get_density_map() const {return dens_;} diff --git a/modules/multifit/include/RadiusOfGyrationRestraint.h b/modules/multifit/include/RadiusOfGyrationRestraint.h index fa88441949..e0f1e99c7a 100644 --- a/modules/multifit/include/RadiusOfGyrationRestraint.h +++ b/modules/multifit/include/RadiusOfGyrationRestraint.h @@ -36,8 +36,8 @@ class IMPMULTIFITEXPORT RadiusOfGyrationRestraint : public Restraint { RadiusOfGyrationRestraint(Particles ps, int num_residues, Float scale = 1.); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(RadiusOfGyrationRestraint); //! Set the predicted radius of gyration used in the restraint void set_radius_of_gyration(Float r) { diff --git a/modules/multifit/include/RigidLeavesRefiner.h b/modules/multifit/include/RigidLeavesRefiner.h index 2edc9328cc..9e63944e6a 100644 --- a/modules/multifit/include/RigidLeavesRefiner.h +++ b/modules/multifit/include/RigidLeavesRefiner.h @@ -19,13 +19,13 @@ class IMPMULTIFITEXPORT RigidLeavesRefiner : public Refiner { public: RigidLeavesRefiner(std::string name = "RigidLeavesRefiner%d") : Refiner(name) {} - virtual bool get_can_refine(Particle *) const IMP_OVERRIDE; + virtual bool get_can_refine(Particle *) const override; #ifndef SWIG using Refiner::get_refined; #endif - virtual const ParticlesTemp get_refined(Particle *) const IMP_OVERRIDE; + virtual const ParticlesTemp get_refined(Particle *) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_OBJECT_METHODS(RigidLeavesRefiner); }; diff --git a/modules/multifit/include/WeightedExcludedVolumeRestraint.h b/modules/multifit/include/WeightedExcludedVolumeRestraint.h index d8fd1da3db..22f4307c33 100644 --- a/modules/multifit/include/WeightedExcludedVolumeRestraint.h +++ b/modules/multifit/include/WeightedExcludedVolumeRestraint.h @@ -43,8 +43,8 @@ class IMPMULTIFITEXPORT WeightedExcludedVolumeRestraint IMP::atom::Mass::get_mass_key()); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(WeightedExcludedVolumeRestraint); #ifndef SWIG diff --git a/modules/multifit/include/fitting_states.h b/modules/multifit/include/fitting_states.h index 9ea05313b8..64063e2768 100644 --- a/modules/multifit/include/fitting_states.h +++ b/modules/multifit/include/fitting_states.h @@ -27,9 +27,9 @@ class IMPMULTIFITEXPORT FittingStates : public domino::ParticleStates { states_(states), fit_state_key_(fit_state_key) {} - virtual unsigned int get_number_of_particle_states() const IMP_OVERRIDE; + virtual unsigned int get_number_of_particle_states() const override; virtual void load_particle_state(unsigned int, Particle *) const - IMP_OVERRIDE; + override; IMP_OBJECT_METHODS(FittingStates); }; diff --git a/modules/multifit/include/merge_tree_utils.h b/modules/multifit/include/merge_tree_utils.h index 9d009f77d2..ec40efaea5 100644 --- a/modules/multifit/include/merge_tree_utils.h +++ b/modules/multifit/include/merge_tree_utils.h @@ -47,8 +47,8 @@ class IMPMULTIFITEXPORT DummyRestraint : public Restraint { p1_(a), p2_(b) {} virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(DummyRestraint); protected: diff --git a/modules/multifit/src/internal/GeometricComplementarity.cpp b/modules/multifit/src/internal/GeometricComplementarity.cpp index d60623e79a..b927bf5090 100644 --- a/modules/multifit/src/internal/GeometricComplementarity.cpp +++ b/modules/multifit/src/internal/GeometricComplementarity.cpp @@ -29,7 +29,7 @@ class SurfaceDistanceMap : public IMP::em::SampledDensityMap { // Resample needs to be overloaded so that the number of layers // is not limited by num_shells_ - void resample() IMP_OVERRIDE; + void resample() override; private: void set_surface_shell(std::vector *shell); diff --git a/modules/npc/include/CompositeRestraint.h b/modules/npc/include/CompositeRestraint.h index 02e66161cc..fbb3004330 100644 --- a/modules/npc/include/CompositeRestraint.h +++ b/modules/npc/include/CompositeRestraint.h @@ -73,8 +73,8 @@ class IMPNPCEXPORT CompositeRestraint : public Restraint { */ ParticleIndexPairs get_connected_pairs() const; - double unprotected_evaluate(DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + double unprotected_evaluate(DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(CompositeRestraint); }; diff --git a/modules/npc/include/MinimumSphereDistancePairScore.h b/modules/npc/include/MinimumSphereDistancePairScore.h index 73429167de..b64de9e93e 100644 --- a/modules/npc/include/MinimumSphereDistancePairScore.h +++ b/modules/npc/include/MinimumSphereDistancePairScore.h @@ -36,9 +36,9 @@ class IMPNPCEXPORT MinimumSphereDistancePairScore : public PairScore { : f_(f), transforms_(transforms) {} virtual double evaluate_index(Model *m, const ParticleIndexPair &pi, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { return IMP::get_particles(m, pis); } IMP_PAIR_SCORE_METHODS(MinimumSphereDistancePairScore); diff --git a/modules/npc/include/ProteinLocalizationRestraint.h b/modules/npc/include/ProteinLocalizationRestraint.h index 1c3d74d155..c3eff6f419 100644 --- a/modules/npc/include/ProteinLocalizationRestraint.h +++ b/modules/npc/include/ProteinLocalizationRestraint.h @@ -43,8 +43,8 @@ class IMPNPCEXPORT ZAxialPositionRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ZAxialPositionRestraint);; }; @@ -72,8 +72,8 @@ class IMPNPCEXPORT ZAxialPositionLowerRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ZAxialPositionLowerRestraint);; }; @@ -101,8 +101,8 @@ class IMPNPCEXPORT ZAxialPositionUpperRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ZAxialPositionUpperRestraint);; }; @@ -132,8 +132,8 @@ class IMPNPCEXPORT YAxialPositionRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(YAxialPositionRestraint);; }; @@ -161,8 +161,8 @@ class IMPNPCEXPORT YAxialPositionLowerRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(YAxialPositionLowerRestraint);; }; @@ -190,8 +190,8 @@ class IMPNPCEXPORT YAxialPositionUpperRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(YAxialPositionUpperRestraint);; }; @@ -221,8 +221,8 @@ class IMPNPCEXPORT XYRadialPositionRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(XYRadialPositionRestraint);; }; @@ -250,8 +250,8 @@ class IMPNPCEXPORT XYRadialPositionLowerRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(XYRadialPositionLowerRestraint);; }; @@ -279,8 +279,8 @@ class IMPNPCEXPORT XYRadialPositionUpperRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(XYRadialPositionUpperRestraint);; }; @@ -309,8 +309,8 @@ class IMPNPCEXPORT ProteinContactRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ProteinContactRestraint);; }; @@ -338,8 +338,8 @@ class IMPNPCEXPORT ProteinChainRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ProteinChainRestraint);; }; @@ -369,8 +369,8 @@ class IMPNPCEXPORT MembraneSurfaceLocationRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(MembraneSurfaceLocationRestraint);; }; @@ -405,8 +405,8 @@ class IMPNPCEXPORT MembraneSurfaceLocationConditionalRestraint : public Restrain #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(MembraneSurfaceLocationConditionalRestraint);; }; @@ -436,8 +436,8 @@ class IMPNPCEXPORT MembraneExclusionRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(MembraneExclusionRestraint);; }; @@ -468,8 +468,8 @@ class IMPNPCEXPORT PoreSideVolumeLocationRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(PoreSideVolumeLocationRestraint);; }; @@ -500,8 +500,8 @@ class IMPNPCEXPORT PerinuclearVolumeLocationRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(PerinuclearVolumeLocationRestraint);; }; @@ -530,8 +530,8 @@ class IMPNPCEXPORT AssemblySymmetryByDistanceRestraint : public Restraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(AssemblySymmetryByDistanceRestraint);; }; @@ -561,8 +561,8 @@ class IMPNPCEXPORT AssemblySymmetryByDihedralRestraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(AssemblySymmetryByDihedralRestraint);; }; @@ -590,8 +590,8 @@ class IMPNPCEXPORT ProteinProximityRestraint #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ProteinProximityRestraint);; }; diff --git a/modules/rmf/include/HierarchyLoadLink.h b/modules/rmf/include/HierarchyLoadLink.h index 7fc0a4b00e..ab69b3c178 100644 --- a/modules/rmf/include/HierarchyLoadLink.h +++ b/modules/rmf/include/HierarchyLoadLink.h @@ -64,7 +64,7 @@ class IMPRMFEXPORT HierarchyLoadLink : public SimpleLoadLink { typedef boost::unordered_map > DM; DM data_; - virtual bool get_is(RMF::NodeConstHandle nh) const IMP_OVERRIDE { + virtual bool get_is(RMF::NodeConstHandle nh) const override { return nh.get_type() == RMF::REPRESENTATION; } virtual void add_link_recursive(Model *m, ParticleIndex root, @@ -74,10 +74,10 @@ class IMPRMFEXPORT HierarchyLoadLink : public SimpleLoadLink { Data &data); virtual void do_add_link(Particle *o, - RMF::NodeConstHandle node) IMP_FINAL IMP_OVERRIDE; + RMF::NodeConstHandle node) IMP_FINAL override; using P::do_create; virtual Particle *do_create(RMF::NodeConstHandle name, - Model *m) IMP_FINAL IMP_OVERRIDE; + Model *m) IMP_FINAL override; void create_recursive(Model *m, ParticleIndex root, ParticleIndex cur, RMF::NodeConstHandle name, ParticleIndexes rigid_bodies, Data &data); @@ -90,7 +90,7 @@ class IMPRMFEXPORT HierarchyLoadLink : public SimpleLoadLink { core::Provenance create_one_provenance(Model *m, RMF::NodeConstHandle node); virtual void do_load_one(RMF::NodeConstHandle nh, - Particle *o) IMP_FINAL IMP_OVERRIDE; + Particle *o) IMP_FINAL override; protected: /** This method is called for the hierarchy.*/ diff --git a/modules/rmf/include/HierarchySaveLink.h b/modules/rmf/include/HierarchySaveLink.h index cd42850d0e..824c1b89f9 100644 --- a/modules/rmf/include/HierarchySaveLink.h +++ b/modules/rmf/include/HierarchySaveLink.h @@ -71,10 +71,10 @@ class IMPRMFEXPORT HierarchySaveLink : public SimpleSaveLink { // Make RMF PROVENANCE nodes corresponding to those in IMP void add_provenance(Model *m, ParticleIndex p, RMF::NodeHandle cur); - virtual void do_add(Particle *p, RMF::NodeHandle cur) IMP_OVERRIDE; + virtual void do_add(Particle *p, RMF::NodeHandle cur) override; virtual void do_save_one(Particle *o, - RMF::NodeHandle nh) IMP_OVERRIDE; - RMF::NodeType get_type(Particle *) const IMP_OVERRIDE { + RMF::NodeHandle nh) override; + RMF::NodeType get_type(Particle *) const override { return RMF::REPRESENTATION; } diff --git a/modules/rmf/include/SaveOptimizerState.h b/modules/rmf/include/SaveOptimizerState.h index 76284e2074..6caad62d4a 100644 --- a/modules/rmf/include/SaveOptimizerState.h +++ b/modules/rmf/include/SaveOptimizerState.h @@ -52,7 +52,7 @@ class IMPRMFEXPORT SaveOptimizerState : public OptimizerState { void update_always(std::string name); // to prevent it from being hidden void update_always() { OptimizerState::update_always(); } - virtual void do_update(unsigned int call_num) IMP_OVERRIDE; + virtual void do_update(unsigned int call_num) override; IMP_OBJECT_METHODS(SaveOptimizerState); }; diff --git a/modules/rmf/include/simple_links.h b/modules/rmf/include/simple_links.h index 423f0d20ea..59b922e798 100644 --- a/modules/rmf/include/simple_links.h +++ b/modules/rmf/include/simple_links.h @@ -35,7 +35,7 @@ class SimpleLoadLink : public LoadLink { protected: virtual void do_load_one(RMF::NodeConstHandle nh, O *o) = 0; - void do_load(RMF::FileConstHandle fh) IMP_OVERRIDE { + void do_load(RMF::FileConstHandle fh) override { IMP_OBJECT_LOG; for (unsigned int i = 0; i < os_.size(); ++i) { IMP_LOG_VERBOSE("Loading " << fh.get_node(nhs_[i]) << std::endl); @@ -135,7 +135,7 @@ class SimpleSaveLink : public SaveLink { protected: virtual void do_save_one(O *o, RMF::NodeHandle nh) = 0; - void do_save(RMF::FileHandle fh) IMP_OVERRIDE { + void do_save(RMF::FileHandle fh) override { for (unsigned int i = 0; i < os_.size(); ++i) { IMP_LOG_VERBOSE("Saving to " << fh.get_node(nhs_[i]) << std::endl); diff --git a/modules/rmf/src/geometry_io.cpp b/modules/rmf/src/geometry_io.cpp index 0823cee980..a9d4241962 100644 --- a/modules/rmf/src/geometry_io.cpp +++ b/modules/rmf/src/geometry_io.cpp @@ -28,11 +28,11 @@ class GeometryLoadLink : public SimpleLoadLink { typedef SimpleLoadLink P; F factory_; RMF::decorator::ColoredFactory colored_factory_; - bool get_is(RMF::NodeConstHandle nh) const IMP_OVERRIDE { + bool get_is(RMF::NodeConstHandle nh) const override { return nh.get_type() == RMF::GEOMETRY && factory_.get_is(nh); } using P::do_create; - G *do_create(RMF::NodeConstHandle name) IMP_OVERRIDE { + G *do_create(RMF::NodeConstHandle name) override { return new G(name.get_name()); } @@ -65,7 +65,7 @@ class GeometrySaveLink : public SimpleSaveLink { typedef SimpleSaveLink P; F factory_; RMF::decorator::ColoredFactory colored_factory_; - RMF::NodeType get_type(G *) const IMP_OVERRIDE { return RMF::GEOMETRY; } + RMF::NodeType get_type(G *) const override { return RMF::GEOMETRY; } public: const F &get_factory() const { return factory_; } @@ -83,7 +83,7 @@ class SphereLoadLink : public GeometryLoadLink P; void do_load_one(RMF::NodeConstHandle nh, - display::SphereGeometry *o) IMP_OVERRIDE { + display::SphereGeometry *o) override { RMF::decorator::BallConst b = get_factory().get(nh); RMF::Vector3 cs = b.get_coordinates(); algebra::Sphere3D s(algebra::Vector3D(cs.begin(), cs.end()), @@ -110,7 +110,7 @@ class SphereSaveLink : public GeometrySaveLink P; void do_save_one(display::SphereGeometry *o, - RMF::NodeHandle nh) IMP_OVERRIDE { + RMF::NodeHandle nh) override { save_sphere(o, nh, P::get_factory()); P::save_color(o, nh); o->set_was_used(true); @@ -127,7 +127,7 @@ class CylinderLoadLink typedef GeometryLoadLink P; void do_load_one(RMF::NodeConstHandle nh, - display::CylinderGeometry *o) IMP_OVERRIDE { + display::CylinderGeometry *o) override { RMF::decorator::CylinderConst b = get_factory().get(nh); RMF::Vector3s cs = b.get_coordinates_list(); algebra::Vector3D vs[2] = {algebra::Vector3D(cs[0]), @@ -163,7 +163,7 @@ class CylinderSaveLink typedef GeometrySaveLink P; void do_save_one(display::CylinderGeometry *o, - RMF::NodeHandle nh) IMP_OVERRIDE { + RMF::NodeHandle nh) override { save_cylinder(o, nh, P::get_factory()); P::save_color(o, nh); o->set_was_used(true); @@ -194,7 +194,7 @@ class SegmentLoadLink typedef GeometryLoadLink P; void do_load_one(RMF::NodeConstHandle nh, - display::SegmentGeometry *o) IMP_OVERRIDE { + display::SegmentGeometry *o) override { RMF::decorator::SegmentConst b = get_factory().get(nh); o->set_geometry(get_segment(b)); P::load_color(nh, o); @@ -218,7 +218,7 @@ class SegmentSaveLink typedef GeometrySaveLink P; void do_save_one(display::SegmentGeometry *o, - RMF::NodeHandle nh) IMP_OVERRIDE { + RMF::NodeHandle nh) override { save_segment(o, nh, P::get_factory()); P::save_color(o, nh); o->set_was_used(true); @@ -234,7 +234,7 @@ class BoxLoadLink : public GeometryLoadLink P; void do_load_one(RMF::NodeConstHandle nh, - display::BoundingBoxGeometry *o) IMP_OVERRIDE { + display::BoundingBoxGeometry *o) override { algebra::BoundingBox3D b; RMF::NodeConstHandles nhs = nh.get_children(); IMP_USAGE_CHECK(nhs.size() == 12, @@ -249,7 +249,7 @@ class BoxLoadLink : public GeometryLoadLinkset_geometry(b); P::load_color(nh, o); } - bool get_is(RMF::NodeConstHandle nh) const IMP_OVERRIDE { + bool get_is(RMF::NodeConstHandle nh) const override { if (nh.get_type() != RMF::GEOMETRY) return false; RMF::NodeConstHandles ch = nh.get_children(); if (ch.size() != 12) return false; @@ -286,13 +286,13 @@ class BoxSaveLink : public GeometrySaveLink P; void do_save_one(display::BoundingBoxGeometry *o, - RMF::NodeHandle nh) IMP_OVERRIDE { + RMF::NodeHandle nh) override { save_box(o, nh, P::get_factory()); P::save_color(o, nh); o->set_was_used(true); } void do_add(display::BoundingBoxGeometry *o, - RMF::NodeHandle nh) IMP_OVERRIDE { + RMF::NodeHandle nh) override { add_box(o, nh); P::do_add(o, nh); } diff --git a/modules/rmf/src/particle_io.cpp b/modules/rmf/src/particle_io.cpp index b021f7f5fc..dffbcd909b 100644 --- a/modules/rmf/src/particle_io.cpp +++ b/modules/rmf/src/particle_io.cpp @@ -58,17 +58,17 @@ class ParticleLoadLink : public SimpleLoadLink { } } } - void do_load_one(RMF::NodeConstHandle nh, Particle *o) IMP_OVERRIDE { + void do_load_one(RMF::NodeConstHandle nh, Particle *o) override { RMF::Category cat = nh.get_file().get_category("IMP"); load_one(o, nh, cat); load_one(o, nh, cat); load_one(o, nh, cat); } - bool get_is(RMF::NodeConstHandle nh) const IMP_OVERRIDE { + bool get_is(RMF::NodeConstHandle nh) const override { return nh.get_type() == RMF::CUSTOM; } using P::do_create; - Particle *do_create(RMF::NodeConstHandle name, Model *m) IMP_OVERRIDE { + Particle *do_create(RMF::NodeConstHandle name, Model *m) override { return new Particle(m, name.get_name()); } @@ -96,12 +96,12 @@ class ParticleSaveLink : public SimpleSaveLink { } } - void do_save_one(Particle *o, RMF::NodeHandle nh) IMP_OVERRIDE { + void do_save_one(Particle *o, RMF::NodeHandle nh) override { save_one(o, o->get_float_keys(), nh, float_); save_one(o, o->get_int_keys(), nh, int_); save_one(o, o->get_string_keys(), nh, string_); } - RMF::NodeType get_type(Particle *) const IMP_OVERRIDE { return RMF::CUSTOM; } + RMF::NodeType get_type(Particle *) const override { return RMF::CUSTOM; } public: ParticleSaveLink(RMF::FileHandle fh) : P("ParticleSaveLink%1%") { diff --git a/modules/rmf/src/restraint_io.cpp b/modules/rmf/src/restraint_io.cpp index 759739631d..dc375d750b 100644 --- a/modules/rmf/src/restraint_io.cpp +++ b/modules/rmf/src/restraint_io.cpp @@ -48,14 +48,14 @@ class RMFRestraint : public Restraint { } return info_; } - RestraintInfo *get_dynamic_info() const IMP_OVERRIDE { return info_; } - RestraintInfo *get_static_info() const IMP_OVERRIDE { return info_; } + RestraintInfo *get_dynamic_info() const override { return info_; } + RestraintInfo *get_static_info() const override { return info_; } #endif double unprotected_evaluate( - IMP::DerivativeAccumulator *accum) const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + IMP::DerivativeAccumulator *accum) const override; + ModelObjectsTemp do_get_inputs() const override; + Restraints do_create_current_decomposition() const override; IMP_OBJECT_METHODS(RMFRestraint); }; @@ -179,7 +179,7 @@ class RestraintLoadLink : public SimpleLoadLink { RMF::StringKeys filenameks_; RMF::StringsKeys filenamesks_; - void do_load_one(RMF::NodeConstHandle nh, Restraint *oi) IMP_OVERRIDE { + void do_load_one(RMF::NodeConstHandle nh, Restraint *oi) override { RMF::NodeConstHandles chs = nh.get_children(); if (sf_.get_is(nh)) { RMF::decorator::ScoreConst d = sf_.get(nh); @@ -196,11 +196,11 @@ class RestraintLoadLink : public SimpleLoadLink { } } - bool get_is(RMF::NodeConstHandle nh) const IMP_OVERRIDE { + bool get_is(RMF::NodeConstHandle nh) const override { return nh.get_type() == RMF::FEATURE; } using P::do_create; - Restraint *do_create(RMF::NodeConstHandle name, Model *m) IMP_OVERRIDE { + Restraint *do_create(RMF::NodeConstHandle name, Model *m) override { RMF::NodeConstHandles chs = name.get_children(); Restraints childr; ParticlesTemp inputs; @@ -493,7 +493,7 @@ class RestraintSaveLink : public SimpleSaveLink { unsigned int max_terms_; boost::unordered_set no_terms_; - void do_add(Restraint *r, RMF::NodeHandle nh) IMP_OVERRIDE { + void do_add(Restraint *r, RMF::NodeHandle nh) override { // handle restraints being in multiple sets all_.push_back(r); rsf_ = new core::RestraintsScoringFunction(all_); @@ -516,7 +516,7 @@ class RestraintSaveLink : public SimpleSaveLink { } } } - void do_save_one(Restraint *o, RMF::NodeHandle nh) IMP_OVERRIDE { + void do_save_one(Restraint *o, RMF::NodeHandle nh) override { IMP_OBJECT_LOG; IMP_LOG_TERSE("Saving restraint info for " << o->get_name() << std::endl); RestraintSaveData &d = data_[o]; @@ -811,11 +811,11 @@ class RestraintSaveLink : public SimpleSaveLink { } } - void do_save(RMF::FileHandle fh) IMP_OVERRIDE { + void do_save(RMF::FileHandle fh) override { rsf_->evaluate(false); P::do_save(fh); } - RMF::NodeType get_type(Restraint *) const IMP_OVERRIDE { + RMF::NodeType get_type(Restraint *) const override { return RMF::FEATURE; } diff --git a/modules/saxs/include/RadiusOfGyrationRestraint.h b/modules/saxs/include/RadiusOfGyrationRestraint.h index d22dd490e4..f4a78ad9e4 100644 --- a/modules/saxs/include/RadiusOfGyrationRestraint.h +++ b/modules/saxs/include/RadiusOfGyrationRestraint.h @@ -37,8 +37,8 @@ class IMPSAXSEXPORT RadiusOfGyrationRestraint : public Restraint { const double end_q_rg = 1.3); virtual double unprotected_evaluate(DerivativeAccumulator* accum) - const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(RadiusOfGyrationRestraint); private: diff --git a/modules/saxs/include/Restraint.h b/modules/saxs/include/Restraint.h index 7643983e04..9cf31a2d0a 100644 --- a/modules/saxs/include/Restraint.h +++ b/modules/saxs/include/Restraint.h @@ -54,12 +54,12 @@ class IMPSAXSEXPORT Restraint : public IMP::Restraint { FormFactorType ff_type = HEAVY_ATOMS); virtual double unprotected_evaluate(IMP::DerivativeAccumulator* accum) - const IMP_OVERRIDE; + const override; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; //! \return Information for writing to RMF files - RestraintInfo *get_static_info() const IMP_OVERRIDE; + RestraintInfo *get_static_info() const override; IMP_OBJECT_METHODS(Restraint); diff --git a/modules/score_functor/include/DistancePairScore.h b/modules/score_functor/include/DistancePairScore.h index bb600e3f45..1f40a2bcb4 100644 --- a/modules/score_functor/include/DistancePairScore.h +++ b/modules/score_functor/include/DistancePairScore.h @@ -39,10 +39,10 @@ class DistancePairScore : public PairScore { virtual double evaluate_index(Model *m, const ParticleIndexPair &pip, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; /** return a reference to the functor that is applied on a pair of particles diff --git a/modules/score_functor/include/DistancePairScoreWithCache.h b/modules/score_functor/include/DistancePairScoreWithCache.h index edc1c1cc2d..bc82308bbc 100644 --- a/modules/score_functor/include/DistancePairScoreWithCache.h +++ b/modules/score_functor/include/DistancePairScoreWithCache.h @@ -40,10 +40,10 @@ class DistancePairScoreWithCache : public PairScore { virtual double evaluate_index(Model *m, const ParticleIndexPair &pip, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; /** return a reference to the functor that is applied on a pair of particles @@ -55,17 +55,17 @@ class DistancePairScoreWithCache : public PairScore { virtual double evaluate_indexes( Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, - unsigned int upper_bound) const IMP_OVERRIDE; + unsigned int upper_bound) const override; virtual double evaluate_indexes_scores( Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, - std::vector &score) const IMP_OVERRIDE; + std::vector &score) const override; virtual double evaluate_indexes_delta( Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector &indexes, - std::vector &score) const IMP_OVERRIDE; + std::vector &score) const override; IMP_OBJECT_METHODS(DistancePairScoreWithCache); }; diff --git a/modules/score_functor/include/ScoreUnaryFunction.h b/modules/score_functor/include/ScoreUnaryFunction.h index 09c20be930..a008b21206 100644 --- a/modules/score_functor/include/ScoreUnaryFunction.h +++ b/modules/score_functor/include/ScoreUnaryFunction.h @@ -25,12 +25,12 @@ class ScoreUnaryFunction : public IMP::UnaryFunction { : UnaryFunction(name), score_(score) {} virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return score_.get_score_and_derivative( nullptr, Array(), feature); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return score_.get_score(nullptr, Array(), feature); } diff --git a/modules/score_functor/include/SurfaceDistancePairScore.h b/modules/score_functor/include/SurfaceDistancePairScore.h index 4869d442e7..fb3e7f9d35 100644 --- a/modules/score_functor/include/SurfaceDistancePairScore.h +++ b/modules/score_functor/include/SurfaceDistancePairScore.h @@ -55,10 +55,10 @@ class SurfaceDistancePairScore : public PairScore { */ virtual double evaluate_index(Model *m, const ParticleIndexPair &pip, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; DistanceScoreT& get_score_functor() { return ds_; } @@ -131,7 +131,7 @@ class SurfaceHeightPairScore : public SurfaceDistancePairScore< virtual double get_distance(const algebra::Vector3D ¢er, const algebra::Vector3D &normal, const algebra::Vector3D &point, - algebra::Vector3D *delta) const IMP_OVERRIDE { + algebra::Vector3D *delta) const override { return internal::get_height_above_surface(center, normal, point, delta); } public: @@ -170,7 +170,7 @@ class SurfaceDepthPairScore : public SurfaceDistancePairScore< virtual double get_distance(const algebra::Vector3D ¢er, const algebra::Vector3D &normal, const algebra::Vector3D &point, - algebra::Vector3D *delta) const IMP_OVERRIDE { + algebra::Vector3D *delta) const override { return internal::get_depth_below_surface(center, normal, point, delta); } public: diff --git a/modules/spb/include/AttributeDistancePairScore.h b/modules/spb/include/AttributeDistancePairScore.h index 39cb56a6f7..43d22ca194 100644 --- a/modules/spb/include/AttributeDistancePairScore.h +++ b/modules/spb/include/AttributeDistancePairScore.h @@ -30,10 +30,10 @@ class IMPSPBEXPORT AttributeDistancePairScore : public PairScore { AttributeDistancePairScore(UnaryFunction *f, FloatKey k); virtual double evaluate_index(IMP::Model *m, const IMP::ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual IMP::ModelObjectsTemp do_get_inputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; // void show(std::ostream &out) const ; diff --git a/modules/spb/include/BoxedMover.h b/modules/spb/include/BoxedMover.h index 7f568309f1..39be81d8f6 100644 --- a/modules/spb/include/BoxedMover.h +++ b/modules/spb/include/BoxedMover.h @@ -30,9 +30,9 @@ class IMPSPBEXPORT BoxedMover : public core::MonteCarloMover { BoxedMover(Particle *p, Float max_tr, algebra::Vector3Ds centers); protected: - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; // IMP_MOVER(BoxedMover); diff --git a/modules/spb/include/CellMover.h b/modules/spb/include/CellMover.h index 04fd88233c..76c95490b3 100644 --- a/modules/spb/include/CellMover.h +++ b/modules/spb/include/CellMover.h @@ -28,9 +28,9 @@ class IMPSPBEXPORT CellMover : public core::MonteCarloMover { // IMP_MOVER(CellMover); protected: - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(CellMover); IMP_SHOWABLE(CellMover); diff --git a/modules/spb/include/ChiSquareMetric.h b/modules/spb/include/ChiSquareMetric.h index 161b75e6fa..608a69a309 100644 --- a/modules/spb/include/ChiSquareMetric.h +++ b/modules/spb/include/ChiSquareMetric.h @@ -41,8 +41,8 @@ class IMPSPBEXPORT ChiSquareMetric : public statistics::Metric { double get_chisquare_exp(unsigned i) const; - double get_distance(unsigned int i, unsigned int j) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + double get_distance(unsigned int i, unsigned int j) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(ChiSquareMetric); // IMP_METRIC(ChiSquareMetric); diff --git a/modules/spb/include/ContactMapMetric.h b/modules/spb/include/ContactMapMetric.h index a95efac890..6a5c3c684d 100644 --- a/modules/spb/include/ContactMapMetric.h +++ b/modules/spb/include/ContactMapMetric.h @@ -37,8 +37,8 @@ class IMPSPBEXPORT ContactMapMetric : public statistics::Metric { Floats get_item(unsigned i) const; // IMP_METRIC(ContactMapMetric); - double get_distance(unsigned int i, unsigned int j) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + double get_distance(unsigned int i, unsigned int j) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(ContactMapMetric); }; diff --git a/modules/spb/include/DiameterRgyrRestraint.h b/modules/spb/include/DiameterRgyrRestraint.h index f3cf8f43b2..0a9d522bde 100644 --- a/modules/spb/include/DiameterRgyrRestraint.h +++ b/modules/spb/include/DiameterRgyrRestraint.h @@ -32,8 +32,8 @@ class IMPSPBEXPORT DiameterRgyrRestraint : public Restraint { DiameterRgyrRestraint(Particles ps, Float diameter, Float rgyr, Float kappa); virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(DiameterRgyrRestraint); }; diff --git a/modules/spb/include/DistanceRMSDMetric.h b/modules/spb/include/DistanceRMSDMetric.h index ec28ae6263..de6ace54fd 100644 --- a/modules/spb/include/DistanceRMSDMetric.h +++ b/modules/spb/include/DistanceRMSDMetric.h @@ -43,8 +43,8 @@ class IMPSPBEXPORT DistanceRMSDMetric : public statistics::Metric { Float get_weight(unsigned i); // IMP_METRIC(DistanceRMSDMetric); - double get_distance(unsigned int i, unsigned int j) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + double get_distance(unsigned int i, unsigned int j) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(DistanceRMSDMetric); }; diff --git a/modules/spb/include/DistanceTerminiRestraint.h b/modules/spb/include/DistanceTerminiRestraint.h index 2b991e7756..781017c0a3 100644 --- a/modules/spb/include/DistanceTerminiRestraint.h +++ b/modules/spb/include/DistanceTerminiRestraint.h @@ -38,8 +38,8 @@ class IMPSPBEXPORT DistanceTerminiRestraint : public IMP::Restraint { /** This macro declares the basic needed methods: evaluate and show */ virtual double unprotected_evaluate(IMP::DerivativeAccumulator* accum) const - IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(DistanceTerminiRestraint); private: diff --git a/modules/spb/include/EM2DRestraint.h b/modules/spb/include/EM2DRestraint.h index 58c4147fb0..f0d51497c7 100644 --- a/modules/spb/include/EM2DRestraint.h +++ b/modules/spb/include/EM2DRestraint.h @@ -61,7 +61,7 @@ class IMPSPBEXPORT EM2DRestraint : public spb::ISDRestraint { double get_element(double fmod, double sigma) const; // get probability - double get_probability() const IMP_OVERRIDE; + double get_probability() const override; /** This macro declares the basic needed methods: evaluate and show */ @@ -72,8 +72,8 @@ class IMPSPBEXPORT EM2DRestraint : public spb::ISDRestraint { // IMP_RESTRAINT( UniformBoundedRestraint); virtual double unprotected_evaluate(IMP::DerivativeAccumulator* accum) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(EM2DRestraint); }; diff --git a/modules/spb/include/Gaussian.h b/modules/spb/include/Gaussian.h index ab0c5d1190..647657fd8b 100644 --- a/modules/spb/include/Gaussian.h +++ b/modules/spb/include/Gaussian.h @@ -34,14 +34,14 @@ class Gaussian : public UnaryFunction { */ virtual DerivativePair evaluate_with_derivative(double feature) const - IMP_OVERRIDE { + override { return DerivativePair(evaluate(feature), -Emin_ * exp(-(feature - Zmin_) * (feature - Zmin_) / sigma_ / sigma_ / 2.0) * (feature - Zmin_) / sigma_ / sigma_); } - virtual double evaluate(double feature) const IMP_OVERRIDE { + virtual double evaluate(double feature) const override { return Emin_ * exp(-(feature - Zmin_) * (feature - Zmin_) / sigma_ / sigma_ / 2.0); } diff --git a/modules/spb/include/KinkPairScore.h b/modules/spb/include/KinkPairScore.h index a4ca322b96..6105cb7259 100644 --- a/modules/spb/include/KinkPairScore.h +++ b/modules/spb/include/KinkPairScore.h @@ -25,10 +25,10 @@ class IMPSPBEXPORT KinkPairScore : public PairScore { KinkPairScore(UnaryFunction *f); virtual double evaluate_index(IMP::Model *m, const IMP::ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual IMP::ModelObjectsTemp do_get_inputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; // void show(std::ostream &out) const ; diff --git a/modules/spb/include/MolecularDynamicsWithWte.h b/modules/spb/include/MolecularDynamicsWithWte.h index e93aef3fa2..84207da990 100644 --- a/modules/spb/include/MolecularDynamicsWithWte.h +++ b/modules/spb/include/MolecularDynamicsWithWte.h @@ -89,9 +89,9 @@ class IMPSPBEXPORT MolecularDynamicsWithWte : public atom::Simulator { void rescale_velocities(Float rescale); // IMP_SIMULATOR(MolecularDynamicsWithWte); - virtual void setup(const ParticleIndexes &ps) IMP_OVERRIDE; - virtual double do_step(const ParticleIndexes &sc, double dt) IMP_OVERRIDE; - virtual bool get_is_simulation_particle(ParticleIndex p) const IMP_OVERRIDE; + virtual void setup(const ParticleIndexes &ps) override; + virtual double do_step(const ParticleIndexes &sc, double dt) override; + virtual bool get_is_simulation_particle(ParticleIndex p) const override; protected: void initialize(); diff --git a/modules/spb/include/MonteCarloWithWte.h b/modules/spb/include/MonteCarloWithWte.h index 2df815a59b..10eaed3458 100644 --- a/modules/spb/include/MonteCarloWithWte.h +++ b/modules/spb/include/MonteCarloWithWte.h @@ -34,7 +34,7 @@ class IMPSPBEXPORT MonteCarloWithWte : public core::MonteCarlo { void update_bias(double score); virtual double do_evaluate( - const ParticleIndexes &moved, bool) const IMP_OVERRIDE; + const ParticleIndexes &moved, bool) const override; double get_spline(double score) const; public: @@ -66,7 +66,7 @@ class IMPSPBEXPORT MonteCarloWithWte : public core::MonteCarlo { } // IMP_MONTE_CARLO(MonteCarloWithWte); - virtual void do_step() IMP_OVERRIDE; + virtual void do_step() override; IMP_OBJECT_METHODS(MonteCarloWithWte); }; diff --git a/modules/spb/include/NuisanceRangeModifier.h b/modules/spb/include/NuisanceRangeModifier.h index fa2075f312..fb73217a90 100644 --- a/modules/spb/include/NuisanceRangeModifier.h +++ b/modules/spb/include/NuisanceRangeModifier.h @@ -22,11 +22,11 @@ class IMPSPBEXPORT NuisanceRangeModifier : public SingletonModifier { // note, Doxygen wants a semicolon at the end of macro lines virtual void apply_index(IMP::Model *m, - IMP::ParticleIndex p) const IMP_OVERRIDE; + IMP::ParticleIndex p) const override; virtual IMP::ModelObjectsTemp do_get_inputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; virtual IMP::ModelObjectsTemp do_get_outputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(NuisanceRangeModifier); IMP_OBJECT_METHODS(NuisanceRangeModifier); diff --git a/modules/spb/include/PbcBoxedMover.h b/modules/spb/include/PbcBoxedMover.h index cc81fe361d..e2a8c2f8e7 100644 --- a/modules/spb/include/PbcBoxedMover.h +++ b/modules/spb/include/PbcBoxedMover.h @@ -33,9 +33,9 @@ class IMPSPBEXPORT PbcBoxedMover : public core::MonteCarloMover { Particle *py, Particle *pz); protected: - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(PbcBoxedMover); IMP_SHOWABLE(PbcBoxedMover); diff --git a/modules/spb/include/PbcBoxedRigidBodyMover.h b/modules/spb/include/PbcBoxedRigidBodyMover.h index bc7a45b59f..832c608992 100644 --- a/modules/spb/include/PbcBoxedRigidBodyMover.h +++ b/modules/spb/include/PbcBoxedRigidBodyMover.h @@ -35,9 +35,9 @@ class IMPSPBEXPORT PbcBoxedRigidBodyMover : public core::MonteCarloMover { Particle *px, Particle *py, Particle *pz); protected: - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(PbcBoxedRigidBodyMover); IMP_SHOWABLE(PbcBoxedRigidBodyMover); diff --git a/modules/spb/include/RMSDMetric.h b/modules/spb/include/RMSDMetric.h index 9368232b67..32d2eb0038 100644 --- a/modules/spb/include/RMSDMetric.h +++ b/modules/spb/include/RMSDMetric.h @@ -29,8 +29,8 @@ class IMPSPBEXPORT RMSDMetric : public statistics::Metric { Float get_weight(unsigned i); // IMP_METRIC(RMSDMetric); - double get_distance(unsigned int i, unsigned int j) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + double get_distance(unsigned int i, unsigned int j) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(RMSDMetric); }; diff --git a/modules/spb/include/RigidBodyNewMover.h b/modules/spb/include/RigidBodyNewMover.h index ce02c457ba..f43ed2bf08 100644 --- a/modules/spb/include/RigidBodyNewMover.h +++ b/modules/spb/include/RigidBodyNewMover.h @@ -37,9 +37,9 @@ class IMPSPBEXPORT RigidBodyNewMover : public core::MonteCarloMover { // IMP_MOVER(RigidBodyNewMover); protected: - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(RigidBodyNewMover); IMP_SHOWABLE(RigidBodyNewMover); diff --git a/modules/spb/include/RigidBodyPackingScore.h b/modules/spb/include/RigidBodyPackingScore.h index 1885118c54..0b52adbc48 100644 --- a/modules/spb/include/RigidBodyPackingScore.h +++ b/modules/spb/include/RigidBodyPackingScore.h @@ -27,10 +27,10 @@ class IMPSPBEXPORT RigidBodyPackingScore : public PairScore { Floats ddb, Floats dde, double kappa); virtual double evaluate_index(IMP::Model *m, const IMP::ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual IMP::ModelObjectsTemp do_get_inputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; // void show(std::ostream &out) const ; diff --git a/modules/spb/include/SameParticlePairFilter.h b/modules/spb/include/SameParticlePairFilter.h index 0701c636e0..91a59bf34e 100644 --- a/modules/spb/include/SameParticlePairFilter.h +++ b/modules/spb/include/SameParticlePairFilter.h @@ -22,10 +22,10 @@ class IMPSPBEXPORT SameParticlePairFilter : public PairPredicate { SameParticlePairFilter(); virtual int get_value_index( - IMP::Model *m, const IMP::ParticleIndexPair &p) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexPair &p) const override; virtual IMP::ModelObjectsTemp do_get_inputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; IMP_PAIR_PREDICATE_METHODS(SameParticlePairFilter); IMP_OBJECT_METHODS(SameParticlePairFilter); diff --git a/modules/spb/include/SameRigidBodyPairFilter.h b/modules/spb/include/SameRigidBodyPairFilter.h index 4e060044ed..1ae4e79ce2 100644 --- a/modules/spb/include/SameRigidBodyPairFilter.h +++ b/modules/spb/include/SameRigidBodyPairFilter.h @@ -22,10 +22,10 @@ class IMPSPBEXPORT SameRigidBodyPairFilter : public PairPredicate { SameRigidBodyPairFilter(); virtual int get_value_index( - IMP::Model *m, const IMP::ParticleIndexPair &p) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexPair &p) const override; virtual IMP::ModelObjectsTemp do_get_inputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; IMP_PAIR_PREDICATE_METHODS(SameRigidBodyPairFilter); IMP_OBJECT_METHODS(SameRigidBodyPairFilter); diff --git a/modules/spb/include/TiltSingletonScore.h b/modules/spb/include/TiltSingletonScore.h index f3908774ca..b61103829a 100644 --- a/modules/spb/include/TiltSingletonScore.h +++ b/modules/spb/include/TiltSingletonScore.h @@ -36,10 +36,10 @@ class IMPSPBEXPORT TiltSingletonScore : public SingletonScore { const algebra::VectorD<3> &v2); virtual double evaluate_index(IMP::Model *m, const IMP::ParticleIndex p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual IMP::ModelObjectsTemp do_get_inputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; IMP_SINGLETON_SCORE_METHODS(TiltSingletonScore); IMP_OBJECT_METHODS(TiltSingletonScore); diff --git a/modules/spb/include/TransformationSymmetry.h b/modules/spb/include/TransformationSymmetry.h index dfa759cd16..07b33708a6 100644 --- a/modules/spb/include/TransformationSymmetry.h +++ b/modules/spb/include/TransformationSymmetry.h @@ -39,11 +39,11 @@ class IMPSPBEXPORT TransformationSymmetry : public SingletonModifier { Particle *py, Particle *pz); virtual void apply_index(IMP::Model *m, - IMP::ParticleIndex p) const IMP_OVERRIDE; + IMP::ParticleIndex p) const override; virtual IMP::ModelObjectsTemp do_get_inputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; virtual IMP::ModelObjectsTemp do_get_outputs( - IMP::Model *m, const IMP::ParticleIndexes &pis) const IMP_OVERRIDE; + IMP::Model *m, const IMP::ParticleIndexes &pis) const override; IMP_SINGLETON_MODIFIER_METHODS(TransformationSymmetry); diff --git a/modules/spb/include/TwoStateGoModelRestraint.h b/modules/spb/include/TwoStateGoModelRestraint.h index c381e128ee..bba498bbcc 100644 --- a/modules/spb/include/TwoStateGoModelRestraint.h +++ b/modules/spb/include/TwoStateGoModelRestraint.h @@ -35,8 +35,8 @@ class IMPSPBEXPORT TwoStateGoModelRestraint : public Restraint { Float Beta, Float Delta, Float Cutoff); virtual double unprotected_evaluate(IMP::DerivativeAccumulator* accum) const - IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; // IMP_RESTRAINT(TwoStateGoModelRestraint); IMP_OBJECT_METHODS(TwoStateGoModelRestraint); diff --git a/modules/spb/include/UniformBoundedRestraint.h b/modules/spb/include/UniformBoundedRestraint.h index bea525abfa..577d1dc900 100644 --- a/modules/spb/include/UniformBoundedRestraint.h +++ b/modules/spb/include/UniformBoundedRestraint.h @@ -34,15 +34,15 @@ class IMPSPBEXPORT UniformBoundedRestraint UniformBoundedRestraint(Particle *p, FloatKey fk, Particle *a, Particle *b); /* call for probability */ - double get_probability() const IMP_OVERRIDE; + double get_probability() const override; /** This macro declares the basic needed methods: evaluate and show */ // IMP_RESTRAINT( UniformBoundedRestraint); // virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(UniformBoundedRestraint); }; diff --git a/modules/statistics/include/ChiSquareMetric.h b/modules/statistics/include/ChiSquareMetric.h index 19ab6ea121..d25763e164 100644 --- a/modules/statistics/include/ChiSquareMetric.h +++ b/modules/statistics/include/ChiSquareMetric.h @@ -51,12 +51,12 @@ class IMPSTATISTICSEXPORT ChiSquareMetric : public Metric { //! get the list of standard deviations for the i-th configuration Floats get_standard_deviation(unsigned i) const; //! get the weight for the i-th configuration - double do_get_weight(unsigned i) const IMP_OVERRIDE; + double do_get_weight(unsigned i) const override; //! get chi2 from experimental data for the i-th configuration double get_chi_square_experimental(unsigned i) const; - double get_distance(unsigned int i, unsigned int j) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + double get_distance(unsigned int i, unsigned int j) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(ChiSquareMetric); }; diff --git a/modules/statistics/include/PartitionalClusteringWithCenter.h b/modules/statistics/include/PartitionalClusteringWithCenter.h index f49b7a228d..62d193aa0a 100644 --- a/modules/statistics/include/PartitionalClusteringWithCenter.h +++ b/modules/statistics/include/PartitionalClusteringWithCenter.h @@ -46,9 +46,9 @@ class IMPSTATISTICSEXPORT PartitionalClusteringWithCenter const algebra::VectorKD &get_cluster_center(unsigned int i) const { return centers_[i]; } - unsigned int get_number_of_clusters() const IMP_OVERRIDE; - const Ints &get_cluster(unsigned int i) const IMP_OVERRIDE; - int get_cluster_representative(unsigned int i) const IMP_OVERRIDE; + unsigned int get_number_of_clusters() const override; + const Ints &get_cluster(unsigned int i) const override; + int get_cluster_representative(unsigned int i) const override; IMP_OBJECT_METHODS(PartitionalClusteringWithCenter); }; diff --git a/modules/statistics/include/RecursivePartitionalClusteringEmbedding.h b/modules/statistics/include/RecursivePartitionalClusteringEmbedding.h index 076a20b0ed..8dc8f83730 100644 --- a/modules/statistics/include/RecursivePartitionalClusteringEmbedding.h +++ b/modules/statistics/include/RecursivePartitionalClusteringEmbedding.h @@ -31,8 +31,8 @@ class IMPSTATISTICSEXPORT RecursivePartitionalClusteringEmbedding PartitionalClustering *clustering); PartitionalClustering *create_full_clustering( PartitionalClustering *center_cluster); - algebra::VectorKD get_point(unsigned int i) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + algebra::VectorKD get_point(unsigned int i) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(RecursivePartitionalClusteringEmbedding); }; diff --git a/modules/statistics/include/RecursivePartitionalClusteringMetric.h b/modules/statistics/include/RecursivePartitionalClusteringMetric.h index 194d9fcda5..3880255d79 100644 --- a/modules/statistics/include/RecursivePartitionalClusteringMetric.h +++ b/modules/statistics/include/RecursivePartitionalClusteringMetric.h @@ -31,8 +31,8 @@ class IMPSTATISTICSEXPORT RecursivePartitionalClusteringMetric : public Metric { PartitionalClustering *clustering); PartitionalClustering *create_full_clustering( PartitionalClustering *center_cluster); - double get_distance(unsigned int i, unsigned int j) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + double get_distance(unsigned int i, unsigned int j) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(RecursivePartitionalClusteringMetric); }; diff --git a/modules/statistics/include/embeddings.h b/modules/statistics/include/embeddings.h index 2d5cf3c48e..ddd3d727e8 100644 --- a/modules/statistics/include/embeddings.h +++ b/modules/statistics/include/embeddings.h @@ -37,8 +37,8 @@ class IMPSTATISTICSEXPORT ConfigurationSetXYZEmbedding : public Embedding { ConfigurationSetXYZEmbedding(ConfigurationSet *cs, SingletonContainerAdaptor pi, bool align = false); - algebra::VectorKD get_point(unsigned int i) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + algebra::VectorKD get_point(unsigned int i) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(ConfigurationSetXYZEmbedding); }; @@ -70,8 +70,8 @@ class IMPSTATISTICSEXPORT ParticleEmbedding : public Embedding { #endif , bool rescale = false); - algebra::VectorKD get_point(unsigned int i) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + algebra::VectorKD get_point(unsigned int i) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(ParticleEmbedding); }; @@ -96,8 +96,8 @@ class IMPSTATISTICSEXPORT VectorDEmbedding : public Embedding { VectorDEmbedding(const algebra::Vector5Ds &vs); VectorDEmbedding(const algebra::Vector6Ds &vs); #endif - algebra::VectorKD get_point(unsigned int i) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + algebra::VectorKD get_point(unsigned int i) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(VectorDEmbedding); }; diff --git a/modules/statistics/include/internal/KMCentersNodeLeaf.h b/modules/statistics/include/internal/KMCentersNodeLeaf.h index effb06a713..05b93b89b3 100644 --- a/modules/statistics/include/internal/KMCentersNodeLeaf.h +++ b/modules/statistics/include/internal/KMCentersNodeLeaf.h @@ -53,16 +53,16 @@ class IMPSTATISTICSEXPORT KMCentersNodeLeaf : public KMCentersNode { the node. The sum of squares is the sum of dot products of each point with itself. */ - void compute_sums() IMP_OVERRIDE; + void compute_sums() override; //! Compute neighbors for centers void get_neighbors(const Ints &cands, KMPointArray *sums, KMPoint *sum_sqs, - Ints *weights) IMP_OVERRIDE; + Ints *weights) override; //! Get assignments for leaf node - void get_assignments(const Ints &cands, Ints &close_center) IMP_OVERRIDE; + void get_assignments(const Ints &cands, Ints &close_center) override; //! Sample a center point c - KMPoint sample_center() IMP_OVERRIDE; - void show(std::ostream &out = std::cout) const IMP_OVERRIDE; + KMPoint sample_center() override; + void show(std::ostream &out = std::cout) const override; protected: Ints data_ps_; // the indexes of data points diff --git a/modules/statistics/include/internal/KMCentersNodeSplit.h b/modules/statistics/include/internal/KMCentersNodeSplit.h index 5f50b34718..70ca11754d 100644 --- a/modules/statistics/include/internal/KMCentersNodeSplit.h +++ b/modules/statistics/include/internal/KMCentersNodeSplit.h @@ -52,11 +52,11 @@ class IMPSTATISTICSEXPORT KMCentersNodeSplit : public KMCentersNode { The sum on a specific dimension is the sum of the sums of the children on that dimension. */ - void compute_sums() IMP_OVERRIDE; + void compute_sums() override; //! Compute neighbors for centers void get_neighbors(const Ints &cands, KMPointArray *sums, KMPoint *sum_sqs, - Ints *weights) IMP_OVERRIDE; - void get_assignments(const Ints &cands, Ints &close_center) IMP_OVERRIDE; + Ints *weights) override; + void get_assignments(const Ints &cands, Ints &close_center) override; /** Let m denote the number of data points descended from this node. Then with probability 1/(2m-1), this cell is chosen. Otherwise, let mL and mR denote the number of points associated @@ -71,10 +71,10 @@ class IMPSTATISTICSEXPORT KMCentersNodeSplit : public KMCentersNode { sampled with probability 1/(2m-1), and the subtrees should be sampled with the given probabilities. */ - KMPoint sample_center() IMP_OVERRIDE; + KMPoint sample_center() override; //! Print node - void show(std::ostream &out = std::cout) const IMP_OVERRIDE; + void show(std::ostream &out = std::cout) const override; protected: int cut_dim_; // dim orthogonal to cutting plane diff --git a/modules/statistics/include/internal/KMFilterCenters.h b/modules/statistics/include/internal/KMFilterCenters.h index ba3bbc19da..4d12e07051 100644 --- a/modules/statistics/include/internal/KMFilterCenters.h +++ b/modules/statistics/include/internal/KMFilterCenters.h @@ -78,7 +78,7 @@ class IMPSTATISTICSEXPORT KMFilterCenters : public KMCenters { //! Generate random centers virtual void generate_random_centers(int k); - void show(std::ostream &out = std::cout) const IMP_OVERRIDE; + void show(std::ostream &out = std::cout) const override; //! move centers to cluster centroids /** Moves each center point to the centroid of its associated cluster. We call compute_distortion() if necessary to compute the weights @@ -204,7 +204,7 @@ class IMPSTATISTICSEXPORT KMFilterCentersResults : public KMCenters { //! Get the assignment of points to centers const Ints *get_assignments() const { return &close_center_; } - void show(std::ostream &out = std::cout) const IMP_OVERRIDE { + void show(std::ostream &out = std::cout) const override { for (int j = 0; j < get_number_of_centers(); j++) { out << " " << std::setw(4) << j << "\t"; print_point(*((*centers_)[j]), out); diff --git a/modules/statistics/include/internal/KMLocalSearchLloyd.h b/modules/statistics/include/internal/KMLocalSearchLloyd.h index 53dd6d8c46..dcafc6a4dd 100644 --- a/modules/statistics/include/internal/KMLocalSearchLloyd.h +++ b/modules/statistics/include/internal/KMLocalSearchLloyd.h @@ -41,31 +41,31 @@ class IMPSTATISTICSEXPORT KMLocalSearchLloyd : public KMLocalSearch { double get_accumulated_rdl() { return (init_trail_dist_ - curr_->get_distortion()) / init_trail_dist_; } - void log_stage(std::ostream &out = std::cout) IMP_OVERRIDE; + void log_stage(std::ostream &out = std::cout) override; void log_run() { IMP_LOG_VERBOSE("" << std::endl); } //! Do base class resetting. Initialize is_new_phase to false and save //! the initial run distortion. - virtual void reset() IMP_OVERRIDE; + virtual void reset() override; //! Do base class processing. If there has been an improvement in distortion, //! save the current solution. - void end_stage() IMP_OVERRIDE; + void end_stage() override; //! Checks if the run is done /** If the number of stages exceeds the maximum stages (total or per run), then we are done. If this is the first stage of the run, then we are not done, and we do beginning of run processing. Otherwise, if the relative distortion loss (RDL) is greater than minimum val then we are done (success). */ - virtual bool is_run_done() IMP_OVERRIDE; + virtual bool is_run_done() override; //! End the run /** If the accumulated RDL is smaller that the minimum predefined accumulated RDL then the run has ended unsuccessfully and we request the start of a new run. Otherwise the run has ended successfully, and we start a new run by saving the current run distortion. */ - void end_run() IMP_OVERRIDE; - void preform_stage() IMP_OVERRIDE; + void end_run() override; + void preform_stage() override; double init_trail_dist_; // initial distortion for a trail bool is_new_trail_; }; diff --git a/modules/statistics/include/internal/TrivialPartitionalClustering.h b/modules/statistics/include/internal/TrivialPartitionalClustering.h index 01da395c30..8003bfaa3e 100644 --- a/modules/statistics/include/internal/TrivialPartitionalClustering.h +++ b/modules/statistics/include/internal/TrivialPartitionalClustering.h @@ -40,9 +40,9 @@ class TrivialPartitionalClustering : public PartitionalClustering { } } } - unsigned int get_number_of_clusters() const IMP_OVERRIDE; - const Ints &get_cluster(unsigned int i) const IMP_OVERRIDE; - int get_cluster_representative(unsigned int i) const IMP_OVERRIDE; + unsigned int get_number_of_clusters() const override; + const Ints &get_cluster(unsigned int i) const override; + int get_cluster_representative(unsigned int i) const override; IMP_OBJECT_METHODS(TrivialPartitionalClustering); }; diff --git a/modules/statistics/include/internal/VQClustering.h b/modules/statistics/include/internal/VQClustering.h index da1e308138..ab5d7bba09 100644 --- a/modules/statistics/include/internal/VQClustering.h +++ b/modules/statistics/include/internal/VQClustering.h @@ -63,7 +63,7 @@ class IMPSTATISTICSEXPORT VQClustering : public ClusteringEngine { void run(DataPoints *starting_centers = nullptr); bool is_part_of_cluster(int data_point_ind, - int cluster_ind) const IMP_OVERRIDE { + int cluster_ind) const override { return (get_cluster_assignment(data_point_ind) == cluster_ind); } @@ -76,12 +76,12 @@ class IMPSTATISTICSEXPORT VQClustering : public ClusteringEngine { return assignment_[data_point_ind]; } - Array1DD get_center(int center_ind) const IMP_OVERRIDE { + Array1DD get_center(int center_ind) const override { IMP_USAGE_CHECK(is_set_, " the clusters have not been assigned " << std::endl); return centers_[center_ind]; } - int get_number_of_clusters() const IMP_OVERRIDE { return k_; } + int get_number_of_clusters() const override { return k_; } void set_random_offset(double o) { par_.random_offset_ = o; } const DataPoints *get_full_data() const { return full_data_; } void set_fast_clustering(); diff --git a/modules/statistics/include/metrics.h b/modules/statistics/include/metrics.h index 2917ffa95d..5f40e038e7 100644 --- a/modules/statistics/include/metrics.h +++ b/modules/statistics/include/metrics.h @@ -25,8 +25,8 @@ class IMPSTATISTICSEXPORT EuclideanMetric : public Metric { public: EuclideanMetric(Embedding *em); - double get_distance(unsigned int i, unsigned int j) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + double get_distance(unsigned int i, unsigned int j) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(EuclideanMetric); }; @@ -52,8 +52,8 @@ class IMPSTATISTICSEXPORT ConfigurationSetRMSDMetric : public Metric { */ ConfigurationSetRMSDMetric(ConfigurationSet *cs, SingletonContainer *sc, bool align = false); - double get_distance(unsigned int i, unsigned int j) const IMP_OVERRIDE; - unsigned int get_number_of_items() const IMP_OVERRIDE; + double get_distance(unsigned int i, unsigned int j) const override; + unsigned int get_number_of_items() const override; IMP_OBJECT_METHODS(ConfigurationSetRMSDMetric); }; diff --git a/modules/symmetry/include/BallMover.h b/modules/symmetry/include/BallMover.h index cc2c784d5c..be8b6e5072 100644 --- a/modules/symmetry/include/BallMover.h +++ b/modules/symmetry/include/BallMover.h @@ -30,9 +30,9 @@ class IMPSYMMETRYEXPORT BallMover : public core::MonteCarloMover { algebra::Vector3Ds ctrs, algebra::Transformation3Ds trs); protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(BallMover); private: diff --git a/modules/symmetry/include/RigidBodyMover.h b/modules/symmetry/include/RigidBodyMover.h index 8b5ca14059..9b81c9e2b7 100644 --- a/modules/symmetry/include/RigidBodyMover.h +++ b/modules/symmetry/include/RigidBodyMover.h @@ -35,9 +35,9 @@ class IMPSYMMETRYEXPORT RigidBodyMover : public core::MonteCarloMover { algebra::Transformation3Ds trs); protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(RigidBodyMover); private: From 509bf6aca44013216900397586cf10706777682a Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 16:51:27 -0800 Subject: [PATCH 038/155] Deprecate our nullptr workaround Since we now require C++11 we can use the 'nullptr' keyword and std::nullptr_t type, so we don't need to create our own workaround type in the IMP namespace. Keep the header around for now though to avoid breaking external modules. --- modules/kernel/include/nullptr.h | 60 ++----------------------- modules/kernel/include/nullptr_macros.h | 8 +--- 2 files changed, 6 insertions(+), 62 deletions(-) diff --git a/modules/kernel/include/nullptr.h b/modules/kernel/include/nullptr.h index 989ffa1174..78ff7b1aa1 100644 --- a/modules/kernel/include/nullptr.h +++ b/modules/kernel/include/nullptr.h @@ -9,62 +9,10 @@ #define IMPKERNEL_NULLPTR_H #include -#include -namespace IMP { -#ifdef IMP_DOXYGEN -/** The C++0x standard adds the nullptr keyword to get around a variety of - problems with NULL. We provide an emulation within the IMP namespace when - it is not available. - - Use "nullptr" in code; the compiler will use our IMP::nullptr emulation - automatically on systems that don't provide a native nullptr implementation. - - If you are not in the IMP namespace, use the IMP_NULLPTR macro rather - than asking for "IMP::nullptr". The latter does not work with some compilers - (e.g. MSVC, which gets confused because nullptr is a keyword). -*/ -const std::nullptr_t nullptr; - -// depending on boost version -#elif(defined(BOOST_NO_CXX11_NULLPTR) || defined(BOOST_NO_NULLPTR)) && \ - !defined(nullptr) - -#if !defined(SWIG) - -#if __GNUC__ &&__GNUC__ == 4 && __GNUC_MINOR__ >= 6 -IMP_GCC_PRAGMA(diagnostic push) -IMP_GCC_PRAGMA(diagnostic ignored "-Wc++0x-compat") -#endif - -struct nullptr_t { - template - operator O *() const { - return static_cast(NULL); - } - /*template - operator O C::*() const { - return static_cast(NULL); - }*/ -}; -template -inline bool operator==(O *a, nullptr_t o) { - return a == static_cast(o); -} -template -inline bool operator!=(O *a, nullptr_t o) { - return a != static_cast(o); -} -extern IMPKERNELEXPORT const nullptr_t nullptr; - -#if __GNUC__ &&__GNUC__ == 4 && __GNUC_MINOR__ >= 6 -IMP_GCC_PRAGMA(diagnostic pop) -#endif - -#else // SWIG -extern const void *const nullptr; -#endif // SWIG -#endif // IMP_DOXYGEN -} +IMPKERNEL_DEPRECATED_HEADER( + 2.17, "Use the nullptr keyword or std::nullptr_t type directly"); +// Does nothing: the nullptr keyword should now be available on all +// supported IMP build platforms #endif /* IMPKERNEL_NULLPTR_H */ diff --git a/modules/kernel/include/nullptr_macros.h b/modules/kernel/include/nullptr_macros.h index cc11a85ce1..a918534043 100644 --- a/modules/kernel/include/nullptr_macros.h +++ b/modules/kernel/include/nullptr_macros.h @@ -10,13 +10,9 @@ #include -#if(defined(BOOST_NO_CXX11_NULLPTR) || defined(BOOST_NO_NULLPTR)) && \ - !defined(nullptr) -#define IMP_NULLPTR IMP::nullptr -#define IMP_NULLPTR_T IMP::nullptr_t -#else +IMPKERNEL_DEPRECATED_HEADER( + 2.17, "Use the nullptr keyword or std::nullptr_t type directly"); #define IMP_NULLPTR nullptr #define IMP_NULLPTR_T std::nullptr_t -#endif // IMP_COMPILER_HAS_NULLPTR #endif /* IMPKERNEL_NULLPTR_MACROS_H */ From 4ad197e06009d64a0fc47a057da205951f5caf49 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 17:08:55 -0800 Subject: [PATCH 039/155] Don't warn when included by SWIG wrappers These headers are still included (via IMP.h) when building SWIG wrappers, even though they're not used, so suppress deprecation warnings here. --- modules/kernel/include/nullptr.h | 2 ++ modules/kernel/include/nullptr_macros.h | 3 +++ 2 files changed, 5 insertions(+) diff --git a/modules/kernel/include/nullptr.h b/modules/kernel/include/nullptr.h index 78ff7b1aa1..b2c5119e43 100644 --- a/modules/kernel/include/nullptr.h +++ b/modules/kernel/include/nullptr.h @@ -10,8 +10,10 @@ #include +#ifndef IMP_SWIG_WRAPPER IMPKERNEL_DEPRECATED_HEADER( 2.17, "Use the nullptr keyword or std::nullptr_t type directly"); +#endif // Does nothing: the nullptr keyword should now be available on all // supported IMP build platforms diff --git a/modules/kernel/include/nullptr_macros.h b/modules/kernel/include/nullptr_macros.h index a918534043..d298fc438a 100644 --- a/modules/kernel/include/nullptr_macros.h +++ b/modules/kernel/include/nullptr_macros.h @@ -10,8 +10,11 @@ #include +#ifndef IMP_SWIG_WRAPPER IMPKERNEL_DEPRECATED_HEADER( 2.17, "Use the nullptr keyword or std::nullptr_t type directly"); +#endif + #define IMP_NULLPTR nullptr #define IMP_NULLPTR_T std::nullptr_t From 840f292c1a3ccb965731d5fbd716bf7cff49e49b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 17:09:58 -0800 Subject: [PATCH 040/155] Use nullptr keyword rather than IMP header --- modules/atom/examples/dope_and_excluded_volume.cpp | 3 +-- modules/benchmark/include/benchmark_macros.h | 3 +-- modules/core/test/test_soft_sphere.cpp | 4 +--- modules/integrative_docking/bin/soap_score.cpp | 5 ++--- modules/kernel/include/ConstVector.h | 1 - modules/kernel/include/CreateLogContext.h | 1 - modules/kernel/include/Restraint.h | 1 - modules/kernel/include/ScoreAccumulator.h | 1 - modules/kernel/include/SetCheckState.h | 1 - modules/kernel/include/SetLogState.h | 1 - modules/kernel/include/exception.h | 1 - modules/kernel/include/internal/PointerBase.h | 1 - modules/kernel/include/internal/swig_helpers_base.h | 4 +--- modules/kernel/include/types.h | 1 - modules/kernel/test/test_pair_memoizer.cpp | 3 +-- modules/kinematics/include/Joint.h | 1 - modules/saxs/bin/cluster_profiles.cpp | 4 +--- modules/saxs/src/Profile.cpp | 9 ++++----- 18 files changed, 12 insertions(+), 33 deletions(-) diff --git a/modules/atom/examples/dope_and_excluded_volume.cpp b/modules/atom/examples/dope_and_excluded_volume.cpp index 76200a9636..dc9dd633b3 100644 --- a/modules/atom/examples/dope_and_excluded_volume.cpp +++ b/modules/atom/examples/dope_and_excluded_volume.cpp @@ -18,7 +18,6 @@ #include #include #include -#include namespace { const double dope_threshold = 16; @@ -85,7 +84,7 @@ int main(int argc, char *argv[]) { for (unsigned int i = 0; i < pips.size(); ++i) { std::cout << "Score is " << score->evaluate_index( - model, pips[i], IMP_NULLPTR) << std::endl; + model, pips[i], nullptr) << std::endl; } return 0; } diff --git a/modules/benchmark/include/benchmark_macros.h b/modules/benchmark/include/benchmark_macros.h index f0a2b3eb0a..fcd6283874 100644 --- a/modules/benchmark/include/benchmark_macros.h +++ b/modules/benchmark/include/benchmark_macros.h @@ -11,7 +11,6 @@ #include #include -#include #include #include #include "internal/control.h" @@ -77,7 +76,7 @@ #define IMP_BENCHMARK_HEAP_CHECKING_END \ if (IMP::benchmark::internal::heap_check_benchmarks) { \ if (!heap_checker->NoLeaks()) std::cerr << "Leaks found\n"; \ - heap_checker.reset(IMP_NULLPTR); \ + heap_checker.reset(nullptr); \ } #else #define IMP_BENCHMARK_HEAP_CHECKING_BEGIN diff --git a/modules/core/test/test_soft_sphere.cpp b/modules/core/test/test_soft_sphere.cpp index 6a1e9e9037..a25e274c88 100644 --- a/modules/core/test/test_soft_sphere.cpp +++ b/modules/core/test/test_soft_sphere.cpp @@ -14,7 +14,6 @@ #include #include #include -#include namespace { @@ -36,8 +35,7 @@ int main(int argc, char *argv[]) { m, p1, IMP::algebra::Sphere3D(IMP::algebra::Vector3D(1, 0, 0), 1)); IMP_NEW(SoftSpherePairScore, ssps, (1)); IMP_TEST_GREATER_THAN( - ssps->evaluate_index(m, IMP::ParticleIndexPair(p0, p1), - IMP_NULLPTR), + ssps->evaluate_index(m, IMP::ParticleIndexPair(p0, p1), nullptr), 0); ssps->set_was_used(true); return 0; diff --git a/modules/integrative_docking/bin/soap_score.cpp b/modules/integrative_docking/bin/soap_score.cpp index 7bad0b18a6..42f3c50dc2 100644 --- a/modules/integrative_docking/bin/soap_score.cpp +++ b/modules/integrative_docking/bin/soap_score.cpp @@ -12,7 +12,6 @@ #include #include -#include #include #include @@ -119,8 +118,8 @@ each pair of PDB file names in the input file filenames.txt.") // init SOAP table float distance_threshold = 15.0; - IMP::score_functor::Soap* soap_distance_score = IMP_NULLPTR; - IMP::score_functor::OrientedSoap* soap_oriented_score = IMP_NULLPTR; + IMP::score_functor::Soap* soap_distance_score = nullptr; + IMP::score_functor::OrientedSoap* soap_oriented_score = nullptr; if (oriented_potentials) { soap_oriented_score = new IMP::score_functor::OrientedSoap(potentials_file); diff --git a/modules/kernel/include/ConstVector.h b/modules/kernel/include/ConstVector.h index cd059079c8..191071dc27 100644 --- a/modules/kernel/include/ConstVector.h +++ b/modules/kernel/include/ConstVector.h @@ -13,7 +13,6 @@ #include "base_macros.h" #include "exception.h" #include "Value.h" -#include #include #include #include diff --git a/modules/kernel/include/CreateLogContext.h b/modules/kernel/include/CreateLogContext.h index 8ad42d28f8..a8639f98f4 100644 --- a/modules/kernel/include/CreateLogContext.h +++ b/modules/kernel/include/CreateLogContext.h @@ -12,7 +12,6 @@ #include #include "raii_macros.h" #include "log.h" -#include #include "Object.h" #if IMP_KERNEL_HAS_LOG4CXX #include diff --git a/modules/kernel/include/Restraint.h b/modules/kernel/include/Restraint.h index 0ebcd07f95..91261ebec8 100644 --- a/modules/kernel/include/Restraint.h +++ b/modules/kernel/include/Restraint.h @@ -17,7 +17,6 @@ #include "base_types.h" #include #include -#include #include IMPKERNEL_BEGIN_NAMESPACE diff --git a/modules/kernel/include/ScoreAccumulator.h b/modules/kernel/include/ScoreAccumulator.h index 0d29a7bec0..22691f704d 100644 --- a/modules/kernel/include/ScoreAccumulator.h +++ b/modules/kernel/include/ScoreAccumulator.h @@ -18,7 +18,6 @@ #include #include #include -#include #include IMPKERNEL_BEGIN_NAMESPACE diff --git a/modules/kernel/include/SetCheckState.h b/modules/kernel/include/SetCheckState.h index 20cc82cdf0..c02d181629 100644 --- a/modules/kernel/include/SetCheckState.h +++ b/modules/kernel/include/SetCheckState.h @@ -13,7 +13,6 @@ #include "enums.h" #include "raii_macros.h" #include "value_macros.h" -#include IMPKERNEL_BEGIN_NAMESPACE class Object; diff --git a/modules/kernel/include/SetLogState.h b/modules/kernel/include/SetLogState.h index 115ce98405..b72271ffbd 100644 --- a/modules/kernel/include/SetLogState.h +++ b/modules/kernel/include/SetLogState.h @@ -12,7 +12,6 @@ #include "enums.h" #include "raii_macros.h" #include "value_macros.h" -#include IMPKERNEL_BEGIN_NAMESPACE class Object; diff --git a/modules/kernel/include/exception.h b/modules/kernel/include/exception.h index 4fd7d84b73..926ceab15a 100644 --- a/modules/kernel/include/exception.h +++ b/modules/kernel/include/exception.h @@ -12,7 +12,6 @@ #include #include "compiler_macros.h" #include "enums.h" -#include "nullptr.h" #include "internal/base_static.h" #include #include diff --git a/modules/kernel/include/internal/PointerBase.h b/modules/kernel/include/internal/PointerBase.h index 469dfb00b0..6b89bd5f3c 100644 --- a/modules/kernel/include/internal/PointerBase.h +++ b/modules/kernel/include/internal/PointerBase.h @@ -14,7 +14,6 @@ #include "../warning_macros.h" #include "../hash.h" #include "../hash_macros.h" -#include "../nullptr.h" #if defined(BOOST_NO_CXX11_NULLPTR) || defined(BOOST_NO_NULLPTR) #include diff --git a/modules/kernel/include/internal/swig_helpers_base.h b/modules/kernel/include/internal/swig_helpers_base.h index 7f3d228ea2..63badf3db1 100644 --- a/modules/kernel/include/internal/swig_helpers_base.h +++ b/modules/kernel/include/internal/swig_helpers_base.h @@ -16,9 +16,7 @@ #include "../Vector.h" #include "../Array.h" #include "../ConstVector.h" -#include "../nullptr_macros.h" #include "IMP/Vector.h" -#include "IMP/nullptr.h" #include #include @@ -84,7 +82,7 @@ struct PyPointer : boost::noncopyable { PyObject* release() { IMP_INTERNAL_CHECK(ptr_->ob_refcnt >= 1, "No refcount"); PyObject* ret = ptr_; - ptr_ = IMP_NULLPTR; + ptr_ = nullptr; return ret; } ~PyPointer() { diff --git a/modules/kernel/include/types.h b/modules/kernel/include/types.h index cda7ead07b..58566dab2a 100644 --- a/modules/kernel/include/types.h +++ b/modules/kernel/include/types.h @@ -12,7 +12,6 @@ #include "value_macros.h" #include "object_macros.h" #include -#include // IMPKERNEL_BEGIN_NAMESPACE namespace IMP { diff --git a/modules/kernel/test/test_pair_memoizer.cpp b/modules/kernel/test/test_pair_memoizer.cpp index 333480e9c6..bc9f0ebe1d 100644 --- a/modules/kernel/test/test_pair_memoizer.cpp +++ b/modules/kernel/test/test_pair_memoizer.cpp @@ -9,7 +9,6 @@ #include #include #include -#include #include #include #include @@ -30,7 +29,7 @@ const int threshold = 2; namespace IMP { struct IP { int *p_; - IP() : p_(IMP_NULLPTR) {} + IP() : p_(nullptr) {} IP(int *p) : p_(p) {} operator int *() const { return p_; } // operator int*(){return p_;} diff --git a/modules/kinematics/include/Joint.h b/modules/kinematics/include/Joint.h index 1e31c06b9a..6932cce69a 100644 --- a/modules/kinematics/include/Joint.h +++ b/modules/kinematics/include/Joint.h @@ -14,7 +14,6 @@ #include #include #include -//#include #include #include #include diff --git a/modules/saxs/bin/cluster_profiles.cpp b/modules/saxs/bin/cluster_profiles.cpp index 9343a5bda7..e6bfda750b 100644 --- a/modules/saxs/bin/cluster_profiles.cpp +++ b/modules/saxs/bin/cluster_profiles.cpp @@ -5,8 +5,6 @@ #include #include -#include - #include #include #include @@ -67,7 +65,7 @@ int main(int argc, char **argv) { } // read the profiles - IMP::saxs::Profile *exp_profile = IMP_NULLPTR; + IMP::saxs::Profile *exp_profile = nullptr; std::map > fit_profiles; bool fit_file = false; // open input file with profile file names - mes format diff --git a/modules/saxs/src/Profile.cpp b/modules/saxs/src/Profile.cpp index 202fd118a1..077a514e91 100644 --- a/modules/saxs/src/Profile.cpp +++ b/modules/saxs/src/Profile.cpp @@ -18,7 +18,6 @@ #include #include #include -#include #include #include @@ -45,7 +44,7 @@ Profile::Profile(double qmin, double qmax, double delta) average_radius_(1.58), average_volume_(17.5), id_(0), - beam_profile_(IMP_NULLPTR) { + beam_profile_(nullptr) { set_was_used(true); ff_table_ = get_default_form_factor_table(); } @@ -55,7 +54,7 @@ Profile::Profile(const std::string& file_name, bool fit_file, double max_q, int experimental_(true), name_(file_name), id_(0), - beam_profile_(IMP_NULLPTR) { + beam_profile_(nullptr) { set_was_used(true); if (fit_file) experimental_ = false; read_SAXS_file(file_name, fit_file, max_q, units); @@ -841,7 +840,7 @@ void Profile::squared_distribution_2_profile( } bool use_beam_profile = false; - if (beam_profile_ != IMP_NULLPTR && beam_profile_->size() > 0) + if (beam_profile_ != nullptr && beam_profile_->size() > 0) use_beam_profile = true; // iterate over intensity profile @@ -891,7 +890,7 @@ void Profile::squared_distributions_2_partial_profiles( } bool use_beam_profile = false; - if (beam_profile_ != IMP_NULLPTR && beam_profile_->size() > 0) + if (beam_profile_ != nullptr && beam_profile_->size() > 0) use_beam_profile = true; // iterate over intensity profile From 75110f748311798ae1015e0f46f6fdc41aa41721 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 17:17:54 -0800 Subject: [PATCH 041/155] Remove test for std::ref We now require C++11 so std::ref is guaranteed to be available. --- modules/kernel/compiler/has_ref.cpp | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100644 modules/kernel/compiler/has_ref.cpp diff --git a/modules/kernel/compiler/has_ref.cpp b/modules/kernel/compiler/has_ref.cpp deleted file mode 100644 index ce2c8d25d5..0000000000 --- a/modules/kernel/compiler/has_ref.cpp +++ /dev/null @@ -1,16 +0,0 @@ -/** - * \file nothing.cpp - * \brief nothing - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - * - */ - -#include - -bool testfunc(char c) { return false; } - -int main(void) { - std::reference_wrapper x = std::ref(testfunc); - return 0; -} From 3c8be8eb816f03541d4eafa34b3e27298821fdfb Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 17:25:05 -0800 Subject: [PATCH 042/155] Require C++11 at CMake time --- cmake_modules/IMPFindC++11.cmake | 92 +++++++++++++++----------------- 1 file changed, 44 insertions(+), 48 deletions(-) diff --git a/cmake_modules/IMPFindC++11.cmake b/cmake_modules/IMPFindC++11.cmake index bf55e3d2fc..3e5e905e03 100644 --- a/cmake_modules/IMPFindC++11.cmake +++ b/cmake_modules/IMPFindC++11.cmake @@ -1,58 +1,54 @@ -if(NOT DEFINED IMP_CXX11) - set(IMP_CXX11 1 CACHE BOOL "Whether to use C++11 if possible") -endif() - # Put flags in a cmake variable so we can set them before running compiler # checks (elsewhere in the build) set(IMP_CXX11_FLAGS "" CACHE INTERNAL "Flags to enable C++11 support" FORCE) -if(IMP_CXX11) - if (APPLE) - execute_process(COMMAND uname -v OUTPUT_VARIABLE DARWIN_VERSION) - string(REGEX MATCH "[0-9]+" DARWIN_VERSION ${DARWIN_VERSION}) - endif() +if (APPLE) + execute_process(COMMAND uname -v OUTPUT_VARIABLE DARWIN_VERSION) + string(REGEX MATCH "[0-9]+" DARWIN_VERSION ${DARWIN_VERSION}) +endif() - if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU") - execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE - GCC_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE) - message(STATUS "GCC version: ${GCC_VERSION}") - if (GCC_VERSION VERSION_GREATER 6.1 OR GCC_VERSION VERSION_EQUAL 6.1) - # gcc 6.1 and up use C++14 by default, so no explicit switch required - # (in fact adding --std=c++11 will break compilation of packages that - # require C++14 features, like CGAL 5). - message(STATUS "Using g++ C++11 (or later) support") - elseif (GCC_VERSION VERSION_GREATER 4.7 OR GCC_VERSION VERSION_EQUAL 4.7) - message(STATUS "Enabling g++ C++11 support") - set(IMP_CXX11_FLAGS "--std=c++11" CACHE INTERNAL "" FORCE) - elseif (GCC_VERSION VERSION_GREATER 4.3 OR GCC_VERSION VERSION_EQUAL 4.3) - message(STATUS "Enabling g++ C++0x support") - set(IMP_CXX11_FLAGS "--std=c++0x" CACHE INTERNAL "" FORCE) - endif() - elseif("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang") - execute_process(COMMAND ${CMAKE_CXX_COMPILER} --version - OUTPUT_VARIABLE CLANG_VERSION) - if(CLANG_VERSION MATCHES "clang version ([0-9.]+)") - set(CLANG_VERSION ${CMAKE_MATCH_1}) - endif() - message(STATUS "clang version: ${CLANG_VERSION}") - # Modern clang (6 or later) uses C++14 by default; don't force older C++11 - if(CLANG_VERSION VERSION_GREATER 6.0) - message(STATUS "Using clang C++11 (or later) support") - # c++11's std::move (which boost/CGAL use) doesn't work until - # OS X 10.9 (Darwin version 13) - elseif(APPLE AND DARWIN_VERSION LESS 13) - message(STATUS "Disabling C++11 for mac os < 10.9") - elseif(BOOST_VERSION LESS 105000) - message(STATUS "Disabling C++11 due to clang and older boost") - else() - message(STATUS "Enabling clang C++11 support") - set(IMP_CXX11_FLAGS "--std=c++11" CACHE INTERNAL "" FORCE) - endif() - elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC") - message(STATUS "Using MSVC C++11 support") +if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE + GCC_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE) + message(STATUS "GCC version: ${GCC_VERSION}") + if (GCC_VERSION VERSION_GREATER 6.1 OR GCC_VERSION VERSION_EQUAL 6.1) + # gcc 6.1 and up use C++14 by default, so no explicit switch required + # (in fact adding --std=c++11 will break compilation of packages that + # require C++14 features, like CGAL 5). + message(STATUS "Using g++ C++11 (or later) support") + elseif (GCC_VERSION VERSION_GREATER 4.7 OR GCC_VERSION VERSION_EQUAL 4.7) + message(STATUS "Enabling g++ C++11 support") + set(IMP_CXX11_FLAGS "--std=c++11" CACHE INTERNAL "" FORCE) + elseif (GCC_VERSION VERSION_GREATER 4.3 OR GCC_VERSION VERSION_EQUAL 4.3) + message(STATUS "Enabling g++ C++0x support") + set(IMP_CXX11_FLAGS "--std=c++0x" CACHE INTERNAL "" FORCE) + else() + message(FATAL_ERROR "IMP requires a C++11 compiler, but this GCC appears to be too old to support C++11") + endif() +elseif("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} --version + OUTPUT_VARIABLE CLANG_VERSION) + if(CLANG_VERSION MATCHES "clang version ([0-9.]+)") + set(CLANG_VERSION ${CMAKE_MATCH_1}) + endif() + message(STATUS "clang version: ${CLANG_VERSION}") + # Modern clang (6 or later) uses C++14 by default; don't force older C++11 + if(CLANG_VERSION VERSION_GREATER 6.0) + message(STATUS "Using clang C++11 (or later) support") + # c++11's std::move (which boost/CGAL use) doesn't work until + # OS X 10.9 (Darwin version 13) + elseif(APPLE AND DARWIN_VERSION LESS 13) + message(FATAL_ERROR "IMP requires a C++11 compiler, but this version of OS X is too old to properly support C++11") + elseif(BOOST_VERSION LESS 105000) + message(FATAL_ERROR "IMP requires a C++11 compiler, but this version of Boost is too old to properly support C++11") else() - message(STATUS "Unknown compiler, not sure what to do about C++11") + message(STATUS "Enabling clang C++11 support") + set(IMP_CXX11_FLAGS "--std=c++11" CACHE INTERNAL "" FORCE) endif() +elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC") + message(STATUS "Using MSVC C++11 support") +else() + message(STATUS "Unknown compiler, not sure what to do about C++11") endif() if(IMP_CXX11_FLAGS) From 541ef84cb69de899e106154087fa218dc519a86e Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 17:27:00 -0800 Subject: [PATCH 043/155] Note deprecated pre-C++11 headers/macros --- ChangeLog.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ChangeLog.md b/ChangeLog.md index d97f95d946..5bcca5ca34 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -6,7 +6,10 @@ ChangeLog {#changelog} functions instead to calculate coarse cross correlation. - IMP now requires a C++11 compiler to build. Most compilers less than 10 years old should support C++11, such as gcc, clang or MS Visual - Studio 2010 or later. + Studio 2010 or later. Various IMP macro and header workarounds for + pre-C++11 environments are thus no longer needed and are deprecated: + `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_UNIQUE_PTR`, + `IMP/nullptr.h`, `IMP/nullptr_macros.h` # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} - OpenCubicSpline now throws a ValueException for out-of-range values, to From 419710ef04055559c3c1f7132353a5b5529ef94a Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 28 Feb 2022 17:38:08 -0800 Subject: [PATCH 044/155] Remove more usage of deprecated nullptr header --- modules/integrative_docking/src/internal/EMFit.cpp | 1 - modules/kinematics/src/CompositeJoint.cpp | 1 - modules/kinematics/src/Joint.cpp | 1 - modules/spb/src/spb_restraint.cpp | 1 - 4 files changed, 4 deletions(-) diff --git a/modules/integrative_docking/src/internal/EMFit.cpp b/modules/integrative_docking/src/internal/EMFit.cpp index 59aa1caeaa..8d65d1c9d4 100644 --- a/modules/integrative_docking/src/internal/EMFit.cpp +++ b/modules/integrative_docking/src/internal/EMFit.cpp @@ -17,7 +17,6 @@ #include #include -#include IMPINTEGRATIVEDOCKING_BEGIN_INTERNAL_NAMESPACE diff --git a/modules/kinematics/src/CompositeJoint.cpp b/modules/kinematics/src/CompositeJoint.cpp index 5a837aef51..4688f2b115 100644 --- a/modules/kinematics/src/CompositeJoint.cpp +++ b/modules/kinematics/src/CompositeJoint.cpp @@ -11,7 +11,6 @@ #include #include #include -#include #include #include diff --git a/modules/kinematics/src/Joint.cpp b/modules/kinematics/src/Joint.cpp index 8925d20267..9bd590f670 100644 --- a/modules/kinematics/src/Joint.cpp +++ b/modules/kinematics/src/Joint.cpp @@ -11,7 +11,6 @@ #include #include #include -#include #include #include diff --git a/modules/spb/src/spb_restraint.cpp b/modules/spb/src/spb_restraint.cpp index e640bf13b0..586711089c 100644 --- a/modules/spb/src/spb_restraint.cpp +++ b/modules/spb/src/spb_restraint.cpp @@ -5,7 +5,6 @@ * Copyright 2007-2022 IMP Inventors. All rights reserved. * */ -#include #include #include #include From c3abd5eed550ecf6d63cad519d48b947913c288b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 1 Mar 2022 10:57:01 -0800 Subject: [PATCH 045/155] Require SWIG 3 for full C++11 support --- ChangeLog.md | 8 ++++---- doc/manual/installation.md | 3 +-- tools/rpm/IMP.spec.in | 8 +++++++- 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index 5bcca5ca34..e7dce436cb 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -4,10 +4,10 @@ ChangeLog {#changelog} # HEAD - The IMP::em::CoarseCC class has been removed. Use similarly-named free functions instead to calculate coarse cross correlation. -- IMP now requires a C++11 compiler to build. Most compilers less than - 10 years old should support C++11, such as gcc, clang or MS Visual - Studio 2010 or later. Various IMP macro and header workarounds for - pre-C++11 environments are thus no longer needed and are deprecated: +- IMP now requires a C++11 compiler and SWIG 3 (or later) to build. Most + compilers less than 10 years old should support C++11, such as gcc, clang + or MS Visual Studio 2010 or later. Various IMP macro and header workarounds + for pre-C++11 environments are thus no longer needed and are deprecated: `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_UNIQUE_PTR`, `IMP/nullptr.h`, `IMP/nullptr_macros.h` diff --git a/doc/manual/installation.md b/doc/manual/installation.md index 391fae19c2..3cb5283315 100644 --- a/doc/manual/installation.md +++ b/doc/manual/installation.md @@ -31,8 +31,7 @@ In order to build %IMP from source, you will need: - [HDF5](https://support.hdfgroup.org/HDF5/) (1.8 or later; 1.10 or 1.12 should also work) - [Python](https://www.python.org) (2.7 or later, or any version of Python 3) -- [SWIG](http://www.swig.org) (1.3.40 or later; 2.0.4 or later is needed - if you want to use Python 3) +- [SWIG](http://www.swig.org) (3 or later) The following prerequisites are _optional_; without them some parts of %IMP will not build, and some will not function optimally. diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in index 4610e622a5..67781068b2 100644 --- a/tools/rpm/IMP.spec.in +++ b/tools/rpm/IMP.spec.in @@ -39,7 +39,13 @@ BuildRequires: python3-devel, symlinks %endif BuildRequires: %{PYTHON2}-devel >= 2.6, gcc-c++ BuildRequires: hdf5-devel >= 1.8 -BuildRequires: swig >= 1.3.40 +%if 0%{?rhel} == 7 +# The default SWIG package in RHEL7 is SWIG 2, but SWIG 3 is provided +# (in the CentOS Extras repository) +BuildRequires: swig3 >= 3.0 +%else +BuildRequires: swig >= 3.0 +%endif BuildRequires: gsl-devel, fftw-devel BuildRequires: zlib-devel, perl, eigen3-devel %if 0%{?fedora} || 0%{?rhel} <= 7 From eae81a9bebfa81a64199a272fa6121cc523f2c79 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 1 Mar 2022 11:15:37 -0800 Subject: [PATCH 046/155] Drop RHEL6 logic We can't build on RHEL6 any more anyway, so drop all the custom RHEL6 logic from the RPM specfile. --- tools/rpm/IMP.spec.in | 56 +++++-------------------------------------- 1 file changed, 6 insertions(+), 50 deletions(-) diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in index 67781068b2..d7c4e28721 100644 --- a/tools/rpm/IMP.spec.in +++ b/tools/rpm/IMP.spec.in @@ -62,39 +62,27 @@ BuildRequires: protobuf-devel Requires: python3-protobuf %endif # No Python protobuf package in RHEL8 -%if 0%{?rhel} >= 6 && 0%{?rhel} <= 7 +%if 0%{?rhel} == 7 Requires: protobuf-python %endif BuildRequires: cmake >= 2.8 BuildRequires: boost-devel >= 1.53 -# RHEL doesn't have a CGAL package, so build without CGAL on RHEL. It also -# doesn't have a new enough OpenCV in the base distribution or in EPEL until -# RHEL7, so disable the em2d module. -# On Fedora, all of these packages are available; add them as dependencies +# RHEL doesn't have a CGAL package, so build without CGAL on RHEL. %if 0%{?fedora} -BuildRequires: CGAL-devel, opencv-devel +BuildRequires: CGAL-devel %endif -%if 0%{?rhel} >= 7 BuildRequires: opencv-devel -%endif # If building in the Sali lab, pass '-D "RHEL_SALI_LAB 1"' to your rpmbuild -# invocation. This will pull in our custom OpenCV (on RHEL6) and CGAL packages +# invocation. This will pull in our custom CGAL package # and bundle the libraries with IMP. # If building outside of the lab and you still want these packages, get them # from https://integrativemodeling.org/build-extras/ %if 0%{?rhel} && 0%{?RHEL_SALI_LAB} -%if 0%{?rhel} < 7 -BuildRequires: opencv-nogui-devel -%endif BuildRequires: CGAL-nogui-devel -%if 0%{?rhel} < 7 -%define bundled libcv\\.so\\|libcxcore\\.so\\|libhighgui.so\\|libTAU\\.so\\|libCGAL\\.so -%else %define bundled libTAU\\.so\\|libCGAL\\.so -%endif %else %define bundled libTAU\\.so %endif @@ -114,13 +102,6 @@ BuildRequires: numpy, scipy Requires: numpy, scipy %endif -# RHEL 6 ships with Python 2.6, which doesn't have the argparse module, -# so pull in the extra package that provides it -%if 0%{?rhel} == 6 -BuildRequires: python-argparse -Requires: python-argparse -%endif - %define cmake_opts -DCMAKE_INSTALL_RPATH=%{_libdir}/IMP # Use user-visible (not "platform") Python on RHEL8 @@ -128,11 +109,7 @@ Requires: python-argparse %define __python3 /usr/bin/python3 %endif -%if 0%{?rhel} == 6 -%define mpiprefix %{nil} -%else %define mpiprefix mpi/ -%endif # Don't build debug source packages; they cause the build to fail with # error: Empty %files file [...]/debugsourcefiles.list @@ -181,11 +158,9 @@ Requires: python3-devel Requires: %{PYTHON2}-devel %endif %if 0%{?fedora} -Requires: CGAL-devel, opencv-devel +Requires: CGAL-devel %endif -%if 0%{?rhel} >= 7 Requires: opencv-devel -%endif %description devel This package contains the include files for building applications that link @@ -396,17 +371,6 @@ for mod in %{MPI_MODULES}; do (cd ${RPM_BUILD_ROOT}%{_libdir} && rm libimp_${mod}.so \ && ln -sf mpich/lib/libimp_${mod}.so.* libimp_${mod}.so) done - -# Add MPI-dependent directory to Python search path -%if 0%{?rhel} == 6 -(cd ${RPM_BUILD_ROOT}%{_libdir}/%{default_python}*/site-packages && cat > imp-mpi.pth < Date: Tue, 1 Mar 2022 13:49:07 -0800 Subject: [PATCH 047/155] Get latest npctransport --- modules/npctransport | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/npctransport b/modules/npctransport index ca1afb458e..a398262bad 160000 --- a/modules/npctransport +++ b/modules/npctransport @@ -1 +1 @@ -Subproject commit ca1afb458ee96f3976a1a294ef0a021cb2c6fa6f +Subproject commit a398262bad35d08c8ffeabff31c7d9a478c1920e From af484f167b98598103737ca439433e84a128e66a Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 1 Mar 2022 13:50:06 -0800 Subject: [PATCH 048/155] Assume 'final' keyword is always available Now that we require C++11, we can use the 'final' keyword. Keep the IMP_FINAL macro for now for backwards compatibility. Provide an IMP_SWIG_FINAL macro for the rare cases where we want to declare a method final for C++ code but still allow SWIG to override it for director classes. --- ChangeLog.md | 2 +- modules/atom/include/Simulator.h | 2 +- modules/core/src/rigid_bodies.cpp | 2 +- modules/kernel/include/OptimizerState.h | 2 +- modules/kernel/include/Particle.h | 4 ++-- modules/kernel/include/compiler_macros.h | 20 ++++++------------- modules/rmf/include/HierarchyLoadLink.h | 6 +++--- .../kernel/classname_macros.h | 8 ++++---- 8 files changed, 19 insertions(+), 27 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index e7dce436cb..8783c54fcf 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -8,7 +8,7 @@ ChangeLog {#changelog} compilers less than 10 years old should support C++11, such as gcc, clang or MS Visual Studio 2010 or later. Various IMP macro and header workarounds for pre-C++11 environments are thus no longer needed and are deprecated: - `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_UNIQUE_PTR`, + `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`, `IMP/nullptr.h`, `IMP/nullptr_macros.h` # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} diff --git a/modules/atom/include/Simulator.h b/modules/atom/include/Simulator.h index 8b6133b001..0d97cff2d3 100644 --- a/modules/atom/include/Simulator.h +++ b/modules/atom/include/Simulator.h @@ -167,7 +167,7 @@ class IMPATOMEXPORT Simulator : public Optimizer { protected: /** @} */ - virtual Float do_optimize(unsigned int max_steps) override IMP_FINAL; + virtual Float do_optimize(unsigned int max_steps) override IMP_SWIG_FINAL; /** Perform any setup operations needed before running a series of simulation steps diff --git a/modules/core/src/rigid_bodies.cpp b/modules/core/src/rigid_bodies.cpp index f8363f6e8c..8e50d4860a 100644 --- a/modules/core/src/rigid_bodies.cpp +++ b/modules/core/src/rigid_bodies.cpp @@ -147,7 +147,7 @@ class NormalizeRotation : public SingletonModifier { Model *m, const ParticleIndexes &pis) const override; virtual void apply_indexes( Model *m, const ParticleIndexes &pis, unsigned int lower_bound, - unsigned int upper_bound) const override IMP_FINAL; + unsigned int upper_bound) const override final; // IMP_SINGLETON_MODIFIER_METHODS(NormalizeRotation); IMP_OBJECT_METHODS(NormalizeRotation); }; diff --git a/modules/kernel/include/OptimizerState.h b/modules/kernel/include/OptimizerState.h index cfeded58b0..e2dd7af4eb 100644 --- a/modules/kernel/include/OptimizerState.h +++ b/modules/kernel/include/OptimizerState.h @@ -124,7 +124,7 @@ class IMPKERNELEXPORT OptimizerState : public ModelObject { virtual ModelObjectsTemp do_get_inputs() const override { return ModelObjectsTemp(); } - virtual ModelObjectsTemp do_get_outputs() const override IMP_FINAL { + virtual ModelObjectsTemp do_get_outputs() const override IMP_SWIG_FINAL { return ModelObjectsTemp(); } diff --git a/modules/kernel/include/Particle.h b/modules/kernel/include/Particle.h index ae2655eb87..73a9ad298d 100644 --- a/modules/kernel/include/Particle.h +++ b/modules/kernel/include/Particle.h @@ -139,10 +139,10 @@ class IMPKERNELEXPORT Particle : public ModelObject { void clear_caches() override; #endif protected: - virtual ModelObjectsTemp do_get_inputs() const override IMP_FINAL { + virtual ModelObjectsTemp do_get_inputs() const override final { return ModelObjectsTemp(); } - virtual ModelObjectsTemp do_get_outputs() const override IMP_FINAL { + virtual ModelObjectsTemp do_get_outputs() const override final { return ModelObjectsTemp(); } }; diff --git a/modules/kernel/include/compiler_macros.h b/modules/kernel/include/compiler_macros.h index 3e9e3fb004..4e6a30196b 100644 --- a/modules/kernel/include/compiler_macros.h +++ b/modules/kernel/include/compiler_macros.h @@ -68,25 +68,17 @@ #define IMP_OVERRIDE override #endif -#if defined(IMP_SWIG_WRAPPER) -#define IMP_COMPILER_HAS_FINAL 0 -#elif defined(__clang__) -#define IMP_COMPILER_HAS_FINAL 1 -#elif defined(__GNUC__) && __cplusplus >= 201103L -// probably should be finer here -#define IMP_COMPILER_HAS_FINAL 1 -#else -#define IMP_COMPILER_HAS_FINAL 0 -#endif - #ifdef IMP_DOXYGEN +#define IMP_FINAL //! Have the compiler report an error if anything overrides this method +#define IMP_SWIG_FINAL +#else +#if defined(IMP_SWIG_WRAPPER) || defined(SWIG) #define IMP_FINAL +#define IMP_SWIG_FINAL #else -#if IMP_COMPILER_HAS_FINAL #define IMP_FINAL final -#else -#define IMP_FINAL +#define IMP_SWIG_FINAL final #endif #endif diff --git a/modules/rmf/include/HierarchyLoadLink.h b/modules/rmf/include/HierarchyLoadLink.h index ab69b3c178..fff11c4ee5 100644 --- a/modules/rmf/include/HierarchyLoadLink.h +++ b/modules/rmf/include/HierarchyLoadLink.h @@ -74,10 +74,10 @@ class IMPRMFEXPORT HierarchyLoadLink : public SimpleLoadLink { Data &data); virtual void do_add_link(Particle *o, - RMF::NodeConstHandle node) IMP_FINAL override; + RMF::NodeConstHandle node) final override; using P::do_create; virtual Particle *do_create(RMF::NodeConstHandle name, - Model *m) IMP_FINAL override; + Model *m) final override; void create_recursive(Model *m, ParticleIndex root, ParticleIndex cur, RMF::NodeConstHandle name, ParticleIndexes rigid_bodies, Data &data); @@ -90,7 +90,7 @@ class IMPRMFEXPORT HierarchyLoadLink : public SimpleLoadLink { core::Provenance create_one_provenance(Model *m, RMF::NodeConstHandle node); virtual void do_load_one(RMF::NodeConstHandle nh, - Particle *o) IMP_FINAL override; + Particle *o) final override; protected: /** This method is called for the hierarchy.*/ diff --git a/tools/build/container_templates/kernel/classname_macros.h b/tools/build/container_templates/kernel/classname_macros.h index 824eb1259f..af9fb917e3 100644 --- a/tools/build/container_templates/kernel/classname_macros.h +++ b/tools/build/container_templates/kernel/classname_macros.h @@ -22,7 +22,7 @@ double evaluate_indexes(Model *m, const PLURALINDEXTYPE &p, \ DerivativeAccumulator *da, unsigned int lower_bound, \ unsigned int upper_bound) \ - const IMP_OVERRIDE IMP_FINAL { \ + const IMP_OVERRIDE final { \ double ret = 0; \ for (unsigned int i = lower_bound; i < upper_bound; ++i) { \ ret += evaluate_index(m, p[i], da); \ @@ -34,7 +34,7 @@ DerivativeAccumulator *da, unsigned int lower_bound, \ unsigned int upper_bound, \ std::vector &score) \ - const IMP_OVERRIDE IMP_FINAL { \ + const IMP_OVERRIDE final { \ double ret = 0; \ for (unsigned int i = lower_bound; i < upper_bound; ++i) { \ double s = evaluate_index(m, p[i], da); \ @@ -48,7 +48,7 @@ DerivativeAccumulator *da, \ const std::vector &indexes, \ std::vector &score) \ - const IMP_OVERRIDE IMP_FINAL { \ + const IMP_OVERRIDE final { \ double ret = 0; \ for (std::vector::const_iterator it = indexes.begin(); \ it != indexes.end(); ++it) { \ @@ -121,7 +121,7 @@ virtual void apply_indexes(Model *m, const PLURALINDEXTYPE &o, \ unsigned int lower_bound, \ unsigned int upper_bound) \ - const IMP_OVERRIDE IMP_FINAL { \ + const IMP_OVERRIDE final { \ for (unsigned int i = lower_bound; i < upper_bound; ++i) { \ apply_index(m, o[i]); \ } \ From eb0097338e2a0f180c39e22d02687cf7b20ccb1b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 1 Mar 2022 14:00:41 -0800 Subject: [PATCH 049/155] Replace more usage of IMP_OVERRIDE with override --- .../benchmark/benchmark_random_collisions.cpp | 4 ++-- modules/container/test/test_non_rigid.cpp | 8 +++---- .../core/benchmark/benchmark_omp_evaluate.cpp | 4 ++-- modules/kernel/test/test_protection.cpp | 4 ++-- .../container/ClassnameContainerSet.h | 16 ++++++------- .../container/ClassnameContainerStatistics.h | 8 +++---- .../container/ClassnamesOptimizerState.h | 2 +- .../DistributeClassnamesScoreState.h | 8 +++---- .../container/EventClassnamesOptimizerState.h | 2 +- .../container/InContainerClassnameFilter.h | 4 ++-- .../container/MinimumClassnameRestraint.h | 8 +++---- .../container/MinimumClassnameScore.h | 6 ++--- .../container/PredicateClassnamesRestraint.h | 6 ++--- .../internal/ClassnameContainerIndex.h | 8 +++---- .../core/classname_predicates.h | 24 +++++++++---------- .../kernel/classname_macros.h | 18 +++++++------- 16 files changed, 65 insertions(+), 65 deletions(-) diff --git a/modules/container/benchmark/benchmark_random_collisions.cpp b/modules/container/benchmark/benchmark_random_collisions.cpp index d9dd13e959..9ad8648ea1 100644 --- a/modules/container/benchmark/benchmark_random_collisions.cpp +++ b/modules/container/benchmark/benchmark_random_collisions.cpp @@ -29,9 +29,9 @@ class ConstPairScore : public PairScore { public: ConstPairScore() {} double evaluate_index(Model *m, const ParticleIndexPair &p, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_PAIR_SCORE_METHODS(ConstPairScore); IMP_OBJECT_METHODS(ConstPairScore); ; diff --git a/modules/container/test/test_non_rigid.cpp b/modules/container/test/test_non_rigid.cpp index 307195b07a..611d3eb527 100644 --- a/modules/container/test/test_non_rigid.cpp +++ b/modules/container/test/test_non_rigid.cpp @@ -23,7 +23,7 @@ class ICMover : public IMP::core::MonteCarloMover { pi_ = pi; ball_ = IMP::algebra::Sphere3D(IMP::algebra::get_zero_vector_d<3>(), r); } - IMP::core::MonteCarloMoverResult do_propose() IMP_OVERRIDE { + IMP::core::MonteCarloMoverResult do_propose() override { IMP::core::NonRigidMember nrm(get_model(), pi_); IMP::algebra::Vector3D ic = nrm.get_internal_coordinates(); old_ = ic; @@ -32,12 +32,12 @@ class ICMover : public IMP::core::MonteCarloMover { return IMP::core::MonteCarloMoverResult( IMP::ParticleIndexes(1, pi_), 1.0); } - void do_reject() IMP_OVERRIDE { + void do_reject() override { IMP::core::NonRigidMember nrm(get_model(), pi_); nrm.set_internal_coordinates(old_); } - void do_accept() IMP_OVERRIDE {} - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { + void do_accept() override {} + IMP::ModelObjectsTemp do_get_inputs() const override { return IMP::ModelObjectsTemp(1, get_model()->get_particle(pi_)); } IMP_OBJECT_METHODS(ICMover); diff --git a/modules/core/benchmark/benchmark_omp_evaluate.cpp b/modules/core/benchmark/benchmark_omp_evaluate.cpp index 35dba949cd..57308d66f3 100644 --- a/modules/core/benchmark/benchmark_omp_evaluate.cpp +++ b/modules/core/benchmark/benchmark_omp_evaluate.cpp @@ -23,8 +23,8 @@ class ExpensiveRestraint : public IMP::Restraint { const IMP::ParticleIndexes &pis) : Restraint(m, "ExpensiveRestraint%1%"), pis_(pis) {} void do_add_score_and_derivatives(IMP::ScoreAccumulator sa) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(ExpensiveRestraint); }; diff --git a/modules/kernel/test/test_protection.cpp b/modules/kernel/test/test_protection.cpp index e9aaad9ef0..bb52187b94 100644 --- a/modules/kernel/test/test_protection.cpp +++ b/modules/kernel/test/test_protection.cpp @@ -24,8 +24,8 @@ class TouchyRestraint : public IMP::Restraint { TouchyRestraint(IMP::Particle *p, IMP::FloatKey fk) : IMP::Restraint(p->get_model(), "Touchy"), p_(p), fk_(fk) {} virtual double unprotected_evaluate(IMP::DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + const override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(TouchyRestraint); }; diff --git a/tools/build/container_templates/container/ClassnameContainerSet.h b/tools/build/container_templates/container/ClassnameContainerSet.h index 2a35de7224..7df99712c4 100644 --- a/tools/build/container_templates/container/ClassnameContainerSet.h +++ b/tools/build/container_templates/container/ClassnameContainerSet.h @@ -27,7 +27,7 @@ class IMPCONTAINEREXPORT ClassnameContainerSet : public ClassnameContainer { static ClassnameContainerSet *get_set(ClassnameContainer *c) { return dynamic_cast(c); } - virtual std::size_t do_get_contents_hash() const IMP_OVERRIDE; + virtual std::size_t do_get_contents_hash() const override; public: //! Construct an empty set @@ -38,11 +38,11 @@ class IMPCONTAINEREXPORT ClassnameContainerSet : public ClassnameContainer { std::string name = "ClassnameContainerSet %1%"); /** \brief apply modifier sm to all classname containers */ - IMP_IMPLEMENT(void do_apply(const ClassnameModifier *sm) const IMP_OVERRIDE); + IMP_IMPLEMENT(void do_apply(const ClassnameModifier *sm) const override); IMP_IMPLEMENT(void do_apply_moved(const ClassnameModifier *sm, const ParticleIndexes &moved_pis, - const ParticleIndexes &reset_pis) const IMP_OVERRIDE); + const ParticleIndexes &reset_pis) const override); template void apply_generic(const M *m) const { @@ -55,7 +55,7 @@ class IMPCONTAINEREXPORT ClassnameContainerSet : public ClassnameContainer { apply_moved(m, moved_pis, reset_pis); } - ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; + ParticleIndexes get_all_possible_indexes() const override; IMP_OBJECT_METHODS(ClassnameContainerSet); /** @name Methods to control the nested container @@ -75,16 +75,16 @@ class IMPCONTAINEREXPORT ClassnameContainerSet : public ClassnameContainer { /**@}*/ #ifndef IMP_DOXYGEN - PLURALINDEXTYPE get_indexes() const IMP_OVERRIDE; - PLURALINDEXTYPE get_range_indexes() const IMP_OVERRIDE; - ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + PLURALINDEXTYPE get_indexes() const override; + PLURALINDEXTYPE get_range_indexes() const override; + ModelObjectsTemp do_get_inputs() const override; #endif protected: //! Insert the contents of the container into output //! instead of output's current content virtual void get_indexes_in_place(PLURALINDEXTYPE& output) - const IMP_OVERRIDE; + const override; }; IMPCONTAINER_END_NAMESPACE diff --git a/tools/build/container_templates/container/ClassnameContainerStatistics.h b/tools/build/container_templates/container/ClassnameContainerStatistics.h index d702b7facc..c610183ecf 100644 --- a/tools/build/container_templates/container/ClassnameContainerStatistics.h +++ b/tools/build/container_templates/container/ClassnameContainerStatistics.h @@ -35,10 +35,10 @@ class IMPCONTAINEREXPORT ClassnameContainerStatistics : public ScoreState { expensive, so it is not done by default. */ void set_track_unique(bool tf); - virtual void do_before_evaluate() IMP_OVERRIDE; - virtual void do_after_evaluate(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_before_evaluate() override; + virtual void do_after_evaluate(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(ClassnameContainerStatistics); }; diff --git a/tools/build/container_templates/container/ClassnamesOptimizerState.h b/tools/build/container_templates/container/ClassnamesOptimizerState.h index 48c4d6bd26..aad88acce0 100644 --- a/tools/build/container_templates/container/ClassnamesOptimizerState.h +++ b/tools/build/container_templates/container/ClassnamesOptimizerState.h @@ -38,7 +38,7 @@ class IMPCONTAINEREXPORT ClassnamesOptimizerState : public OptimizerState { ClassnamesOptimizerState(ClassnameContainerAdaptor c, ClassnameModifier *gf, std::string name = "ClassnamesOptimizerState %1%"); - virtual void update() IMP_OVERRIDE; + virtual void update() override; IMP_OBJECT_METHODS(ClassnamesOptimizerState); }; diff --git a/tools/build/container_templates/container/DistributeClassnamesScoreState.h b/tools/build/container_templates/container/DistributeClassnamesScoreState.h index 34ff52a730..056e05fac0 100644 --- a/tools/build/container_templates/container/DistributeClassnamesScoreState.h +++ b/tools/build/container_templates/container/DistributeClassnamesScoreState.h @@ -51,10 +51,10 @@ class IMPCONTAINEREXPORT DistributeClassnamesScoreState : public ScoreState { data_.push_back(Data(c, predicate, value)); return c; } - virtual void do_before_evaluate() IMP_OVERRIDE; - virtual void do_after_evaluate(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_before_evaluate() override; + virtual void do_after_evaluate(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(DistributeClassnamesScoreState); }; diff --git a/tools/build/container_templates/container/EventClassnamesOptimizerState.h b/tools/build/container_templates/container/EventClassnamesOptimizerState.h index 3a5c151c28..96e110abcb 100644 --- a/tools/build/container_templates/container/EventClassnamesOptimizerState.h +++ b/tools/build/container_templates/container/EventClassnamesOptimizerState.h @@ -32,7 +32,7 @@ class IMPCONTAINEREXPORT EventClassnamesOptimizerState : public OptimizerState { int min_count, int max_count, std::string name = "ConstClassnamePredicate%1%"); - virtual void update() IMP_OVERRIDE; + virtual void update() override; IMP_OBJECT_METHODS(EventClassnamesOptimizerState); }; diff --git a/tools/build/container_templates/container/InContainerClassnameFilter.h b/tools/build/container_templates/container/InContainerClassnameFilter.h index b4cf1d5cd2..3a31749d4e 100644 --- a/tools/build/container_templates/container/InContainerClassnameFilter.h +++ b/tools/build/container_templates/container/InContainerClassnameFilter.h @@ -36,11 +36,11 @@ class IMPCONTAINEREXPORT InContainerClassnameFilter std::string name = "ClassnameFilter %1%"); virtual int get_value_index(Model *, PASSINDEXTYPE vt) const - IMP_OVERRIDE { + override { return c_->get_contains(vt); } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pi) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pi) const override { ModelObjectsTemp ret = IMP::get_particles(m, pi); ret.push_back(c_); return ret; diff --git a/tools/build/container_templates/container/MinimumClassnameRestraint.h b/tools/build/container_templates/container/MinimumClassnameRestraint.h index 79780c5d5b..c0564cfee5 100644 --- a/tools/build/container_templates/container/MinimumClassnameRestraint.h +++ b/tools/build/container_templates/container/MinimumClassnameRestraint.h @@ -35,17 +35,17 @@ class IMPCONTAINEREXPORT MinimumClassnameRestraint : public Restraint { public: double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(MinimumClassnameRestraint); ; //! Set the number of lowest scores to use. void set_n(unsigned int n) { n_ = n; } #ifndef IMP_DOXYGEN - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + Restraints do_create_current_decomposition() const override; double unprotected_evaluate_if_good(DerivativeAccumulator *da, - double max) const IMP_OVERRIDE; + double max) const override; #endif }; diff --git a/tools/build/container_templates/container/MinimumClassnameScore.h b/tools/build/container_templates/container/MinimumClassnameScore.h index 2839ca760b..271aa02eb8 100644 --- a/tools/build/container_templates/container/MinimumClassnameScore.h +++ b/tools/build/container_templates/container/MinimumClassnameScore.h @@ -26,15 +26,15 @@ class IMPCONTAINEREXPORT MinimumClassnameScore : public ClassnameScore { MinimumClassnameScore(const ClassnameScoresTemp &scores, unsigned int n = 1, std::string name = "ClassnameScore %1%"); virtual double evaluate_index(Model *m, PASSINDEXTYPE vt, - DerivativeAccumulator *da) const IMP_OVERRIDE; + DerivativeAccumulator *da) const override; virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE; + Model *m, const ParticleIndexes &pis) const override; IMP_CLASSNAME_SCORE_METHODS(MinimumClassnameScore); IMP_OBJECT_METHODS(MinimumClassnameScore); Restraints do_create_current_decomposition(Model *m, PASSINDEXTYPE vt) const - IMP_OVERRIDE; + override; }; IMP_OBJECTS(MinimumClassnameScore, MinimumClassnameScores); diff --git a/tools/build/container_templates/container/PredicateClassnamesRestraint.h b/tools/build/container_templates/container/PredicateClassnamesRestraint.h index 303a1da099..3b941828e9 100644 --- a/tools/build/container_templates/container/PredicateClassnamesRestraint.h +++ b/tools/build/container_templates/container/PredicateClassnamesRestraint.h @@ -91,8 +91,8 @@ class IMPCONTAINEREXPORT PredicateClassnamesRestraint : public Restraint { public: void do_add_score_and_derivatives(IMP::ScoreAccumulator sa) const - IMP_OVERRIDE; - IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + IMP::ModelObjectsTemp do_get_inputs() const override; #ifndef SWIG //! use at own risk - for efficiency in case e.g. all scores use same inputs @@ -118,7 +118,7 @@ class IMPCONTAINEREXPORT PredicateClassnamesRestraint : public Restraint { get_score_for_predicate(int predicate) const; - Restraints do_create_current_decomposition() const IMP_OVERRIDE; + Restraints do_create_current_decomposition() const override; }; diff --git a/tools/build/container_templates/container/internal/ClassnameContainerIndex.h b/tools/build/container_templates/container/internal/ClassnameContainerIndex.h index 73acdeabab..90774796c4 100644 --- a/tools/build/container_templates/container/internal/ClassnameContainerIndex.h +++ b/tools/build/container_templates/container/internal/ClassnameContainerIndex.h @@ -33,10 +33,10 @@ class IMPCONTAINEREXPORT ClassnameContainerIndex : public ScoreState { if (handle_permutations_) i = IMP::internal::get_canonical(i); return contents_.find(i) != contents_.end(); } - virtual void do_before_evaluate() IMP_OVERRIDE; - virtual void do_after_evaluate(DerivativeAccumulator *da) IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_outputs() const IMP_OVERRIDE; + virtual void do_before_evaluate() override; + virtual void do_after_evaluate(DerivativeAccumulator *da) override; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual ModelObjectsTemp do_get_outputs() const override; IMP_OBJECT_METHODS(ClassnameContainerIndex); }; diff --git a/tools/build/container_templates/core/classname_predicates.h b/tools/build/container_templates/core/classname_predicates.h index f4cad3b669..55740956c2 100644 --- a/tools/build/container_templates/core/classname_predicates.h +++ b/tools/build/container_templates/core/classname_predicates.h @@ -26,11 +26,11 @@ class IMPCOREEXPORT ConstantClassnamePredicate : public ClassnamePredicate { ConstantClassnamePredicate(int v, std::string name = "ConstClassnamePredicate%1%"); virtual int get_value_index(Model *, PASSINDEXTYPE) const - IMP_OVERRIDE { + override { return v_; } virtual ModelObjectsTemp do_get_inputs( - Model *, const ParticleIndexes &) const IMP_OVERRIDE { + Model *, const ParticleIndexes &) const override { return ModelObjectsTemp(); } IMP_CLASSNAME_PREDICATE_METHODS(ConstantClassnamePredicate); @@ -48,11 +48,11 @@ class IMPCOREEXPORT UnorderedTypeClassnamePredicate UnorderedTypeClassnamePredicate(std::string name = "UnorderedTypeClassnamePredicate%1%"); virtual int get_value_index(Model *m, PASSINDEXTYPE pi) const - IMP_OVERRIDE { + override { return internal::get_type_hash(m, pi); } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { ModelObjectsTemp ret; ret += IMP::get_particles(m, pis); return ret; @@ -77,14 +77,14 @@ class IMPCOREEXPORT OrderedTypeClassnamePredicate : public ClassnamePredicate { } //! Compute the predicate for types of specific pi virtual int get_value_index(Model *m, PASSINDEXTYPE pi) const - IMP_OVERRIDE { + override { return internal::get_ordered_type_hash(m, pi); } //! Setup for a batch of calls to get_value_index_in_batch() //! (used for improving performance) virtual void setup_for_get_value_index_in_batch(Model* m) const - IMP_OVERRIDE{ + override{ cached_particle_type_ids_table_= m->IMP::internal::IntAttributeTable::access_attribute_data(Typed::get_type_key()); cached_n_particle_types_= ParticleType::get_number_unique(); @@ -94,7 +94,7 @@ class IMPCOREEXPORT OrderedTypeClassnamePredicate : public ClassnamePredicate { //! for a batch of calls. Call setup_for_get_value_index_in_batch() //! right before calling a batch of those, otherwise unexpected behavior. virtual int get_value_index_in_batch(Model* m, PASSINDEXTYPE pi) const - IMP_OVERRIDE{ + override{ IMP_UNUSED(m); return internal::get_ordered_type_hash( pi, cached_particle_type_ids_table_, @@ -102,7 +102,7 @@ class IMPCOREEXPORT OrderedTypeClassnamePredicate : public ClassnamePredicate { } virtual ModelObjectsTemp do_get_inputs( - Model *m, const ParticleIndexes &pis) const IMP_OVERRIDE { + Model *m, const ParticleIndexes &pis) const override { ModelObjectsTemp ret; ret += IMP::get_particles(m, pis); return ret; @@ -116,11 +116,11 @@ class IMPCOREEXPORT AllSameClassnamePredicate : public ClassnamePredicate { public: AllSameClassnamePredicate(std::string name = "AllSameClassnamePredicate%1%"); virtual int get_value_index(Model *m, PASSINDEXTYPE pi) const - IMP_OVERRIDE { + override { return internal::get_all_same(m, pi); } virtual ModelObjectsTemp do_get_inputs( - Model *, const ParticleIndexes &) const IMP_OVERRIDE { + Model *, const ParticleIndexes &) const override { return ModelObjectsTemp(); } IMP_CLASSNAME_PREDICATE_METHODS(AllSameClassnamePredicate); @@ -136,14 +136,14 @@ class IMPCOREEXPORT CoinFlipClassnamePredicate : public ClassnamePredicate { CoinFlipClassnamePredicate(double p, std::string name = "CoinFlipClassnamePredicate%1%"); virtual int get_value_index(Model *, PASSINDEXTYPE) const - IMP_OVERRIDE { + override { if (rng_(random_number_generator) < p_) return 1; else return 0; } virtual ModelObjectsTemp do_get_inputs( - Model *, const ParticleIndexes &) const IMP_OVERRIDE { + Model *, const ParticleIndexes &) const override { return ModelObjectsTemp(); } IMP_CLASSNAME_PREDICATE_METHODS(CoinFlipClassnamePredicate); diff --git a/tools/build/container_templates/kernel/classname_macros.h b/tools/build/container_templates/kernel/classname_macros.h index af9fb917e3..d72dec16e0 100644 --- a/tools/build/container_templates/kernel/classname_macros.h +++ b/tools/build/container_templates/kernel/classname_macros.h @@ -22,7 +22,7 @@ double evaluate_indexes(Model *m, const PLURALINDEXTYPE &p, \ DerivativeAccumulator *da, unsigned int lower_bound, \ unsigned int upper_bound) \ - const IMP_OVERRIDE final { \ + const override final { \ double ret = 0; \ for (unsigned int i = lower_bound; i < upper_bound; ++i) { \ ret += evaluate_index(m, p[i], da); \ @@ -34,7 +34,7 @@ DerivativeAccumulator *da, unsigned int lower_bound, \ unsigned int upper_bound, \ std::vector &score) \ - const IMP_OVERRIDE final { \ + const override final { \ double ret = 0; \ for (unsigned int i = lower_bound; i < upper_bound; ++i) { \ double s = evaluate_index(m, p[i], da); \ @@ -48,7 +48,7 @@ DerivativeAccumulator *da, \ const std::vector &indexes, \ std::vector &score) \ - const IMP_OVERRIDE final { \ + const override final { \ double ret = 0; \ for (std::vector::const_iterator it = indexes.begin(); \ it != indexes.end(); ++it) { \ @@ -61,7 +61,7 @@ double evaluate_if_good_indexes( \ Model *m, const PLURALINDEXTYPE &p, DerivativeAccumulator *da, \ double max, unsigned int lower_bound, \ - unsigned int upper_bound) const IMP_OVERRIDE { \ + unsigned int upper_bound) const override { \ double ret = 0; \ for (unsigned int i = lower_bound; i < upper_bound; ++i) { \ ret += evaluate_if_good_index(m, p[i], da, max - ret); \ @@ -83,7 +83,7 @@ } \ return ret; \ } \ - Ints get_value_index(Model *m, const PLURALINDEXTYPE &o) const IMP_OVERRIDE {\ + Ints get_value_index(Model *m, const PLURALINDEXTYPE &o) const override { \ Ints ret(o.size()); \ for (unsigned int i = 0; i < o.size(); ++i) { \ ret[i] += Name::get_value_index(m, o[i]); \ @@ -121,7 +121,7 @@ virtual void apply_indexes(Model *m, const PLURALINDEXTYPE &o, \ unsigned int lower_bound, \ unsigned int upper_bound) \ - const IMP_OVERRIDE final { \ + const override final { \ for (unsigned int i = lower_bound; i < upper_bound; ++i) { \ apply_index(m, o[i]); \ } \ @@ -139,7 +139,7 @@ const ParticleIndexes &moved_pis, \ const ParticleIndexes &reset_pis) const, \ { apply_generic_moved(sm, moved_pis, reset_pis); }); \ - virtual ParticleIndexes get_all_possible_indexes() const IMP_OVERRIDE; \ + virtual ParticleIndexes get_all_possible_indexes() const override; \ IMP_OBJECT_METHODS(Name) #endif @@ -148,11 +148,11 @@ IMP::ClassnameContainer::do_apply_moved() */ #define IMP_CLASSNAME_CONTAINER_METHODS(Name) \ - void do_apply(const ClassnameModifier *sm) const IMP_OVERRIDE { \ + void do_apply(const ClassnameModifier *sm) const override { \ apply_generic(sm); } \ void do_apply_moved(const ClassnameModifier *sm, \ const ParticleIndexes &moved_pis, \ - const ParticleIndexes &reset_pis) const IMP_OVERRIDE { \ + const ParticleIndexes &reset_pis) const override { \ apply_generic_moved(sm, moved_pis, reset_pis); } #endif /* IMPKERNEL_CLASSNAME_MACROS_H */ From 1d1c917cca5dc82ce00821a2c1444cc598e481db Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 4 Mar 2022 12:17:32 -0800 Subject: [PATCH 050/155] Reenable 32-bit Windows tests These tests work again with our new 32-bit Windows setup, with a newer MSVS and scipy plus Python 3. The skip-check logic doesn't work on Python 3 anyway as sys.maxint has been removed. --- modules/saxs_merge/test/test_merge.py | 5 ----- modules/saxs_merge/test/test_merge2.py | 5 ----- 2 files changed, 10 deletions(-) diff --git a/modules/saxs_merge/test/test_merge.py b/modules/saxs_merge/test/test_merge.py index 8393352377..8206ffed2e 100755 --- a/modules/saxs_merge/test/test_merge.py +++ b/modules/saxs_merge/test/test_merge.py @@ -1,6 +1,5 @@ #!/usr/bin/env python -import sys import os import tempfile import copy @@ -75,10 +74,6 @@ def setUp(self): import numpy except ImportError: self.skipTest("could not import scipy and numpy") - # Calling scipy.linalg.cho_solve() causes python/wineserver - # to deadlock so that python.exe never exits, on our Wine setup - if sys.platform == 'win32' and sys.maxsize == sys.maxint: - self.skipTest("does not work on 32-bit Windows") merge = self.import_python_application('saxs_merge') self.SAXSProfile = merge.SAXSProfile self.merge = merge diff --git a/modules/saxs_merge/test/test_merge2.py b/modules/saxs_merge/test/test_merge2.py index 6257778dfc..155731abf1 100755 --- a/modules/saxs_merge/test/test_merge2.py +++ b/modules/saxs_merge/test/test_merge2.py @@ -1,6 +1,5 @@ #!/usr/bin/env python -import sys import os import tempfile import copy @@ -62,10 +61,6 @@ def setUp(self): import numpy except ImportError: self.skipTest("could not import scipy and numpy") - # Calling scipy.linalg.cho_solve() causes python/wineserver - # to deadlock so that python.exe never exits, on our Wine setup - if sys.platform == 'win32' and sys.maxsize == sys.maxint: - self.skipTest("does not work on 32-bit Windows") merge = self.import_python_application('saxs_merge') self.SAXSProfile = merge.SAXSProfile self.merge = merge From 6eaf4402903cce4bad29fea036a149379a7cb36b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 4 Mar 2022 12:53:17 -0800 Subject: [PATCH 051/155] Drop Python 2, update bundled DLLs for 32-bit We now use MSVS2015 rather than MSVS2010 to build on 32-bit, and have dropped Python 2 support, so update accordingly. --- tools/w32/make-package.sh | 45 ++++++++++++++++++++++----------------- 1 file changed, 26 insertions(+), 19 deletions(-) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 48a2c222b2..ccbf4b3854 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -55,8 +55,13 @@ cp ${TOOLDIR}/pkg-README.txt ${ROOT}/README.txt || exit 1 # Move pure Python code to Windows location mkdir ${ROOT}/python || exit 1 mkdir ${ROOT}/python/ihm || exit 1 -mv ${ROOT}/pylib/2.7/*.py ${ROOT}/pylib/2.7/IMP ${ROOT}/python || exit 1 -mv ${ROOT}/pylib/2.7/ihm/*.py ${ROOT}/python/ihm || exit 1 +if [ "${BITS}" = "32" ]; then + mv ${ROOT}/pylib/3.6/*.py ${ROOT}/pylib/3.6/IMP ${ROOT}/python || exit 1 + mv ${ROOT}/pylib/3.6/ihm/*.py ${ROOT}/python/ihm || exit 1 +else + mv ${ROOT}/pylib/2.7/*.py ${ROOT}/pylib/2.7/IMP ${ROOT}/python || exit 1 + mv ${ROOT}/pylib/2.7/ihm/*.py ${ROOT}/python/ihm || exit 1 +fi rm -rf ${ROOT}/pylib/*/*.py ${ROOT}/pylib/*/ihm/*.py ${ROOT}/pylib/*/IMP || exit 1 # Patch IMP/__init__.py, ihm/__init__.py, and RMF.py so they can find Python @@ -80,7 +85,11 @@ for app in ${ROOT}/bin/*; do done # Make Python version-specific directories for extensions (.pyd) -PYVERS="2.7 3.6 3.7 3.8 3.9 3.10" +if [ "${BITS}" = "32" ]; then + PYVERS="3.6 3.7 3.8 3.9 3.10" +else + PYVERS="2.7 3.6 3.7 3.8 3.9 3.10" +fi for PYVER in ${PYVERS}; do mkdir ${ROOT}/python/python${PYVER} || exit 1 mkdir ${ROOT}/python/python${PYVER}/_ihm_pyd || exit 1 @@ -108,32 +117,30 @@ rm -rf ${ROOT}/bin/imp_example_app.exe \ rm -rf `find ${ROOT} -name .svn` if [ "${BITS}" = "32" ]; then - PYVERS="27 36 37 38 39 310" + PYVERS="36 37 38 39 310" MAKENSIS="makensis" # Add redist MSVC runtime DLLs DLLSRC=/usr/lib/w32comp/windows/system - cp ${DLLSRC}/msvc*100.dll ${ROOT}/bin || exit 1 + cp ${DLLSRC}/msvc*140.dll ${ROOT}/bin || exit 1 # Add other DLL dependencies cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ - ${DLLSRC}/boost_filesystem-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_program_options-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_system-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_date_time-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_graph-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_regex-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_thread-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_random-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_iostreams-vc100-mt-1_53.dll \ - ${DLLSRC}/boost_zlib-vc100-mt-1_53.dll \ - ${DLLSRC}/CGAL-vc100-mt-4.1.dll \ + ${DLLSRC}/boost_filesystem-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_program_options-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_system-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_date_time-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_graph-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_regex-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_thread-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_random-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_iostreams-vc140-mt-x32-1_72.dll \ + ${DLLSRC}/boost_zlib-vc140-mt-x32-1_72.dll \ ${DLLSRC}/libgmp-10.dll \ ${DLLSRC}/libmpfr-4.dll \ ${DLLSRC}/libfftw3-3.dll \ ${DLLSRC}/libTAU1.dll \ ${DLLSRC}/zlib1.dll \ - ${DLLSRC}/opencv_core220.dll ${DLLSRC}/opencv_highgui220.dll \ - ${DLLSRC}/opencv_ffmpeg220.dll \ - ${DLLSRC}/opencv_imgproc220.dll ${ROOT}/bin || exit 1 + ${DLLSRC}/opencv_core455.dll ${DLLSRC}/opencv_highgui455.dll \ + ${DLLSRC}/opencv_imgproc455.dll ${ROOT}/bin || exit 1 else PYVERS="27 36 37 38 39 310" MAKENSIS="makensis -DIMP_64BIT" From ce7c8b41b33343bc19aee0ce24a45362374bc99a Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 4 Mar 2022 13:39:52 -0800 Subject: [PATCH 052/155] Remove redundant implementation of vector::data() Every compiler we support now provides std::vector::data() so we no longer need our own implementation (which was provided for MSVC 2008 for Windows Python 2.7 conda builds). This reverts commit fa0a1b45b23bc45642114f024c9d68fc3ea7d77b. --- modules/kernel/include/Vector.h | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/modules/kernel/include/Vector.h b/modules/kernel/include/Vector.h index e6b01f1aa2..0760609932 100644 --- a/modules/kernel/include/Vector.h +++ b/modules/kernel/include/Vector.h @@ -72,24 +72,6 @@ class Vector : public Value push_back(T(*it)); } } - - // MSVC 2008 doesn't support std::vector::data() (technically it requires - // a C++11 compiler), so provide an implementation - T* data() { - if (empty()) { - return NULL; - } else { - return &front(); - } - } - const T* data() const { - if (empty()) { - return NULL; - } else { - return &front(); - } - } - #else template Vector(It b, It e) From 3e92f6c8228a91c362db7801ed0c5d427df1228b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 4 Mar 2022 14:35:35 -0800 Subject: [PATCH 053/155] Use C++11 range-based for loop We should have C++11 on all supported compilers now, so we should be able to use range-based for loops for cleaner code. --- modules/misc/src/DecayPairContainerOptimizerState.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/misc/src/DecayPairContainerOptimizerState.cpp b/modules/misc/src/DecayPairContainerOptimizerState.cpp index 1293fc65db..e6764e1856 100644 --- a/modules/misc/src/DecayPairContainerOptimizerState.cpp +++ b/modules/misc/src/DecayPairContainerOptimizerState.cpp @@ -23,7 +23,7 @@ DecayPairContainerOptimizerState::DecayPairContainerOptimizerState( void DecayPairContainerOptimizerState::do_update(unsigned int) { IMP_OBJECT_LOG; ParticleIndexPairs to_remove; - IMP_FOREACH(ParticleIndexPair pip, output_->get_contents()) { + for(ParticleIndexPair pip : output_->get_contents()) { if (pred_->get_value_index(input_->get_model(), pip) == 0) { to_remove.push_back(pip); } From 2da4fca419074e1b8c895fee85e16a46e40abbaa Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Sat, 5 Mar 2022 13:35:16 -0800 Subject: [PATCH 054/155] Don't include python3 cache files in Windows package --- tools/w32/make-package.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index ccbf4b3854..1344dd2afe 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -56,6 +56,8 @@ cp ${TOOLDIR}/pkg-README.txt ${ROOT}/README.txt || exit 1 mkdir ${ROOT}/python || exit 1 mkdir ${ROOT}/python/ihm || exit 1 if [ "${BITS}" = "32" ]; then + # Remove .pyc files + find ${ROOT} -name __pycache__ -exec rm -rf \{\} \; 2>/dev/null mv ${ROOT}/pylib/3.6/*.py ${ROOT}/pylib/3.6/IMP ${ROOT}/python || exit 1 mv ${ROOT}/pylib/3.6/ihm/*.py ${ROOT}/python/ihm || exit 1 else From 3c00c1f74c840757cddac54fdad4843cb45a7c09 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Sat, 5 Mar 2022 18:52:50 -0800 Subject: [PATCH 055/155] Assume range-based for is always available Since we require C++11, we can use range-based for syntax directly now rather than using the IMP_FOREACH macro (but keep it around for backwards compatibility). --- ChangeLog.md | 6 +++--- modules/kernel/include/compiler_macros.h | 9 +-------- 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index 8783c54fcf..dd4a893d5f 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -5,11 +5,11 @@ ChangeLog {#changelog} - The IMP::em::CoarseCC class has been removed. Use similarly-named free functions instead to calculate coarse cross correlation. - IMP now requires a C++11 compiler and SWIG 3 (or later) to build. Most - compilers less than 10 years old should support C++11, such as gcc, clang - or MS Visual Studio 2010 or later. Various IMP macro and header workarounds + recent compilers should support C++11, such as gcc, clang + or MS Visual Studio 2015 or later. Various IMP macro and header workarounds for pre-C++11 environments are thus no longer needed and are deprecated: `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`, - `IMP/nullptr.h`, `IMP/nullptr_macros.h` + `IMP_FOREACH`, `IMP/nullptr.h`, and `IMP/nullptr_macros.h`. # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} - OpenCubicSpline now throws a ValueException for out-of-range values, to diff --git a/modules/kernel/include/compiler_macros.h b/modules/kernel/include/compiler_macros.h index 4e6a30196b..b10adf2737 100644 --- a/modules/kernel/include/compiler_macros.h +++ b/modules/kernel/include/compiler_macros.h @@ -8,15 +8,8 @@ #ifndef IMPKERNEL_COMPILER_MACROS_H #define IMPKERNEL_COMPILER_MACROS_H -#include -#include -#if defined(BOOST_NO_CXX11_RANGE_BASED_FOR) -#include -#define IMP_FOREACH(v, r) BOOST_FOREACH(v, r) -#else -/** Use C++11 range-based for if available or BOOST_FOREACH if not. */ +// Deprecated: just use C++11 range-based for instead #define IMP_FOREACH(v, r) for (v : r) -#endif #define IMP_STRINGIFY(x) #x From 4f85c079ac7a955ed00a041595fd673c33b43a5e Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Sat, 5 Mar 2022 19:10:07 -0800 Subject: [PATCH 056/155] Replace IMP_FOREACH with range-based for loop --- .../include/AllBipartitePairContainer.h | 4 +- .../container/src/ConnectingPairContainer.cpp | 2 +- modules/container/test/test_non_rigid.cpp | 4 +- modules/core/src/ExcludedVolumeRestraint.cpp | 2 +- .../core/src/IncrementalScoringFunction.cpp | 2 +- modules/core/src/rigid_bodies.cpp | 10 ++--- modules/kernel/include/container_macros.h | 2 +- modules/kernel/src/Model.cpp | 4 +- modules/kernel/src/Model_dependencies.cpp | 45 +++++++++---------- modules/kernel/src/Optimizer.cpp | 2 +- modules/kernel/src/dependency_graph.cpp | 4 +- modules/kernel/src/particle_index.cpp | 4 +- .../container/classnames.cpp | 36 +++++++-------- 13 files changed, 59 insertions(+), 62 deletions(-) diff --git a/modules/container/include/AllBipartitePairContainer.h b/modules/container/include/AllBipartitePairContainer.h index ce466a1ba4..a065eb85f0 100644 --- a/modules/container/include/AllBipartitePairContainer.h +++ b/modules/container/include/AllBipartitePairContainer.h @@ -43,8 +43,8 @@ class IMPCONTAINEREXPORT AllBipartitePairContainer : public PairContainer { // needed. validate_readable(); ParticleIndexPairs pips; - IMP_FOREACH(ParticleIndex pa, a_->get_contents()) { - IMP_FOREACH(ParticleIndex pb, b_->get_contents()) { + for(ParticleIndex pa : a_->get_contents()) { + for(ParticleIndex pb : b_->get_contents()) { pips.push_back(ParticleIndexPair(pa, pb)); } } diff --git a/modules/container/src/ConnectingPairContainer.cpp b/modules/container/src/ConnectingPairContainer.cpp index d6d174987f..c6cc82e8eb 100644 --- a/modules/container/src/ConnectingPairContainer.cpp +++ b/modules/container/src/ConnectingPairContainer.cpp @@ -113,7 +113,7 @@ ModelObjectsTemp ConnectingPairContainer::get_score_state_inputs() const { ModelObjectsTemp ret = get_particles(get_model(), sc_->get_indexes()); ret.push_back(sc_); ret.push_back(mv_); - IMP_FOREACH(ModelObject * mo, ret) { + for(ModelObject * mo : ret) { IMP_UNUSED(mo); IMP_INTERNAL_CHECK(mo, "Null object found in " << ret); } diff --git a/modules/container/test/test_non_rigid.cpp b/modules/container/test/test_non_rigid.cpp index 611d3eb527..f8bf7eadc4 100644 --- a/modules/container/test/test_non_rigid.cpp +++ b/modules/container/test/test_non_rigid.cpp @@ -46,7 +46,7 @@ class ICMover : public IMP::core::MonteCarloMover { IMP::core::MonteCarloMovers create_ic_movers(IMP::Model *m, IMP::ParticleIndexes pis) { IMP::core::MonteCarloMovers ret; - IMP_FOREACH(IMP::ParticleIndex pi, pis) { + for(IMP::ParticleIndex pi : pis) { ret.push_back(new ICMover(m, pi, 1)); } return ret; @@ -95,7 +95,7 @@ IMP::ParticleIndexes add_non_rigid(IMP::Model *m, } void move(IMP::core::MonteCarloMovers mvs) { - IMP_FOREACH(IMP::core::MonteCarloMover * m, mvs) { + for(IMP::core::MonteCarloMover * m : mvs) { m->propose(); m->accept(); } diff --git a/modules/core/src/ExcludedVolumeRestraint.cpp b/modules/core/src/ExcludedVolumeRestraint.cpp index 360d426b67..97c0be8085 100644 --- a/modules/core/src/ExcludedVolumeRestraint.cpp +++ b/modules/core/src/ExcludedVolumeRestraint.cpp @@ -166,7 +166,7 @@ double ExcludedVolumeRestraint::unprotected_evaluate(DerivativeAccumulator *da) } IMP_UNUSED(recomputed); double ret = 0; - IMP_FOREACH(ParticleIndexPair pi, cur_list_) { + for(ParticleIndexPair pi : cur_list_) { ret += ssps_->evaluate_index(get_model(), pi, da); } #if IMP_HAS_CHECKS >= IMP_INTERNAL diff --git a/modules/core/src/IncrementalScoringFunction.cpp b/modules/core/src/IncrementalScoringFunction.cpp index 587f8c698d..0eef009ee6 100644 --- a/modules/core/src/IncrementalScoringFunction.cpp +++ b/modules/core/src/IncrementalScoringFunction.cpp @@ -104,7 +104,7 @@ void IncrementalScoringFunction::create_scoring_functions() { } Vector crs; - IMP_FOREACH(ParticleIndex pi, all_) { + for(ParticleIndex pi : all_) { RestraintsTemp cr = get_dependent_restraints(get_model(), pi); /* Remove any duplicates in cr (could happen with rigid bodies) */ std::sort(cr.begin(), cr.end()); diff --git a/modules/core/src/rigid_bodies.cpp b/modules/core/src/rigid_bodies.cpp index 8e50d4860a..12650371ba 100644 --- a/modules/core/src/rigid_bodies.cpp +++ b/modules/core/src/rigid_bodies.cpp @@ -546,14 +546,14 @@ void RigidBody::teardown_particle(RigidBody rb) { rb.on_change(); { const ParticleIndexes &members = rb.get_member_particle_indexes(); - IMP_FOREACH(ParticleIndex pi, members) { + for(ParticleIndex pi : members) { internal::remove_required_attributes_for_member(rb.get_model(), pi); } } { const ParticleIndexes &members = rb.get_body_member_particle_indexes(); - IMP_FOREACH(ParticleIndex pi, members) { + for(ParticleIndex pi : members) { internal::remove_required_attributes_for_body_member(rb.get_model(), pi); } } @@ -569,7 +569,7 @@ void RigidBody::set_reference_frame_from_members( "Can't initialize a rigid body reference frame " << "with < 3 particles."); Model *m = get_model(); - IMP_FOREACH(ParticleIndex pi, rms) { + for(ParticleIndex pi : rms) { local.push_back(RigidMember(m, pi).get_internal_coordinates()); global.push_back(RigidMember(m, pi).get_coordinates()); } @@ -577,7 +577,7 @@ void RigidBody::set_reference_frame_from_members( algebra::get_transformation_aligning_first_to_second(local, global); set_reference_frame_lazy(algebra::ReferenceFrame3D(t3)); IMP_IF_CHECK(USAGE_AND_INTERNAL) { - IMP_FOREACH(ParticleIndex pi, rms) { + for(ParticleIndex pi : rms) { algebra::Vector3D local = RigidBodyMember(m, pi).get_internal_coordinates(); algebra::Vector3D back = t3.get_transformed(local); @@ -1082,7 +1082,7 @@ void show_rigid_body_hierarchy(RigidBody rb, TextOutput out) { if (core::RigidBody::get_is_setup(m, pi)) { out.get_stream() << " + " << m->get_particle_name(pi) << std::endl; core::RigidBody rb(m, pi); - IMP_FOREACH(ParticleIndex ch, + for(ParticleIndex ch : rb.get_member_particle_indexes() + rb.get_body_member_particle_indexes()) { queue.push_back(boost::make_tuple(prefix1 + " ", prefix1 + " ", ch)); diff --git a/modules/kernel/include/container_macros.h b/modules/kernel/include/container_macros.h index 2f80b06ae9..ef1cf80eaa 100644 --- a/modules/kernel/include/container_macros.h +++ b/modules/kernel/include/container_macros.h @@ -311,7 +311,7 @@ #define IMP_CONTAINER_FOREACH_IMPL(ContainerType, container, operation, tname) \ IMPKERNEL_DEPRECATED_MACRO(2.2, \ - "Use get_contents() and a IMP_FOREACH macro."); \ + "Use get_contents() and a for loop."); \ do { \ if (container->get_provides_access()) { \ const tname ContainerType::ContainedIndexTypes& imp_foreach_indexes = \ diff --git a/modules/kernel/src/Model.cpp b/modules/kernel/src/Model.cpp index d3c8198a83..adb1f440d6 100644 --- a/modules/kernel/src/Model.cpp +++ b/modules/kernel/src/Model.cpp @@ -122,7 +122,7 @@ ParticleIndexes Model::get_particle_indexes() { ModelObjectsTemp Model::get_model_objects() const { ModelObjectsTemp ret; ret.reserve(dependency_graph_.size()); - IMP_FOREACH(const DependencyGraph::value_type & vt, dependency_graph_) { + for(const DependencyGraph::value_type & vt : dependency_graph_) { ret.push_back(const_cast(vt.first)); } return ret; @@ -199,7 +199,7 @@ void Model::do_destroy() { IMP_OBJECT_LOG; IMP_LOG_TERSE("Destroying model" << std::endl); // make sure we clear their data to free model objects they are keeping alive - IMP_FOREACH(Particle * p, particle_index_) { + for(Particle * p : particle_index_) { if (p) { remove_particle(p->get_index()); } diff --git a/modules/kernel/src/Model_dependencies.cpp b/modules/kernel/src/Model_dependencies.cpp index 084b61911c..c4cc77ffce 100644 --- a/modules/kernel/src/Model_dependencies.cpp +++ b/modules/kernel/src/Model_dependencies.cpp @@ -56,8 +56,8 @@ ScoreStatesTemp Model::get_descendent_score_states(const ModelObject *mo) void Model::do_check_inputs_and_outputs(const ModelObject *mo) const { { - IMP_FOREACH(ModelObject * i, - dependency_graph_.find(mo)->second.get_inputs()) { + for(ModelObject * i : + dependency_graph_.find(mo)->second.get_inputs()) { ModelObjectsTemp readers = dependency_graph_.find(i)->second.get_readers(); IMP_INTERNAL_CHECK( @@ -67,8 +67,8 @@ void Model::do_check_inputs_and_outputs(const ModelObject *mo) const { } } { - IMP_FOREACH(ModelObject * o, - dependency_graph_.find(mo)->second.get_outputs()) { + for(ModelObject * o : + dependency_graph_.find(mo)->second.get_outputs()) { ModelObjectsTemp writers = dependency_graph_.find(o)->second.get_writers(); IMP_INTERNAL_CHECK( @@ -82,7 +82,7 @@ void Model::do_check_inputs_and_outputs(const ModelObject *mo) const { void Model::do_check_readers_and_writers(const ModelObject *mo) const { { ModelObjectsTemp readers = dependency_graph_.find(mo)->second.get_readers(); - IMP_FOREACH(ModelObject * r, readers) { + for(ModelObject * r : readers) { IMP_INTERNAL_CHECK(dependency_graph_.find(r) != dependency_graph_.end(), "Reader " << r->get_name() << " of " << mo->get_name() << " not in graph" << std::endl); @@ -99,7 +99,7 @@ void Model::do_check_readers_and_writers(const ModelObject *mo) const { const ModelObjectsTemp &writers = dependency_graph_.find(mo)->second.get_writers(); IMP_UNUSED(writers); - IMP_FOREACH(ModelObject * w, writers) { + for(ModelObject * w : writers) { IMP_INTERNAL_CHECK(dependency_graph_.find(w) != dependency_graph_.end(), "Reader " << w->get_name() << " of " << mo->get_name() << " not in graph" << std::endl); @@ -141,7 +141,7 @@ void Model::do_check_update_order(const ScoreState *ss) const { void Model::do_check_not_in_readers_and_writers(const ModelObject *mo) const { IMP_UNUSED(mo); // for fast builds - IMP_FOREACH(DependencyGraph::value_type vt, dependency_graph_) { + for(DependencyGraph::value_type vt : dependency_graph_) { ModelObjectsTemp readers = vt.second.get_readers(); IMP_INTERNAL_CHECK( std::find(readers.begin(), readers.end(), mo) == readers.end(), @@ -202,10 +202,10 @@ void Model::check_dependency_invariants() const { IMP_IF_CHECK(USAGE_AND_INTERNAL) { IMP_LOG_TERSE("Checking dependency invariants" << std::endl); ModelObjectsTemp without; - IMP_FOREACH(const DependencyGraph::value_type & vt, dependency_graph_) { + for(const DependencyGraph::value_type & vt : dependency_graph_) { check_dependency_invariants(vt.first); } - IMP_FOREACH(const ModelObject * mo, no_dependencies_) { + for(const ModelObject * mo : no_dependencies_) { IMP_UNUSED(mo); IMP_INTERNAL_CHECK( dependency_graph_.find(mo) != dependency_graph_.end(), @@ -245,7 +245,7 @@ void Model::update() { set_has_all_dependencies(true); ScoreStatesTemp sst; - IMP_FOREACH(DependencyGraph::value_type & vt, dependency_graph_) { + for(DependencyGraph::value_type & vt : dependency_graph_) { ModelObject *mo = const_cast(vt.first); ScoreState *ss = dynamic_cast(mo); if (ss) { @@ -289,7 +289,7 @@ void Model::do_add_dependencies(const ModelObject *cmo) { { std::sort(outputs.begin(), outputs.end()); outputs.erase(std::unique(outputs.begin(), outputs.end()), outputs.end()); - IMP_FOREACH(ModelObject * out, outputs) { + for(ModelObject * out : outputs) { dependency_graph_[out].access_writers().push_back(mo); do_clear_required_score_states(out); } @@ -309,7 +309,7 @@ void Model::do_add_dependencies(const ModelObject *cmo) { IMP_INTERNAL_CHECK( filtered_inputs.size() + input_outputs.size() == inputs.size(), "Sizes don't add up"); - IMP_FOREACH(ModelObject * in, filtered_inputs) { + for(ModelObject * in : filtered_inputs) { dependency_graph_[in].access_readers().push_back(mo); } dependency_graph_[mo].set_inputs(filtered_inputs); @@ -327,12 +327,10 @@ void Model::do_clear_required_score_states(ModelObject *mo) { required_score_states_.erase(mo); IMP_CHECK_OBJECT(mo); mo->handle_set_has_required_score_states(false); - IMP_FOREACH(ModelObject * in, - dependency_graph_.find(mo)->second.get_readers()) { + for(ModelObject * in : dependency_graph_.find(mo)->second.get_readers()) { do_clear_required_score_states(in); } - IMP_FOREACH(ModelObject * in, - dependency_graph_.find(mo)->second.get_outputs()) { + for(ModelObject * in : dependency_graph_.find(mo)->second.get_outputs()) { do_clear_required_score_states(in); } } @@ -345,7 +343,7 @@ void Model::do_clear_dependencies(const ModelObject *cmo) { do_clear_required_score_states(mo); } NodeInfo &ni = dependency_graph_.find(cmo)->second; - IMP_FOREACH(ModelObject * in, ni.get_inputs()) { + for(ModelObject * in : ni.get_inputs()) { // for teardown if (dependency_graph_.find(in) == dependency_graph_.end()) continue; Vector &cur = @@ -359,7 +357,7 @@ void Model::do_clear_dependencies(const ModelObject *cmo) { } ni.set_inputs(Edges()); - IMP_FOREACH(ModelObject * out, ni.get_outputs()) { + for(ModelObject * out : ni.get_outputs()) { if (dependency_graph_.find(out) == dependency_graph_.end()) continue; Vector &cur = dependency_graph_.find(out)->second.access_writers(); @@ -376,7 +374,7 @@ void Model::do_clear_dependencies(const ModelObject *cmo) { dependencies_age_ = age_counter_; { // down stream might be affected (eg SetContainers) Edges readers = ni.get_readers(); - IMP_FOREACH(ModelObject * reader, readers) { + for(ModelObject * reader : readers) { do_clear_dependencies(reader); } } @@ -422,15 +420,14 @@ void Model::do_set_has_required_score_states(ModelObject *mo, bool tf) { IMP_OBJECT_LOG; if (tf) { ScoreStates all; - IMP_FOREACH(ModelObject * input, - dependency_graph_.find(mo)->second.get_inputs()) { + for(ModelObject * input : dependency_graph_.find(mo)->second.get_inputs()) { do_set_has_required_score_states(input, true); all += required_score_states_.find(input)->second; ScoreState *ss = dynamic_cast(input); if (ss) all.push_back(ss); } - IMP_FOREACH(ModelObject * input, - dependency_graph_.find(mo)->second.get_writers()) { + for(ModelObject * input : + dependency_graph_.find(mo)->second.get_writers()) { do_set_has_required_score_states(input, true); all += required_score_states_.find(input)->second; ScoreState *ss = dynamic_cast(input); @@ -467,7 +464,7 @@ void Model::do_remove_model_object(ModelObject *mo) { // clean up stray references { Edges readers = dependency_graph_.find(mo)->second.get_readers(); - IMP_FOREACH(ModelObject * r, readers) { do_clear_dependencies(r); } + for(ModelObject * r : readers) { do_clear_dependencies(r); } } IMP_INTERNAL_CHECK(dependency_graph_.find(mo) != dependency_graph_.end(), "Not in dependency graph"); diff --git a/modules/kernel/src/Optimizer.cpp b/modules/kernel/src/Optimizer.cpp index 650027634f..ddbf9bb56a 100644 --- a/modules/kernel/src/Optimizer.cpp +++ b/modules/kernel/src/Optimizer.cpp @@ -32,7 +32,7 @@ Optimizer::~Optimizer() {} void Optimizer::update_states() const { IMP_LOG_VERBOSE("Updating OptimizerStates " << std::flush); - IMP_FOREACH(ScoreState * ss, get_required_score_states()) { + for(ScoreState * ss : get_required_score_states()) { ss->before_evaluate(); } for (OptimizerStateConstIterator it = optimizer_states_begin(); diff --git a/modules/kernel/src/dependency_graph.cpp b/modules/kernel/src/dependency_graph.cpp index 6751731d8b..b5793f3df9 100644 --- a/modules/kernel/src/dependency_graph.cpp +++ b/modules/kernel/src/dependency_graph.cpp @@ -346,8 +346,8 @@ MOVector do_get_dependent(ModelObject *mo) { if (r) { ret.push_back(r); } - IMP_FOREACH(ModelObject * cur, - mo->get_model()->get_dependency_graph_outputs(mo)) { + for(ModelObject * cur : + mo->get_model()->get_dependency_graph_outputs(mo)) { ret += do_get_dependent(cur); } return ret; diff --git a/modules/kernel/src/particle_index.cpp b/modules/kernel/src/particle_index.cpp index 8df16ca4e6..08c1d77f34 100644 --- a/modules/kernel/src/particle_index.cpp +++ b/modules/kernel/src/particle_index.cpp @@ -48,12 +48,12 @@ ParticleIndexPairsAdaptor::ParticleIndexPairsAdaptor( : ParticleIndexPairs(get_indexes(ps)) {} namespace { -/* Check to make sure that IMP_FOREACH compiles correctly */ +/* Check to make sure that range-based for compiles correctly */ void foreach_test() IMP_UNUSED_FUNCTION; void foreach_test() { ParticleIndexes pis; ParticleIndexesAdaptor pia(pis); - IMP_FOREACH(ParticleIndex pi, pia) { IMP_UNUSED(pi); } + for(ParticleIndex pi : pia) { IMP_UNUSED(pi); } } } IMPKERNEL_END_NAMESPACE diff --git a/tools/build/container_templates/container/classnames.cpp b/tools/build/container_templates/container/classnames.cpp index d9b93fc333..cf8fb12cec 100644 --- a/tools/build/container_templates/container/classnames.cpp +++ b/tools/build/container_templates/container/classnames.cpp @@ -46,7 +46,7 @@ ClassnameContainerIndex::ClassnameContainerIndex(ClassnameContainerAdaptor c, void ClassnameContainerIndex::build() { contents_.clear(); - IMP_FOREACH(INDEXTYPE it, container_->get_contents()) { + for(INDEXTYPE it : container_->get_contents()) { contents_.insert(IMP::internal::get_canonical(it)); } } @@ -82,7 +82,7 @@ ClassnameContainerSet::ClassnameContainerSet(const ClassnameContainersTemp &in, PLURALINDEXTYPE ClassnameContainerSet::get_indexes() const { PLURALINDEXTYPE sum; - IMP_FOREACH(ClassnameContainer * c, get_classname_containers()) { + for(ClassnameContainer * c : get_classname_containers()) { PLURALINDEXTYPE const& cur= c->get_contents(); sum.insert(sum.end(), cur.begin(), cur.end()); } @@ -95,7 +95,7 @@ void ClassnameContainerSet::get_indexes_in_place (PLURALINDEXTYPE& output) const { output.clear(); - IMP_FOREACH(ClassnameContainer * c, get_classname_containers()) { + for(ClassnameContainer * c : get_classname_containers()) { PLURALINDEXTYPE const& cur = c->get_contents(); output.insert(output.end(), cur.begin(), cur.end()); } @@ -103,7 +103,7 @@ ClassnameContainerSet::get_indexes_in_place PLURALINDEXTYPE ClassnameContainerSet::get_range_indexes() const { PLURALINDEXTYPE sum; - IMP_FOREACH(ClassnameContainer * c, get_classname_containers()) { + for(ClassnameContainer * c : get_classname_containers()) { PLURALINDEXTYPE cur = c->get_range_indexes(); sum.insert(sum.end(), cur.begin(), cur.end()); } @@ -115,7 +115,7 @@ IMP_LIST_IMPL(ClassnameContainerSet, ClassnameContainer, ClassnameContainers); void ClassnameContainerSet::do_apply(const ClassnameModifier *sm) const { - IMP_FOREACH(ClassnameContainer * c, get_classname_containers()) { + for(ClassnameContainer * c : get_classname_containers()) { c->apply(sm); } } @@ -124,14 +124,14 @@ void ClassnameContainerSet::do_apply_moved( const ClassnameModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const { - IMP_FOREACH(ClassnameContainer * c, get_classname_containers()) { + for(ClassnameContainer * c : get_classname_containers()) { c->apply_moved(sm, moved_pis, reset_pis); } } ParticleIndexes ClassnameContainerSet::get_all_possible_indexes() const { ParticleIndexes ret; - IMP_FOREACH(ClassnameContainer * c, get_classname_containers()) { + for(ClassnameContainer * c : get_classname_containers()) { ret += c->get_all_possible_indexes(); } return ret; @@ -144,7 +144,7 @@ ModelObjectsTemp ClassnameContainerSet::do_get_inputs() const { std::size_t ClassnameContainerSet::do_get_contents_hash() const { std::size_t ret = 0; - IMP_FOREACH(ClassnameContainer * c, get_classname_containers()) { + for(ClassnameContainer * c : get_classname_containers()) { boost::hash_combine(ret, c->get_contents_hash()); } return ret; @@ -261,7 +261,7 @@ void DistributeClassnamesScoreState::update_lists_if_necessary() const { input_version_ = h; Vector output(data_.size()); - IMP_FOREACH(INDEXTYPE it, input_->get_contents()) { + for(INDEXTYPE it : input_->get_contents()) { for (unsigned int i = 0; i < data_.size(); ++i) { if (data_[i].get<1>()->get_value_index(get_model(), it) == data_[i].get<2>()) { @@ -298,7 +298,7 @@ EventClassnamesOptimizerState::EventClassnamesOptimizerState( void EventClassnamesOptimizerState::update() { int met = 0; Model *m = get_optimizer()->get_model(); - IMP_FOREACH(INDEXTYPE it, container_->get_contents()) { + for(INDEXTYPE it : container_->get_contents()) { if (pred_->get_value_index(m, it) == v_) ++met; } if (met >= min_ && met < max_) { @@ -359,7 +359,7 @@ ClassnameMinimumMS find_minimal_set_ClassnameMinimum(C *c, F *f, IMP_LOG_VERBOSE("Finding Minimum " << n << " of " << c->get_number() << std::endl); ClassnameMinimumMS bestn(n); - IMP_FOREACH(INDEXTYPE it, c->get_contents()) { + for(INDEXTYPE it : c->get_contents()) { double score = f->evaluate_index(c->get_model(), it, nullptr); IMP_LOG_VERBOSE("Found " << score << " for " << it << std::endl); bestn.insert(score, it); @@ -514,7 +514,7 @@ void PredicateClassnamesRestraint::do_add_score_and_derivatives( // no longer parallizable update_lists_if_necessary(); typedef std::pair LP; - IMP_FOREACH(const LP & lp, lists_) { + for(const LP & lp : lists_) { IMP_LOG_VERBOSE("Evaluating score for predicate value " << lp.first << std::endl); ClassnameScore* score= get_score_for_predicate(lp.first); @@ -534,7 +534,7 @@ ModelObjectsTemp PredicateClassnamesRestraint::do_get_inputs() const { ret += predicate_->get_inputs(get_model(), all); if(!is_get_inputs_ignores_individual_scores_){ typedef std::pair > SP; - IMP_FOREACH(const SP & sp, scores_) { + for(const SP & sp : scores_) { ret += sp.second->get_inputs(get_model(), all); } } @@ -545,11 +545,11 @@ Restraints PredicateClassnamesRestraint::do_create_current_decomposition() const { Restraints ret; typedef std::pair LP; - IMP_FOREACH(const LP & lp, lists_) { + for(const LP & lp : lists_) { if(lists_.size()>0){ ClassnameScore* score= get_score_for_predicate(lp.first); if(IMP_LIKELY(score != nullptr)){ - IMP_FOREACH(PASSINDEXTYPE it, lp.second) { + for(PASSINDEXTYPE it : lp.second) { Restraints r = score->create_current_decomposition(get_model(), it); ret += r; @@ -576,15 +576,15 @@ void PredicateClassnamesRestraint::update_lists_if_necessary() const { } #else typedef std::pair LP; - IMP_FOREACH(LP & lp, lists_) { + for(LP & lp : lists_) { lp.second.clear(); } #endif predicate_->setup_for_get_value_index_in_batch(get_model()); - IMP_FOREACH(INDEXTYPE it, input_->get_contents()) { + for(INDEXTYPE it : input_->get_contents()) { int bin = predicate_->get_value_index_in_batch(get_model(), it); lists_[bin].push_back(it); - } // IMP_FOREACH + } } From 78e490bc64faac2ce4fd5d14397ced8f5ecbf72e Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Sun, 6 Mar 2022 09:04:11 -0800 Subject: [PATCH 057/155] Fix bundling of 32-bit Windows DLLs Add missing Visual Studio 2015 redistributable DLLs and OpenCV dependencies, but don't bundle the APIset forwarder DLLs, which are expected to be installed on all systems. --- tools/w32/make-package.sh | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 1344dd2afe..159282e5db 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -123,7 +123,8 @@ if [ "${BITS}" = "32" ]; then MAKENSIS="makensis" # Add redist MSVC runtime DLLs DLLSRC=/usr/lib/w32comp/windows/system - cp ${DLLSRC}/msvc*140.dll ${ROOT}/bin || exit 1 + cp ${DLLSRC}/msvc*140.dll ${DLLSRC}/concrt140.dll \ + ${DLLSRC}/vcruntime140.dll ${ROOT}/bin || exit 1 # Add other DLL dependencies cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ ${DLLSRC}/boost_filesystem-vc140-mt-x32-1_72.dll \ @@ -142,6 +143,7 @@ if [ "${BITS}" = "32" ]; then ${DLLSRC}/libTAU1.dll \ ${DLLSRC}/zlib1.dll \ ${DLLSRC}/opencv_core455.dll ${DLLSRC}/opencv_highgui455.dll \ + ${DLLSRC}/opencv_imgcodecs455.dll ${DLLSRC}/opencv_videoio455.dll \ ${DLLSRC}/opencv_imgproc455.dll ${ROOT}/bin || exit 1 else PYVERS="27 36 37 38 39 310" @@ -195,6 +197,10 @@ echo "oleaut32.dll" >> w32.dlls echo "user32.dll" >> w32.dlls echo "wsock32.dll" >> w32.dlls echo "ws2_32.dll" >> w32.dlls +for crt in convert environment filesystem heap locale math multibyte \ + runtime stdio string time utility; do + echo "api-ms-win-crt-${crt}-l1-1-0.dll" >> w32.dlls +done # People that want to run MPI-enabled binaries will need their own copy # of MS-MPI - we don't bundle it. From cdf1e54fb45e0f757a312a36cc27b9b7333d0967 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 10:23:59 -0800 Subject: [PATCH 058/155] Bundle api-ms* DLLs since conda-forge does --- tools/w32/make-package.sh | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 159282e5db..84ca2abcfc 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -124,7 +124,11 @@ if [ "${BITS}" = "32" ]; then # Add redist MSVC runtime DLLs DLLSRC=/usr/lib/w32comp/windows/system cp ${DLLSRC}/msvc*140.dll ${DLLSRC}/concrt140.dll \ - ${DLLSRC}/vcruntime140.dll ${ROOT}/bin || exit 1 + ${DLLSRC}/vcruntime140.dll ${DLLSRC}/ucrtbase.dll ${ROOT}/bin || exit 1 + for crt in convert environment filesystem heap locale math multibyte \ + runtime stdio string time utility; do + cp ${DLLSRC}/api-ms-win-crt-${crt}-l1-1-0.dll ${ROOT}/bin || exit 1 + done # Add other DLL dependencies cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ ${DLLSRC}/boost_filesystem-vc140-mt-x32-1_72.dll \ @@ -197,10 +201,6 @@ echo "oleaut32.dll" >> w32.dlls echo "user32.dll" >> w32.dlls echo "wsock32.dll" >> w32.dlls echo "ws2_32.dll" >> w32.dlls -for crt in convert environment filesystem heap locale math multibyte \ - runtime stdio string time utility; do - echo "api-ms-win-crt-${crt}-l1-1-0.dll" >> w32.dlls -done # People that want to run MPI-enabled binaries will need their own copy # of MS-MPI - we don't bundle it. From 3087090cddf7e859bc33a17b81256689d3057ef0 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 10:26:35 -0800 Subject: [PATCH 059/155] Add more standard Windows DLLs --- tools/w32/make-package.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 84ca2abcfc..0dac1eeb75 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -201,6 +201,10 @@ echo "oleaut32.dll" >> w32.dlls echo "user32.dll" >> w32.dlls echo "wsock32.dll" >> w32.dlls echo "ws2_32.dll" >> w32.dlls +echo "mf.dll" >> w32.dlls +echo "mfplat.dll" >> w32.dlls +echo "mfreadwrite.dll" >> w32.dlls +echo "shlwapi.dll" >> w32.dlls # People that want to run MPI-enabled binaries will need their own copy # of MS-MPI - we don't bundle it. From 87dcdab01185cbaef0d0983e915b1c87dedab6b6 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 13:33:17 -0800 Subject: [PATCH 060/155] Use MSVS2015 for both 32-bit and 64-bit Both 32-bit and 64-bit Windows IMP builds now use Visual Studio 2015, and dropped Python 2, so we can consolidate the logic here. --- tools/w32/make-package.sh | 113 ++++++++++++++------------------------ tools/w32/w32-install.nsi | 2 - 2 files changed, 41 insertions(+), 74 deletions(-) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 0dac1eeb75..0599b628b7 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -3,15 +3,15 @@ # Make a Win32 installer # First run the following in the binary directory to install files: -# cmake -DCMAKE_INSTALL_PYTHONDIR=/pylib/2.7 \ -# -DSWIG_PYTHON_LIBRARIES=$w32py/2.7/lib/python27.lib \ -# -DPYTHON_INCLUDE_DIRS=$w32py/2.7/include/ \ -# -DPYTHON_INCLUDE_PATH=$w32py/2.7/include/ \ -# -DPYTHON_LIBRARIES=$w32py/2.7/lib/python27.lib +# cmake -DCMAKE_INSTALL_PYTHONDIR=/pylib/3.6 \ +# -DSWIG_PYTHON_LIBRARIES=$w32py/3.6/lib/python36.lib \ +# -DPYTHON_INCLUDE_DIRS=$w32py/3.6/include/ \ +# -DPYTHON_INCLUDE_PATH=$w32py/3.6/include/ \ +# -DPYTHON_LIBRARIES=$w32py/3.6/lib/python36.lib # make DESTDIR=`pwd`/w32-inst install # # Where $w32py is the path containing Python headers and libraries. -# Repeat for all desired Python versions (2.7, 3.6, 3.7, 3.8, 3.9, and 3.10 +# Repeat for all desired Python versions (3.6, 3.7, 3.8, 3.9, and 3.10 # for us) # # Then run (still in the binary directory) @@ -55,15 +55,12 @@ cp ${TOOLDIR}/pkg-README.txt ${ROOT}/README.txt || exit 1 # Move pure Python code to Windows location mkdir ${ROOT}/python || exit 1 mkdir ${ROOT}/python/ihm || exit 1 -if [ "${BITS}" = "32" ]; then - # Remove .pyc files - find ${ROOT} -name __pycache__ -exec rm -rf \{\} \; 2>/dev/null - mv ${ROOT}/pylib/3.6/*.py ${ROOT}/pylib/3.6/IMP ${ROOT}/python || exit 1 - mv ${ROOT}/pylib/3.6/ihm/*.py ${ROOT}/python/ihm || exit 1 -else - mv ${ROOT}/pylib/2.7/*.py ${ROOT}/pylib/2.7/IMP ${ROOT}/python || exit 1 - mv ${ROOT}/pylib/2.7/ihm/*.py ${ROOT}/python/ihm || exit 1 -fi + +# Remove .pyc files +find ${ROOT} -name __pycache__ -exec rm -rf \{\} \; 2>/dev/null +mv ${ROOT}/pylib/3.6/*.py ${ROOT}/pylib/3.6/IMP ${ROOT}/python || exit 1 +mv ${ROOT}/pylib/3.6/ihm/*.py ${ROOT}/python/ihm || exit 1 + rm -rf ${ROOT}/pylib/*/*.py ${ROOT}/pylib/*/ihm/*.py ${ROOT}/pylib/*/IMP || exit 1 # Patch IMP/__init__.py, ihm/__init__.py, and RMF.py so they can find Python @@ -87,11 +84,7 @@ for app in ${ROOT}/bin/*; do done # Make Python version-specific directories for extensions (.pyd) -if [ "${BITS}" = "32" ]; then - PYVERS="3.6 3.7 3.8 3.9 3.10" -else - PYVERS="2.7 3.6 3.7 3.8 3.9 3.10" -fi +PYVERS="3.6 3.7 3.8 3.9 3.10" for PYVER in ${PYVERS}; do mkdir ${ROOT}/python/python${PYVER} || exit 1 mkdir ${ROOT}/python/python${PYVER}/_ihm_pyd || exit 1 @@ -118,66 +111,42 @@ rm -rf ${ROOT}/bin/imp_example_app.exe \ # Remove any .svn directories rm -rf `find ${ROOT} -name .svn` +PYVERS="36 37 38 39 310" if [ "${BITS}" = "32" ]; then - PYVERS="36 37 38 39 310" MAKENSIS="makensis" - # Add redist MSVC runtime DLLs DLLSRC=/usr/lib/w32comp/windows/system - cp ${DLLSRC}/msvc*140.dll ${DLLSRC}/concrt140.dll \ - ${DLLSRC}/vcruntime140.dll ${DLLSRC}/ucrtbase.dll ${ROOT}/bin || exit 1 - for crt in convert environment filesystem heap locale math multibyte \ - runtime stdio string time utility; do - cp ${DLLSRC}/api-ms-win-crt-${crt}-l1-1-0.dll ${ROOT}/bin || exit 1 - done - # Add other DLL dependencies - cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ - ${DLLSRC}/boost_filesystem-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_program_options-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_system-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_date_time-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_graph-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_regex-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_thread-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_random-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_iostreams-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/boost_zlib-vc140-mt-x32-1_72.dll \ - ${DLLSRC}/libgmp-10.dll \ - ${DLLSRC}/libmpfr-4.dll \ - ${DLLSRC}/libfftw3-3.dll \ - ${DLLSRC}/libTAU1.dll \ - ${DLLSRC}/zlib1.dll \ - ${DLLSRC}/opencv_core455.dll ${DLLSRC}/opencv_highgui455.dll \ - ${DLLSRC}/opencv_imgcodecs455.dll ${DLLSRC}/opencv_videoio455.dll \ - ${DLLSRC}/opencv_imgproc455.dll ${ROOT}/bin || exit 1 else - PYVERS="27 36 37 38 39 310" MAKENSIS="makensis -DIMP_64BIT" - # Add redist MSVC runtime DLLs DLLSRC=/usr/lib/w64comp/windows/system32 - cp ${DLLSRC}/msvc*110.dll ${ROOT}/bin || exit 1 - # Add other DLL dependencies - cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ - ${DLLSRC}/boost_filesystem-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_program_options-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_system-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_date_time-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_graph-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_regex-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_thread-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_random-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_iostreams-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_zlib-vc110-mt-1_55.dll \ - ${DLLSRC}/boost_chrono-vc110-mt-1_55.dll \ - ${DLLSRC}/CGAL-vc110-mt-4.4.dll \ - ${DLLSRC}/libgmp-10.dll \ - ${DLLSRC}/libmpfr-4.dll \ - ${DLLSRC}/libfftw3-3.dll \ - ${DLLSRC}/libTAU1.dll \ - ${DLLSRC}/zlib1.dll \ - ${DLLSRC}/opencv_core248.dll ${DLLSRC}/opencv_highgui248.dll \ - ${DLLSRC}/opencv_imgproc248.dll ${ROOT}/bin || exit 1 fi +# Add redist MSVC runtime DLLs +cp ${DLLSRC}/msvc*140.dll ${DLLSRC}/concrt140.dll \ +${DLLSRC}/vcruntime140.dll ${DLLSRC}/ucrtbase.dll ${ROOT}/bin || exit 1 +for crt in convert environment filesystem heap locale math multibyte \ + runtime stdio string time utility; do + cp ${DLLSRC}/api-ms-win-crt-${crt}-l1-1-0.dll ${ROOT}/bin || exit 1 +done +# Add other DLL dependencies +cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ + ${DLLSRC}/boost_filesystem-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_program_options-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_system-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_date_time-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_graph-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_regex-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_thread-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_random-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_iostreams-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_zlib-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/libgmp-10.dll \ + ${DLLSRC}/libmpfr-4.dll \ + ${DLLSRC}/libfftw3-3.dll \ + ${DLLSRC}/libTAU1.dll \ + ${DLLSRC}/zlib1.dll \ + ${DLLSRC}/opencv_core455.dll ${DLLSRC}/opencv_highgui455.dll \ + ${DLLSRC}/opencv_imgcodecs455.dll ${DLLSRC}/opencv_videoio455.dll \ + ${DLLSRC}/opencv_imgproc455.dll ${ROOT}/bin || exit 1 # Check all installed binaries for DLL dependencies, to make sure we # didn't miss any diff --git a/tools/w32/w32-install.nsi b/tools/w32/w32-install.nsi index a95de830ad..5191c296f5 100644 --- a/tools/w32/w32-install.nsi +++ b/tools/w32/w32-install.nsi @@ -81,7 +81,6 @@ Section "" WriteRegDWORD HKLM "${UNINST_KEY}" "NoModify" 1 WriteRegDWORD HKLM "${UNINST_KEY}" "NoRepair" 1 - WriteRegStr HKLM "Software\Python\PythonCore\2.7\PythonPath\${PRODVER}" "" "$INSTDIR\python" WriteRegStr HKLM "Software\Python\PythonCore\3.6${PYTHON_ARCH_SUFFIX}\PythonPath\${PRODVER}" "" "$INSTDIR\python" WriteRegStr HKLM "Software\Python\PythonCore\3.7${PYTHON_ARCH_SUFFIX}\PythonPath\${PRODVER}" "" "$INSTDIR\python" WriteRegStr HKLM "Software\Python\PythonCore\3.8${PYTHON_ARCH_SUFFIX}\PythonPath\${PRODVER}" "" "$INSTDIR\python" @@ -115,7 +114,6 @@ Section "Uninstall" DeleteRegKey /ifempty HKLM "Software\${PRODVER}" DeleteRegKey HKLM "${UNINST_KEY}" - DeleteRegKey HKLM "Software\Python\PythonCore\2.7\PythonPath\${PRODVER}" DeleteRegKey HKLM "Software\Python\PythonCore\3.6${PYTHON_ARCH_SUFFIX}\PythonPath\${PRODVER}" DeleteRegKey HKLM "Software\Python\PythonCore\3.7${PYTHON_ARCH_SUFFIX}\PythonPath\${PRODVER}" DeleteRegKey HKLM "Software\Python\PythonCore\3.8${PYTHON_ARCH_SUFFIX}\PythonPath\${PRODVER}" From b1a850ba76122d3d5acbe94d9d4bc36b7c76faf0 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 13:36:43 -0800 Subject: [PATCH 061/155] Drop Windows XP/Vista support We now build with Visual Studio 2015, which almost certainly doesn't support Windows XP, long discontinued by Microsoft. --- tools/w32/w32-install.nsi | 27 ++++++--------------------- 1 file changed, 6 insertions(+), 21 deletions(-) diff --git a/tools/w32/w32-install.nsi b/tools/w32/w32-install.nsi index 5191c296f5..412598c294 100644 --- a/tools/w32/w32-install.nsi +++ b/tools/w32/w32-install.nsi @@ -127,27 +127,12 @@ Function .onInit SetRegView 64 !endif -!ifdef IMP_64BIT - ${If} ${AtLeastWinVista} - Goto version_check_done - ${Else} - MessageBox MB_OK \ - "IMP (64 bit) can only be installed on Windows Vista or later. \ - Use the 32 bit version on older versions of Windows." /SD IDOK - Quit - ${EndIf} -!else - ${If} ${IsWinXP} - ${AndIf} ${AtLeastServicePack} 2 - ${OrIf} ${AtLeastWin2003} - Goto version_check_done - ${Else} - MessageBox MB_OK \ - "IMP can only be installed on Windows XP Service Pack 2 or later." \ - /SD IDOK - Quit - ${EndIf} -!endif +${If} ${AtLeastWin7} + Goto version_check_done +${Else} + MessageBox MB_OK "IMP can only be installed on Windows 7 or later." /SD IDOK + Quit +${EndIf} version_check_done: FunctionEnd From 82b278ab06f1b7762419c8b22bf2b29e1e6da493 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 13:43:00 -0800 Subject: [PATCH 062/155] Note that we now require C++11 --- doc/manual/code_conventions.md | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/doc/manual/code_conventions.md b/doc/manual/code_conventions.md index 7a8de0379c..30209e3afd 100644 --- a/doc/manual/code_conventions.md +++ b/doc/manual/code_conventions.md @@ -121,11 +121,8 @@ As a result, such functions do not need to obey all the coding conventions (but we recommend that they do). # C++ 11 {#codeconv_cxx11} -%IMP now turns on C++ 11 support when it can. However, since compilers -are still quite variable in which C++ 11 features they support, it is -not advisable to use them directly in %IMP code at this point. To aid -in their use when practical we provide several helper macros: -- `IMP_OVERRIDE` inserts the `override` keyword when available -- `IMP_FINAL` inserts the `final` keyword when available - -More will come. +Latest %IMP requires a compiler that supports C++ 11, unlike older versions. +Thus, C++ 11 features, such as the `override`, `final`, `auto` and `nullptr` +keywords, and range-based for loops, can be used where appropriate. +The old compatibility macros (such as `IMP_OVERRIDE`, `IMP_FINAL`, +`IMP_NULLPTR` and `IMP_FOREACH`) should no longer be used. From 01106a0d60aa4fa53b0401a177fa678d59738aa1 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 13:46:47 -0800 Subject: [PATCH 063/155] Remove obsolete file We no longer need our own nullptr type. --- modules/kernel/src/nullptr.cpp | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 modules/kernel/src/nullptr.cpp diff --git a/modules/kernel/src/nullptr.cpp b/modules/kernel/src/nullptr.cpp deleted file mode 100644 index 75022aa179..0000000000 --- a/modules/kernel/src/nullptr.cpp +++ /dev/null @@ -1,15 +0,0 @@ -/** - * \file base_types.cpp \brief Base types. - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - * - */ - -#include "IMP/nullptr.h" - -namespace IMP { -#if (defined(BOOST_NO_CXX11_NULLPTR) || defined(BOOST_NO_NULLPTR)) && \ - !defined(nullptr) -const nullptr_t nullptr = nullptr_t(); -#endif -} From 6549a9b7571a37cf50d7621a15a58895999abeb9 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 14:02:40 -0800 Subject: [PATCH 064/155] Replace IMP_FOREACH with range-based for loop --- modules/algebra/examples/grid.cpp | 2 +- modules/algebra/include/VectorBaseD.h | 4 ++-- modules/algebra/src/Gaussian3D.cpp | 2 +- modules/algebra/src/Sphere3D.cpp | 16 ++++++------- modules/algebra/src/vector_generators.cpp | 10 ++++---- .../atom/benchmark/benchmark_md_charmm.cpp | 2 +- modules/atom/include/BondPairContainer.h | 2 +- modules/atom/include/hierarchy_tools.h | 2 +- .../include/internal/SelectionPredicate.h | 4 ++-- .../src/RemoveRigidMotionOptimizerState.cpp | 2 +- .../src/RemoveTranslationOptimizerState.cpp | 2 +- modules/atom/src/Representation.cpp | 2 +- modules/atom/src/Selection.cpp | 18 +++++++-------- .../src/VelocityScalingOptimizerState.cpp | 2 +- modules/atom/src/hierarchy_tools.cpp | 23 +++++++++---------- modules/atom/src/pdb.cpp | 6 ++--- .../src/internal/MovedSingletonContainer.cpp | 12 ++++------ modules/display/include/geometry_macros.h | 5 ++-- modules/display/src/Writer.cpp | 2 +- modules/display/test/test_isosurface.cpp | 2 +- modules/em/include/DensityMap.h | 2 +- .../include/internal/create_decomposition.h | 2 +- modules/kinematics/include/KinematicForest.h | 4 ++-- .../kinematics/include/ProteinKinematics.h | 2 +- modules/rmf/bin/rmf_display.cpp | 2 +- modules/rmf/bin/rmf_simplify.cpp | 2 +- modules/rmf/include/simple_links.h | 2 +- modules/rmf/src/HierarchyLoadLink.cpp | 8 +++---- modules/rmf/src/HierarchySaveLink.cpp | 8 +++---- modules/rmf/src/frames.cpp | 4 ++-- modules/rmf/src/geometry_io.cpp | 2 +- .../rmf/src/internal/atom_links_gaussians.cpp | 4 ++-- .../src/internal/atom_links_rigid_bodies.cpp | 23 +++++++++---------- .../rmf/src/internal/atom_links_static.cpp | 6 ++--- modules/rmf/src/internal/atom_links_xyzs.cpp | 10 ++++---- .../src/internal/hierarchy_links_helpers.cpp | 2 +- modules/rmf/src/internal/link_helpers.cpp | 4 ++-- modules/rmf/src/restraint_io.cpp | 23 +++++++++---------- 38 files changed, 112 insertions(+), 118 deletions(-) diff --git a/modules/algebra/examples/grid.cpp b/modules/algebra/examples/grid.cpp index 65fd1b8aa2..a26d480352 100644 --- a/modules/algebra/examples/grid.cpp +++ b/modules/algebra/examples/grid.cpp @@ -26,7 +26,7 @@ int main(int argc, char *argv[]) { double> Grid; Grid grid(1, bb, 0); // fill it with a gradient - IMP_FOREACH(Grid::Index i, grid.get_all_indexes()) { + for(Grid::Index i : grid.get_all_indexes()) { IMP::algebra::Vector3D c = grid.get_center(i); grid[i] = IMP::algebra::get_distance(c, IMP::algebra::Vector3D(10, 10, 10)); } diff --git a/modules/algebra/include/VectorBaseD.h b/modules/algebra/include/VectorBaseD.h index d0a11cfd00..968e78fd94 100644 --- a/modules/algebra/include/VectorBaseD.h +++ b/modules/algebra/include/VectorBaseD.h @@ -77,7 +77,7 @@ class VectorBaseD : public GeometricPrimitiveD { ValueException); } IMP_IF_CHECK(USAGE) { - IMP_FOREACH(double f, r) { + for(double f : r) { IMP_UNUSED(f); IMP_USAGE_CHECK(!IMP::is_nan(f), "NaN passed to constructor"); } @@ -93,7 +93,7 @@ class VectorBaseD : public GeometricPrimitiveD { ValueException); } IMP_IF_CHECK(USAGE) { - IMP_FOREACH(double f, r) { + for(double f : r) { IMP_USAGE_CHECK(!IMP::is_nan(f), "NaN passed in equals"); } } diff --git a/modules/algebra/src/Gaussian3D.cpp b/modules/algebra/src/Gaussian3D.cpp index 3f462ea9d1..28b4a1fdb5 100644 --- a/modules/algebra/src/Gaussian3D.cpp +++ b/modules/algebra/src/Gaussian3D.cpp @@ -94,7 +94,7 @@ DensityGrid get_rasterized(const Gaussian3Ds &gmm, const Floats &weights, double pre(get_gaussian_eval_prefactor(determinant)); Eigen::Vector3d center(gmm[ng].get_center().get_data()); IMP_INTERNAL_CHECK(invertible, "matrix wasn't invertible! uh oh!"); - IMP_FOREACH(const DensityGrid::Index & i, ret.get_all_indexes()) { + for(const DensityGrid::Index & i : ret.get_all_indexes()) { Eigen::Vector3d r(get_vec_from_center(i, ret, center)); update_value(&ret, i, r, inverse, pre, weights[ng]); } diff --git a/modules/algebra/src/Sphere3D.cpp b/modules/algebra/src/Sphere3D.cpp index 7cf64e2fef..f441820d12 100644 --- a/modules/algebra/src/Sphere3D.cpp +++ b/modules/algebra/src/Sphere3D.cpp @@ -73,7 +73,7 @@ Sphere3Ds get_simplified_from_volume(Sphere3Ds in, const double resolution = 1.0 / maximum_allowed_error_angstroms; const double probe = maximum_allowed_error_angstroms; - IMP_FOREACH(Sphere3D & s, in) { + for(Sphere3D & s : in) { s = Sphere3D(s.get_center(), s.get_radius() + probe); } @@ -93,7 +93,7 @@ Sphere3Ds get_simplified_from_volume(Sphere3Ds in, SphereIndex si(i); unsigned int nn = nns->get_nearest_neighbor(in[i].get_center()); double r = get_distance(sps[nn], in[i].get_center()); - IMP_FOREACH(Vector3D v, sps) { + for(Vector3D v : sps) { IMP_INTERNAL_CHECK(get_distance(v, in[i].get_center()) > .9 * r, "Bad nearest neighbor. Found one at " << v << " with distance " @@ -103,7 +103,7 @@ Sphere3Ds get_simplified_from_volume(Sphere3Ds in, IMP::Ints support = nns->get_in_ball(in[i].get_center(), r + 1.0 / resolution); - IMP_FOREACH(int i, support) { supports[si].insert(SPIndex(i)); } + for(int i : support) { supports[si].insert(SPIndex(i)); } radii[si] = r + .5 / resolution; /*cpout << ".sphere " << in[i].get_center()[0] << " " << in[i].get_center()[1] << " " << in[i].get_center()[2] << " " << r @@ -118,8 +118,8 @@ Sphere3Ds get_simplified_from_volume(Sphere3Ds in, if (0) SupportedPair(); // suppress warning IMP_KERNEL_LARGE_UNORDERED_MAP supported; typedef std::pair SupportsPair; - IMP_FOREACH(const SupportsPair & ps, supports) { - IMP_FOREACH(SPIndex spi, ps.second) { supported[spi].insert(ps.first); } + for(const SupportsPair & ps : supports) { + for(SPIndex spi : ps.second) { supported[spi].insert(ps.first); } } IMP_LOG_TERSE("Generating output." << std::endl); @@ -129,7 +129,7 @@ Sphere3Ds get_simplified_from_volume(Sphere3Ds in, IMP_USAGE_CHECK(!supports.empty(), "Out of spheres"); SphereIndex max; double max_score = 0; - IMP_FOREACH(const SupportsPair & sp, supports) { + for(const SupportsPair & sp : supports) { double score = sp.second.size(); if (score > max_score) { max_score = score; @@ -137,8 +137,8 @@ Sphere3Ds get_simplified_from_volume(Sphere3Ds in, } } SPIndexSet max_supports = supports.find(max)->second; - IMP_FOREACH(SPIndex spi, max_supports) { - IMP_FOREACH(SphereIndex si, supported.find(spi)->second) { + for(SPIndex spi : max_supports) { + for(SphereIndex si : supported.find(spi)->second) { if (si != max) { supports[si].erase(spi); if (supports[si].empty()) supports.erase(si); diff --git a/modules/algebra/src/vector_generators.cpp b/modules/algebra/src/vector_generators.cpp index 0cb28c4406..c55034cc45 100644 --- a/modules/algebra/src/vector_generators.cpp +++ b/modules/algebra/src/vector_generators.cpp @@ -196,24 +196,24 @@ Vector3Ds get_uniform_surface_cover(const Sphere3Ds &in, const double scale = 1.0 / resolution; BoundingBox3D bb; - IMP_FOREACH(Sphere3D s, in) { bb += get_bounding_box(s); } + for(Sphere3D s : in) { bb += get_bounding_box(s); } bb += scale; typedef DenseGrid3D Grid; Grid grid(scale, bb, 0); - IMP_FOREACH(Sphere3D s, in) { + for(Sphere3D s : in) { BoundingBox3D bb = get_bounding_box(s); - IMP_FOREACH(Grid::Index i, grid.get_indexes(bb)) { + for(Grid::Index i : grid.get_indexes(bb)) { Vector3D c = grid.get_center(i); if (get_distance(c, s.get_center()) <= s.get_radius()) { grid[i] = 1; } } } - IMP_FOREACH(Sphere3D s, in) { + for(Sphere3D s : in) { double a = get_surface_area(s); double n = a * resolution * resolution; - IMP_FOREACH(Vector3D v, get_uniform_surface_cover(s, std::ceil(n))) { + for(Vector3D v : get_uniform_surface_cover(s, std::ceil(n))) { if (!grid[v]) { ret.push_back(v); } diff --git a/modules/atom/benchmark/benchmark_md_charmm.cpp b/modules/atom/benchmark/benchmark_md_charmm.cpp index 676c04848c..68a649b1ac 100644 --- a/modules/atom/benchmark/benchmark_md_charmm.cpp +++ b/modules/atom/benchmark/benchmark_md_charmm.cpp @@ -66,7 +66,7 @@ int do_benchmark() { // Get a list of all atoms in the protein, and put it in a container atom::Hierarchies atoms = get_by_type(prot, ATOM_TYPE); // work around added atoms not being marked as optimized - IMP_FOREACH(atom::Hierarchy atom, atoms) { + for(atom::Hierarchy atom : atoms) { core::XYZ(atom).set_coordinates_are_optimized(true); } IMP_NEW(ListSingletonContainer, cont, (m, IMP::internal::get_index(atoms))); diff --git a/modules/atom/include/BondPairContainer.h b/modules/atom/include/BondPairContainer.h index f50c515417..47e09a0295 100644 --- a/modules/atom/include/BondPairContainer.h +++ b/modules/atom/include/BondPairContainer.h @@ -37,7 +37,7 @@ class IMPATOMEXPORT BondPairContainer : public PairContainer { public: template void apply_generic(F* f) const { - IMP_FOREACH(ParticleIndex pi, sc_->get_contents()) { + for(ParticleIndex pi : sc_->get_contents()) { Bond bp(get_model(), pi); f->apply_index(get_model(), ParticleIndexPair( bp.get_bonded(0).get_particle_index(), diff --git a/modules/atom/include/hierarchy_tools.h b/modules/atom/include/hierarchy_tools.h index c3175fd39c..4c14f9144d 100644 --- a/modules/atom/include/hierarchy_tools.h +++ b/modules/atom/include/hierarchy_tools.h @@ -212,7 +212,7 @@ class HierarchiesGeometry : public display::SingletonsGeometry { : SingletonsGeometry(sc), res_(resolution) {} display::Geometries get_components() const override { display::Geometries ret; - IMP_FOREACH(ParticleIndex pi, get_container()->get_contents()) { + for(ParticleIndex pi : get_container()->get_contents()) { Model *m = get_container()->get_model(); if (components_.find(pi) == components_.end()) { IMP_NEW(HierarchyGeometry, g, (atom::Hierarchy(m, pi), res_)); diff --git a/modules/atom/include/internal/SelectionPredicate.h b/modules/atom/include/internal/SelectionPredicate.h index a045ce92e0..3b2d844cc5 100644 --- a/modules/atom/include/internal/SelectionPredicate.h +++ b/modules/atom/include/internal/SelectionPredicate.h @@ -107,7 +107,7 @@ class ListSelectionPredicate : public SelectionPredicate { SelectionPredicates predicates_; void clone_predicates(ListSelectionPredicate *s) { s->predicates_.reserve(predicates_.size()); - IMP_FOREACH(SelectionPredicate *p, predicates_) { + for(SelectionPredicate *p : predicates_) { s->predicates_.push_back(p->clone(false)); } } @@ -129,7 +129,7 @@ class ListSelectionPredicate : public SelectionPredicate { virtual int setup_bitset(int index) override { index = SelectionPredicate::setup_bitset(index); /* Set indexes for subpredicates */ - IMP_FOREACH(SelectionPredicate *p, predicates_) { + for(SelectionPredicate *p : predicates_) { index = p->setup_bitset(index); } return index; diff --git a/modules/atom/src/RemoveRigidMotionOptimizerState.cpp b/modules/atom/src/RemoveRigidMotionOptimizerState.cpp index 8a72e7ea33..d01ab37a80 100644 --- a/modules/atom/src/RemoveRigidMotionOptimizerState.cpp +++ b/modules/atom/src/RemoveRigidMotionOptimizerState.cpp @@ -16,7 +16,7 @@ IMPATOM_BEGIN_NAMESPACE RemoveRigidMotionOptimizerState::RemoveRigidMotionOptimizerState( Model *m, ParticleIndexesAdaptor pis) : OptimizerState(m, "RemoveRigidMotionOptimizerState%1%") { - IMP_FOREACH(ParticleIndex pi, pis) { + for(ParticleIndex pi : pis) { pis_.push_back(m->get_particle(pi)); } } diff --git a/modules/atom/src/RemoveTranslationOptimizerState.cpp b/modules/atom/src/RemoveTranslationOptimizerState.cpp index ca68a94b2a..75ea0c3208 100644 --- a/modules/atom/src/RemoveTranslationOptimizerState.cpp +++ b/modules/atom/src/RemoveTranslationOptimizerState.cpp @@ -16,7 +16,7 @@ IMPATOM_BEGIN_NAMESPACE RemoveTranslationOptimizerState::RemoveTranslationOptimizerState( Model *m, ParticleIndexesAdaptor pis) : OptimizerState(m, "RemoveTranslationOptimizerState%1%") { - IMP_FOREACH(ParticleIndex pi, pis) { + for(ParticleIndex pi : pis) { pis_.push_back(m->get_particle(pi)); } } diff --git a/modules/atom/src/Representation.cpp b/modules/atom/src/Representation.cpp index 323843c66c..aa0ce215a5 100644 --- a/modules/atom/src/Representation.cpp +++ b/modules/atom/src/Representation.cpp @@ -20,7 +20,7 @@ IMPATOM_BEGIN_NAMESPACE double get_resolution(Model* m, ParticleIndex pi) { double min = std::numeric_limits::max(); - IMP_FOREACH(Hierarchy l, get_leaves(Hierarchy(m, pi))) { + for(Hierarchy l : get_leaves(Hierarchy(m, pi))) { double cur = core::XYZR(l).get_radius(); IMP_USAGE_CHECK(cur > 0, "Particle " << l << " has an invalid radius"); min = std::min(min, cur); diff --git a/modules/atom/src/Selection.cpp b/modules/atom/src/Selection.cpp index 383fc113c0..d5ef206d4d 100644 --- a/modules/atom/src/Selection.cpp +++ b/modules/atom/src/Selection.cpp @@ -137,7 +137,7 @@ namespace { return MATCH_WITH_CHILDREN; } bool no_match = false, cached_match = true; - IMP_FOREACH(internal::SelectionPredicate *p, predicates_) { + for(internal::SelectionPredicate *p : predicates_) { MatchType v = p->get_value_index(m, pi, bs); if (v == MISMATCH) { return MISMATCH; @@ -180,7 +180,7 @@ namespace { return MATCH_WITH_CHILDREN; } bool no_match = false, no_cached_match = false; - IMP_FOREACH(internal::SelectionPredicate *p, predicates_) { + for(internal::SelectionPredicate *p : predicates_) { MatchType v = p->get_value_index(m, pi, bs); if (v == MATCH_WITH_CHILDREN) { return MATCH_WITH_CHILDREN; @@ -223,7 +223,7 @@ namespace { return MATCH_WITH_CHILDREN; } bool no_match = false, match = false; - IMP_FOREACH(internal::SelectionPredicate *p, predicates_) { + for(internal::SelectionPredicate *p : predicates_) { MatchType v = p->get_value_index(m, pi, bs); if (v == MATCH_WITH_CHILDREN || v == MATCH_SELF_ONLY) { match = !match; @@ -544,7 +544,7 @@ ExpandResults expand_children_search(Model *m, RepresentationType representation_type) { Hierarchy h(m, pi); ExpandResults ret; - IMP_FOREACH(Hierarchy c, h.get_children()) { + for(Hierarchy c : h.get_children()) { ExpandResult r = expand_search(m, c, resolution, representation_type); if (r.get_indexes().size()>0) ret.push_back(r); } @@ -579,9 +579,9 @@ Selection::SearchResult Selection::search( bool children_covered = true; bool matched = (val == internal::SelectionPredicate::MATCH_WITH_CHILDREN || val == internal::SelectionPredicate::MATCH_SELF_ONLY); - IMP_FOREACH(ExpandResult chlist, cur_children) { + for(ExpandResult chlist : cur_children) { found_rep_node |= chlist.get_from_rep(); - IMP_FOREACH(ParticleIndex ch, chlist.get_indexes()) { + for(ParticleIndex ch : chlist.get_indexes()) { SearchResult curr = search(m, ch, parent, with_representation, found_rep_node); matched |= curr.get_match(); if (curr.get_match()) { @@ -629,10 +629,10 @@ Selection::get_selected_particle_indexes(bool with_representation) const { IMP_LOG_TERSE("Processing selection on " << h_ << " with predicates " << std::endl); IMP_LOG_WRITE(VERBOSE, show_predicate(predicate_, IMP_STREAM)); - IMP_FOREACH(ParticleIndex pi, h_) { + for(ParticleIndex pi : h_) { ExpandResult res = expand_search(m_, pi, resolution_, representation_type_); - IMP_FOREACH(ParticleIndex rpi, res.get_indexes()) { + for(ParticleIndex rpi : res.get_indexes()) { ret += search(m_, rpi, base, with_representation, res.get_from_rep()).get_indexes(); } } @@ -835,7 +835,7 @@ Restraint *create_connectivity_restraint(const Selections &s, double x0, double k, std::string name) { IMP_IF_CHECK(USAGE) { boost::unordered_set used; - IMP_FOREACH(const Selection & sel, s) { + for(const Selection & sel : s) { ParticleIndexes cur = sel.get_selected_particle_indexes(); int old = used.size(); IMP_UNUSED(old); diff --git a/modules/atom/src/VelocityScalingOptimizerState.cpp b/modules/atom/src/VelocityScalingOptimizerState.cpp index b01ce395e6..4660958d79 100644 --- a/modules/atom/src/VelocityScalingOptimizerState.cpp +++ b/modules/atom/src/VelocityScalingOptimizerState.cpp @@ -15,7 +15,7 @@ VelocityScalingOptimizerState::VelocityScalingOptimizerState( Model *m, ParticleIndexesAdaptor pis, double temp) : OptimizerState(m, "VelocityScalingOptimizerState%1%"), temperature_(temp) { - IMP_FOREACH(ParticleIndex pi, pis) { + for(ParticleIndex pi : pis) { pis_.push_back(m->get_particle(pi)); } } diff --git a/modules/atom/src/hierarchy_tools.cpp b/modules/atom/src/hierarchy_tools.cpp index 851635cfd3..63624629ee 100644 --- a/modules/atom/src/hierarchy_tools.cpp +++ b/modules/atom/src/hierarchy_tools.cpp @@ -442,8 +442,7 @@ void transform_impl( } else if (core::XYZ::get_is_setup(m, cur)) { core::transform(core::XYZ(m, cur), tr); } - IMP_FOREACH(ParticleIndex pi, - atom::Hierarchy(m, cur).get_children_indexes()) { + for(ParticleIndex pi : atom::Hierarchy(m, cur).get_children_indexes()) { transform_impl(m, pi, tr, rigid_bodies); } } @@ -455,7 +454,7 @@ void transform(atom::Hierarchy h, const algebra::Transformation3D &tr) { boost::unordered_map rigid_bodies; transform_impl(m, h.get_particle_index(), tr, rigid_bodies); - IMP_FOREACH(const RBP & rbp, rigid_bodies) { + for(const RBP & rbp : rigid_bodies) { core::RigidBody rb(m, rbp.first); ParticleIndexes members = rb.get_member_indexes(); if (rbp.second.size() != members.size()) { @@ -477,7 +476,7 @@ void assign_residues(IMP::atom::Hierarchy in, IMP_FUNCTION_LOG; IMP_KERNEL_LARGE_UNORDERED_MAP > indexes; - IMP_FOREACH(IMP::atom::Hierarchy l, IMP::atom::get_leaves(in)) { + for(IMP::atom::Hierarchy l : IMP::atom::get_leaves(in)) { IMP::core::XYZR d(l); IMP::Ints cur; if (IMP::atom::Atom::get_is_setup(l) && @@ -497,7 +496,7 @@ void assign_residues(IMP::atom::Hierarchy in, } IMP::atom::Hierarchy min; double min_distance = std::numeric_limits::max(); - IMP_FOREACH(IMP::atom::Hierarchy c, out) { + for(IMP::atom::Hierarchy c : out) { double cur_dist = IMP::core::get_distance(IMP::core::XYZR(c), d); if (cur_dist < min_distance) { min_distance = cur_dist; @@ -508,7 +507,7 @@ void assign_residues(IMP::atom::Hierarchy in, } typedef std::pair > IP; - IMP_FOREACH(IP ip, indexes) { + for(IP ip : indexes) { IMP::atom::Fragment::setup_particle( ip.first, IMP::Ints(ip.second.begin(), ip.second.end())); IMP::atom::Mass::setup_particle( @@ -519,7 +518,7 @@ void assign_residues(IMP::atom::Hierarchy in, void add_bonds(const IMP::atom::Hierarchies &out) { IMP_FUNCTION_LOG; - IMP_FOREACH(IMP::atom::Hierarchy c, out) { + for(IMP::atom::Hierarchy c : out) { IMP::atom::Bonded::setup_particle(c); } IMP::set_progress_display("adding bonds", out.size()); @@ -529,7 +528,7 @@ void add_bonds(const IMP::atom::Hierarchies &out) { for (unsigned int j = 0; j < i; ++j) { IMP::Ints ij = IMP::atom::Fragment(out[j]).get_residue_indexes(); std::sort(ij.begin(), ij.end()); - IMP_FOREACH(int iic, ii) { + for(int iic : ii) { if (std::binary_search(ij.begin(), ij.end(), iic + 1) || std::binary_search(ij.begin(), ij.end(), iic - 1) || std::binary_search(ij.begin(), ij.end(), iic)) { @@ -551,7 +550,7 @@ Hierarchy create_simplified_from_volume(Hierarchy h, double resolution) { IMP_FUNCTION_LOG; Model *m = h.get_model(); IMP::algebra::Sphere3Ds in_spheres; - IMP_FOREACH(IMP::atom::Hierarchy child, IMP::atom::get_leaves(h)) { + for(IMP::atom::Hierarchy child : IMP::atom::get_leaves(h)) { in_spheres.push_back(IMP::core::XYZR(child).get_sphere()); } @@ -563,7 +562,7 @@ Hierarchy create_simplified_from_volume(Hierarchy h, double resolution) { << out_spheres.size() << std::endl); IMP::atom::Hierarchies leaves; - IMP_FOREACH(IMP::algebra::Sphere3D s, out_spheres) { + for(IMP::algebra::Sphere3D s : out_spheres) { IMP::ParticleIndex cur = m->add_particle("fragment"); leaves.push_back(IMP::atom::Hierarchy::setup_particle(m, cur)); IMP::core::XYZR::setup_particle(m, cur, s); @@ -571,7 +570,7 @@ Hierarchy create_simplified_from_volume(Hierarchy h, double resolution) { assign_residues(h, leaves); add_bonds(leaves); Hierarchy ret = Hierarchy::setup_particle(m, m->add_particle(h->get_name())); - IMP_FOREACH(Hierarchy c, leaves) { ret.add_child(c); } + for(Hierarchy c : leaves) { ret.add_child(c); } return ret; } @@ -589,7 +588,7 @@ Hierarchy create_simplified_assembly_from_volume(Hierarchy h, } else { Hierarchy ret = Hierarchy::setup_particle( h.get_model(), h.get_model()->add_particle(h->get_name())); - IMP_FOREACH(Hierarchy c, h.get_children()) { + for(Hierarchy c : h.get_children()) { ret.add_child(create_simplified_assembly_from_volume(c, resolution)); } return ret; diff --git a/modules/atom/src/pdb.cpp b/modules/atom/src/pdb.cpp index d71f0623d5..ce9a13f427 100644 --- a/modules/atom/src/pdb.cpp +++ b/modules/atom/src/pdb.cpp @@ -498,7 +498,7 @@ WritePDBOptimizerState::WritePDBOptimizerState(const atom::Hierarchies mh, std::string filename) : OptimizerState(mh[0].get_model(), filename + "Writer"), filename_(filename) { - IMP_FOREACH(atom::Hierarchy h, mh) { pis_.push_back(h.get_particle_index()); } + for(atom::Hierarchy h : mh) { pis_.push_back(h.get_particle_index()); } } void WritePDBOptimizerState::do_update(unsigned int call) { @@ -506,7 +506,7 @@ void WritePDBOptimizerState::do_update(unsigned int call) { bool append = (call != 0); std::string filename; Hierarchies hs; - IMP_FOREACH(ParticleIndex pi, pis_) { + for(ParticleIndex pi : pis_) { hs.push_back(Hierarchy(get_model(), pi)); } try { @@ -525,7 +525,7 @@ void WritePDBOptimizerState::do_update(unsigned int call) { ModelObjectsTemp WritePDBOptimizerState::do_get_inputs() const { ModelObjectsTemp ret; - IMP_FOREACH(ParticleIndex pi, pis_) { + for(ParticleIndex pi : pis_) { ret += get_leaves(Hierarchy(get_model(), pi)); } return ret; diff --git a/modules/core/src/internal/MovedSingletonContainer.cpp b/modules/core/src/internal/MovedSingletonContainer.cpp index acec3449f9..9f1a5ce96e 100644 --- a/modules/core/src/internal/MovedSingletonContainer.cpp +++ b/modules/core/src/internal/MovedSingletonContainer.cpp @@ -131,7 +131,7 @@ void XYZRMovedSingletonContainer::do_reset_moved() { IMP_OBJECT_LOG; IMP_LOG_TERSE("Resetting moved particles" << std::endl); IMP_CONTAINER_ACCESS(SingletonContainer, get_singleton_container(), { - IMP_FOREACH(int m, moved_) { + for(int m : moved_) { backup_[m] = XYZR(get_model(), imp_indexes[m]).get_sphere(); } @@ -220,8 +220,7 @@ ParticleIndexes RigidMovedSingletonContainer::do_initialize() { backup_.clear(); rbs_members_.clear(); bodies_.clear(); - IMP_FOREACH(ParticleIndex pi, - get_singleton_container()->get_contents()) { + for(ParticleIndex pi : get_singleton_container()->get_contents()) { do_initialize_particle(pi); } for (unsigned int i = 0; i < bodies_.size(); ++i) { @@ -240,7 +239,7 @@ void RigidMovedSingletonContainer::do_reset_all() { void RigidMovedSingletonContainer::do_reset_moved() { IMP_OBJECT_LOG; - IMP_FOREACH(int m, moved_) { backup_[m] = get_data(bodies_[m]); } + for(int m : moved_) { backup_[m] = get_data(bodies_[m]); } moved_.clear(); } @@ -254,7 +253,7 @@ std::ostream &operator<<( ParticleIndexes> &m) { typedef std::pair P; out << "{"; - IMP_FOREACH(P p, m) { out << p.first << ": " << p.second << ", "; } + for(P p : m) { out << p.first << ": " << p.second << ", "; } out << "}"; return out; } @@ -325,8 +324,7 @@ RigidMovedSingletonContainer::RigidMovedSingletonContainer( ModelObjectsTemp RigidMovedSingletonContainer::get_extra_inputs() const { ModelObjectsTemp ret; - IMP_FOREACH(ParticleIndex pi, - get_singleton_container()->get_contents()) { + for(ParticleIndex pi : get_singleton_container()->get_contents()) { if (core::RigidMember::get_is_setup(get_model(), pi)) { RigidBody rb = core::RigidMember(get_model(), pi).get_rigid_body(); ret.push_back(rb); diff --git a/modules/display/include/geometry_macros.h b/modules/display/include/geometry_macros.h index 03b801bcf1..6ccb84d9b8 100644 --- a/modules/display/include/geometry_macros.h +++ b/modules/display/include/geometry_macros.h @@ -149,7 +149,7 @@ : display::SingletonsGeometry(sc) {} \ display::Geometries get_components() const override { \ display::Geometries ret; \ - IMP_FOREACH(ParticleIndex pi, get_container()->get_contents()) { \ + for(ParticleIndex pi : get_container()->get_contents()) { \ Decorator d(get_container()->get_model(), pi); \ action; \ } \ @@ -179,8 +179,7 @@ Name##sGeometry(PairContainer *sc) : display::PairsGeometry(sc) {} \ display::Geometries get_components() const override { \ display::Geometries ret; \ - IMP_FOREACH(ParticleIndexPair pip, \ - get_container()->get_contents()) { \ + for(ParticleIndexPair pip : get_container()->get_contents()) { \ Decorator d0(get_container()->get_model(), pip[0]); \ Decorator d1(get_container()->get_model(), pip[1]); \ action; \ diff --git a/modules/display/src/Writer.cpp b/modules/display/src/Writer.cpp index 02fee3f4ec..8ac3a5a573 100644 --- a/modules/display/src/Writer.cpp +++ b/modules/display/src/Writer.cpp @@ -58,7 +58,7 @@ void TextWriter::do_set_frame() { Writer *create_writer(std::string name) { typedef std::pair > MP; - IMP_FOREACH(MP mp, internal::get_writer_factory_table()) { + for(MP mp : internal::get_writer_factory_table()) { if (boost::algorithm::ends_with(name, mp.first)) { return mp.second->create(name); } diff --git a/modules/display/test/test_isosurface.cpp b/modules/display/test/test_isosurface.cpp index e95ffc867c..181fef401e 100644 --- a/modules/display/test/test_isosurface.cpp +++ b/modules/display/test/test_isosurface.cpp @@ -10,7 +10,7 @@ int main(int argc, char *argv[]) { typedef IMP::algebra::DenseGrid3D G; G g(2.5, IMP::algebra::BoundingBox3D(IMP::algebra::Vector3D(-10, -10, -10), IMP::algebra::Vector3D(10, 10, 10))); - IMP_FOREACH(G::Index i, g.get_all_indexes()) { + for(G::Index i : g.get_all_indexes()) { double m = g.get_center(i).get_magnitude(); g[i] = 100 - m; } diff --git a/modules/em/include/DensityMap.h b/modules/em/include/DensityMap.h index 99f75002ad..841db29ebf 100644 --- a/modules/em/include/DensityMap.h +++ b/modules/em/include/DensityMap.h @@ -665,7 +665,7 @@ inline DensityMap *create_density_map( IMP_USAGE_CHECK(arg.get_number_of_voxels(2) == static_cast(ret->get_header()->get_nz()), "Z voxels don't match"); - IMP_FOREACH(typename Grid::Index i, arg.get_all_indexes()) { + for(typename Grid::Index i : arg.get_all_indexes()) { long vi = ret->xyz_ind2voxel(i[0], i[1], i[2]); ret->set_value(vi, arg[vi]); } diff --git a/modules/kernel/include/internal/create_decomposition.h b/modules/kernel/include/internal/create_decomposition.h index 9fc2e03377..980baa424e 100644 --- a/modules/kernel/include/internal/create_decomposition.h +++ b/modules/kernel/include/internal/create_decomposition.h @@ -23,7 +23,7 @@ Restraints create_current_decomposition(Model *m, Score *score, IMP_USAGE_CHECK(m, "nullptr passed for the Model."); IMP_USAGE_CHECK(score, "nullptr passed for the Score."); Restraints ret; - IMP_FOREACH(typename Container::ContainedIndexType i, c->get_contents()) { + for(typename Container::ContainedIndexType i : c->get_contents()) { double cscore = score->evaluate_index(m, i, nullptr); if (cscore != 0) { std::ostringstream oss; diff --git a/modules/kinematics/include/KinematicForest.h b/modules/kinematics/include/KinematicForest.h index 83a7ba666e..77715b107f 100644 --- a/modules/kinematics/include/KinematicForest.h +++ b/modules/kinematics/include/KinematicForest.h @@ -168,7 +168,7 @@ class IMPKINEMATICSEXPORT KinematicForest //! update_all_external_coordinates() or update_all_internal_coordinates(), //! respectively. void transform_safe(IMP::algebra::Transformation3D tr){ - IMP_FOREACH(KinematicNode root, roots_){ + for(KinematicNode root : roots_){ IMP::core::transform(root, tr); mark_internal_coordinates_changed(); // technically, roots reference frames is a part of the internal tree coordinates, so external coordinates will need to be updated at some point } @@ -267,7 +267,7 @@ class IMPKINEMATICSEXPORT KinematicForest */ void apply_transform_safely(IMP::algebra::Transformation3D tr) { - IMP_FOREACH(KinematicNode root, roots_){ + for(KinematicNode root : roots_){ IMP::core::transform(root, tr); mark_internal_coordinates_changed(); // technically, roots reference frames is a part of the internal tree coordinates, so external coordinates will need to be updated at some point } diff --git a/modules/kinematics/include/ProteinKinematics.h b/modules/kinematics/include/ProteinKinematics.h index 5e01001c32..28f0895420 100644 --- a/modules/kinematics/include/ProteinKinematics.h +++ b/modules/kinematics/include/ProteinKinematics.h @@ -181,7 +181,7 @@ class IMPKINEMATICSEXPORT ProteinKinematics : public IMP::Object { //! root(s) of the kinematic structure DihedralAngleRevoluteJoints get_ordered_joints() { DihedralAngleRevoluteJoints ret; - IMP_FOREACH(Joint *j, kf_->get_ordered_joints() ){ + for(Joint *j : kf_->get_ordered_joints() ){ ret.push_back(dynamic_cast(j)); } return ret; diff --git a/modules/rmf/bin/rmf_display.cpp b/modules/rmf/bin/rmf_display.cpp index 15b7446dfe..b190452e72 100644 --- a/modules/rmf/bin/rmf_display.cpp +++ b/modules/rmf/bin/rmf_display.cpp @@ -82,7 +82,7 @@ int main(int argc, char **argv) { IMP::display::create_writer(output); if (frame_step == 0) frame_step = std::numeric_limits::max(); int cur_frame = 0; - IMP_FOREACH(RMF::FrameID frame_iteration, rh.get_frames()) { + for(RMF::FrameID frame_iteration : rh.get_frames()) { w->set_frame(cur_frame++); IMP::rmf::load_frame(rh, frame_iteration); for (unsigned int i = 0; i < hs.size(); ++i) { diff --git a/modules/rmf/bin/rmf_simplify.cpp b/modules/rmf/bin/rmf_simplify.cpp index f86c6239bd..937c5f4f65 100644 --- a/modules/rmf/bin/rmf_simplify.cpp +++ b/modules/rmf/bin/rmf_simplify.cpp @@ -28,7 +28,7 @@ int main(int argc, char *argv[]) { IMP::atom::add_bonds(hr); } - IMP_FOREACH(IMP::atom::Hierarchy c, + for(IMP::atom::Hierarchy c : IMP::atom::get_by_type(hr, IMP::atom::CHAIN_TYPE)) { IMP::atom::Hierarchy cur = create_simplified_assembly_from_volume(c, resolution); diff --git a/modules/rmf/include/simple_links.h b/modules/rmf/include/simple_links.h index 59b922e798..9f5da0b5b8 100644 --- a/modules/rmf/include/simple_links.h +++ b/modules/rmf/include/simple_links.h @@ -106,7 +106,7 @@ class SimpleLoadLink : public LoadLink { set_was_used(true); RMF::NodeConstHandles chs = rt.get_children(); RMF::NodeConstHandles matching_chs; - IMP_FOREACH(RMF::NodeConstHandle ch, rt.get_children()) { + for(RMF::NodeConstHandle ch : rt.get_children()) { IMP_LOG_VERBOSE("Checking " << ch << std::endl); if (get_is(ch)) matching_chs.push_back(ch); } diff --git a/modules/rmf/src/HierarchyLoadLink.cpp b/modules/rmf/src/HierarchyLoadLink.cpp index 64f3a55af4..8b9828c668 100644 --- a/modules/rmf/src/HierarchyLoadLink.cpp +++ b/modules/rmf/src/HierarchyLoadLink.cpp @@ -53,7 +53,7 @@ void HierarchyLoadLink::create_recursive(Model *m, Floats bresols, gresols; std::map rep_map; if (af_.get_is(name)) { - IMP_FOREACH(RMF::NodeConstHandle alt, + for(RMF::NodeConstHandle alt : af_.get(name).get_alternatives(RMF::PARTICLE)) { if (alt == name) continue; ParticleIndex cur_rep = m->add_particle(alt.get_name()); @@ -68,7 +68,7 @@ void HierarchyLoadLink::create_recursive(Model *m, } IMP_LOG_TERSE("Found particle alternative " << alt << std::endl); } - IMP_FOREACH(RMF::NodeConstHandle alt, + for(RMF::NodeConstHandle alt : af_.get(name).get_alternatives(RMF::GAUSSIAN_PARTICLE)) { if (alt == name) continue; ParticleIndex cur_rep = m->add_particle(alt.get_name()); @@ -92,7 +92,7 @@ void HierarchyLoadLink::create_recursive(Model *m, data.load_xyzs.setup_particle(name, m, cur, rigid_bodies); data.load_gaussians.setup_particle(name, m, cur, rigid_bodies); - IMP_FOREACH(RMF::NodeConstHandle ch, name.get_children()) { + for(RMF::NodeConstHandle ch : name.get_children()) { if (ch.get_type() == RMF::REPRESENTATION) { if (rep_map.find(ch) == rep_map.end()) { ParticleIndex child = m->add_particle(ch.get_name()); @@ -260,7 +260,7 @@ void HierarchyLoadLink::add_link_recursive(Model *m, do_link_particle(m, root, cur, node); RMF::NodeConstHandles nchs; - IMP_FOREACH(RMF::NodeConstHandle ch, node.get_children()) { + for(RMF::NodeConstHandle ch : node.get_children()) { if (ch.get_type() == RMF::REPRESENTATION) { nchs.push_back(ch); } diff --git a/modules/rmf/src/HierarchySaveLink.cpp b/modules/rmf/src/HierarchySaveLink.cpp index 6e3919af25..e25d49a2cc 100644 --- a/modules/rmf/src/HierarchySaveLink.cpp +++ b/modules/rmf/src/HierarchySaveLink.cpp @@ -69,7 +69,7 @@ void HierarchySaveLink::add_recursive(Model *m, ParticleIndex root, { atom::Hierarchies reps = rep.get_representations(atom::BALLS); int i = 0; /* Skip first (default) resolution */ - IMP_FOREACH(atom::Hierarchy cr, reps) { + for(atom::Hierarchy cr : reps) { i++; if (cr.get_particle_index() == p) continue; RMF::NodeHandle cn = cur.get_file().add_node @@ -86,7 +86,7 @@ void HierarchySaveLink::add_recursive(Model *m, ParticleIndex root, atom::Hierarchies reps = rep.get_representations(atom::DENSITIES); Floats gresols = rep.get_resolutions(atom::DENSITIES); int i = -1; - IMP_FOREACH(atom::Hierarchy cr, reps) { + for(atom::Hierarchy cr : reps) { i++; if (cr.get_particle_index() == p) continue; RMF::NodeHandle cn = cur.get_file().add_node @@ -131,10 +131,10 @@ void HierarchySaveLink::add_recursive(Model *m, ParticleIndex root, if (!prep_nodes.empty() || !grep_nodes.empty()) { RMF::decorator::Alternatives ad = af_.get(cur); - IMP_FOREACH(RMF::NodeHandle nh, prep_nodes) { + for(RMF::NodeHandle nh : prep_nodes) { ad.add_alternative(nh, RMF::PARTICLE); } - IMP_FOREACH(RMF::NodeHandle nh, grep_nodes) { + for(RMF::NodeHandle nh : grep_nodes) { ad.add_alternative(nh, RMF::GAUSSIAN_PARTICLE); } } diff --git a/modules/rmf/src/frames.cpp b/modules/rmf/src/frames.cpp index dc9157fd8a..bc81ee829f 100644 --- a/modules/rmf/src/frames.cpp +++ b/modules/rmf/src/frames.cpp @@ -21,7 +21,7 @@ void load_frame(RMF::FileConstHandle fh, RMF::FrameID frame) { std::string what; try { fh.set_current_frame(frame); - IMP_FOREACH(LoadLink * ll, internal::get_load_linkers(fh)) { ll->load(fh); } + for(LoadLink * ll : internal::get_load_linkers(fh)) { ll->load(fh); } } catch (const std::exception& e) { except = true; @@ -39,7 +39,7 @@ RMF::FrameID save_frame(RMF::FileHandle file, std::string name) { try { file.set_producer("IMP " + get_module_version()); RMF::FrameID cur = file.add_frame(name, RMF::FRAME); - IMP_FOREACH(SaveLink * ll, internal::get_save_linkers(file)) { + for(SaveLink * ll : internal::get_save_linkers(file)) { ll->save(file); } file.flush(); diff --git a/modules/rmf/src/geometry_io.cpp b/modules/rmf/src/geometry_io.cpp index a9d4241962..2cc8f367fe 100644 --- a/modules/rmf/src/geometry_io.cpp +++ b/modules/rmf/src/geometry_io.cpp @@ -239,7 +239,7 @@ class BoxLoadLink : public GeometryLoadLinkget_particle_name(pp.second) << std::endl); RMF::Vector3 sd = @@ -61,7 +61,7 @@ void HierarchySaveGaussians::setup_node(Model *m, } void HierarchySaveGaussians::save(Model *m, RMF::FileHandle fh) { - IMP_FOREACH(Pair pp, gaussians_) { + for(Pair pp : gaussians_) { gaussian_factory_.get(fh.get_node(pp.first)) .set_frame_variances(RMF::Vector3( core::Gaussian(m, pp.second).get_gaussian().get_variances())); diff --git a/modules/rmf/src/internal/atom_links_rigid_bodies.cpp b/modules/rmf/src/internal/atom_links_rigid_bodies.cpp index 8e94bae16e..91bf0382aa 100644 --- a/modules/rmf/src/internal/atom_links_rigid_bodies.cpp +++ b/modules/rmf/src/internal/atom_links_rigid_bodies.cpp @@ -156,7 +156,7 @@ void HierarchyLoadRigidBodies::fix_rigid_body(Model *m, const RB &in) const { // core::RigidMembers rms=in.second; core::RigidBody rb(m, in.rb); ParticleIndexes rigid_bits; - IMP_FOREACH(ParticleIndex pi, in.members) { + for(ParticleIndex pi : in.members) { if (core::RigidMember::get_is_setup(rb.get_model(), pi)) { rigid_bits.push_back(pi); } @@ -169,7 +169,7 @@ void HierarchyLoadRigidBodies::fix_rigid_body(Model *m, const RB &in) const { rb.set_reference_frame_from_members(rigid_bits); algebra::ReferenceFrame3D rf = rb.get_reference_frame(); // fix rigid bodies that aren't rigid - IMP_FOREACH(ParticleIndex mb, in.members) { + for(ParticleIndex mb : in.members) { if (core::NonRigidMember::get_is_setup(rb.get_model(), mb)) { fix_internal_coordinates(rb, rf, core::RigidBodyMember(rb.get_model(), mb)); @@ -186,7 +186,7 @@ void HierarchyLoadRigidBodies::initialize_rigid_body(Model *m, RB &in) const { core::get_initial_reference_frame(m, in.members); IMP_LOG_TERSE("Initial rf is " << rf << std::endl); rb.set_reference_frame_lazy(rf); - IMP_FOREACH(ParticleIndex pi, in.members) { + for(ParticleIndex pi : in.members) { core::RigidBodyMember rbm(m, pi); if (core::RigidBody::get_is_setup(m, pi)) { algebra::Transformation3D lc = @@ -208,14 +208,14 @@ void HierarchyLoadRigidBodies::initialize_rigid_body(Model *m, RB &in) const { } void HierarchyLoadRigidBodies::load(RMF::FileConstHandle fh, Model *m) { - IMP_FOREACH(Pair pp, global_) { + for(Pair pp : global_) { IMP_LOG_VERBOSE("Loading global rigid body " << m->get_particle_name(pp.second) << std::endl); algebra::ReferenceFrame3D rf( get_transformation(fh.get_node(pp.first), reference_frame_factory_)); core::RigidBody(m, pp.second).set_reference_frame_lazy(rf); } - IMP_FOREACH(Pair pp, local_) { + for(Pair pp : local_) { IMP_LOG_VERBOSE("Loading local rigid body " << m->get_particle_name(pp.second) << std::endl); algebra::ReferenceFrame3D rf( @@ -229,14 +229,14 @@ void HierarchyLoadRigidBodies::update_rigid_bodies(RMF::FileConstHandle, Model *m) { /* Make sure that the global coordinates of any nested rigid bodies are set from their parents */ - IMP_FOREACH(Pair pp, global_) { + for(Pair pp : global_) { core::RigidBody rb(m, pp.second); rb.update_members(); } // backwards compat typedef std::pair P; - IMP_FOREACH(P & pp, rigid_body_compositions_) { + for(P & pp : rigid_body_compositions_) { if (!pp.second.initialized) { initialize_rigid_body(m, pp.second); } else { @@ -255,7 +255,7 @@ HierarchySaveRigidBodies::HierarchySaveRigidBodies(RMF::FileHandle f) ParticleIndex HierarchySaveRigidBodies::fill_external( Model *m, ParticleIndex p) { RMF_SMALL_UNORDERED_SET rbs; - IMP_FOREACH(ParticleIndex ch, + for(ParticleIndex ch : atom::Hierarchy(m, p).get_children_indexes()) { ParticleIndex cur = fill_external(m, ch); rbs.insert(cur); @@ -274,8 +274,7 @@ ParticleIndex HierarchySaveRigidBodies::fill_external( *rbs.begin() != IMP::get_invalid_index()) { externals_[p] = *rbs.begin(); external_index_[externals_[p]] = externals_[p].get_index(); - IMP_FOREACH(ParticleIndex ch, - atom::Hierarchy(m, p).get_children_indexes()) { + for(ParticleIndex ch : atom::Hierarchy(m, p).get_children_indexes()) { not_externals_.insert(ch); externals_.erase(ch); } @@ -325,14 +324,14 @@ void HierarchySaveRigidBodies::setup_node( } void HierarchySaveRigidBodies::save(Model *m, RMF::FileHandle fh) { - IMP_FOREACH(Pair pp, global_) { + for(Pair pp : global_) { copy_to_frame_reference_frame(core::RigidBody(m, pp.second) .get_reference_frame() .get_transformation_to(), fh.get_node(pp.first), reference_frame_factory_); } - IMP_FOREACH(Pair pp, local_) { + for(Pair pp : local_) { copy_to_frame_reference_frame( core::RigidBodyMember(m, pp.second).get_internal_transformation(), fh.get_node(pp.first), reference_frame_factory_); diff --git a/modules/rmf/src/internal/atom_links_static.cpp b/modules/rmf/src/internal/atom_links_static.cpp index 47b1250742..d906fd29a7 100644 --- a/modules/rmf/src/internal/atom_links_static.cpp +++ b/modules/rmf/src/internal/atom_links_static.cpp @@ -380,7 +380,7 @@ void HierarchyLoadBonds::setup_bonds(RMF::NodeConstHandle n, Model *m, atom::create_bond(get_bonded(p0), get_bonded(p1), atom::Bond::SINGLE); } } else { - IMP_FOREACH(RMF::NodeConstHandle c, n.get_children()) { + for(RMF::NodeConstHandle c : n.get_children()) { setup_bonds(c, m, p); } } @@ -391,7 +391,7 @@ atom::Bonds get_rep_bonds(atom::Hierarchy h) { IMP_FUNCTION_LOG; atom::Bonds ret; if (atom::Representation::get_is_setup(h)) { - IMP_FOREACH(atom::Hierarchy r, + for(atom::Hierarchy r : atom::Representation(h).get_representations(atom::BALLS)) { if (r != h) { ret += atom::get_internal_bonds(r); @@ -399,7 +399,7 @@ atom::Bonds get_rep_bonds(atom::Hierarchy h) { } IMP_LOG_VERBOSE("Found " << ret.size() << " alt bonds" << std::endl); } else { - IMP_FOREACH(atom::Hierarchy ch, h.get_children()) { + for(atom::Hierarchy ch : h.get_children()) { ret += get_rep_bonds(ch); } } diff --git a/modules/rmf/src/internal/atom_links_xyzs.cpp b/modules/rmf/src/internal/atom_links_xyzs.cpp index bbcce0d53e..24937ef1f9 100644 --- a/modules/rmf/src/internal/atom_links_xyzs.cpp +++ b/modules/rmf/src/internal/atom_links_xyzs.cpp @@ -82,13 +82,13 @@ void HierarchyLoadXYZs::link_particle( } void HierarchyLoadXYZs::load(RMF::FileConstHandle fh, Model *m) { - IMP_FOREACH(Pair pp, global_) { + for(Pair pp : global_) { IMP_LOG_VERBOSE("Loading global coordinates for " << m->get_particle_name(pp.second) << std::endl); algebra::Vector3D rf(get_coordinates(fh.get_node(pp.first), ip_factory_)); core::XYZ(m, pp.second).set_coordinates(rf); } - IMP_FOREACH(Pair pp, local_) { + for(Pair pp : local_) { IMP_LOG_VERBOSE("Loading local coordinates for " << m->get_particle_name(pp.second) << std::endl); algebra::Vector3D rf(get_coordinates(fh.get_node(pp.first), ip_factory_)); @@ -127,11 +127,11 @@ void HierarchySaveXYZs::setup_node( } void HierarchySaveXYZs::save(Model *m, RMF::FileHandle fh) { - IMP_FOREACH(Pair pp, global_) { + for(Pair pp : global_) { copy_to_frame_particle(core::XYZ(m, pp.second).get_coordinates(), fh.get_node(pp.first), ip_factory_); } - IMP_FOREACH(Triplet pp, rigid_nonmember_) { + for(Triplet pp : rigid_nonmember_) { /* Transform global coordinates to those relative to the "parent" rigid body */ algebra::Vector3D global_coord @@ -142,7 +142,7 @@ void HierarchySaveXYZs::save(Model *m, RMF::FileHandle fh) { rf.get_transformation_from().get_transformed(global_coord), fh.get_node(pp.first), ip_factory_); } - IMP_FOREACH(Pair pp, local_) { + for(Pair pp : local_) { copy_to_frame_particle( core::RigidBodyMember(m, pp.second).get_internal_coordinates(), fh.get_node(pp.first), ip_factory_); diff --git a/modules/rmf/src/internal/hierarchy_links_helpers.cpp b/modules/rmf/src/internal/hierarchy_links_helpers.cpp index ad52418757..292cc2f69e 100644 --- a/modules/rmf/src/internal/hierarchy_links_helpers.cpp +++ b/modules/rmf/src/internal/hierarchy_links_helpers.cpp @@ -31,7 +31,7 @@ std::string get_good_name_to_atom_node(Model *m, ParticleIndex h) { // object if no children exist RMF::NodeConstHandle get_previous_rmf_provenance(RMF::NodeConstHandle node) { RMF::NodeConstHandles nchs; - IMP_FOREACH(RMF::NodeConstHandle ch, node.get_children()) { + for(RMF::NodeConstHandle ch : node.get_children()) { if (ch.get_type() == RMF::PROVENANCE) { nchs.push_back(ch); } diff --git a/modules/rmf/src/internal/link_helpers.cpp b/modules/rmf/src/internal/link_helpers.cpp index 25160a972b..ca3923aaf3 100644 --- a/modules/rmf/src/internal/link_helpers.cpp +++ b/modules/rmf/src/internal/link_helpers.cpp @@ -37,7 +37,7 @@ unsigned int get_save_linker_index(std::string st) { LoadLinks get_load_linkers(RMF::FileConstHandle fh) { LoadLinks ret; typedef std::pair P; - IMP_FOREACH(P kl, known_load_linkers) { + for(P kl : known_load_linkers) { if (fh.get_has_associated_data(kl.second)) { ret.push_back(fh.get_associated_data(kl.second)); } @@ -49,7 +49,7 @@ LoadLinks get_load_linkers(RMF::FileConstHandle fh) { SaveLinks get_save_linkers(RMF::FileHandle fh) { SaveLinks ret; typedef std::pair P; - IMP_FOREACH(P kl, known_save_linkers) { + for(P kl : known_save_linkers) { if (fh.get_has_associated_data(kl.second)) { ret.push_back(fh.get_associated_data(kl.second)); } diff --git a/modules/rmf/src/restraint_io.cpp b/modules/rmf/src/restraint_io.cpp index dc375d750b..cab6240f61 100644 --- a/modules/rmf/src/restraint_io.cpp +++ b/modules/rmf/src/restraint_io.cpp @@ -189,7 +189,7 @@ class RestraintLoadLink : public SimpleLoadLink { } else { oi->set_last_score(0); } - IMP_FOREACH(RMF::NodeConstHandle ch, chs) { + for(RMF::NodeConstHandle ch : chs) { if (ch.get_type() == RMF::ORGANIZATIONAL) { load_restraint_particles(ch); } @@ -205,7 +205,7 @@ class RestraintLoadLink : public SimpleLoadLink { Restraints childr; ParticlesTemp inputs; std::vector static_pis, dynamic_pis; - IMP_FOREACH(RMF::NodeConstHandle ch, chs) { + for(RMF::NodeConstHandle ch : chs) { if (ch.get_type() == RMF::FEATURE) { childr.push_back(do_create(ch, m)); add_link(childr.back(), ch); @@ -214,7 +214,7 @@ class RestraintLoadLink : public SimpleLoadLink { } } if (rf_.get_is(name)) { - IMP_FOREACH(RMF::NodeConstHandle an, rf_.get(name).get_representation()) { + for(RMF::NodeConstHandle an : rf_.get(name).get_representation()) { IMP_LOG_TERSE("Found alias child to " << an.get_name() << " of type " << an.get_type() << std::endl); Particle *p = get_association(an); @@ -248,7 +248,7 @@ class RestraintLoadLink : public SimpleLoadLink { } void load_restraint_particles(RMF::NodeConstHandle parent) { - IMP_FOREACH(RMF::NodeConstHandle ch, parent.get_children()) { + for(RMF::NodeConstHandle ch : parent.get_children()) { Particle *p = get_association(ch); if (p) { load_particle(ch, p->get_model(), p->get_index()); @@ -262,10 +262,10 @@ class RestraintLoadLink : public SimpleLoadLink { (or its children) */ void create_restraint_particles(RMF::NodeConstHandle parent, Model *m) { RMF::NodeConstHandles chs = parent.get_children(); - IMP_FOREACH(RMF::NodeConstHandle ch, chs) { + for(RMF::NodeConstHandle ch : chs) { if (ch.get_type() == RMF::ORGANIZATIONAL) { ParticleIndexes pis; - IMP_FOREACH(RMF::NodeConstHandle pch, ch.get_children()) { + for(RMF::NodeConstHandle pch : ch.get_children()) { Pointer pi = new IMP::Particle(m, pch.get_name()); set_association(pch, pi.get(), true); } @@ -280,7 +280,7 @@ class RestraintLoadLink : public SimpleLoadLink { std::vector &static_pis, std::vector &dynamic_pis) { ParticleIndexes pis; - IMP_FOREACH(RMF::NodeConstHandle ch, parent.get_children()) { + for(RMF::NodeConstHandle ch : parent.get_children()) { Particle *p = get_association(ch); pis.push_back(p->get_index()); setup_particle(ch, m, p->get_index()); @@ -562,7 +562,7 @@ class RestraintSaveLink : public SimpleSaveLink { no_terms_.insert(o); // delete old children } else { - IMP_FOREACH(Restraint * r, rs) { + for(Restraint * r : rs) { Subset s(get_input_particles(r->get_inputs())); double score = r->get_last_score(); r->set_was_used(true); @@ -853,7 +853,7 @@ void add_restraints_as_bonds(RMF::FileHandle fh, const Restraints &rs) { RMF::decorator::BondFactory bf(fh); Restraints decomp; - IMP_FOREACH(Restraint * r, rs) { + for(Restraint * r : rs) { Pointer rd = r->create_decomposition(); if (rd == r) { decomp.push_back(rd); @@ -864,12 +864,11 @@ void add_restraints_as_bonds(RMF::FileHandle fh, const Restraints &rs) { } RMF::NodeHandle bdr = fh.get_root_node().add_child("restraint bonds", RMF::ORGANIZATIONAL); - IMP_FOREACH(Restraint * bd, decomp) { + for(Restraint * bd : decomp) { Subset s(get_input_particles(bd->get_inputs())); bd->set_was_used(bd); RMF::NodeHandles inputs; - IMP_FOREACH(Particle * cur, - get_input_particles(bd->get_inputs())) { + for(Particle * cur : get_input_particles(bd->get_inputs())) { RMF::NodeHandle n = get_node_from_association(fh, cur); if (n != RMF::NodeHandle()) { inputs.push_back(n); From 0e2c1e2121cc95679a3f2165575c4b5911f99307 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 14:05:40 -0800 Subject: [PATCH 065/155] Get latest PMI1 --- modules/pmi1 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/pmi1 b/modules/pmi1 index 3bf65bedb2..f5f17e5b29 160000 --- a/modules/pmi1 +++ b/modules/pmi1 @@ -1 +1 @@ -Subproject commit 3bf65bedb2f8db6f74e392148636cca24d071ed7 +Subproject commit f5f17e5b298316599a68c71183ac7ccc3139643d From c5791be6630003fb6e1e350d1b332e8d518cb234 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 14:06:19 -0800 Subject: [PATCH 066/155] Get latest npctransport --- modules/npctransport | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/npctransport b/modules/npctransport index a398262bad..34f49afef9 160000 --- a/modules/npctransport +++ b/modules/npctransport @@ -1 +1 @@ -Subproject commit a398262bad35d08c8ffeabff31c7d9a478c1920e +Subproject commit 34f49afef95d800c2aafaad6f2918f8d4cd1e542 From e71aa9eb635f22c5a1eea41fddc676e89892603c Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 14:06:51 -0800 Subject: [PATCH 067/155] Squashed 'modules/pmi/' changes from 86cd0b6b86..4c3ece6809 4c3ece6809 Use older pytest-flake8 on Python 2 daf8e6e4e5 Use C++11 'override' keyword git-subtree-dir: modules/pmi git-subtree-split: 4c3ece680994a508c6c737d8641c4b541abede19 --- modules/pmi/include/CompositeRestraint.h | 5 ++--- modules/pmi/include/MembraneRestraint.h | 4 ++-- modules/pmi/include/TransformMover.h | 6 +++--- modules/pmi/tools/setup_ci.sh | 9 ++++++++- 4 files changed, 15 insertions(+), 9 deletions(-) diff --git a/modules/pmi/include/CompositeRestraint.h b/modules/pmi/include/CompositeRestraint.h index fa077cd38b..00b0fc806f 100644 --- a/modules/pmi/include/CompositeRestraint.h +++ b/modules/pmi/include/CompositeRestraint.h @@ -90,9 +90,8 @@ class IMPPMIEXPORT CompositeRestraint : public Restraint //double get_probability() const {return 0.0;} virtual double - unprotected_evaluate(DerivativeAccumulator *accum) - const IMP_OVERRIDE; - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + unprotected_evaluate(DerivativeAccumulator *accum) const override; + virtual ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(CompositeRestraint); virtual double get_probability() const diff --git a/modules/pmi/include/MembraneRestraint.h b/modules/pmi/include/MembraneRestraint.h index 853f54a3aa..e34da1d5a8 100644 --- a/modules/pmi/include/MembraneRestraint.h +++ b/modules/pmi/include/MembraneRestraint.h @@ -43,8 +43,8 @@ class IMPPMIEXPORT MembraneRestraint : public isd::ISDRestraint { double get_score_inside(double z, double z_slope_center_lower, double z_slope_center_upper) const; virtual double unprotected_evaluate(DerivativeAccumulator *) const - IMP_OVERRIDE; - virtual IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; + override; + virtual IMP::ModelObjectsTemp do_get_inputs() const override; IMP_OBJECT_METHODS(MembraneRestraint); }; diff --git a/modules/pmi/include/TransformMover.h b/modules/pmi/include/TransformMover.h index bdfaf1981d..56efb3f0df 100644 --- a/modules/pmi/include/TransformMover.h +++ b/modules/pmi/include/TransformMover.h @@ -119,9 +119,9 @@ pis_.push_back(pi); IMP::algebra::Transformation3D get_last_transformation() const { return tt_; } protected: - virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE; - virtual core::MonteCarloMoverResult do_propose() IMP_OVERRIDE; - virtual void do_reject() IMP_OVERRIDE; + virtual ModelObjectsTemp do_get_inputs() const override; + virtual core::MonteCarloMoverResult do_propose() override; + virtual void do_reject() override; IMP_OBJECT_METHODS(TransformMover); }; diff --git a/modules/pmi/tools/setup_ci.sh b/modules/pmi/tools/setup_ci.sh index 27870d3441..22bf86f27f 100755 --- a/modules/pmi/tools/setup_ci.sh +++ b/modules/pmi/tools/setup_ci.sh @@ -13,4 +13,11 @@ conda config --remove channels defaults # get conda-forge, not main, packages conda create --yes -q -n python${python_version} -c salilab -c conda-forge python=${python_version} pip scipy matplotlib imp-nightly gxx_linux-64 eigen swig cmake eval "$(conda shell.bash hook)" conda activate python${python_version} -pip install pytest-cov coverage pytest-flake8 + +if [ ${python_version} = "2.7" ]; then + # pytest-flake8 1.1.0 tries to import contextlib.redirect_stdout, which + # isn't present in Python 2 + pip install pytest-cov coverage 'pytest-flake8<1.1' +else + pip install pytest-cov coverage pytest-flake8 +fi From f1579fd13d1e250024a264421d5a7431b9556f12 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 14:16:54 -0800 Subject: [PATCH 068/155] Use C++11 math/set types We can now use std::copysign, std::tgamma, std::log1p and std::unordered_set since we require C++11, and so no longer need to use the Boost types. --- modules/em/src/BayesEM3D.cpp | 25 +++++++++++-------------- modules/isd/src/FStudentT.cpp | 7 +++---- modules/isd/src/GammaPrior.cpp | 7 +++---- 3 files changed, 17 insertions(+), 22 deletions(-) diff --git a/modules/em/src/BayesEM3D.cpp b/modules/em/src/BayesEM3D.cpp index a83d807ab0..7151a82cca 100644 --- a/modules/em/src/BayesEM3D.cpp +++ b/modules/em/src/BayesEM3D.cpp @@ -10,10 +10,8 @@ #include #include #include -#include -#include -#include -#include +#include +#include IMPEM_BEGIN_NAMESPACE @@ -135,16 +133,16 @@ FloatPair bayesem3d_get_logabssumexp(double x, double y, double sx, double sy) { } if (x > y) { - return FloatPair(x + boost::math::log1p(sx * sy * exp(y - x)), sx); + return FloatPair(x + std::log1p(sx * sy * exp(y - x)), sx); } else { - return FloatPair(y + boost::math::log1p(sx * sy * exp(x - y)), sy); + return FloatPair(y + std::log1p(sx * sy * exp(x - y)), sy); } } FloatPair bayesem3d_get_logabssumprodexp(double x, double y, double wx, double wy) { - double sx = boost::math::copysign(1.0, wx); - double sy = boost::math::copysign(1.0, wy); + double sx = std::copysign(1.0, wx); + double sy = std::copysign(1.0, wy); return bayesem3d_get_logabssumexp(x + log(wx * sx), y + log(wy * sy), sx, sy); } @@ -159,9 +157,9 @@ double bayesem3d_get_logsumexp(double x, double y) { } if (x > y) { - return x + boost::math::log1p(exp(y - x)); + return x + std::log1p(exp(y - x)); } else { - return y + boost::math::log1p(exp(x - y)); + return y + std::log1p(exp(x - y)); } } @@ -295,7 +293,7 @@ DensityMap *bayesem3d_get_density_from_particle(DensityMap *em, int nxny = em_header->get_nx() * em_header->get_ny(); int znxny; - boost::unordered_set visited_voxels; + std::unordered_set visited_voxels; for (unsigned int ii = 0; ii < xyzr.size(); ii++) { double px = xyzr[ii].get_x(); @@ -329,9 +327,8 @@ DensityMap *bayesem3d_get_density_from_particle(DensityMap *em, } } - for (boost::unordered_set::iterator vv = visited_voxels.begin(); - vv != visited_voxels.end(); ++vv) { - vals[*vv] = exp(vals[*vv]) - 1.; + for (auto &vv : visited_voxels) { + vals[vv] = exp(vals[vv]) - 1.; } return ret.release(); diff --git a/modules/isd/src/FStudentT.cpp b/modules/isd/src/FStudentT.cpp index e0cc3d5e72..b8e71b0a1c 100644 --- a/modules/isd/src/FStudentT.cpp +++ b/modules/isd/src/FStudentT.cpp @@ -8,8 +8,7 @@ #include #include #include -#include -#include +#include IMPISD_BEGIN_NAMESPACE @@ -65,7 +64,7 @@ double FStudentT::do_evaluate() const { update_cached_values(); // update t2 return boost::math::lgamma(.5 * nu_) - boost::math::lgamma(.5 * (N_ + nu_)) + .5 * N_ * std::log(IMP::PI * nu_) + N_ * std::log(sigma_) + - .5 * (N_ + nu_) * boost::math::log1p(t2_ / nu_) - LogJX_; + .5 * (N_ + nu_) * std::log1p(t2_ / nu_) - LogJX_; } double FStudentT::evaluate_derivative_Fx(double Fx) const { @@ -96,7 +95,7 @@ double FStudentT::evaluate_derivative_sigma() const { double FStudentT::evaluate_derivative_nu() const { return .5 * (-1 + boost::math::digamma(.5 * nu_) - boost::math::digamma(.5 * (N_ + nu_)) + - boost::math::log1p(t2_ / nu_) + (N_ + nu_) / (nu_ + t2_)); + std::log1p(t2_ / nu_) + (N_ + nu_) / (nu_ + t2_)); } IMPISD_END_NAMESPACE diff --git a/modules/isd/src/GammaPrior.cpp b/modules/isd/src/GammaPrior.cpp index 6a71012a0f..4af2b3f27a 100644 --- a/modules/isd/src/GammaPrior.cpp +++ b/modules/isd/src/GammaPrior.cpp @@ -8,8 +8,7 @@ #include #include -#include -#include +#include IMPISD_BEGIN_NAMESPACE @@ -26,7 +25,7 @@ GammaPrior::unprotected_evaluate(DerivativeAccumulator *accum) const IMP::isd::Scale sig(p_); double prob=0.0; double s=sig.get_scale()/10; - double gam = boost::math::tgamma(k_) * std::pow(theta_, k_); + double gam = std::tgamma(k_) * std::pow(theta_, k_); prob = std::pow(s, k_-1) * std::exp(-s/theta_)/gam; if (accum) { @@ -40,7 +39,7 @@ double GammaPrior::evaluate_at(Float val) const { double prob=0.0; - double gam = boost::math::tgamma(k_) * std::pow(theta_, k_); + double gam = std::tgamma(k_) * std::pow(theta_, k_); prob = std::pow(val, k_-1) * std::exp(-val/theta_)/gam; double score = -1*log (prob); From 9a40f110e3b1dfb574120d9848b1b03355ae8681 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 15:29:09 -0800 Subject: [PATCH 069/155] Assume 'noexcept' keyword is always available Use 'noexcept' keyword (which requires C++11, now supported) instead of the IMP_NOEXCEPT macro or 'throw()' (which is removed in C++20). --- ChangeLog.md | 2 +- doc/manual/code_conventions.md | 8 ++++---- modules/kernel/include/compiler_macros.h | 15 +------------- modules/kernel/include/exception.h | 20 +++++++++---------- .../include/internal/input_output_exception.h | 2 +- modules/kernel/src/exception.cpp | 18 ++++++++--------- .../src/internal/input_output_exception.cpp | 2 +- 7 files changed, 27 insertions(+), 40 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index dd4a893d5f..730821a43f 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -9,7 +9,7 @@ ChangeLog {#changelog} or MS Visual Studio 2015 or later. Various IMP macro and header workarounds for pre-C++11 environments are thus no longer needed and are deprecated: `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`, - `IMP_FOREACH`, `IMP/nullptr.h`, and `IMP/nullptr_macros.h`. + `IMP_FOREACH`, `IMP_NOEXCEPT`, `IMP/nullptr.h`, and `IMP/nullptr_macros.h`. # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} - OpenCubicSpline now throws a ValueException for out-of-range values, to diff --git a/doc/manual/code_conventions.md b/doc/manual/code_conventions.md index 30209e3afd..1772fe05be 100644 --- a/doc/manual/code_conventions.md +++ b/doc/manual/code_conventions.md @@ -122,7 +122,7 @@ As a result, such functions do not need to obey all the coding conventions # C++ 11 {#codeconv_cxx11} Latest %IMP requires a compiler that supports C++ 11, unlike older versions. -Thus, C++ 11 features, such as the `override`, `final`, `auto` and `nullptr` -keywords, and range-based for loops, can be used where appropriate. -The old compatibility macros (such as `IMP_OVERRIDE`, `IMP_FINAL`, -`IMP_NULLPTR` and `IMP_FOREACH`) should no longer be used. +Thus, C++ 11 features, such as the `override`, `final`, `auto`, `noexcept` +and `nullptr` keywords, and range-based for loops, can be used where +appropriate. The old compatibility macros (such as `IMP_OVERRIDE`, `IMP_FINAL`, +`IMP_NOEXCEPT`, `IMP_NULLPTR` and `IMP_FOREACH`) should no longer be used. diff --git a/modules/kernel/include/compiler_macros.h b/modules/kernel/include/compiler_macros.h index b10adf2737..b8c344d543 100644 --- a/modules/kernel/include/compiler_macros.h +++ b/modules/kernel/include/compiler_macros.h @@ -75,24 +75,11 @@ #endif #endif -#if defined(__GNUC__) && __cplusplus >= 201103L -#define IMP_HAS_NOEXCEPT 1 -#elif defined(__clang__) && defined(__has_feature) -#define IMP_HAS_NOEXCEPT __has_feature(cxx_noexcept) -#else -#define IMP_HAS_NOEXCEPT 0 -#endif - -#if IMP_HAS_NOEXCEPT +// Deprecated: just use 'noexcept' directly #define IMP_NOEXCEPT noexcept #define IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(Name) \ Name(const Name &) = default; \ Name &operator=(const Name &) = default -#else -// probably should be finer here -#define IMP_NOEXCEPT throw() -#define IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(Name) -#endif #if defined(__clang__) || defined(__GNUC__) #define IMP_PRAGMA(x) _Pragma(IMP_STRINGIFY(x)) diff --git a/modules/kernel/include/exception.h b/modules/kernel/include/exception.h index 926ceab15a..698de26346 100644 --- a/modules/kernel/include/exception.h +++ b/modules/kernel/include/exception.h @@ -52,11 +52,11 @@ class IMPKERNELEXPORT Exception { public: #if defined(SWIG) || defined(IMP_DOXYGEN) - const char *what() const IMP_NOEXCEPT; + const char *what() const noexcept; #endif IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(Exception); Exception(const char *message); - ~Exception() IMP_NOEXCEPT; + ~Exception() noexcept; }; #endif @@ -106,7 +106,7 @@ struct IMPKERNELEXPORT InternalException IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(InternalException); InternalException(const char *msg = "Fatal error") : std::runtime_error(msg) {} - ~InternalException() IMP_NOEXCEPT; + ~InternalException() noexcept; }; //! An exception for an invalid usage of \imp @@ -127,7 +127,7 @@ class IMPKERNELEXPORT UsageException public: IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(UsageException); UsageException(const char *t) : std::runtime_error(t) {} - ~UsageException() IMP_NOEXCEPT; + ~UsageException() noexcept; }; //! An exception for an invalid value being passed to \imp @@ -137,7 +137,7 @@ class IMPKERNELEXPORT ValueException : public Exception { public: IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(ValueException); ValueException(const char *t) : Exception(t) {} - ~ValueException() IMP_NOEXCEPT; + ~ValueException() noexcept; }; //! An exception for an invalid type being passed to \imp @@ -147,7 +147,7 @@ class IMPKERNELEXPORT TypeException : public Exception { public: IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(TypeException); TypeException(const char *t) : Exception(t) {} - ~TypeException() IMP_NOEXCEPT; + ~TypeException() noexcept; }; //! An exception for a request for an invalid member of a container @@ -158,7 +158,7 @@ class IMPKERNELEXPORT IndexException : public Exception { IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(IndexException); //! Create exception with an error message IndexException(const char *t) : Exception(t) {} - ~IndexException() IMP_NOEXCEPT; + ~IndexException() noexcept; }; //! An input/output exception @@ -174,7 +174,7 @@ class IMPKERNELEXPORT IOException : public Exception { public: IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(IOException); IOException(const char *t) : Exception(t) {} - ~IOException() IMP_NOEXCEPT; + ~IOException() noexcept; }; /** \brief An exception which is thrown when the Model has @@ -190,7 +190,7 @@ class IMPKERNELEXPORT ModelException : public Exception { IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(ModelException); //! Create exception with an error message ModelException(const char *t) : Exception(t) {} - ~ModelException() IMP_NOEXCEPT; + ~ModelException() noexcept; }; //! An exception that signifies some event occurred. @@ -205,7 +205,7 @@ class IMPKERNELEXPORT EventException : public Exception { IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(EventException); //! Create exception with an error message EventException(const char *t = "") : Exception(t) {} - ~EventException() IMP_NOEXCEPT; + ~EventException() noexcept; }; #endif diff --git a/modules/kernel/include/internal/input_output_exception.h b/modules/kernel/include/internal/input_output_exception.h index 30a3577f90..13fc80b3c8 100644 --- a/modules/kernel/include/internal/input_output_exception.h +++ b/modules/kernel/include/internal/input_output_exception.h @@ -24,7 +24,7 @@ struct IMPKERNELEXPORT InputOutputException : public std::runtime_error { InputOutputException(int particle_index, int operation, int entity, std::string key_name); InputOutputException(std::string container_name, int entity); - ~InputOutputException() IMP_NOEXCEPT; + ~InputOutputException() noexcept; enum AccessEntity { NO_ENTITY, ATTRIBUTE, diff --git a/modules/kernel/src/exception.cpp b/modules/kernel/src/exception.cpp index cce0b2d4bc..22a5d9a2d1 100644 --- a/modules/kernel/src/exception.cpp +++ b/modules/kernel/src/exception.cpp @@ -14,24 +14,24 @@ void handle_error(const char *message) { // this method is just here to provide a place to break in the debugger } -Exception::~Exception() throw() {} +Exception::~Exception() noexcept {} Exception::Exception(const char *message) : std::runtime_error(message) {} -InternalException::~InternalException() throw() {} +InternalException::~InternalException() noexcept {} -UsageException::~UsageException() throw() {} +UsageException::~UsageException() noexcept {} -IndexException::~IndexException() throw() {} +IndexException::~IndexException() noexcept {} -ValueException::~ValueException() throw() {} +ValueException::~ValueException() noexcept {} -ModelException::~ModelException() throw() {} +ModelException::~ModelException() noexcept {} -EventException::~EventException() throw() {} +EventException::~EventException() noexcept {} -IOException::~IOException() throw() {} +IOException::~IOException() noexcept {} -TypeException::~TypeException() throw() {} +TypeException::~TypeException() noexcept {} IMPKERNEL_END_NAMESPACE diff --git a/modules/kernel/src/internal/input_output_exception.cpp b/modules/kernel/src/internal/input_output_exception.cpp index 3ae6299d8e..19c498a75f 100644 --- a/modules/kernel/src/internal/input_output_exception.cpp +++ b/modules/kernel/src/internal/input_output_exception.cpp @@ -27,7 +27,7 @@ InputOutputException::InputOutputException(std::string container_name, operation_(operation), entity_(NO_ENTITY) {} -InputOutputException::~InputOutputException() throw() {} +InputOutputException::~InputOutputException() noexcept {} std::string InputOutputException::get_message(ModelObject *o) const { std::ostringstream oss; From 9824bac6c66fdec9abb7c2a0cebe764677ecdf66 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 15:52:27 -0800 Subject: [PATCH 070/155] Use %pythonbegin to add header to SWIG output Since we now require SWIG 3, we can rely on the %pythonbegin directive rather than patching the output file. --- tools/build/make_swig_wrapper.py | 15 +-------------- tools/build/setup_swig_wrappers.py | 7 +++++++ 2 files changed, 8 insertions(+), 14 deletions(-) diff --git a/tools/build/make_swig_wrapper.py b/tools/build/make_swig_wrapper.py index db8af80131..9e6c1f4024 100755 --- a/tools/build/make_swig_wrapper.py +++ b/tools/build/make_swig_wrapper.py @@ -66,19 +66,11 @@ def run_swig(outputdir, options): def patch_py_wrapper(infile, outfile, module): """Patch Python wrappers. - Work around SWIG bugs. Also add custom header; this is more properly - done by SWIG's %pythonbegin directive, but only very recent versions - of SWIG understand that.""" + Work around SWIG bugs.""" # outfile might be a symlink if os.path.exists(outfile): os.unlink(outfile) outfh = open(outfile, "w") - in_initial_comment = True - header = """# This wrapper is part of IMP, -# Copyright 2007-2022 IMP Inventors. All rights reserved. - -from __future__ import print_function, division, absolute_import -""" with open(infile) as infh: for line in infh: if module == 'kernel': @@ -86,11 +78,6 @@ def patch_py_wrapper(infile, outfile, module): # https://github.com/swig/swig/issues/583 line = line.replace('except Exception:', 'except:') outfh.write(line) - if in_initial_comment and not line.startswith('#'): - in_initial_comment = False - outfh.write(header) - if in_initial_comment: - raise IOError("Empty SWIG wrapper file") outfh.close() diff --git a/tools/build/setup_swig_wrappers.py b/tools/build/setup_swig_wrappers.py index 4ab294326b..bc271f4f6a 100755 --- a/tools/build/setup_swig_wrappers.py +++ b/tools/build/setup_swig_wrappers.py @@ -50,6 +50,13 @@ def build_wrapper(module, finder, sorted, target, source): """%%module(directors="1", allprotected="1", moduleimport="import $module") "%s" %%feature("autodoc", 1); +%%pythonbegin %%{ +# This wrapper is part of IMP, +# Copyright 2007-2022 IMP Inventors. All rights reserved. + +from __future__ import print_function, division, absolute_import +%%} + /* '#' formats in parsing or building Python values (e.g. in PyObject_CallFunction) use Py_ssize_t, not int, for lengths in Python >= 2.5 */ From b5a6adccb015b14c5a1507443e05480a67557514 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 23:11:33 -0800 Subject: [PATCH 071/155] Fix type used in for loop --- modules/algebra/src/Sphere3D.cpp | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/modules/algebra/src/Sphere3D.cpp b/modules/algebra/src/Sphere3D.cpp index f441820d12..e353d5e74b 100644 --- a/modules/algebra/src/Sphere3D.cpp +++ b/modules/algebra/src/Sphere3D.cpp @@ -117,8 +117,7 @@ Sphere3Ds get_simplified_from_volume(Sphere3Ds in, typedef std::pair SupportedPair; if (0) SupportedPair(); // suppress warning IMP_KERNEL_LARGE_UNORDERED_MAP supported; - typedef std::pair SupportsPair; - for(const SupportsPair & ps : supports) { + for(const auto &ps : supports) { for(SPIndex spi : ps.second) { supported[spi].insert(ps.first); } } @@ -129,7 +128,7 @@ Sphere3Ds get_simplified_from_volume(Sphere3Ds in, IMP_USAGE_CHECK(!supports.empty(), "Out of spheres"); SphereIndex max; double max_score = 0; - for(const SupportsPair & sp : supports) { + for(const auto &sp : supports) { double score = sp.second.size(); if (score > max_score) { max_score = score; From aff6bffd91b07d98ca084724f11830117557183a Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 23:15:11 -0800 Subject: [PATCH 072/155] Fix type in for loop --- modules/atom/src/hierarchy_tools.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/atom/src/hierarchy_tools.cpp b/modules/atom/src/hierarchy_tools.cpp index 63624629ee..17dba9c0c0 100644 --- a/modules/atom/src/hierarchy_tools.cpp +++ b/modules/atom/src/hierarchy_tools.cpp @@ -450,11 +450,10 @@ void transform_impl( void transform(atom::Hierarchy h, const algebra::Transformation3D &tr) { Model *m = h.get_model(); - typedef std::pair RBP; boost::unordered_map rigid_bodies; transform_impl(m, h.get_particle_index(), tr, rigid_bodies); - for(const RBP & rbp : rigid_bodies) { + for(const auto &rbp : rigid_bodies) { core::RigidBody rb(m, rbp.first); ParticleIndexes members = rb.get_member_indexes(); if (rbp.second.size() != members.size()) { From 21c0efc0635c1ec5ddb5c65a812d1db9d0c62f1d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 7 Mar 2022 23:29:41 -0800 Subject: [PATCH 073/155] Simplify some loops using ranged-for --- modules/algebra/include/grid_storages.h | 15 +++---- modules/cgal/src/internal/union_of_balls.cpp | 44 +++++++++---------- modules/kernel/pyext/IMP_kernel.argparse.i | 8 ++-- modules/kernel/src/Particle.cpp | 4 +- modules/kernel/src/io.cpp | 6 +-- modules/npc/include/CompositeRestraint.h | 5 +-- modules/npc/src/CompositeRestraint.cpp | 31 ++++++------- .../src/MinimumSphereDistancePairScore.cpp | 5 +-- modules/rmf/src/particle_io.cpp | 22 +++++----- modules/rmf/src/restraint_io.cpp | 21 ++++----- .../include/DistancePairScoreWithCache.h | 9 ++-- modules/score_functor/include/OrientedSoap.h | 8 ++-- 12 files changed, 74 insertions(+), 104 deletions(-) diff --git a/modules/algebra/include/grid_storages.h b/modules/algebra/include/grid_storages.h index 0fa1ccaee3..d6f80c11db 100644 --- a/modules/algebra/include/grid_storages.h +++ b/modules/algebra/include/grid_storages.h @@ -341,9 +341,8 @@ class SparseGridStorageD : public Base { template Functor apply(const Grid &g, Functor f) const { - for (typename Data::const_iterator it = data_.begin(); it != data_.end(); - ++it) { - f(g, it->first, g.get_center(it->first)); + for (const auto &it : data_) { + f(g, it.first, g.get_center(it.first)); } return f; } @@ -353,10 +352,9 @@ class SparseGridStorageD : public Base { IMP_USAGE_CHECK(!data_.empty(), "No voxels in grid."); GridIndexD reti = data_.begin()->first; ExtendedGridIndexD ret(reti.begin(), reti.end()); - for (typename Data::const_iterator it = data_.begin(); it != data_.end(); - ++it) { + for (const auto &it : data_) { for (unsigned int i = 0; i < ret.get_dimension(); ++i) { - ret.access_data().get_data()[i] = std::min(ret[i], it->first[i]); + ret.access_data().get_data()[i] = std::min(ret[i], it.first[i]); } } return ret; @@ -366,10 +364,9 @@ class SparseGridStorageD : public Base { IMP_USAGE_CHECK(!data_.empty(), "No voxels in grid."); GridIndexD reti = data_.begin()->first; ExtendedGridIndexD ret(reti.begin(), reti.end()); - for (typename Data::const_iterator it = data_.begin(); it != data_.end(); - ++it) { + for (const auto &it : data_) { for (unsigned int i = 0; i < ret.get_dimension(); ++i) { - ret.access_data().get_data()[i] = std::min(ret[i], it->first[i]); + ret.access_data().get_data()[i] = std::min(ret[i], it.first[i]); } } return ret; diff --git a/modules/cgal/src/internal/union_of_balls.cpp b/modules/cgal/src/internal/union_of_balls.cpp index f01e94c68a..9f00120759 100644 --- a/modules/cgal/src/internal/union_of_balls.cpp +++ b/modules/cgal/src/internal/union_of_balls.cpp @@ -1780,10 +1780,9 @@ std::pair computeVolumetrics(Alpha_shape const &A) { A.get_alpha_shape_vertices(std::back_inserter(vertices), Alpha_shape::SINGULAR, 0); #endif - for (std::list::iterator cit = vertices.begin(); - cit != vertices.end(); ++cit) { - tmpV += spacefill.ball_V((*cit)->point()); - tmpA += spacefill.ball_A((*cit)->point()); + for (Vertex_handle &cit : vertices) { + tmpV += spacefill.ball_V(cit->point()); + tmpA += spacefill.ball_A(cit->point()); } } volumeAccumulator += tmpV; @@ -1805,12 +1804,11 @@ std::pair computeVolumetrics(Alpha_shape const &A) { A.get_alpha_shape_edges(std::back_inserter(edges), Alpha_shape::SINGULAR, 0); #endif - for (std::list::iterator cit = edges.begin(); cit != edges.end(); - ++cit) { - tmpV -= spacefill.ballInter2_V(cit->first->vertex(cit->second)->point(), - cit->first->vertex(cit->third)->point()); - tmpA -= spacefill.ballInter2_A(cit->first->vertex(cit->second)->point(), - cit->first->vertex(cit->third)->point()); + for (Edge &cit : edges) { + tmpV -= spacefill.ballInter2_V(cit.first->vertex(cit.second)->point(), + cit.first->vertex(cit.third)->point()); + tmpA -= spacefill.ballInter2_A(cit.first->vertex(cit.second)->point(), + cit.first->vertex(cit.third)->point()); } } volumeAccumulator += tmpV; @@ -1844,16 +1842,15 @@ std::pair computeVolumetrics(Alpha_shape const &A) { A.get_alpha_shape_facets(std::back_inserter(facets), Alpha_shape::SINGULAR, 0); #endif - for (std::list::iterator cit = facets.begin(); cit != facets.end(); - ++cit) { + for (Facet &cit : facets) { tmpV += spacefill.ballInter3_V( - cit->first->vertex((cit->second + 1) & 3)->point(), - cit->first->vertex((cit->second + 2) & 3)->point(), - cit->first->vertex((cit->second + 3) & 3)->point()); + cit.first->vertex((cit.second + 1) & 3)->point(), + cit.first->vertex((cit.second + 2) & 3)->point(), + cit.first->vertex((cit.second + 3) & 3)->point()); tmpA += spacefill.ballInter3_A( - cit->first->vertex((cit->second + 1) & 3)->point(), - cit->first->vertex((cit->second + 2) & 3)->point(), - cit->first->vertex((cit->second + 3) & 3)->point()); + cit.first->vertex((cit.second + 1) & 3)->point(), + cit.first->vertex((cit.second + 2) & 3)->point(), + cit.first->vertex((cit.second + 3) & 3)->point()); } facets.clear(); #if CGAL_VERSION_NR > 1030701000 @@ -1889,8 +1886,7 @@ std::pair computeVolumetrics(Alpha_shape const &A) { A.get_alpha_shape_cells(std::back_inserter(cells), Alpha_shape::INTERIOR, 0); #endif - for (std::list::iterator cit = cells.begin(); - cit != cells.end(); ++cit) { + for (Cell_handle &cit : cells) { // tmpA-= // ballInter4_A((*cit)->vertex(0)->point(),(*cit)->vertex(1)->point(), // (*cit)->vertex(2)->point(),(*cit)->vertex(3)->point()); @@ -1898,11 +1894,11 @@ std::pair computeVolumetrics(Alpha_shape const &A) { // ballInter4_V((*cit)->vertex(0)->point(),(*cit)->vertex(1)->point(), // (*cit)->vertex(2)->point(),(*cit)->vertex(3)->point()); tmpA -= spacefill.ballInter4and3_A( - (*cit)->vertex(0)->point(), (*cit)->vertex(1)->point(), - (*cit)->vertex(2)->point(), (*cit)->vertex(3)->point()); + cit->vertex(0)->point(), cit->vertex(1)->point(), + cit->vertex(2)->point(), cit->vertex(3)->point()); tmpV -= spacefill.ballInter4and3_V( - (*cit)->vertex(0)->point(), (*cit)->vertex(1)->point(), - (*cit)->vertex(2)->point(), (*cit)->vertex(3)->point()); + cit->vertex(0)->point(), cit->vertex(1)->point(), + cit->vertex(2)->point(), cit->vertex(3)->point()); } } volumeAccumulator += tmpV; diff --git a/modules/kernel/pyext/IMP_kernel.argparse.i b/modules/kernel/pyext/IMP_kernel.argparse.i index 140e5497e3..ce6d4c0aea 100644 --- a/modules/kernel/pyext/IMP_kernel.argparse.i +++ b/modules/kernel/pyext/IMP_kernel.argparse.i @@ -10,11 +10,9 @@ extern IMPKERNELEXPORT Flag help_advanced; void get_flag_subset(const boost::program_options::options_description &f, unsigned ntokens, Strings &s) { - for (std::vector >::const_iterator - it = f.options().begin(); it != f.options().end(); ++it) { - if (it->get()->semantic()->min_tokens() == ntokens) { - s.push_back(it->get()->long_name()); + for (const auto &it : f.options()) { + if (it.get()->semantic()->min_tokens() == ntokens) { + s.push_back(it.get()->long_name()); } } } diff --git a/modules/kernel/src/Particle.cpp b/modules/kernel/src/Particle.cpp index 1923c333fd..2f40be234a 100644 --- a/modules/kernel/src/Particle.cpp +++ b/modules/kernel/src/Particle.cpp @@ -96,9 +96,7 @@ void Particle::show(std::ostream &out) const { if (!fks.empty()) { preout << "float attributes:" << std::endl; preout.set_prefix(" "); - for (FloatKeys::const_iterator it = fks.begin(); it != fks.end(); - ++it) { - FloatKey k = *it; + for (const FloatKey &k : fks) { preout << k << ": "; preout << get_model()->get_attribute(k, id_, false); preout << " (" << get_model()->get_derivative(k, id_, false) << ") "; diff --git a/modules/kernel/src/io.cpp b/modules/kernel/src/io.cpp index f88f5a363c..5c980a37bb 100644 --- a/modules/kernel/src/io.cpp +++ b/modules/kernel/src/io.cpp @@ -80,10 +80,8 @@ void read_particles_from_buffer(const Vector &buffer, read_particles_from_buffer(&buffer.front(), buffer.size() * sizeof(double), particles, keys); Model *m = particles[0]->get_model(); - ParticleIndexes pis = m->get_particle_indexes(); - for (ParticleIndexes::iterator pi = pis.begin(); pi != pis.end(); - ++pi) { - IMP::check_particle(m, *pi); + for (ParticleIndex pi : m->get_particle_indexes()) { + IMP::check_particle(m, pi); } } diff --git a/modules/npc/include/CompositeRestraint.h b/modules/npc/include/CompositeRestraint.h index fbb3004330..db6357d52b 100644 --- a/modules/npc/include/CompositeRestraint.h +++ b/modules/npc/include/CompositeRestraint.h @@ -59,9 +59,8 @@ class IMPNPCEXPORT CompositeRestraint : public Restraint { /** The restraint will ensure that at least one Particle of each type is present in the composite. */ void add_type(ParticleIndexes ps) { - for (ParticleIndexes::const_iterator it = ps.begin(); it != ps.end(); - ++it) { - tps_.push_back(TypedParticle(num_particle_types_, *it)); + for (const ParticleIndex &it : ps) { + tps_.push_back(TypedParticle(num_particle_types_, it)); } ++num_particle_types_; } diff --git a/modules/npc/src/CompositeRestraint.cpp b/modules/npc/src/CompositeRestraint.cpp index b3e0e64e6f..22b47a1b19 100644 --- a/modules/npc/src/CompositeRestraint.cpp +++ b/modules/npc/src/CompositeRestraint.cpp @@ -65,10 +65,9 @@ namespace { // Build new graph containing only the mst edges FullGraphWeightMap weight_map = boost::get(boost::edge_weight, full_g); - for (std::vector::const_iterator it = mst.begin(); - it != mst.end(); ++it) { - boost::add_edge(boost::source(*it, full_g), - boost::target(*it, full_g), weight_map[*it], g); + for (const FullGraphEdge &it : mst) { + boost::add_edge(boost::source(it, full_g), + boost::target(it, full_g), weight_map[it], g); } } @@ -91,9 +90,8 @@ namespace { int num_particle_types) { boost::dynamic_bitset<> have_types(num_particle_types); have_types.set(); - for (std::vector::const_iterator it = subset_so_far.begin(); - it != subset_so_far.end(); ++it) { - have_types.reset(tps[*it].first); + for (const Vertex &it : subset_so_far) { + have_types.reset(tps[it].first); } return have_types.none(); } @@ -187,10 +185,9 @@ namespace { const TypedParticles &tps, ParticleIndexPairs &pis) { pis.reserve(edges.size()); - for (std::vector::const_iterator it = edges.begin(); - it != edges.end(); ++it) { - int i = boost::target(*it, g); - int j = boost::source(*it, g); + for (const Edge &it : edges) { + int i = boost::target(it, g); + int j = boost::source(it, g); pis.push_back(ParticleIndexPair(tps[i].second, tps[j].second)); } } @@ -209,10 +206,9 @@ double CompositeRestraint::unprotected_evaluate(DerivativeAccumulator *accum) ParticleIndexPairs pis; get_particles_from_edges(edges, g, tps_, pis); IMP_LOG_VERBOSE("Minimum subtree is ["); - for (ParticleIndexPairs::const_iterator it = pis.begin(); it != pis.end(); - ++it) { - IMP_LOG_VERBOSE("(" << get_model()->get_particle_name((*it)[0]) - << ", " << get_model()->get_particle_name((*it)[1]) + for (const ParticleIndexPair &it : pis) { + IMP_LOG_VERBOSE("(" << get_model()->get_particle_name(it[0]) + << ", " << get_model()->get_particle_name(it[1]) << ") "); } IMP_LOG_VERBOSE("]" << std::endl); @@ -244,9 +240,8 @@ ModelObjectsTemp CompositeRestraint::do_get_inputs() const { ModelObjectsTemp ret; ret.reserve(tps_.size()); Model *m = get_model(); - for (TypedParticles::const_iterator it = tps_.begin(); it != tps_.end(); - ++it) { - ret.push_back(m->get_particle(it->second)); + for (const TypedParticle &it : tps_) { + ret.push_back(m->get_particle(it.second)); } return ret; } diff --git a/modules/npc/src/MinimumSphereDistancePairScore.cpp b/modules/npc/src/MinimumSphereDistancePairScore.cpp index 529fc7bbec..b3dae2d8d6 100644 --- a/modules/npc/src/MinimumSphereDistancePairScore.cpp +++ b/modules/npc/src/MinimumSphereDistancePairScore.cpp @@ -23,9 +23,8 @@ double MinimumSphereDistancePairScore::evaluate_index(Model *m, double dist2_min = algebra::get_squared_distance(c0, c1_orig); /* Find transformation that gives the minimum pairwise distance */ - for (algebra::Transformation3Ds::const_iterator it = transforms_.begin(); - it != transforms_.end(); ++it) { - algebra::Vector3D c1_transformed = (*it) * c1_orig; + for (const algebra::Transformation3D &it : transforms_) { + algebra::Vector3D c1_transformed = it * c1_orig; double dist2 = algebra::get_squared_distance(c0, c1_transformed); if (dist2 < dist2_min) { c1_min = c1_transformed; diff --git a/modules/rmf/src/particle_io.cpp b/modules/rmf/src/particle_io.cpp index dffbcd909b..a6eec6953c 100644 --- a/modules/rmf/src/particle_io.cpp +++ b/modules/rmf/src/particle_io.cpp @@ -29,10 +29,9 @@ class ParticleLoadLink : public SimpleLoadLink { map[ks[i]] = ik; IMP_LOG_TERSE("Found " << ks[i] << " with " << ik << std::endl); } - for (typename boost::unordered_map::const_iterator it = map.begin(); - it != map.end(); ++it) { - IMP_LOG_TERSE("Added key assoc " << fh.get_name(it->first) << " with " - << it->second << std::endl); + for (const auto &item : map) { + IMP_LOG_TERSE("Added key assoc " << fh.get_name(item.first) << " with " + << item.second << std::endl); } } template @@ -42,18 +41,17 @@ class ParticleLoadLink : public SimpleLoadLink { load_keys(nh.get_file(), cat, map); /*RMF::show_hierarchy_with_values(nh, frame);*/ - for (typename boost::unordered_map::const_iterator it = map.begin(); - it != map.end(); ++it) { - if (nh.get_has_value(it->first)) { - IK ik = it->second; + for (const auto &it : map) { + if (nh.get_has_value(it.first)) { + IK ik = it.second; if (o->has_attribute(ik)) { - o->set_value(ik, nh.get_value(it->first)); + o->set_value(ik, nh.get_value(it.first)); } else { - o->add_attribute(ik, nh.get_value(it->first)); + o->add_attribute(ik, nh.get_value(it.first)); } } else { - if (o->has_attribute(it->second)) { - o->remove_attribute(it->second); + if (o->has_attribute(it.second)) { + o->remove_attribute(it.second); } } } diff --git a/modules/rmf/src/restraint_io.cpp b/modules/rmf/src/restraint_io.cpp index cab6240f61..d6ac5f510d 100644 --- a/modules/rmf/src/restraint_io.cpp +++ b/modules/rmf/src/restraint_io.cpp @@ -395,9 +395,8 @@ class RestraintLoadLink : public SimpleLoadLink { RMF::Strings rvalue = nh.get_value(k); // Convert RMF relative paths to absolute Strings value; - for (RMF::Strings::const_iterator it = rvalue.begin(); - it != rvalue.end(); ++it) { - value.push_back(RMF::internal::get_absolute_path(fh.get_path(), *it)); + for (const auto &it : rvalue) { + value.push_back(RMF::internal::get_absolute_path(fh.get_path(), it)); } r->get_info()->add_filenames(fh.get_name(k), value); } @@ -641,9 +640,8 @@ class RestraintSaveLink : public SimpleSaveLink { imp_restraint_fn_cat_, ri->get_filenames_key(i)); Strings value = ri->get_filenames_value(i); RMF::Strings rvalue; - for (Strings::const_iterator it = value.begin(); - it != value.end(); ++it) { - rvalue.push_back(RMF::internal::get_relative_path(fh.get_path(), *it)); + for (const auto &it : value) { + rvalue.push_back(RMF::internal::get_relative_path(fh.get_path(), it)); } nh.set_frame_value(key, rvalue); } @@ -709,9 +707,8 @@ class RestraintSaveLink : public SimpleSaveLink { imp_restraint_fn_cat_, ri->get_filenames_key(i)); Strings value = ri->get_filenames_value(i); RMF::Strings rvalue; - for (Strings::const_iterator it = value.begin(); - it != value.end(); ++it) { - rvalue.push_back(RMF::internal::get_relative_path(fh.get_path(), *it)); + for (const auto &it : value) { + rvalue.push_back(RMF::internal::get_relative_path(fh.get_path(), it)); } nh.set_static_value(key, rvalue); } @@ -748,8 +745,7 @@ class RestraintSaveLink : public SimpleSaveLink { } void save_dynamic_particles(RMF::FileHandle file, ParticlesTemp ps) { - for (ParticlesTemp::iterator pit = ps.begin(); pit != ps.end(); ++pit) { - Particle *p = *pit; + for (Particle *p : ps) { RMF::NodeHandle nh = get_node_from_association(file, p); save_node(p->get_model(), p->get_index(), nh); } @@ -758,8 +754,7 @@ class RestraintSaveLink : public SimpleSaveLink { void add_static_particles(RMF::NodeHandle parent, ParticlesTemp ps) { RMF::FileHandle file = parent.get_file(); RMF::decorator::AliasFactory af(file); - for (ParticlesTemp::iterator pit = ps.begin(); pit != ps.end(); ++pit) { - Particle *p = *pit; + for (Particle *p : ps) { std::string nicename = RMF::get_as_node_name(p->get_name()); if (get_has_associated_node(file, p)) { RMF::NodeHandle c = parent.add_child(nicename, RMF::ALIAS); diff --git a/modules/score_functor/include/DistancePairScoreWithCache.h b/modules/score_functor/include/DistancePairScoreWithCache.h index bc82308bbc..d0b2e022f4 100644 --- a/modules/score_functor/include/DistancePairScoreWithCache.h +++ b/modules/score_functor/include/DistancePairScoreWithCache.h @@ -107,11 +107,10 @@ DistancePairScoreWithCache::evaluate_indexes_delta( const std::vector &indexes, std::vector &score) const { double ret = 0; ds_.check_cache_valid(m); - for (std::vector::const_iterator it = indexes.begin(); - it != indexes.end(); ++it) { - double s = evaluate_index_with_cache(m, p[*it], da); - ret = ret - score[*it] + s; - score[*it] = s; + for (unsigned it : indexes) { + double s = evaluate_index_with_cache(m, p[it], da); + ret = ret - score[it] + s; + score[it] = s; } return ret; } diff --git a/modules/score_functor/include/OrientedSoap.h b/modules/score_functor/include/OrientedSoap.h index 5050e69477..4fbdecbb73 100644 --- a/modules/score_functor/include/OrientedSoap.h +++ b/modules/score_functor/include/OrientedSoap.h @@ -93,11 +93,9 @@ class OrientedSoap : public ScoreWithCache { const DList &doublets1 = doublets_.get_for_atom(a1); if (doublets1.size() > 0) { const DList &doublets2 = doublets_.get_for_atom(a2); - for (DList::const_iterator dit1 = doublets1.begin(); - dit1 != doublets1.end(); ++dit1) { - for (DList::const_iterator dit2 = doublets2.begin(); - dit2 != doublets2.end(); ++dit2) { - score += score_doublets(a1, a2, distbin, *dit1, *dit2); + for (const internal::SoapModelDoublet &dit1 : doublets1) { + for (const internal::SoapModelDoublet &dit2 : doublets2) { + score += score_doublets(a1, a2, distbin, dit1, dit2); } } } From 0828d4d86b1c0ad93a8de5117489c9adcbe3cb3f Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 8 Mar 2022 08:59:03 -0800 Subject: [PATCH 074/155] Bundle api-ms-win-core DLLs too --- tools/w32/make-package.sh | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 0599b628b7..9f090a6d3d 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -127,6 +127,16 @@ for crt in convert environment filesystem heap locale math multibyte \ runtime stdio string time utility; do cp ${DLLSRC}/api-ms-win-crt-${crt}-l1-1-0.dll ${ROOT}/bin || exit 1 done +for core in console-l1-1-0 datetime-l1-1-0 debug-l1-1-0 errorhandling-l1-1-0 \ + file-l1-1-0 file-l1-2-0 file-l2-1-0 handle-l1-1-0 heap-l1-1-0 \ + interlocked-l1-1-0 libraryloader-l1-1-0 localization-l1-2-0 \ + memory-l1-1-0 namedpipe-l1-1-0 processenvironment-l1-1-0 \ + processthreads-l1-1-0 processthreads-l1-1-1 profile-l1-1-0 \ + rtlsupport-l1-1-0 string-l1-1-0 synch-l1-1-0 synch-l1-2-0 \ + sysinfo-l1-1-0 timezone-l1-1-0 util-l1-1-0; do + cp ${DLLSRC}/api-ms-win-core-${core}.dll ${ROOT}/bin || exit 1 +done + # Add other DLL dependencies cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ ${DLLSRC}/boost_filesystem-vc140-mt-x${BITS}-1_72.dll \ From 2e7bf2d68a04baa34725a6838c7921b4b964e18d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 8 Mar 2022 18:27:19 -0800 Subject: [PATCH 075/155] Go back to MSVS2012 for 64-bit Windows for now Our MSVS2015 setup results in a lot of test failures, so stick with 2012 for now. --- tools/w32/make-package.sh | 102 ++++++++++++++++++++++++-------------- 1 file changed, 64 insertions(+), 38 deletions(-) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 9f090a6d3d..7367d5c709 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -56,6 +56,9 @@ cp ${TOOLDIR}/pkg-README.txt ${ROOT}/README.txt || exit 1 mkdir ${ROOT}/python || exit 1 mkdir ${ROOT}/python/ihm || exit 1 +# Drop Python 2 +rm -rf ${ROOT}/pylib/2.7/ + # Remove .pyc files find ${ROOT} -name __pycache__ -exec rm -rf \{\} \; 2>/dev/null mv ${ROOT}/pylib/3.6/*.py ${ROOT}/pylib/3.6/IMP ${ROOT}/python || exit 1 @@ -115,49 +118,72 @@ PYVERS="36 37 38 39 310" if [ "${BITS}" = "32" ]; then MAKENSIS="makensis" DLLSRC=/usr/lib/w32comp/windows/system + + # Add redist MSVC runtime DLLs + cp ${DLLSRC}/msvc*140.dll ${DLLSRC}/concrt140.dll \ + ${DLLSRC}/vcruntime140.dll ${DLLSRC}/ucrtbase.dll ${ROOT}/bin || exit 1 + for crt in convert environment filesystem heap locale math multibyte \ + runtime stdio string time utility; do + cp ${DLLSRC}/api-ms-win-crt-${crt}-l1-1-0.dll ${ROOT}/bin || exit 1 + done + for core in console-l1-1-0 datetime-l1-1-0 debug-l1-1-0 errorhandling-l1-1-0 \ + file-l1-1-0 file-l1-2-0 file-l2-1-0 handle-l1-1-0 heap-l1-1-0 \ + interlocked-l1-1-0 libraryloader-l1-1-0 localization-l1-2-0 \ + memory-l1-1-0 namedpipe-l1-1-0 processenvironment-l1-1-0 \ + processthreads-l1-1-0 processthreads-l1-1-1 profile-l1-1-0 \ + rtlsupport-l1-1-0 string-l1-1-0 synch-l1-1-0 synch-l1-2-0 \ + sysinfo-l1-1-0 timezone-l1-1-0 util-l1-1-0; do + cp ${DLLSRC}/api-ms-win-core-${core}.dll ${ROOT}/bin || exit 1 + done + + # Add other DLL dependencies + cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ + ${DLLSRC}/boost_filesystem-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_program_options-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_system-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_date_time-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_graph-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_regex-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_thread-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_random-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_iostreams-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/boost_zlib-vc140-mt-x${BITS}-1_72.dll \ + ${DLLSRC}/libgmp-10.dll \ + ${DLLSRC}/libmpfr-4.dll \ + ${DLLSRC}/libfftw3-3.dll \ + ${DLLSRC}/libTAU1.dll \ + ${DLLSRC}/zlib1.dll \ + ${DLLSRC}/opencv_core455.dll ${DLLSRC}/opencv_highgui455.dll \ + ${DLLSRC}/opencv_imgcodecs455.dll ${DLLSRC}/opencv_videoio455.dll \ + ${DLLSRC}/opencv_imgproc455.dll ${ROOT}/bin || exit 1 else MAKENSIS="makensis -DIMP_64BIT" DLLSRC=/usr/lib/w64comp/windows/system32 + # Add redist MSVC runtime DLLs + cp ${DLLSRC}/msvc*110.dll ${ROOT}/bin || exit 1 + # Add other DLL dependencies + cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ + ${DLLSRC}/boost_filesystem-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_program_options-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_system-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_date_time-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_graph-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_regex-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_thread-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_random-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_iostreams-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_zlib-vc110-mt-1_55.dll \ + ${DLLSRC}/boost_chrono-vc110-mt-1_55.dll \ + ${DLLSRC}/CGAL-vc110-mt-4.4.dll \ + ${DLLSRC}/libgmp-10.dll \ + ${DLLSRC}/libmpfr-4.dll \ + ${DLLSRC}/libfftw3-3.dll \ + ${DLLSRC}/libTAU1.dll \ + ${DLLSRC}/zlib1.dll \ + ${DLLSRC}/opencv_core248.dll ${DLLSRC}/opencv_highgui248.dll \ + ${DLLSRC}/opencv_imgproc248.dll ${ROOT}/bin || exit 1 fi -# Add redist MSVC runtime DLLs -cp ${DLLSRC}/msvc*140.dll ${DLLSRC}/concrt140.dll \ -${DLLSRC}/vcruntime140.dll ${DLLSRC}/ucrtbase.dll ${ROOT}/bin || exit 1 -for crt in convert environment filesystem heap locale math multibyte \ - runtime stdio string time utility; do - cp ${DLLSRC}/api-ms-win-crt-${crt}-l1-1-0.dll ${ROOT}/bin || exit 1 -done -for core in console-l1-1-0 datetime-l1-1-0 debug-l1-1-0 errorhandling-l1-1-0 \ - file-l1-1-0 file-l1-2-0 file-l2-1-0 handle-l1-1-0 heap-l1-1-0 \ - interlocked-l1-1-0 libraryloader-l1-1-0 localization-l1-2-0 \ - memory-l1-1-0 namedpipe-l1-1-0 processenvironment-l1-1-0 \ - processthreads-l1-1-0 processthreads-l1-1-1 profile-l1-1-0 \ - rtlsupport-l1-1-0 string-l1-1-0 synch-l1-1-0 synch-l1-2-0 \ - sysinfo-l1-1-0 timezone-l1-1-0 util-l1-1-0; do - cp ${DLLSRC}/api-ms-win-core-${core}.dll ${ROOT}/bin || exit 1 -done - -# Add other DLL dependencies -cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ - ${DLLSRC}/boost_filesystem-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_program_options-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_system-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_date_time-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_graph-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_regex-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_thread-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_random-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_iostreams-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/boost_zlib-vc140-mt-x${BITS}-1_72.dll \ - ${DLLSRC}/libgmp-10.dll \ - ${DLLSRC}/libmpfr-4.dll \ - ${DLLSRC}/libfftw3-3.dll \ - ${DLLSRC}/libTAU1.dll \ - ${DLLSRC}/zlib1.dll \ - ${DLLSRC}/opencv_core455.dll ${DLLSRC}/opencv_highgui455.dll \ - ${DLLSRC}/opencv_imgcodecs455.dll ${DLLSRC}/opencv_videoio455.dll \ - ${DLLSRC}/opencv_imgproc455.dll ${ROOT}/bin || exit 1 - # Check all installed binaries for DLL dependencies, to make sure we # didn't miss any dumpbin /DEPENDENTS ${ROOT}/bin/*.exe ${ROOT}/bin/*.dll ${ROOT}/python/*/*.pyd \ From 641d152d5b29f991d1eacc83784f970b9a2b66ff Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 8 Mar 2022 19:44:28 -0800 Subject: [PATCH 076/155] Revert "Use C++11 math/set types" Since we had to drop MSVS2015 on 64-bit Windows for now, we are still on MSVS2012, which doesn't support these C++11 math/set types. Use Boost equivalents. This reverts commit f1579fd13d1e250024a264421d5a7431b9556f12. --- modules/em/src/BayesEM3D.cpp | 25 ++++++++++++++----------- modules/isd/src/FStudentT.cpp | 7 ++++--- modules/isd/src/GammaPrior.cpp | 7 ++++--- 3 files changed, 22 insertions(+), 17 deletions(-) diff --git a/modules/em/src/BayesEM3D.cpp b/modules/em/src/BayesEM3D.cpp index 7151a82cca..a83d807ab0 100644 --- a/modules/em/src/BayesEM3D.cpp +++ b/modules/em/src/BayesEM3D.cpp @@ -10,8 +10,10 @@ #include #include #include -#include -#include +#include +#include +#include +#include IMPEM_BEGIN_NAMESPACE @@ -133,16 +135,16 @@ FloatPair bayesem3d_get_logabssumexp(double x, double y, double sx, double sy) { } if (x > y) { - return FloatPair(x + std::log1p(sx * sy * exp(y - x)), sx); + return FloatPair(x + boost::math::log1p(sx * sy * exp(y - x)), sx); } else { - return FloatPair(y + std::log1p(sx * sy * exp(x - y)), sy); + return FloatPair(y + boost::math::log1p(sx * sy * exp(x - y)), sy); } } FloatPair bayesem3d_get_logabssumprodexp(double x, double y, double wx, double wy) { - double sx = std::copysign(1.0, wx); - double sy = std::copysign(1.0, wy); + double sx = boost::math::copysign(1.0, wx); + double sy = boost::math::copysign(1.0, wy); return bayesem3d_get_logabssumexp(x + log(wx * sx), y + log(wy * sy), sx, sy); } @@ -157,9 +159,9 @@ double bayesem3d_get_logsumexp(double x, double y) { } if (x > y) { - return x + std::log1p(exp(y - x)); + return x + boost::math::log1p(exp(y - x)); } else { - return y + std::log1p(exp(x - y)); + return y + boost::math::log1p(exp(x - y)); } } @@ -293,7 +295,7 @@ DensityMap *bayesem3d_get_density_from_particle(DensityMap *em, int nxny = em_header->get_nx() * em_header->get_ny(); int znxny; - std::unordered_set visited_voxels; + boost::unordered_set visited_voxels; for (unsigned int ii = 0; ii < xyzr.size(); ii++) { double px = xyzr[ii].get_x(); @@ -327,8 +329,9 @@ DensityMap *bayesem3d_get_density_from_particle(DensityMap *em, } } - for (auto &vv : visited_voxels) { - vals[vv] = exp(vals[vv]) - 1.; + for (boost::unordered_set::iterator vv = visited_voxels.begin(); + vv != visited_voxels.end(); ++vv) { + vals[*vv] = exp(vals[*vv]) - 1.; } return ret.release(); diff --git a/modules/isd/src/FStudentT.cpp b/modules/isd/src/FStudentT.cpp index b8e71b0a1c..e0cc3d5e72 100644 --- a/modules/isd/src/FStudentT.cpp +++ b/modules/isd/src/FStudentT.cpp @@ -8,7 +8,8 @@ #include #include #include -#include +#include +#include IMPISD_BEGIN_NAMESPACE @@ -64,7 +65,7 @@ double FStudentT::do_evaluate() const { update_cached_values(); // update t2 return boost::math::lgamma(.5 * nu_) - boost::math::lgamma(.5 * (N_ + nu_)) + .5 * N_ * std::log(IMP::PI * nu_) + N_ * std::log(sigma_) + - .5 * (N_ + nu_) * std::log1p(t2_ / nu_) - LogJX_; + .5 * (N_ + nu_) * boost::math::log1p(t2_ / nu_) - LogJX_; } double FStudentT::evaluate_derivative_Fx(double Fx) const { @@ -95,7 +96,7 @@ double FStudentT::evaluate_derivative_sigma() const { double FStudentT::evaluate_derivative_nu() const { return .5 * (-1 + boost::math::digamma(.5 * nu_) - boost::math::digamma(.5 * (N_ + nu_)) + - std::log1p(t2_ / nu_) + (N_ + nu_) / (nu_ + t2_)); + boost::math::log1p(t2_ / nu_) + (N_ + nu_) / (nu_ + t2_)); } IMPISD_END_NAMESPACE diff --git a/modules/isd/src/GammaPrior.cpp b/modules/isd/src/GammaPrior.cpp index 4af2b3f27a..6a71012a0f 100644 --- a/modules/isd/src/GammaPrior.cpp +++ b/modules/isd/src/GammaPrior.cpp @@ -8,7 +8,8 @@ #include #include -#include +#include +#include IMPISD_BEGIN_NAMESPACE @@ -25,7 +26,7 @@ GammaPrior::unprotected_evaluate(DerivativeAccumulator *accum) const IMP::isd::Scale sig(p_); double prob=0.0; double s=sig.get_scale()/10; - double gam = std::tgamma(k_) * std::pow(theta_, k_); + double gam = boost::math::tgamma(k_) * std::pow(theta_, k_); prob = std::pow(s, k_-1) * std::exp(-s/theta_)/gam; if (accum) { @@ -39,7 +40,7 @@ double GammaPrior::evaluate_at(Float val) const { double prob=0.0; - double gam = std::tgamma(k_) * std::pow(theta_, k_); + double gam = boost::math::tgamma(k_) * std::pow(theta_, k_); prob = std::pow(val, k_-1) * std::exp(-val/theta_)/gam; double score = -1*log (prob); From 067f32379e9bf7d1fc53375382d5420122fcacc4 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 9 Mar 2022 10:47:23 -0800 Subject: [PATCH 077/155] Don't redistribute API sets We shouldn't need to redistribute the API sets (api-ms*.dll) or the universal C runtime, as a) these should be installed on any up to date Windows 7 system (or on Win10 by default) and b) Microsoft recommends (or requires in some docs) that they not be redistributed. At any rate, most IMP users will have already installed Python 3, which requires the same DLLs. --- tools/w32/make-package.sh | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 7367d5c709..3dc10130dc 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -120,21 +120,8 @@ if [ "${BITS}" = "32" ]; then DLLSRC=/usr/lib/w32comp/windows/system # Add redist MSVC runtime DLLs - cp ${DLLSRC}/msvc*140.dll ${DLLSRC}/concrt140.dll \ - ${DLLSRC}/vcruntime140.dll ${DLLSRC}/ucrtbase.dll ${ROOT}/bin || exit 1 - for crt in convert environment filesystem heap locale math multibyte \ - runtime stdio string time utility; do - cp ${DLLSRC}/api-ms-win-crt-${crt}-l1-1-0.dll ${ROOT}/bin || exit 1 - done - for core in console-l1-1-0 datetime-l1-1-0 debug-l1-1-0 errorhandling-l1-1-0 \ - file-l1-1-0 file-l1-2-0 file-l2-1-0 handle-l1-1-0 heap-l1-1-0 \ - interlocked-l1-1-0 libraryloader-l1-1-0 localization-l1-2-0 \ - memory-l1-1-0 namedpipe-l1-1-0 processenvironment-l1-1-0 \ - processthreads-l1-1-0 processthreads-l1-1-1 profile-l1-1-0 \ - rtlsupport-l1-1-0 string-l1-1-0 synch-l1-1-0 synch-l1-2-0 \ - sysinfo-l1-1-0 timezone-l1-1-0 util-l1-1-0; do - cp ${DLLSRC}/api-ms-win-core-${core}.dll ${ROOT}/bin || exit 1 - done + cp ${DLLSRC}/msvcp140.dll ${DLLSRC}/concrt140.dll ${DLLSRC}/vcruntime140.dll \ + ${ROOT}/bin || exit 1 # Add other DLL dependencies cp ${DLLSRC}/hdf5.dll ${DLLSRC}/libgsl.dll ${DLLSRC}/libgslcblas.dll \ @@ -211,6 +198,25 @@ echo "mfplat.dll" >> w32.dlls echo "mfreadwrite.dll" >> w32.dlls echo "shlwapi.dll" >> w32.dlls +# Also exclude Universal C runtime and Windows API sets, which +# should be present on any up to date Windows 7 system (via KB2999226), +# or by default in Windows 10. +echo "ucrtbase.dll" >> w32.dlls + +for crt in convert environment filesystem heap locale math multibyte \ + runtime stdio string time utility; do + echo "api-ms-win-crt-${crt}-l1-1-0.dll" >> w32.dlls +done +for core in console-l1-1-0 datetime-l1-1-0 debug-l1-1-0 errorhandling-l1-1-0 \ + file-l1-1-0 file-l1-2-0 file-l2-1-0 handle-l1-1-0 heap-l1-1-0 \ + interlocked-l1-1-0 libraryloader-l1-1-0 localization-l1-2-0 \ + memory-l1-1-0 namedpipe-l1-1-0 processenvironment-l1-1-0 \ + processthreads-l1-1-0 processthreads-l1-1-1 profile-l1-1-0 \ + rtlsupport-l1-1-0 string-l1-1-0 synch-l1-1-0 synch-l1-2-0 \ + sysinfo-l1-1-0 timezone-l1-1-0 util-l1-1-0; do + echo "api-ms-win-core-${core}.dll" >> w32.dlls +done + # People that want to run MPI-enabled binaries will need their own copy # of MS-MPI - we don't bundle it. echo "msmpi.dll" >> w32.dlls From 425a8a6f60f120cc847d7ab2c5783a14eff35ac4 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 9 Mar 2022 11:01:17 -0800 Subject: [PATCH 078/155] Restore workaround for non-noexcept compilers Unfortunately MSVS2012 does not support the 'noexcept' or 'default' specifiers, so restore our workaround. This reverts commit 9a40f110e3b1dfb574120d9848b1b03355ae8681. --- ChangeLog.md | 2 +- doc/manual/code_conventions.md | 8 ++++---- modules/kernel/include/compiler_macros.h | 15 +++++++++++++- modules/kernel/include/exception.h | 20 +++++++++---------- .../include/internal/input_output_exception.h | 2 +- modules/kernel/src/exception.cpp | 18 ++++++++--------- .../src/internal/input_output_exception.cpp | 2 +- 7 files changed, 40 insertions(+), 27 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index 730821a43f..dd4a893d5f 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -9,7 +9,7 @@ ChangeLog {#changelog} or MS Visual Studio 2015 or later. Various IMP macro and header workarounds for pre-C++11 environments are thus no longer needed and are deprecated: `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`, - `IMP_FOREACH`, `IMP_NOEXCEPT`, `IMP/nullptr.h`, and `IMP/nullptr_macros.h`. + `IMP_FOREACH`, `IMP/nullptr.h`, and `IMP/nullptr_macros.h`. # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} - OpenCubicSpline now throws a ValueException for out-of-range values, to diff --git a/doc/manual/code_conventions.md b/doc/manual/code_conventions.md index 1772fe05be..30209e3afd 100644 --- a/doc/manual/code_conventions.md +++ b/doc/manual/code_conventions.md @@ -122,7 +122,7 @@ As a result, such functions do not need to obey all the coding conventions # C++ 11 {#codeconv_cxx11} Latest %IMP requires a compiler that supports C++ 11, unlike older versions. -Thus, C++ 11 features, such as the `override`, `final`, `auto`, `noexcept` -and `nullptr` keywords, and range-based for loops, can be used where -appropriate. The old compatibility macros (such as `IMP_OVERRIDE`, `IMP_FINAL`, -`IMP_NOEXCEPT`, `IMP_NULLPTR` and `IMP_FOREACH`) should no longer be used. +Thus, C++ 11 features, such as the `override`, `final`, `auto` and `nullptr` +keywords, and range-based for loops, can be used where appropriate. +The old compatibility macros (such as `IMP_OVERRIDE`, `IMP_FINAL`, +`IMP_NULLPTR` and `IMP_FOREACH`) should no longer be used. diff --git a/modules/kernel/include/compiler_macros.h b/modules/kernel/include/compiler_macros.h index b8c344d543..b10adf2737 100644 --- a/modules/kernel/include/compiler_macros.h +++ b/modules/kernel/include/compiler_macros.h @@ -75,11 +75,24 @@ #endif #endif -// Deprecated: just use 'noexcept' directly +#if defined(__GNUC__) && __cplusplus >= 201103L +#define IMP_HAS_NOEXCEPT 1 +#elif defined(__clang__) && defined(__has_feature) +#define IMP_HAS_NOEXCEPT __has_feature(cxx_noexcept) +#else +#define IMP_HAS_NOEXCEPT 0 +#endif + +#if IMP_HAS_NOEXCEPT #define IMP_NOEXCEPT noexcept #define IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(Name) \ Name(const Name &) = default; \ Name &operator=(const Name &) = default +#else +// probably should be finer here +#define IMP_NOEXCEPT throw() +#define IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(Name) +#endif #if defined(__clang__) || defined(__GNUC__) #define IMP_PRAGMA(x) _Pragma(IMP_STRINGIFY(x)) diff --git a/modules/kernel/include/exception.h b/modules/kernel/include/exception.h index 698de26346..926ceab15a 100644 --- a/modules/kernel/include/exception.h +++ b/modules/kernel/include/exception.h @@ -52,11 +52,11 @@ class IMPKERNELEXPORT Exception { public: #if defined(SWIG) || defined(IMP_DOXYGEN) - const char *what() const noexcept; + const char *what() const IMP_NOEXCEPT; #endif IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(Exception); Exception(const char *message); - ~Exception() noexcept; + ~Exception() IMP_NOEXCEPT; }; #endif @@ -106,7 +106,7 @@ struct IMPKERNELEXPORT InternalException IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(InternalException); InternalException(const char *msg = "Fatal error") : std::runtime_error(msg) {} - ~InternalException() noexcept; + ~InternalException() IMP_NOEXCEPT; }; //! An exception for an invalid usage of \imp @@ -127,7 +127,7 @@ class IMPKERNELEXPORT UsageException public: IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(UsageException); UsageException(const char *t) : std::runtime_error(t) {} - ~UsageException() noexcept; + ~UsageException() IMP_NOEXCEPT; }; //! An exception for an invalid value being passed to \imp @@ -137,7 +137,7 @@ class IMPKERNELEXPORT ValueException : public Exception { public: IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(ValueException); ValueException(const char *t) : Exception(t) {} - ~ValueException() noexcept; + ~ValueException() IMP_NOEXCEPT; }; //! An exception for an invalid type being passed to \imp @@ -147,7 +147,7 @@ class IMPKERNELEXPORT TypeException : public Exception { public: IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(TypeException); TypeException(const char *t) : Exception(t) {} - ~TypeException() noexcept; + ~TypeException() IMP_NOEXCEPT; }; //! An exception for a request for an invalid member of a container @@ -158,7 +158,7 @@ class IMPKERNELEXPORT IndexException : public Exception { IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(IndexException); //! Create exception with an error message IndexException(const char *t) : Exception(t) {} - ~IndexException() noexcept; + ~IndexException() IMP_NOEXCEPT; }; //! An input/output exception @@ -174,7 +174,7 @@ class IMPKERNELEXPORT IOException : public Exception { public: IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(IOException); IOException(const char *t) : Exception(t) {} - ~IOException() noexcept; + ~IOException() IMP_NOEXCEPT; }; /** \brief An exception which is thrown when the Model has @@ -190,7 +190,7 @@ class IMPKERNELEXPORT ModelException : public Exception { IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(ModelException); //! Create exception with an error message ModelException(const char *t) : Exception(t) {} - ~ModelException() noexcept; + ~ModelException() IMP_NOEXCEPT; }; //! An exception that signifies some event occurred. @@ -205,7 +205,7 @@ class IMPKERNELEXPORT EventException : public Exception { IMP_CXX11_DEFAULT_COPY_CONSTRUCTOR(EventException); //! Create exception with an error message EventException(const char *t = "") : Exception(t) {} - ~EventException() noexcept; + ~EventException() IMP_NOEXCEPT; }; #endif diff --git a/modules/kernel/include/internal/input_output_exception.h b/modules/kernel/include/internal/input_output_exception.h index 13fc80b3c8..30a3577f90 100644 --- a/modules/kernel/include/internal/input_output_exception.h +++ b/modules/kernel/include/internal/input_output_exception.h @@ -24,7 +24,7 @@ struct IMPKERNELEXPORT InputOutputException : public std::runtime_error { InputOutputException(int particle_index, int operation, int entity, std::string key_name); InputOutputException(std::string container_name, int entity); - ~InputOutputException() noexcept; + ~InputOutputException() IMP_NOEXCEPT; enum AccessEntity { NO_ENTITY, ATTRIBUTE, diff --git a/modules/kernel/src/exception.cpp b/modules/kernel/src/exception.cpp index 22a5d9a2d1..cce0b2d4bc 100644 --- a/modules/kernel/src/exception.cpp +++ b/modules/kernel/src/exception.cpp @@ -14,24 +14,24 @@ void handle_error(const char *message) { // this method is just here to provide a place to break in the debugger } -Exception::~Exception() noexcept {} +Exception::~Exception() throw() {} Exception::Exception(const char *message) : std::runtime_error(message) {} -InternalException::~InternalException() noexcept {} +InternalException::~InternalException() throw() {} -UsageException::~UsageException() noexcept {} +UsageException::~UsageException() throw() {} -IndexException::~IndexException() noexcept {} +IndexException::~IndexException() throw() {} -ValueException::~ValueException() noexcept {} +ValueException::~ValueException() throw() {} -ModelException::~ModelException() noexcept {} +ModelException::~ModelException() throw() {} -EventException::~EventException() noexcept {} +EventException::~EventException() throw() {} -IOException::~IOException() noexcept {} +IOException::~IOException() throw() {} -TypeException::~TypeException() noexcept {} +TypeException::~TypeException() throw() {} IMPKERNEL_END_NAMESPACE diff --git a/modules/kernel/src/internal/input_output_exception.cpp b/modules/kernel/src/internal/input_output_exception.cpp index 19c498a75f..3ae6299d8e 100644 --- a/modules/kernel/src/internal/input_output_exception.cpp +++ b/modules/kernel/src/internal/input_output_exception.cpp @@ -27,7 +27,7 @@ InputOutputException::InputOutputException(std::string container_name, operation_(operation), entity_(NO_ENTITY) {} -InputOutputException::~InputOutputException() noexcept {} +InputOutputException::~InputOutputException() throw() {} std::string InputOutputException::get_message(ModelObject *o) const { std::ostringstream oss; From 45791079c12d964f97094da4840cb49cea72a600 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 9 Mar 2022 11:04:40 -0800 Subject: [PATCH 079/155] Don't use throw() throw() has been removed in C++20. Use our IMP_NOEXCEPT macro instead which will expand to 'noexcept' in most cases. --- modules/kernel/src/exception.cpp | 18 +++++++++--------- .../src/internal/input_output_exception.cpp | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/kernel/src/exception.cpp b/modules/kernel/src/exception.cpp index cce0b2d4bc..9c7e6d4407 100644 --- a/modules/kernel/src/exception.cpp +++ b/modules/kernel/src/exception.cpp @@ -14,24 +14,24 @@ void handle_error(const char *message) { // this method is just here to provide a place to break in the debugger } -Exception::~Exception() throw() {} +Exception::~Exception() IMP_NOEXCEPT {} Exception::Exception(const char *message) : std::runtime_error(message) {} -InternalException::~InternalException() throw() {} +InternalException::~InternalException() IMP_NOEXCEPT {} -UsageException::~UsageException() throw() {} +UsageException::~UsageException() IMP_NOEXCEPT {} -IndexException::~IndexException() throw() {} +IndexException::~IndexException() IMP_NOEXCEPT {} -ValueException::~ValueException() throw() {} +ValueException::~ValueException() IMP_NOEXCEPT {} -ModelException::~ModelException() throw() {} +ModelException::~ModelException() IMP_NOEXCEPT {} -EventException::~EventException() throw() {} +EventException::~EventException() IMP_NOEXCEPT {} -IOException::~IOException() throw() {} +IOException::~IOException() IMP_NOEXCEPT {} -TypeException::~TypeException() throw() {} +TypeException::~TypeException() IMP_NOEXCEPT {} IMPKERNEL_END_NAMESPACE diff --git a/modules/kernel/src/internal/input_output_exception.cpp b/modules/kernel/src/internal/input_output_exception.cpp index 3ae6299d8e..144be7ae5b 100644 --- a/modules/kernel/src/internal/input_output_exception.cpp +++ b/modules/kernel/src/internal/input_output_exception.cpp @@ -27,7 +27,7 @@ InputOutputException::InputOutputException(std::string container_name, operation_(operation), entity_(NO_ENTITY) {} -InputOutputException::~InputOutputException() throw() {} +InputOutputException::~InputOutputException() IMP_NOEXCEPT {} std::string InputOutputException::get_message(ModelObject *o) const { std::ostringstream oss; From c0dec038a1df964a5adc2b620edf77e9a37800ef Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 9 Mar 2022 16:15:42 -0800 Subject: [PATCH 080/155] Squashed 'modules/rmf/dependency/RMF/' changes from e0424dd8ab..7f8c4cab38 7f8c4cab38 Use nullptr rather than NULL f5a99d19b0 Add better workaround for flat_map[] segfault ae9e321aee Don't use throw() ce4956109b Restore workaround for non-noexcept compilers 9ffb254dff Use C++11 range-based for instead of RMF_FOREACH eeb0979927 Use 'noexcept' keyword, since we require C++11 f5ecbb748b Use 'override' keyword, since we require C++11 04411a9f67 Require C++11, so we can use 'final' keyword git-subtree-dir: modules/rmf/dependency/RMF git-subtree-split: 7f8c4cab382ba3fa44bb7129eafd90301199fe76 --- modules/rmf/dependency/RMF/ChangeLog.md | 7 + .../RMF/benchmark/benchmark_rmf.cpp | 10 +- modules/rmf/dependency/RMF/bin/rmf_cat.cpp | 2 +- modules/rmf/dependency/RMF/bin/rmf_slice.cpp | 2 +- .../rmf/dependency/RMF/bin/rmf_transform.cpp | 2 +- .../RMF/cmake_modules/IMPFindC++11.cmake | 94 ++++++------ .../RMF/include/RMF/HDF5/ConstDataSetD.h | 17 +-- .../RMF/include/RMF/HDF5/DataSetD.h | 8 +- .../dependency/RMF/include/RMF/HDF5/handle.h | 2 +- .../dependency/RMF/include/RMF/HDF5/types.h | 2 +- .../rmf/dependency/RMF/include/RMF/Nullable.h | 2 +- .../RMF/include/RMF/compiler_macros.h | 30 +--- .../include/RMF/decorator/representation.h | 6 +- .../dependency/RMF/include/RMF/exceptions.h | 2 +- .../RMF/include/RMF/infrastructure_macros.h | 7 +- .../include/RMF/internal/SharedDataCategory.h | 2 +- .../RMF/include/RMF/internal/SharedDataData.h | 6 - .../RMF/include/RMF/internal/SharedDataKeys.h | 6 +- .../RMF/include/RMF/internal/swig_helpers.h | 2 +- .../rmf/dependency/RMF/plugins/vmd/Data.cpp | 24 ++-- .../dependency/RMF/plugins/vmd/Data_read.cpp | 15 +- .../dependency/RMF/src/FileConstHandle.cpp | 2 +- .../rmf/dependency/RMF/src/TraverseHelper.cpp | 2 +- .../dependency/RMF/src/backend/BackwardsIO.h | 96 ++++++------- modules/rmf/dependency/RMF/src/backend/IO.cpp | 8 +- .../dependency/RMF/src/backend/KeyFilter.h | 6 +- .../RMF/src/backend/avro/encode_decode.h | 4 +- .../RMF/src/backend/avro/encode_decode_util.h | 2 +- .../RMF/src/backend/avro/factory.cpp | 12 +- .../rmf/dependency/RMF/src/backend/avro/io.h | 136 +++++++++--------- .../src/backend/deprecated_avro/create.cpp | 18 +-- .../deprecated_hdf5/HDF5SharedData.cpp | 2 +- .../backend/deprecated_hdf5/HDF5SharedData.h | 8 +- .../src/backend/deprecated_hdf5/create.cpp | 6 +- .../RMF/src/decorator/alternatives.cpp | 10 +- modules/rmf/dependency/RMF/src/exceptions.cpp | 12 +- .../rmf/dependency/RMF/src/hdf5_wrapper.cpp | 20 +-- modules/rmf/dependency/RMF/src/info.cpp | 6 +- .../RMF/src/internal/clone_shared_data.h | 25 ++-- .../rmf/dependency/RMF/src/internal/paths.cpp | 2 +- .../RMF/src/internal/shared_data_equality.h | 8 +- .../RMF/src/internal/shared_data_maps.h | 2 +- .../rmf/dependency/RMF/src/show_hierarchy.cpp | 10 +- modules/rmf/dependency/RMF/src/signature.cpp | 10 +- modules/rmf/dependency/RMF/src/utility.cpp | 4 +- modules/rmf/dependency/RMF/src/validate.cpp | 2 +- .../rmf/dependency/RMF/test/test_ranges.cpp | 2 +- 47 files changed, 313 insertions(+), 350 deletions(-) diff --git a/modules/rmf/dependency/RMF/ChangeLog.md b/modules/rmf/dependency/RMF/ChangeLog.md index 5c23cc5472..7f6ca62bd7 100644 --- a/modules/rmf/dependency/RMF/ChangeLog.md +++ b/modules/rmf/dependency/RMF/ChangeLog.md @@ -1,6 +1,13 @@ Change Log {#changelog} ========== +# HEAD +- RMF now requires a C++11 compiler and SWIG 3 (or later) to build. Most + recent compilers should support C++11, such as gcc, clang + or MS Visual Studio 2015 or later. Various macro and header workarounds + for pre-C++11 environments are thus no longer needed and are deprecated: + `RMF_FINAL`, `RMF_OVERRIDE`, `RMF_CANEXCEPT`, `RMF_FOREACH`. + # 1.3.1 - 2021-12-01 # {#changelog_1_3_1} - Various build fixes for newer versions of gcc and clang. - Build fixes for Fedora 33 or later. diff --git a/modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp b/modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp index afe2b7af5b..709acc51b6 100644 --- a/modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp +++ b/modules/rmf/dependency/RMF/benchmark/benchmark_rmf.cpp @@ -110,7 +110,7 @@ std::pair create_frame(RMF::FileHandle fh, int frame) { RMF::Vector3 ret(0, 0, 0); std::size_t total_size = 0; - RMF_FOREACH(RMF::NodeID n, atoms) { + for(RMF::NodeID n : atoms) { RMF::Vector3 v((n.get_index() + 0 + frame) / 17.0, (n.get_index() + 1 + frame) / 19.0, (n.get_index() + 2 + frame) / 23.0); @@ -125,7 +125,7 @@ std::pair create_frame(RMF::FileHandle fh, boost::tuple create(RMF::FileHandle file, RMF::NodeIDs& atoms) { std::size_t hierarchy_size = create_hierarchy(file); - RMF_FOREACH(RMF::NodeID n, file.get_node_ids()) { + for(RMF::NodeID n : file.get_node_ids()) { if (file.get_node(n).get_children().empty()) { atoms.push_back(n); } @@ -166,9 +166,9 @@ double traverse(RMF::FileConstHandle file) { double load(RMF::FileConstHandle file, const RMF::NodeIDs& nodes) { RMF::decorator::IntermediateParticleFactory ipcf(file); RMF::Vector3 v(0, 0, 0); - RMF_FOREACH(RMF::FrameID fr, file.get_frames()) { + for(RMF::FrameID fr : file.get_frames()) { file.set_current_frame(fr); - RMF_FOREACH(RMF::NodeID n, nodes) { + for(RMF::NodeID n : nodes) { RMF::Vector3 cur = ipcf.get(file.get_node(n)).get_coordinates(); v[0] += cur[0]; v[1] += cur[1]; @@ -208,7 +208,7 @@ void benchmark_traverse(RMF::FileConstHandle file, std::string type) { void benchmark_load(RMF::FileConstHandle file, std::string type) { RMF::NodeIDs nodes; RMF::decorator::ParticleFactory ipcf(file); - RMF_FOREACH(RMF::NodeID n, file.get_node_ids()) { + for(RMF::NodeID n : file.get_node_ids()) { if (ipcf.get_is(file.get_node(n))) nodes.push_back(n); } boost::timer timer; diff --git a/modules/rmf/dependency/RMF/bin/rmf_cat.cpp b/modules/rmf/dependency/RMF/bin/rmf_cat.cpp index cc89df7675..c0d11e1555 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_cat.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_cat.cpp @@ -44,7 +44,7 @@ int main(int argc, char** argv) { RMF::clone_static_frame(rh, orh); } orh.set_description(orh.get_description() + "\n" + rh.get_description()); - RMF_FOREACH(RMF::FrameID ni, rh.get_frames()) { + for(RMF::FrameID ni : rh.get_frames()) { rh.set_current_frame(ni); orh.add_frame(rh.get_name(ni), rh.get_type(ni)); RMF::clone_loaded_frame(rh, orh); diff --git a/modules/rmf/dependency/RMF/bin/rmf_slice.cpp b/modules/rmf/dependency/RMF/bin/rmf_slice.cpp index 893a6f906f..072b8afd5f 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_slice.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_slice.cpp @@ -36,7 +36,7 @@ int main(int argc, char** argv) { RMF::clone_static_frame(rh, orh); if(!quiet) std::cout << "Copying frames"; unsigned num_copied = 0; - RMF_FOREACH(RMF::FrameID f, rh.get_frames()) { + for(RMF::FrameID f : rh.get_frames()) { if (f.get_index() < static_cast(start_frame)) continue; if ((f.get_index() - start_frame) % step_frame != 0) continue; rh.set_current_frame(f); diff --git a/modules/rmf/dependency/RMF/bin/rmf_transform.cpp b/modules/rmf/dependency/RMF/bin/rmf_transform.cpp index c2b6654cdc..25cee949b7 100644 --- a/modules/rmf/dependency/RMF/bin/rmf_transform.cpp +++ b/modules/rmf/dependency/RMF/bin/rmf_transform.cpp @@ -116,7 +116,7 @@ int main(int argc, char** argv) { RMF::decorator::BallFactory bf(rh); RMF::decorator::CylinderFactory cf(rh); RMF::decorator::SegmentFactory sf(rh); - RMF_FOREACH(RMF::FrameID frame, rhi.get_frames()) { + for(RMF::FrameID frame : rhi.get_frames()) { RMF::clone_loaded_frame(rhi, rh); RMF_INFO("Processing frame " << frame); rh.set_current_frame(frame); diff --git a/modules/rmf/dependency/RMF/cmake_modules/IMPFindC++11.cmake b/modules/rmf/dependency/RMF/cmake_modules/IMPFindC++11.cmake index 509bec1a71..f5ce215ee6 100644 --- a/modules/rmf/dependency/RMF/cmake_modules/IMPFindC++11.cmake +++ b/modules/rmf/dependency/RMF/cmake_modules/IMPFindC++11.cmake @@ -1,59 +1,55 @@ -if(NOT DEFINED IMP_CXX11) - set(IMP_CXX11 1 CACHE BOOL "Whether to use C++11 if possible") -endif() - # Put flags in a cmake variable so we can set them before running compiler # checks (elsewhere in the build) set(IMP_CXX11_FLAGS "" CACHE INTERNAL "Flags to enable C++11 support" FORCE) -if(IMP_CXX11) - if (APPLE) - execute_process(COMMAND uname -v OUTPUT_VARIABLE DARWIN_VERSION) - string(REGEX MATCH "[0-9]+" DARWIN_VERSION ${DARWIN_VERSION}) - endif() +if (APPLE) + execute_process(COMMAND uname -v OUTPUT_VARIABLE DARWIN_VERSION) + string(REGEX MATCH "[0-9]+" DARWIN_VERSION ${DARWIN_VERSION}) +endif() - if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU") - execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE - GCC_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE) - message(STATUS "GCC version: ${GCC_VERSION}") - if (GCC_VERSION VERSION_GREATER 6.1 OR GCC_VERSION VERSION_EQUAL 6.1) - # gcc 6.1 and up use C++14 by default, so no explicit switch required - # (in fact adding --std=c++11 will break compilation of packages that - # require C++14 features, like CGAL 5). - message(STATUS "Using g++ C++11 (or later) support") - elseif (GCC_VERSION VERSION_GREATER 4.7 OR GCC_VERSION VERSION_EQUAL 4.7) - message(STATUS "Enabling g++ C++11 support") - set(IMP_CXX11_FLAGS "--std=c++11" CACHE INTERNAL "" FORCE) - elseif (GCC_VERSION VERSION_GREATER 4.3 OR GCC_VERSION VERSION_EQUAL 4.3) - message(STATUS "Enabling g++ C++0x support") - set(IMP_CXX11_FLAGS "--std=c++0x" CACHE INTERNAL "" FORCE) - endif() - elseif("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang") - execute_process(COMMAND ${CMAKE_CXX_COMPILER} --version - OUTPUT_VARIABLE CLANG_VERSION) - if(CLANG_VERSION MATCHES "clang version ([0-9.]+)") - set(CLANG_VERSION ${CMAKE_MATCH_1}) - endif() - message(STATUS "clang version: ${CLANG_VERSION}") - # Modern clang (6 or later) uses C++14 by default; don't force older C++11 - if(CLANG_VERSION VERSION_GREATER 6.0) - message(STATUS "Enabling clang C++17 support") - set(IMP_CXX11_FLAGS "--std=c++17" CACHE INTERNAL "" FORCE) - # c++11's std::move (which boost/CGAL use) doesn't work until - # OS X 10.9 (Darwin version 13) - elseif(APPLE AND DARWIN_VERSION LESS 13) - message(STATUS "Disabling C++11 for mac os < 10.9") - elseif(BOOST_VERSION LESS 105000) - message(STATUS "Disabling C++11 due to clang and older boost") - else() - message(STATUS "Enabling clang C++11 support") - set(IMP_CXX11_FLAGS "--std=c++11" CACHE INTERNAL "" FORCE) - endif() - elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC") - message(STATUS "Using MSVC C++11 support") +if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE + GCC_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE) + message(STATUS "GCC version: ${GCC_VERSION}") + if (GCC_VERSION VERSION_GREATER 6.1 OR GCC_VERSION VERSION_EQUAL 6.1) + # gcc 6.1 and up use C++14 by default, so no explicit switch required + # (in fact adding --std=c++11 will break compilation of packages that + # require C++14 features, like CGAL 5). + message(STATUS "Using g++ C++11 (or later) support") + elseif (GCC_VERSION VERSION_GREATER 4.7 OR GCC_VERSION VERSION_EQUAL 4.7) + message(STATUS "Enabling g++ C++11 support") + set(IMP_CXX11_FLAGS "--std=c++11" CACHE INTERNAL "" FORCE) + elseif (GCC_VERSION VERSION_GREATER 4.3 OR GCC_VERSION VERSION_EQUAL 4.3) + message(STATUS "Enabling g++ C++0x support") + set(IMP_CXX11_FLAGS "--std=c++0x" CACHE INTERNAL "" FORCE) + else() + message(FATAL_ERROR "IMP requires a C++11 compiler, but this GCC appears to be too old to support C++11") + endif() +elseif("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang") + execute_process(COMMAND ${CMAKE_CXX_COMPILER} --version + OUTPUT_VARIABLE CLANG_VERSION) + if(CLANG_VERSION MATCHES "clang version ([0-9.]+)") + set(CLANG_VERSION ${CMAKE_MATCH_1}) + endif() + message(STATUS "clang version: ${CLANG_VERSION}") + # Modern clang (6 or later) uses C++14 by default; don't force older C++11 + if(CLANG_VERSION VERSION_GREATER 6.0) + message(STATUS "Enabling clang C++17 support") + set(IMP_CXX11_FLAGS "--std=c++17" CACHE INTERNAL "" FORCE) + # c++11's std::move (which boost/CGAL use) doesn't work until + # OS X 10.9 (Darwin version 13) + elseif(APPLE AND DARWIN_VERSION LESS 13) + message(FATAL_ERROR "IMP requires a C++11 compiler, but this version of OS X is too old to properly support C++11") + elseif(BOOST_VERSION LESS 105000) + message(FATAL_ERROR "IMP requires a C++11 compiler, but this version of Boost is too old to properly support C++11") else() - message(STATUS "Unknown compiler, not sure what to do about C++11") + message(STATUS "Enabling clang C++11 support") + set(IMP_CXX11_FLAGS "--std=c++11" CACHE INTERNAL "" FORCE) endif() +elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC") + message(STATUS "Using MSVC C++11 support") +else() + message(STATUS "Unknown compiler, not sure what to do about C++11") endif() if(IMP_CXX11_FLAGS) diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h index 273f08bcad..9f718b0dbb 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/ConstDataSetD.h @@ -72,7 +72,7 @@ class ConstDataSetD : public ConstDataSetAttributes { } void initialize() { hsize_t one = 1; - data_->ids_.open(H5Screate_simple(1, &one, NULL), &H5Sclose); + data_->ids_.open(H5Screate_simple(1, &one, nullptr), &H5Sclose); std::fill(data_->ones_, data_->ones_ + D, 1); // pos_.reset(new hsize_t[dim_]); // sel_= new SharedHandle(H5Dget_space(h_->get_hid()), &H5Sclose); @@ -139,19 +139,19 @@ class ConstDataSetD : public ConstDataSetAttributes { // must be second hsize_t ret[D]; std::fill(ret, ret + D, -1); - RMF_HDF5_CALL(H5Sget_simple_extent_dims(get_data_space(), ret, NULL)); + RMF_HDF5_CALL(H5Sget_simple_extent_dims(get_data_space(), ret, nullptr)); RMF_INTERNAL_CHECK(ret[D - 1] < 1000000, "extents not returned properly"); if (ret[D - 1] > 0) { // some versions will spew an error on this // we will call this function again before rds_ is needed // std::cout << "initializing row to " << ret[data_->dim_-1] << std::endl; - data_->rds_.open(H5Screate_simple(1, ret + D - 1, NULL), &H5Sclose); + data_->rds_.open(H5Screate_simple(1, ret + D - 1, nullptr), &H5Sclose); } else { // std::cout << "clearing row data" << std::endl; data_->rds_.close(); } RMF_HDF5_CALL(H5Sget_simple_extent_dims(get_data_space(), - data_->size_.begin(), NULL)); + data_->size_.begin(), nullptr)); } public: @@ -182,7 +182,7 @@ class ConstDataSetD : public ConstDataSetAttributes { // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose); RMF_HDF5_CALL(H5Sselect_hyperslab(get_data_space(), H5S_SELECT_SET, ijk.get(), data_->ones_, data_->ones_, - NULL)); + nullptr)); return TypeTraits::read_value_dataset( Object::get_handle(), data_->ids_.get_hid(), get_data_space()); } @@ -199,7 +199,8 @@ class ConstDataSetD : public ConstDataSetAttributes { size[D - 1] = get_size()[D - 1]; // set last to size of row // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose); RMF_HDF5_CALL(H5Sselect_hyperslab(get_data_space(), H5S_SELECT_SET, - ijk.get(), data_->ones_, &size[0], NULL)); + ijk.get(), data_->ones_, &size[0], + nullptr)); return TypeTraits::read_values_dataset(Object::get_handle(), get_row_data_space().get_hid(), get_data_space(), size[D - 1]); @@ -216,8 +217,8 @@ class ConstDataSetD : public ConstDataSetAttributes { // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose); RMF_HDF5_CALL(H5Sselect_hyperslab(get_data_space(), H5S_SELECT_SET, lb.get(), data_->ones_, size.get(), - NULL)); - RMF_HDF5_HANDLE(input, H5Screate_simple(1, &total, NULL), &H5Sclose); + nullptr)); + RMF_HDF5_HANDLE(input, H5Screate_simple(1, &total, nullptr), &H5Sclose); typename TypeTraits::Types ret = TypeTraits::read_values_dataset( Object::get_handle(), input, get_data_space(), total); RMF_INTERNAL_CHECK(ret.size() == total, "Size mismatch"); diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h index c6eac2435f..6315a2a0c5 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/DataSetD.h @@ -58,7 +58,7 @@ class DataSetD : public MutableAttributes > { // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose); RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET, ijk.get(), P::get_ones(), P::get_ones(), - NULL)); + nullptr)); TypeTraits::write_value_dataset(Object::get_handle(), P::get_input_data_space().get_hid(), P::get_data_space(), value); @@ -77,7 +77,7 @@ class DataSetD : public MutableAttributes > { // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose); RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET, ijk.get(), P::get_ones(), &size[0], - NULL)); + nullptr)); TypeTraits::write_values_dataset(Object::get_handle(), P::get_row_data_space().get_hid(), P::get_data_space(), value); @@ -104,9 +104,9 @@ class DataSetD : public MutableAttributes > { // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose); RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET, lb.get(), P::get_ones(), size.get(), - NULL)); + nullptr)); hsize_t sz = value.size(); - RMF_HDF5_HANDLE(input, H5Screate_simple(1, &sz, NULL), &H5Sclose); + RMF_HDF5_HANDLE(input, H5Screate_simple(1, &sz, nullptr), &H5Sclose); TypeTraits::write_values_dataset(Object::get_handle(), input, P::get_data_space(), value); } diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h index 75b11e8256..6b99342e0a 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/handle.h @@ -49,7 +49,7 @@ class RMFEXPORT Handle : public boost::noncopyable { IOException); } } - Handle() : h_(-1), f_(NULL) {} + Handle() : h_(-1), f_(nullptr) {} hid_t get_hid() const { RMF_USAGE_CHECK(h_ >= 0, "Uninitialized handle used."); return h_; diff --git a/modules/rmf/dependency/RMF/include/RMF/HDF5/types.h b/modules/rmf/dependency/RMF/include/RMF/HDF5/types.h index f22e102a8e..e5eda41472 100644 --- a/modules/rmf/dependency/RMF/include/RMF/HDF5/types.h +++ b/modules/rmf/dependency/RMF/include/RMF/HDF5/types.h @@ -205,7 +205,7 @@ struct SimplePluralTraits { if (data.len > 0) { data.p = const_cast(&v[0]); } else { - data.p = NULL; + data.p = nullptr; } RMF_HDF5_CALL( H5Dwrite(d, get_hdf5_memory_type(), iss, s, H5P_DEFAULT, &data)); diff --git a/modules/rmf/dependency/RMF/include/RMF/Nullable.h b/modules/rmf/dependency/RMF/include/RMF/Nullable.h index dd36c7434f..af5aa9adfa 100644 --- a/modules/rmf/dependency/RMF/include/RMF/Nullable.h +++ b/modules/rmf/dependency/RMF/include/RMF/Nullable.h @@ -58,7 +58,7 @@ class Nullable { /** For python since it nicely becomes None. */ const T* get_ptr() const { if (get_is_null()) - return NULL; + return nullptr; else return &v_; } diff --git a/modules/rmf/dependency/RMF/include/RMF/compiler_macros.h b/modules/rmf/dependency/RMF/include/RMF/compiler_macros.h index ec16614de8..ecbcd589be 100644 --- a/modules/rmf/dependency/RMF/include/RMF/compiler_macros.h +++ b/modules/rmf/dependency/RMF/include/RMF/compiler_macros.h @@ -21,35 +21,11 @@ #endif #endif -#ifdef __clang__ -#define RMF_COMPILER_HAS_OVERRIDE 1 -#elif defined(__GNUC__) && __cplusplus >= 201103L -// probably should be finer here -#define RMF_COMPILER_HAS_OVERRIDE 1 -#else -#define RMF_COMPILER_HAS_OVERRIDE 0 -#endif - -#if RMF_COMPILER_HAS_OVERRIDE +// Deprecated; just use 'override' keyword instead #define RMF_OVERRIDE override -#else -#define RMF_OVERRIDE -#endif -#ifdef __clang__ -#define RMF_COMPILER_HAS_FINAL 1 -#elif defined(__GNUC__) && __cplusplus >= 201103L -// probably should be finer here -#define RMF_COMPILER_HAS_FINAL 1 -#else -#define RMF_COMPILER_HAS_FINAL 0 -#endif - -#if RMF_COMPILER_HAS_FINAL +// Deprecated; just use 'final' keyword instead #define RMF_FINAL final -#else -#define RMF_FINAL -#endif #if defined(__GNUC__) && __cplusplus >= 201103L #define RMF_HAS_NOEXCEPT 1 @@ -159,7 +135,7 @@ #define RMF_GCC_PROTOTYPES #endif -// Warn about missing RMF_OVERRIDE on virtual methods if gcc is new enough +// Warn about missing override on virtual methods if gcc is new enough #if __GNUC__ > 5 || (__GNUC__ == 5 && __GNUC_MINOR__ >= 1) #ifdef RMF_SWIG_WRAPPER #define RMF_GCC_OVERRIDE diff --git a/modules/rmf/dependency/RMF/include/RMF/decorator/representation.h b/modules/rmf/dependency/RMF/include/RMF/decorator/representation.h index 58db831460..303c9e3b5e 100644 --- a/modules/rmf/dependency/RMF/include/RMF/decorator/representation.h +++ b/modules/rmf/dependency/RMF/include/RMF/decorator/representation.h @@ -33,7 +33,7 @@ class RepresentationConst : public Decorator { template std::vector get_it(const Ints &in) const { std::vector ret; - RMF_FOREACH(int i, in) { + for(int i : in) { ret.push_back(get_node().get_file().get_node(NodeID(i))); } return ret; @@ -77,13 +77,13 @@ class Representation : public RepresentationConst { Ints set_it(const std::vector &in) const { Ints ret; ret.reserve(in.size()); - RMF_FOREACH(T n, in) { ret.push_back(n.get_id().get_index()); } + for(T n : in) { ret.push_back(n.get_id().get_index()); } return ret; } Ints set_it(const NodeIDs &in) { Ints ret; ret.reserve(in.size()); - RMF_FOREACH(NodeID n, in) { ret.push_back(n.get_index()); } + for(NodeID n : in) { ret.push_back(n.get_index()); } return ret; } diff --git a/modules/rmf/dependency/RMF/include/RMF/exceptions.h b/modules/rmf/dependency/RMF/include/RMF/exceptions.h index 16aef81af6..85b3c989eb 100644 --- a/modules/rmf/dependency/RMF/include/RMF/exceptions.h +++ b/modules/rmf/dependency/RMF/include/RMF/exceptions.h @@ -31,7 +31,7 @@ class RMFEXPORT Exception : public virtual std::exception, public: RMF_CXX11_DEFAULT_COPY_CONSTRUCTOR(Exception); Exception(); - const char* what() const RMF_NOEXCEPT RMF_OVERRIDE; + const char* what() const RMF_NOEXCEPT override; virtual ~Exception() RMF_NOEXCEPT; }; diff --git a/modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h b/modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h index 03402303db..a1e02a519c 100644 --- a/modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h +++ b/modules/rmf/dependency/RMF/include/RMF/infrastructure_macros.h @@ -17,12 +17,9 @@ #include #include #include -#if defined(BOOST_NO_CXX11_RANGE_BASED_FOR) || BOOST_VERSION < 105300 -#define RMF_FOREACH(v, r) BOOST_FOREACH(v, r) -#include // IWYU pragma: export -#else + +// Deprecated: just use range-based for directly #define RMF_FOREACH(v, r) for (v : r) -#endif RMF_ENABLE_WARNINGS diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataCategory.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataCategory.h index 492c12d57e..3acff368c3 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataCategory.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataCategory.h @@ -42,7 +42,7 @@ class SharedDataCategory { SharedDataCategory() {} Categories get_categories() const { Categories ret; - RMF_FOREACH(const CategoryData::From::value_type & it, data_.from_name) { + for(const auto &it : data_.from_name) { ret.push_back(it.second); } return ret; diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData.h index 989e044606..30889c7dd7 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataData.h @@ -28,15 +28,9 @@ struct KeyData : public RMF_LARGE_UNORDERED_MAP { KeyData() {} }; -// boost flat_map::operator[] segfaults on Fedora 32+; use std::map instead template -#if __GNUC__ >= 10 -struct TypeData : std::map, KeyData > { - typedef std::map, KeyData > P; -#else struct TypeData : RMF_SMALL_UNORDERED_MAP, KeyData > { typedef RMF_SMALL_UNORDERED_MAP, KeyData > P; -#endif // Mac OS 10.8 and earlier clang needs this for some reason TypeData() {} TypeData(const TypeData& o) : P(o) {} diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h index 05d776b5ba..2712f44cb2 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/SharedDataKeys.h @@ -82,16 +82,14 @@ class SharedDataKeys { } std::vector > ret; ret.reserve(data_.category_keys.find(cat)->second.size()); - RMF_FOREACH(typename Keys::KeyInfo::value_type it, - data_.category_keys.find(cat)->second) { + for(auto it : data_.category_keys.find(cat)->second) { ret.push_back(it.second); } return ret; } std::vector > get_keys(Traits) const { std::vector > ret; - typedef std::pair, Category> KP; - RMF_FOREACH(KP kp, data_.key_categories) { ret.push_back(kp.first); } + for(const auto &kp : data_.key_categories) { ret.push_back(kp.first); } return ret; } diff --git a/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h b/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h index 85dc2f6a71..68b4ad37f3 100644 --- a/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h +++ b/modules/rmf/dependency/RMF/include/RMF/internal/swig_helpers.h @@ -42,7 +42,7 @@ struct PyPointer : boost::noncopyable { PyObject* release() { RMF_INTERNAL_CHECK(ptr_->ob_refcnt >= 1, "No refcount"); PyObject* ret = ptr_; - ptr_ = NULL; + ptr_ = nullptr; return ret; } ~PyPointer() { diff --git a/modules/rmf/dependency/RMF/plugins/vmd/Data.cpp b/modules/rmf/dependency/RMF/plugins/vmd/Data.cpp index 56d6269a0e..313002d23e 100644 --- a/modules/rmf/dependency/RMF/plugins/vmd/Data.cpp +++ b/modules/rmf/dependency/RMF/plugins/vmd/Data.cpp @@ -91,7 +91,7 @@ double Data::get_resolution() { int Data::get_show_restraints() { bool has_restraints = false; - RMF_FOREACH(RMF::NodeID n, file_.get_node_ids()) { + for(RMF::NodeID n : file_.get_node_ids()) { if (rcf_.get_is(file_.get_node(n))) { has_restraints = true; break; @@ -157,7 +157,7 @@ Data::handle_alternative(RMF::NodeConstHandle cur, int body, } else { RMF::NodeConstHandles alts = altf_.get(cur).get_alternatives(RMF::PARTICLE); int alt = 1; - RMF_FOREACH(RMF::NodeConstHandle c, + for(RMF::NodeConstHandle c : boost::make_iterator_range(alts.begin() + 1, alts.end())) { altid[0] = 'A' + alt; boost::array cur = fill_bodies(c, body, chain, resid, resname, @@ -202,7 +202,7 @@ boost::array Data::fill_bodies(RMF::NodeConstHandle cur, int body, my_copy_n(rf_.get(cur).get_residue_type(), 8, resname.begin()); } - RMF_FOREACH(RMF::NodeConstHandle c, cur.get_children()) { + for(RMF::NodeConstHandle c : cur.get_children()) { boost::array count = fill_bodies(c, body, chain, resid, resname, altid, segment, resolution); for (unsigned int i = 0; i < 2; ++i) { @@ -225,11 +225,11 @@ boost::array Data::fill_bodies(RMF::NodeConstHandle cur, int body, void Data::fill_index() { int cur_index = -1; - RMF_FOREACH(const Body & body, bodies_) { - RMF_FOREACH(const AtomInfo & n, body.particles) { + for(const Body & body : bodies_) { + for(const AtomInfo & n : body.particles) { index_[n.node_id] = ++cur_index; } - RMF_FOREACH(const AtomInfo & n, body.balls) { + for(const AtomInfo & n : body.balls) { index_[n.node_id] = ++cur_index; } } @@ -251,7 +251,7 @@ void Data::fill_graphics(RMF::NodeConstHandle cur, size = cf_.get(cur).get_radius(); } RMF::Vector3 last_coords = tr.get_global_coordinates(coords[0]); - RMF_FOREACH(const RMF::Vector3 & cc, + for(const RMF::Vector3 & cc : boost::make_iterator_range(coords.begin() + 1, coords.end())) { molfile_graphics_t g; g.type = type; @@ -263,7 +263,7 @@ void Data::fill_graphics(RMF::NodeConstHandle cur, graphics_.push_back(g); } } - RMF_FOREACH(RMF::NodeConstHandle c, cur.get_children()) { + for(RMF::NodeConstHandle c : cur.get_children()) { fill_graphics(c, tr); } } @@ -282,7 +282,7 @@ void Data::handle_bond(RMF::NodeConstHandle cur) { void Data::handle_restraint(RMF::NodeConstHandle cur) { bool child_feature = false; - RMF_FOREACH(RMF::NodeConstHandle c, cur.get_children()) { + for(RMF::NodeConstHandle c : cur.get_children()) { if (c.get_type() == RMF::FEATURE) { child_feature = true; break; @@ -312,7 +312,7 @@ void Data::fill_bonds(RMF::NodeConstHandle cur) { if (show_restraints_ & RESTRAINTS && cur.get_type() == RMF::FEATURE) { handle_restraint(cur); } - RMF_FOREACH(RMF::NodeConstHandle c, cur.get_children()) { fill_bonds(c); } + for(RMF::NodeConstHandle c : cur.get_children()) { fill_bonds(c); } } void Data::copy_basics(const AtomInfo &n, molfile_atom_t *out) { @@ -327,7 +327,7 @@ void Data::copy_basics(const AtomInfo &n, molfile_atom_t *out) { molfile_atom_t *Data::copy_particles(const std::vector &atoms, molfile_atom_t *out) { - RMF_FOREACH(const AtomInfo & n, atoms) { + for(const AtomInfo & n : atoms) { copy_basics(n, out); RMF::NodeConstHandle cur = file_.get_node(n.node_id); @@ -353,7 +353,7 @@ molfile_atom_t *Data::copy_particles(const std::vector &atoms, molfile_atom_t *Data::copy_balls(const std::vector &balls, molfile_atom_t *out) { - RMF_FOREACH(AtomInfo n, balls) { + for(AtomInfo n : balls) { copy_basics(n, out); RMF::NodeConstHandle cur = file_.get_node(n.node_id); diff --git a/modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp b/modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp index 64e91a5278..471c952c42 100644 --- a/modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp +++ b/modules/rmf/dependency/RMF/plugins/vmd/Data_read.cpp @@ -14,7 +14,7 @@ namespace RMF_vmd { int Data::read_structure(int *optflags, molfile_atom_t *out) { RMF_INFO("Reading structure"); - RMF_FOREACH(const Body & body, bodies_) { + for(const Body & body : bodies_) { out = copy_particles(body.particles, out); out = copy_balls(body.balls, out); } @@ -29,21 +29,21 @@ int Data::read_timestep(molfile_timestep_t *frame) { frame->physical_time = curf.get_index(); float *coords = frame->coords; file_.set_current_frame(RMF::FrameID(curf.get_index())); - RMF_FOREACH(const Body & body, bodies_) { + for(const Body & body : bodies_) { RMF::CoordinateTransformer tr; double offset = (bounds_[1][0] - bounds_[0][0] + max_radius_ * 3) * body.state; - RMF_FOREACH(RMF::decorator::ReferenceFrameConst rf, body.frames) { + for(RMF::decorator::ReferenceFrameConst rf : body.frames) { tr = RMF::CoordinateTransformer(tr, rf); } - RMF_FOREACH(const AtomInfo & n, body.particles) { + for(const AtomInfo & n : body.particles) { RMF::Vector3 cc = pf_.get(file_.get_node(n.node_id)).get_coordinates(); cc = tr.get_global_coordinates(cc); cc[0] += offset; std::copy(cc.begin(), cc.end(), coords); coords += 3; } - RMF_FOREACH(const AtomInfo & n, body.balls) { + for(const AtomInfo & n : body.balls) { RMF::Vector3 cc = bf_.get(file_.get_node(n.node_id)).get_coordinates(); cc = tr.get_global_coordinates(cc); cc[0] += offset; @@ -93,8 +93,7 @@ int Data::read_bonds(int *nbonds, int **fromptr, int **toptr, bond_type_names_.push_back(restraint_bond_type_name_.get()); *bondtypename = &bond_type_names_[0]; - RMF_FOREACH(int bt, - boost::make_iterator_range(*bondtype, *bondtype + *nbonds)) { + for(int bt : boost::make_iterator_range(*bondtype, *bondtype + *nbonds)) { RMF_UNUSED(bt); RMF_INTERNAL_CHECK(bt >= 0 && bt < *nbondtypes, "Invalid bond type "); } @@ -105,7 +104,7 @@ int Data::read_timestep_metadata(molfile_timestep_metadata_t *data) { RMF_INFO("Reading timestep data"); data->count = file_.get_number_of_frames(); int na = 0; - RMF_FOREACH(const Body & bd, bodies_) { + for(const Body & bd : bodies_) { na += bd.particles.size() + bd.balls.size(); } data->avg_bytes_per_timestep = sizeof(float) * 3 * na; diff --git a/modules/rmf/dependency/RMF/src/FileConstHandle.cpp b/modules/rmf/dependency/RMF/src/FileConstHandle.cpp index 8e50148c36..824d256eb0 100644 --- a/modules/rmf/dependency/RMF/src/FileConstHandle.cpp +++ b/modules/rmf/dependency/RMF/src/FileConstHandle.cpp @@ -67,7 +67,7 @@ FileConstHandle open_rmf_buffer_read_only(BufferConstHandle buffer) { FrameIDs FileConstHandle::get_root_frames() const { FrameIDs ret; - RMF_FOREACH(FrameID fr, get_frames()) { + for(FrameID fr : get_frames()) { if (get_parents(fr).empty()) ret.push_back(fr); } return ret; diff --git a/modules/rmf/dependency/RMF/src/TraverseHelper.cpp b/modules/rmf/dependency/RMF/src/TraverseHelper.cpp index 54c3cab2fe..c414d03e38 100644 --- a/modules/rmf/dependency/RMF/src/TraverseHelper.cpp +++ b/modules/rmf/dependency/RMF/src/TraverseHelper.cpp @@ -95,7 +95,7 @@ unsigned int TraverseHelper::get_index(NodeID n) const { std::vector TraverseHelper::get_children() const { std::vector ret; // handle alternatives later - RMF_FOREACH(NodeConstHandle ch, NodeConstHandle::get_children()) { + for(NodeConstHandle ch : NodeConstHandle::get_children()) { if (data_->state_filter_ != -1 && data_->state_factory_.get_is(ch) && data_->state_factory_.get(ch).get_state_index() != data_->state_filter_) continue; diff --git a/modules/rmf/dependency/RMF/src/backend/BackwardsIO.h b/modules/rmf/dependency/RMF/src/backend/BackwardsIO.h index 43acb4c9ab..c6f326b69d 100644 --- a/modules/rmf/dependency/RMF/src/backend/BackwardsIO.h +++ b/modules/rmf/dependency/RMF/src/backend/BackwardsIO.h @@ -63,7 +63,7 @@ RMF_ENABLE_WARNINGS namespace RMF { template ID get_key_const(Category cat, std::string name, Traits, SDC *sd) const { - RMF_FOREACH(ID k, sd->get_keys(cat, Traits())) { + for(ID k : sd->get_keys(cat, Traits())) { if (sd->get_name(k) == name) return k; } return ID(); @@ -71,9 +71,8 @@ RMF_ENABLE_WARNINGS namespace RMF { template void filter_vector(Filter &filter, Category cat) const { - RMF_FOREACH(std::string key_name, - get_vector_names(cat, RMF_VECTOR())) { - RMF_FOREACH(std::string subkey_name, + for(std::string key_name : get_vector_names(cat, RMF_VECTOR())) { + for(std::string subkey_name : get_vector_subkey_names(key_name, RMF_VECTOR())) { filter.add_float_key(cat, subkey_name); RMF_TRACE("Filtering " << subkey_name); @@ -83,9 +82,8 @@ RMF_ENABLE_WARNINGS namespace RMF { template void filter_vectors(Filter &filter, Category cat) const { - RMF_FOREACH(std::string key_name, - get_vectors_names(cat, RMF_VECTOR())) { - RMF_FOREACH(std::string subkey_name, + for(std::string key_name : get_vectors_names(cat, RMF_VECTOR())) { + for(std::string subkey_name : get_vectors_subkey_names(key_name, RMF_VECTOR())) { filter.add_floats_key(cat, subkey_name); RMF_TRACE("Filtering " << subkey_name); @@ -142,7 +140,7 @@ RMF_ENABLE_WARNINGS namespace RMF { ret = sd_->get_static_value(NodeID(0), key); } typedef std::pair > KP; - RMF_FOREACH(KP kp, get_vector_names_map(RMF_VECTOR())) { + for(KP kp : get_vector_names_map(RMF_VECTOR())) { ret.push_back(kp.first); } std::sort(ret.begin(), ret.end()); @@ -161,7 +159,7 @@ RMF_ENABLE_WARNINGS namespace RMF { ret = sd_->get_static_value(NodeID(0), key); } typedef std::pair > KP; - RMF_FOREACH(KP kp, get_vectors_names_map(RMF_VECTOR())) { + for(KP kp : get_vectors_names_map(RMF_VECTOR())) { ret.push_back(kp.first); } std::sort(ret.begin(), ret.end()); @@ -174,7 +172,7 @@ RMF_ENABLE_WARNINGS namespace RMF { typedef ID > > Key; typedef boost::tuple Data; RMF_LARGE_UNORDERED_MAP map; - RMF_FOREACH(std::string key_name, + for(std::string key_name : get_vector_names(category_b, RMF_VECTOR())) { boost::array subkey_names = get_vector_subkey_names(key_name, RMF_VECTOR()); @@ -187,9 +185,8 @@ RMF_ENABLE_WARNINGS namespace RMF { } } if (map.empty()) return; - typedef std::pair KP; - RMF_FOREACH(KP kp, map) { - RMF_FOREACH(NodeID n, internal::get_nodes(sdb)) { + for(const auto &kp : map) { + for(NodeID n : internal::get_nodes(sdb)) { double v = H::get(sdb, n, kp.first); if (!FloatTraits::get_is_null_value(v)) { RMF_VECTOR &old = H::access(sdb, n, kp.second.template get<0>()); @@ -208,7 +205,7 @@ RMF_ENABLE_WARNINGS namespace RMF { typedef boost::array, D> Data; RMF_LARGE_UNORDERED_MAP map; Strings key_names; - RMF_FOREACH(VectorKey k, keys) { + for(VectorKey k : keys) { std::string name = sda->get_name(k); key_names.push_back(name); boost::array subkey_names = @@ -225,9 +222,8 @@ RMF_ENABLE_WARNINGS namespace RMF { sdb->set_static_value(NodeID(0), k, key_names); } - typedef std::pair KP; - RMF_FOREACH(KP kp, map) { - RMF_FOREACH(NodeID n, internal::get_nodes(sda)) { + for(const auto &kp : map) { + for(NodeID n : internal::get_nodes(sda)) { RMF_VECTOR v = H::get(sda, n, kp.first); if (!Traits >::get_is_null_value(v)) { for (unsigned int i = 0; i < D; ++i) { @@ -243,7 +239,7 @@ RMF_ENABLE_WARNINGS namespace RMF { typedef Vector3sKey Key; typedef boost::tuple Data; RMF_LARGE_UNORDERED_MAP map; - RMF_FOREACH(std::string key_name, + for(std::string key_name : get_vectors_names(category_b, RMF_VECTOR<3>())) { boost::array subkey_names = get_vectors_subkey_names(key_name, RMF_VECTOR<3>()); @@ -256,9 +252,8 @@ RMF_ENABLE_WARNINGS namespace RMF { } } if (map.empty()) return; - typedef std::pair KP; - RMF_FOREACH(KP kp, map) { - RMF_FOREACH(NodeID n, internal::get_nodes(sdb)) { + for(const auto &kp : map) { + for(NodeID n : internal::get_nodes(sdb)) { Floats v = H::get(sdb, n, kp.first); if (!v.empty()) { std::vector > &old = @@ -281,7 +276,7 @@ RMF_ENABLE_WARNINGS namespace RMF { typedef boost::array, 3> Data; RMF_LARGE_UNORDERED_MAP map; Strings key_names; - RMF_FOREACH(VectorKey k, keys) { + for(VectorKey k : keys) { std::string name = sda->get_name(k); key_names.push_back(name); boost::array subkey_names = @@ -298,9 +293,8 @@ RMF_ENABLE_WARNINGS namespace RMF { sdb->set_static_value(NodeID(0), k, key_names); } - typedef std::pair KP; - RMF_FOREACH(KP kp, map) { - RMF_FOREACH(NodeID n, internal::get_nodes(sda)) { + for(const auto &kp : map) { + for(NodeID n : internal::get_nodes(sda)) { std::vector > v = H::get(sda, n, kp.first); if (!v.empty()) { for (unsigned int i = 0; i < 3; ++i) { @@ -318,7 +312,7 @@ RMF_ENABLE_WARNINGS namespace RMF { template ID get_alias_key(const SDA *a) { Category alias_cat; - RMF_FOREACH(Category cur_cat, a->get_categories()) { + for(Category cur_cat : a->get_categories()) { if (a->get_name(cur_cat) == "alias") { alias_cat = cur_cat; } @@ -326,7 +320,7 @@ RMF_ENABLE_WARNINGS namespace RMF { if (alias_cat == Category()) return ID(); ID alias_key; - RMF_FOREACH(ID nik_cur, + for(ID nik_cur : a->get_keys(alias_cat, backward_types::NodeIDTraits())) { if (a->get_name(nik_cur) == "aliased") { alias_key = nik_cur; @@ -347,13 +341,13 @@ RMF_ENABLE_WARNINGS namespace RMF { IntsKey rep_key = b->get_key(feature_category, "representation", IntsTraits()); - RMF_FOREACH(NodeID n, internal::get_nodes(b)) { + for(NodeID n : internal::get_nodes(b)) { if (b->get_type(n) == FEATURE) { RMF_TRACE("Processing restraint node " << b->get_name(n)); // make a copy as it can change NodeIDs chs = b->get_children(n); Ints val; - RMF_FOREACH(NodeID ch, chs) { + for(NodeID ch : chs) { if (b->get_type(ch) == ALIAS) { RMF_TRACE("Found alias child " << b->get_name(ch)); val.push_back(a->get_static_value(ch, alias_key).get_index()); @@ -376,7 +370,7 @@ RMF_ENABLE_WARNINGS namespace RMF { Category bond_cat = b->get_category("bond"); IntKey k0 = b->get_key(bond_cat, "bonded 0", IntTraits()); IntKey k1 = b->get_key(bond_cat, "bonded 1", IntTraits()); - RMF_FOREACH(NodeID n, internal::get_nodes(a)) { + for(NodeID n : internal::get_nodes(a)) { if (a->get_type(n) == BOND) { NodeIDs ch = a->get_children(n); if (ch.size() == 2 && a->get_type(ch[0]) == ALIAS && @@ -433,7 +427,7 @@ RMF_ENABLE_WARNINGS namespace RMF { if (cidk != backward_types::IndexKey()) { StringKey cidsk = shared_data->get_key(category, "chain id", StringTraits()); - RMF_FOREACH(NodeID ni, internal::get_nodes(shared_data)) { + for(NodeID ni : internal::get_nodes(shared_data)) { int ci = H::get(sd_.get(), ni, cidk); if (!backward_types::IndexTraits::get_is_null_value(ci)) { H::set(shared_data, ni, cidsk, std::string(1, ci = 'A')); @@ -449,7 +443,7 @@ RMF_ENABLE_WARNINGS namespace RMF { if (rtk != StringKey() && bk != IntKey() && ek != IntKey()) { IntKey rik = shared_data->get_key(category, "residue index", IntTraits()); - RMF_FOREACH(NodeID ni, internal::get_nodes(shared_data)) { + for(NodeID ni : internal::get_nodes(shared_data)) { std::string rt = H::get(shared_data, ni, rtk); if (!rt.empty()) { int b = H::get(shared_data, ni, bk); @@ -468,7 +462,7 @@ RMF_ENABLE_WARNINGS namespace RMF { FloatKey nbk = shared_data->get_key(category, "rgb color blue", FloatTraits()); if (bk != FloatKey()) { - RMF_FOREACH(NodeID ni, internal::get_nodes(shared_data)) { + for(NodeID ni : internal::get_nodes(shared_data)) { float v = H::get(shared_data, ni, bk); if (!FloatTraits::get_is_null_value(v)) { H::set(shared_data, ni, nbk, v); @@ -512,9 +506,8 @@ RMF_ENABLE_WARNINGS namespace RMF { virtual ~BackwardsIO() { flush(); } protected: - virtual void load_static_frame(internal::SharedData *shared_data) - RMF_OVERRIDE { - RMF_FOREACH(Category category, shared_data->get_categories()) { + virtual void load_static_frame(internal::SharedData *shared_data) override { + for(Category category : shared_data->get_categories()) { load_frame_category(category, shared_data, internal::StaticValues()); } @@ -522,36 +515,33 @@ RMF_ENABLE_WARNINGS namespace RMF { load_restraints(sd_.get(), shared_data); } - virtual void save_static_frame(internal::SharedData *shared_data) - RMF_OVERRIDE { - RMF_FOREACH(Category category, shared_data->get_categories()) { + virtual void save_static_frame(internal::SharedData *shared_data) override { + for(Category category : shared_data->get_categories()) { save_frame_category(category, shared_data, internal::StaticValues()); } } - virtual void load_file(internal::SharedData *shared_data) RMF_OVERRIDE { + virtual void load_file(internal::SharedData *shared_data) override { sd_->reload(); RMF_INFO("Loading file"); RMF::internal::clone_file(sd_.get(), shared_data); shared_data->set_file_type(sd_->get_file_type()); - RMF_FOREACH(FrameID id, internal::get_frames(sd_.get())) { + for(FrameID id : internal::get_frames(sd_.get())) { shared_data->add_frame_data(id, "", FRAME); } RMF_TRACE("Found " << sd_->get_number_of_frames() << " frames."); - RMF_FOREACH(Category c, sd_->get_categories()) { + for(Category c : sd_->get_categories()) { shared_data->get_category(sd_->get_name(c)); } } - virtual void save_file(const internal::SharedData *shared_data) - RMF_OVERRIDE { + virtual void save_file(const internal::SharedData *shared_data) override { RMF_INFO("Saving file"); RMF::internal::clone_file(shared_data, sd_.get()); flush(); } - virtual void save_loaded_frame(internal::SharedData *shared_data) - RMF_OVERRIDE { + virtual void save_loaded_frame(internal::SharedData *shared_data) override { RMF_INFO("Saving frame " << shared_data->get_loaded_frame()); FrameID cur = shared_data->get_loaded_frame(); RMF_USAGE_CHECK(cur.get_index() == sd_->get_number_of_frames(), @@ -565,34 +555,32 @@ RMF_ENABLE_WARNINGS namespace RMF { RMF_INTERNAL_CHECK(nfid == cur, "Number of frames don't match."); } sd_->set_loaded_frame(cur); - RMF_FOREACH(Category category, shared_data->get_categories()) { + for(Category category : shared_data->get_categories()) { save_frame_category(category, shared_data, internal::LoadedValues()); } } - virtual void load_loaded_frame(internal::SharedData *shared_data) - RMF_OVERRIDE { + virtual void load_loaded_frame(internal::SharedData *shared_data) override { RMF_INFO("Loading frame " << shared_data->get_loaded_frame()); FrameID cur = shared_data->get_loaded_frame(); sd_->set_loaded_frame(cur); - RMF_FOREACH(Category category, sd_->get_categories()) { + for(Category category : sd_->get_categories()) { load_frame_category(category, shared_data, internal::LoadedValues()); } } - virtual void load_hierarchy(internal::SharedData *shared_data) - RMF_OVERRIDE { + virtual void load_hierarchy(internal::SharedData *shared_data) override { RMF_INFO("Loading hierarchy"); RMF::internal::clone_hierarchy(sd_.get(), shared_data); } virtual void save_hierarchy(const internal::SharedData *shared_data) - RMF_OVERRIDE { + override { RMF_INFO("Saving hierarchy"); RMF::internal::clone_hierarchy(shared_data, sd_.get()); } - virtual void flush() RMF_OVERRIDE { sd_->flush(); } + virtual void flush() override { sd_->flush(); } }; } // namespace internal diff --git a/modules/rmf/dependency/RMF/src/backend/IO.cpp b/modules/rmf/dependency/RMF/src/backend/IO.cpp index 49e79a7d01..d69a57798c 100644 --- a/modules/rmf/dependency/RMF/src/backend/IO.cpp +++ b/modules/rmf/dependency/RMF/src/backend/IO.cpp @@ -55,7 +55,7 @@ boost::shared_ptr create_file(const std::string &name) { test_buffers[name] = BufferHandle(); return create_buffer(test_buffers.find(name)->second); } else { - RMF_FOREACH(boost::shared_ptr f, factories) { + for(boost::shared_ptr f : factories) { if (!boost::algorithm::ends_with(name, f->get_file_extension())) continue; boost::shared_ptr cur = f->create_file(name); if (cur) return cur; @@ -64,7 +64,7 @@ boost::shared_ptr create_file(const std::string &name) { return boost::shared_ptr(); } boost::shared_ptr create_buffer(BufferHandle buffer) { - RMF_FOREACH(boost::shared_ptr f, factories) { + for(boost::shared_ptr f : factories) { boost::shared_ptr cur = f->create_buffer(buffer); if (cur) return cur; } @@ -74,7 +74,7 @@ boost::shared_ptr read_file(const std::string &name) { if (boost::algorithm::ends_with(name, "_rmf_test_buffer")) { return read_buffer(test_buffers.find(name)->second); } else { - RMF_FOREACH(boost::shared_ptr f, factories) { + for(boost::shared_ptr f : factories) { // if (!boost::algorithm::ends_with(name, f->get_file_extension())) // continue; try { @@ -89,7 +89,7 @@ boost::shared_ptr read_file(const std::string &name) { return boost::shared_ptr(); } boost::shared_ptr read_buffer(BufferConstHandle buffer) { - RMF_FOREACH(boost::shared_ptr f, factories) { + for(boost::shared_ptr f : factories) { boost::shared_ptr cur = f->read_buffer(buffer); if (cur) return cur; } diff --git a/modules/rmf/dependency/RMF/src/backend/KeyFilter.h b/modules/rmf/dependency/RMF/src/backend/KeyFilter.h index 0359ac74dc..dc3c530530 100644 --- a/modules/rmf/dependency/RMF/src/backend/KeyFilter.h +++ b/modules/rmf/dependency/RMF/src/backend/KeyFilter.h @@ -31,7 +31,7 @@ class KeyFilter : public SharedDataAdaptor { public: KeyFilter(SD* sd) : P(sd) {} void add_index_key(Category cat, std::string name) { - RMF_FOREACH(backward_types::IndexKey k, + for(backward_types::IndexKey k : P::sync_->get_keys(cat, backward_types::IndexTraits())) { if (P::sync_->get_name(k) == name) { index_keys_.push_back(k); @@ -41,7 +41,7 @@ class KeyFilter : public SharedDataAdaptor { } } void add_float_key(Category cat, std::string name) { - RMF_FOREACH(FloatKey k, P::sync_->get_keys(cat, FloatTraits())) { + for(FloatKey k : P::sync_->get_keys(cat, FloatTraits())) { if (P::sync_->get_name(k) == name) { float_keys_.push_back(k); std::sort(float_keys_.begin(), float_keys_.end()); @@ -50,7 +50,7 @@ class KeyFilter : public SharedDataAdaptor { } } void add_floats_key(Category cat, std::string name) { - RMF_FOREACH(FloatsKey k, P::sync_->get_keys(cat, FloatsTraits())) { + for(FloatsKey k : P::sync_->get_keys(cat, FloatsTraits())) { if (P::sync_->get_name(k) == name) { floats_keys_.push_back(k); std::sort(floats_keys_.begin(), floats_keys_.end()); diff --git a/modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h b/modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h index 9e2afb6338..ba7f34f011 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h +++ b/modules/rmf/dependency/RMF/src/backend/avro/encode_decode.h @@ -562,7 +562,7 @@ struct codec_traits { } std::vector nodes; internal_avro::decode(d, nodes); - RMF_FOREACH(const RMF::avro2::HierarchyNode & hn, nodes) { + for(const RMF::avro2::HierarchyNode & hn : nodes) { v.nodes.resize( std::max(v.nodes.size(), hn.id.get_index() + 1)); v.nodes[hn.id.get_index()].name = hn.name; @@ -570,7 +570,7 @@ struct codec_traits { v.nodes[hn.id.get_index()] .parents.insert(v.nodes[hn.id.get_index()].parents.end(), hn.parents.begin(), hn.parents.end()); - RMF_FOREACH(RMF::NodeID ch, hn.parents) { + for(RMF::NodeID ch : hn.parents) { v.nodes.resize( std::max(v.nodes.size(), ch.get_index() + 1)); v.nodes[ch.get_index()].children.push_back(hn.id); diff --git a/modules/rmf/dependency/RMF/src/backend/avro/encode_decode_util.h b/modules/rmf/dependency/RMF/src/backend/avro/encode_decode_util.h index 93ab7b4b4a..e97e64d097 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/encode_decode_util.h +++ b/modules/rmf/dependency/RMF/src/backend/avro/encode_decode_util.h @@ -25,7 +25,7 @@ inline void sort_key(const KeyInfo& ki, KeyMaps& maps) { } inline void sort_keys(const std::vector& in, KeyData& out) { - RMF_FOREACH(const KeyInfo & k, in) { + for(const KeyInfo & k : in) { switch (k.type) { case INT: sort_key(k, out.int_keys); diff --git a/modules/rmf/dependency/RMF/src/backend/avro/factory.cpp b/modules/rmf/dependency/RMF/src/backend/avro/factory.cpp index cff2127c12..998bc8e0fc 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/factory.cpp +++ b/modules/rmf/dependency/RMF/src/backend/avro/factory.cpp @@ -32,7 +32,7 @@ namespace avro2 { template class Avro2IOFileFactory : public backends::IOFactory { public: - virtual std::string get_file_extension() const RMF_OVERRIDE { + virtual std::string get_file_extension() const override { if (OLD) return ".rmf3"; if (GZIP) return ".rmfz"; @@ -40,22 +40,22 @@ class Avro2IOFileFactory : public backends::IOFactory { return ".rmf"; } virtual boost::shared_ptr read_file(const std::string &name) - const RMF_OVERRIDE { + const override { return boost::make_shared > >(name); } virtual boost::shared_ptr create_file(const std::string &name) - const RMF_OVERRIDE { + const override { return boost::make_shared > >(name); } }; class Avro2IOBufferFactory : public backends::IOFactory { public: - virtual std::string get_file_extension() const RMF_OVERRIDE { + virtual std::string get_file_extension() const override { return ".none"; } virtual boost::shared_ptr read_buffer(BufferConstHandle buffer) - const RMF_OVERRIDE { + const override { try { return boost::make_shared > >( buffer); @@ -66,7 +66,7 @@ class Avro2IOBufferFactory : public backends::IOFactory { } } virtual boost::shared_ptr create_buffer(BufferHandle buffer) - const RMF_OVERRIDE { + const override { return boost::make_shared >(buffer); } }; diff --git a/modules/rmf/dependency/RMF/src/backend/avro/io.h b/modules/rmf/dependency/RMF/src/backend/avro/io.h index e28c228722..cc3530720f 100644 --- a/modules/rmf/dependency/RMF/src/backend/avro/io.h +++ b/modules/rmf/dependency/RMF/src/backend/avro/io.h @@ -40,20 +40,15 @@ struct Avro2IO : public backends::IO { public: template Avro2IO(T t); - virtual void save_loaded_frame(internal::SharedData *shared_data) - RMF_OVERRIDE; - virtual void load_loaded_frame(internal::SharedData *shared_data) - RMF_OVERRIDE; - virtual void save_static_frame(internal::SharedData *shared_data) - RMF_OVERRIDE; - virtual void load_static_frame(internal::SharedData *shared_data) - RMF_OVERRIDE; - virtual void load_file(internal::SharedData *shared_data) RMF_OVERRIDE; - virtual void save_file(const internal::SharedData *shared_data) RMF_OVERRIDE; - virtual void load_hierarchy(internal::SharedData *shared_data) RMF_OVERRIDE; - virtual void save_hierarchy(const internal::SharedData *shared_data) - RMF_OVERRIDE; - virtual void flush() RMF_OVERRIDE; + virtual void save_loaded_frame(internal::SharedData *shared_data) override; + virtual void load_loaded_frame(internal::SharedData *shared_data) override; + virtual void save_static_frame(internal::SharedData *shared_data) override; + virtual void load_static_frame(internal::SharedData *shared_data) override; + virtual void load_file(internal::SharedData *shared_data) override; + virtual void save_file(const internal::SharedData *shared_data) override; + virtual void load_hierarchy(internal::SharedData *shared_data) override; + virtual void save_hierarchy(const internal::SharedData *shared_data) override; + virtual void flush() override; virtual ~Avro2IO(); }; @@ -63,7 +58,7 @@ template void load(internal::SharedData *shared_data, const KeyMaps &keys, internal::TypeData &data, Loader) { typedef std::pair, Category> KKP; - RMF_FOREACH(KKP kp, keys.category) { + for(KKP kp : keys.category) { shared_data->ensure_key(kp.second, kp.first, keys.name.find(kp.first)->second, Traits()); } @@ -76,10 +71,10 @@ void load(internal::SharedData *shared_data, const KeyMaps &keys, template bool save(KeyType key_type, internal::SharedData *shared_data, KeyMaps &keys, std::vector *keys_changed, - internal::TypeData &data, - internal::TypeData *change_data, Loader) { + internal::TypeData &data, Loader, + internal::TypeData *change_data = nullptr) { bool ret = false; - RMF_FOREACH(ID k, shared_data->get_keys(Traits())) { + for(ID k : shared_data->get_keys(Traits())) { if (keys.category.find(k) == keys.category.end()) { ret = true; std::string name = shared_data->get_name(k); @@ -100,14 +95,14 @@ bool save(KeyType key_type, internal::SharedData *shared_data, } if (change_data) { - RMF_FOREACH(typename internal::TypeData::const_reference kpd, + for(typename internal::TypeData::const_reference kpd : Loader::get_data(shared_data, Traits())) { if (data.find(kpd.first) == data.end() && !kpd.second.empty()) { ret = true; change_data->operator[](kpd.first) = kpd.second; data[kpd.first] = kpd.second; } else { - RMF_FOREACH(typename internal::KeyData::const_reference npd, + for(typename internal::KeyData::const_reference npd : kpd.second) { if (data[kpd.first].find(npd.first) == data[kpd.first].end()) { ret = true; @@ -128,8 +123,7 @@ template void load_all(const std::vector > &categories, internal::SharedData *shared_data, const KeyData &keys, DataTypes &data, Loader) { - typedef std::pair CP; - RMF_FOREACH(CP cp, categories) { + for(const auto &cp : categories) { shared_data->ensure_category(cp.first, cp.second); } load(shared_data, keys.float_keys, data.float_data, Loader()); @@ -158,43 +152,57 @@ bool save_all(FileData &file_data, FileDataChanges &file_data_changes, file_data_changes.categories.push_back(file_data.categories.back()); } - ret = save(FLOAT, shared_data, file_data.keys.float_keys, - &file_data_changes.keys, data.float_data, - data_changes ? &data_changes->float_data : NULL, Loader()) || - ret; - ret = save(INT, shared_data, file_data.keys.int_keys, &file_data_changes.keys, - data.int_data, data_changes ? &data_changes->int_data : NULL, - Loader()) || - ret; - ret = save(STRING, shared_data, file_data.keys.string_keys, - &file_data_changes.keys, data.string_data, - data_changes ? &data_changes->string_data : NULL, Loader()) || - ret; - ret = save(FLOATS, shared_data, file_data.keys.floats_keys, - &file_data_changes.keys, data.floats_data, - data_changes ? &data_changes->floats_data : NULL, Loader()) || - ret; - ret = save(INTS, shared_data, file_data.keys.ints_keys, - &file_data_changes.keys, data.ints_data, - data_changes ? &data_changes->ints_data : NULL, Loader()) || - ret; - ret = save(STRINGS, shared_data, file_data.keys.strings_keys, - &file_data_changes.keys, data.strings_data, - data_changes ? &data_changes->strings_data : NULL, Loader()) || - ret; - - ret = save(VECTOR3, shared_data, file_data.keys.vector3_keys, - &file_data_changes.keys, data.vector3_data, - data_changes ? &data_changes->vector3_data : NULL, Loader()) || - ret; - ret = save(VECTOR4, shared_data, file_data.keys.vector4_keys, - &file_data_changes.keys, data.vector4_data, - data_changes ? &data_changes->vector4_data : NULL, Loader()) || - ret; - ret = save(VECTOR3S, shared_data, file_data.keys.vector3s_keys, - &file_data_changes.keys, data.vector3s_data, - data_changes ? &data_changes->vector3s_data : NULL, Loader()) || - ret; + // This duplication is quite ugly but works around a (compiler?) bug; + // although nullptr was passed for change_data to save(), it tried to + // dereference it anyway and caused a segfault + if (data_changes) { + ret = save(FLOAT, shared_data, file_data.keys.float_keys, + &file_data_changes.keys, data.float_data, Loader(), + &data_changes->float_data) || ret; + ret = save(INT, shared_data, file_data.keys.int_keys, + &file_data_changes.keys, data.int_data, Loader(), + &data_changes->int_data) || ret; + ret = save(STRING, shared_data, file_data.keys.string_keys, + &file_data_changes.keys, data.string_data, Loader(), + &data_changes->string_data) || ret; + ret = save(FLOATS, shared_data, file_data.keys.floats_keys, + &file_data_changes.keys, data.floats_data, Loader(), + &data_changes->floats_data) || ret; + ret = save(INTS, shared_data, file_data.keys.ints_keys, + &file_data_changes.keys, data.ints_data, Loader(), + &data_changes->ints_data) || ret; + ret = save(STRINGS, shared_data, file_data.keys.strings_keys, + &file_data_changes.keys, data.strings_data, Loader(), + &data_changes->strings_data) || ret; + ret = save(VECTOR3, shared_data, file_data.keys.vector3_keys, + &file_data_changes.keys, data.vector3_data, Loader(), + &data_changes->vector3_data) || ret; + ret = save(VECTOR4, shared_data, file_data.keys.vector4_keys, + &file_data_changes.keys, data.vector4_data, Loader(), + &data_changes->vector4_data) || ret; + ret = save(VECTOR3S, shared_data, file_data.keys.vector3s_keys, + &file_data_changes.keys, data.vector3s_data, Loader(), + &data_changes->vector3s_data) || ret; + } else { + ret = save(FLOAT, shared_data, file_data.keys.float_keys, + &file_data_changes.keys, data.float_data, Loader()) || ret; + ret = save(INT, shared_data, file_data.keys.int_keys, + &file_data_changes.keys, data.int_data, Loader()) || ret; + ret = save(STRING, shared_data, file_data.keys.string_keys, + &file_data_changes.keys, data.string_data, Loader()) || ret; + ret = save(FLOATS, shared_data, file_data.keys.floats_keys, + &file_data_changes.keys, data.floats_data, Loader()) || ret; + ret = save(INTS, shared_data, file_data.keys.ints_keys, + &file_data_changes.keys, data.ints_data, Loader()) || ret; + ret = save(STRINGS, shared_data, file_data.keys.strings_keys, + &file_data_changes.keys, data.strings_data, Loader()) || ret; + ret = save(VECTOR3, shared_data, file_data.keys.vector3_keys, + &file_data_changes.keys, data.vector3_data, Loader()) || ret; + ret = save(VECTOR4, shared_data, file_data.keys.vector4_keys, + &file_data_changes.keys, data.vector4_data, Loader()) || ret; + ret = save(VECTOR3S, shared_data, file_data.keys.vector3s_keys, + &file_data_changes.keys, data.vector3s_data, Loader()) || ret; + } return ret; } @@ -231,7 +239,7 @@ void Avro2IO::save_loaded_frame(internal::SharedData *shared_data) { frame_.parents = FrameIDs(fd.parents.begin(), fd.parents.end()); frame_.type = fd.type; frame_.name = fd.name; - save_all(file_data_, file_data_changes_, shared_data, frame_.data, NULL, + save_all(file_data_, file_data_changes_, shared_data, frame_.data, nullptr, internal::LoadedValues()); } @@ -266,16 +274,16 @@ void Avro2IO::load_file(internal::SharedData *shared_data) { shared_data->set_description(file_data_.description); shared_data->set_producer(file_data_.producer); typedef std::pair FDP; - RMF_FOREACH(FDP fdp, file_data_.frames) { + for(FDP fdp : file_data_.frames) { shared_data->add_frame_data(fdp.first, fdp.second.name, fdp.second.type); - RMF_FOREACH(FrameID p, fdp.second.parents) { + for(FrameID p : fdp.second.parents) { shared_data->add_child_frame(p, fdp.first); } } shared_data->set_file_type("rmf3"); typedef std::pair CP; - RMF_FOREACH(CP cp, file_data_.categories) { + for(CP cp : file_data_.categories) { shared_data->ensure_category(cp.first, cp.second); } } @@ -302,7 +310,7 @@ void Avro2IO::load_hierarchy(internal::SharedData *shared_data) { template void Avro2IO::save_hierarchy(const internal::SharedData *shared_data) { - RMF_FOREACH(NodeID n, get_nodes(shared_data)) { + for(NodeID n : get_nodes(shared_data)) { HierarchyNode cur; cur.id = n; bool cur_dirty = false; diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp index d8c4c3780f..fea467079e 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp @@ -45,30 +45,30 @@ typedef backends::BackwardsIO > AvroReaderShareData; struct SingleTextAvroFactory : public RMF::backends::IOFactory { - virtual std::string get_file_extension() const RMF_OVERRIDE { + virtual std::string get_file_extension() const override { return ".rmf-text"; } virtual boost::shared_ptr read_file( - const std::string& name) const RMF_OVERRIDE { + const std::string& name) const override { return boost::make_shared(name, false, true); } virtual boost::shared_ptr create_file( - const std::string& name) const RMF_OVERRIDE { + const std::string& name) const override { return boost::make_shared(name, true, false); } virtual ~SingleTextAvroFactory() {} }; struct SingleAvroFactory : public SingleTextAvroFactory { - virtual std::string get_file_extension() const RMF_OVERRIDE { + virtual std::string get_file_extension() const override { return ".rmfa"; } /*virtual boost::shared_ptr create_buffer( - BufferHandle buffer) const RMF_OVERRIDE { + BufferHandle buffer) const override { return boost::make_shared(buffer); }*/ virtual boost::shared_ptr read_buffer( - BufferConstHandle buffer) const RMF_OVERRIDE { + BufferConstHandle buffer) const override { try { return boost::make_shared(buffer); } @@ -81,15 +81,15 @@ struct SingleAvroFactory : public SingleTextAvroFactory { }; struct MultipleAvroFactory : public RMF::backends::IOFactory { - virtual std::string get_file_extension() const RMF_OVERRIDE { + virtual std::string get_file_extension() const override { return ".rmf-avro"; } virtual boost::shared_ptr read_file( - const std::string& name) const RMF_OVERRIDE { + const std::string& name) const override { return boost::make_shared(name, false, true); } virtual boost::shared_ptr create_file( - const std::string& name) const RMF_OVERRIDE { + const std::string& name) const override { return boost::make_shared(name, true, false); } virtual ~MultipleAvroFactory() {} diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp index 42eacf4fbc..341f8adc63 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp @@ -93,7 +93,7 @@ void HDF5SharedData::open_things(bool create, bool read_only) { void HDF5SharedData::initialize_keys(int) { Categories cats = get_categories(); - RMF_FOREACH(Category cat, cats) { RMF_FOREACH_BACKWARDS_TYPE(RMF_LIST_KEYS); } + for(Category cat : cats) { RMF_FOREACH_BACKWARDS_TYPE(RMF_LIST_KEYS); } initialize_keys(get_category("link"), "nodeid", NodeIDTraits()); } diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h index 3d89bc92a0..e9ee640a78 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h @@ -137,7 +137,7 @@ class HDF5SharedData : public backends::BackwardsIOBase { kcname, arity, TypeTraits::HDF5Traits::get_name(), true); cache_.resize( std::max(cache_.size(), static_cast(category_index + 1)), - NULL); + nullptr); cache_.replace(category_index, new DS()); cache_[category_index].set_current_frame(frame_.get_index()); cache_[category_index].set(file, nm); @@ -173,7 +173,7 @@ class HDF5SharedData : public backends::BackwardsIOBase { kcname, arity, TypeTraits::HDF5Traits::get_name(), false); cache_.resize( std::max(cache_.size(), static_cast(category_index + 1)), - NULL); + nullptr); cache_.replace(category_index, new DS()); cache_[category_index].set(file, nm); } @@ -210,7 +210,7 @@ class HDF5SharedData : public backends::BackwardsIOBase { cache_[cat.get_index()][pfi] .resize(std::max(cache_[cat.get_index()][pfi].size(), static_cast(type_index + 1)), - NULL); + nullptr); cache_[cat.get_index()][pfi].replace(type_index, new DS()); cache_[cat.get_index()][pfi][type_index].set(file, nm); } @@ -591,7 +591,7 @@ class HDF5SharedData : public backends::BackwardsIOBase { std::vector > ret; typename NameKeyMap::const_iterator oit = name_key_map_.find(cat); if (oit == name_key_map_.end()) return ret; - RMF_FOREACH(NameKeyInnerMap::const_reference rt, oit->second) { + for(NameKeyInnerMap::const_reference rt : oit->second) { if (key_data_map_.find(rt.second)->second.type_index == TypeTraits::HDF5Traits::get_index()) { ret.push_back(ID(rt.second)); diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp index 15b5dac967..78da7e9f15 100644 --- a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp +++ b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp @@ -33,15 +33,15 @@ namespace { typedef backends::BackwardsIO MIO; struct HDF5Factory : public RMF::backends::IOFactory { - virtual std::string get_file_extension() const RMF_OVERRIDE { + virtual std::string get_file_extension() const override { return ".rmf-hdf5"; } virtual boost::shared_ptr read_file( - const std::string& name) const RMF_OVERRIDE { + const std::string& name) const override { return boost::make_shared(name, false, true); } virtual boost::shared_ptr create_file( - const std::string& name) const RMF_OVERRIDE { + const std::string& name) const override { return boost::make_shared(name, true, false); } virtual ~HDF5Factory() {} diff --git a/modules/rmf/dependency/RMF/src/decorator/alternatives.cpp b/modules/rmf/dependency/RMF/src/decorator/alternatives.cpp index 7efda60130..5e126ce5fb 100644 --- a/modules/rmf/dependency/RMF/src/decorator/alternatives.cpp +++ b/modules/rmf/dependency/RMF/src/decorator/alternatives.cpp @@ -26,7 +26,7 @@ std::pair get_resolution_impl(NodeConstHandle root, IntermediateParticleFactory ipcf, GaussianParticleFactory gpf) { std::pair ret(std::numeric_limits::max(), false); - RMF_FOREACH(NodeConstHandle ch, root.get_children()) { + for(NodeConstHandle ch : root.get_children()) { std::pair cur = get_resolution_impl(ch, ipcf, gpf); ret.first = std::min(ret.first, cur.first); ret.second = ret.second || cur.second; @@ -139,7 +139,7 @@ NodeConstHandle AlternativesConst::get_alternative(RepresentationType type, NodeConstHandles AlternativesConst::get_alternatives(RepresentationType type) const { NodeConstHandles ret; - RMF_FOREACH(NodeID nid, get_alternatives_impl(type)) { + for(NodeID nid : get_alternatives_impl(type)) { ret.push_back(get_node().get_file().get_node(nid)); } return ret; @@ -162,11 +162,11 @@ Floats get_resolutions_impl(NodeConstHandle root, AlternativesFactory af, RepresentationType type) { Floats ret; if (af.get_is(root)) { - RMF_FOREACH(NodeConstHandle a, af.get(root).get_alternatives(type)) { + for(NodeConstHandle a : af.get(root).get_alternatives(type)) { ret.push_back(get_resolution(a)); } } else { - RMF_FOREACH(NodeConstHandle ch, root.get_children()) { + for(NodeConstHandle ch : root.get_children()) { Floats cur = get_resolutions_impl(ch, af, type); ret.insert(ret.end(), cur.begin(), cur.end()); } @@ -184,7 +184,7 @@ Floats get_resolutions(NodeConstHandle root, RepresentationType type, double lb = unclustered[0]; double ub = lb; Floats ret; - RMF_FOREACH(double r, unclustered) { + for(double r : unclustered) { if (r > lb + accuracy) { ret.push_back(.5 * (lb + ub)); lb = r; diff --git a/modules/rmf/dependency/RMF/src/exceptions.cpp b/modules/rmf/dependency/RMF/src/exceptions.cpp index a1bf374afa..761ced4e2f 100644 --- a/modules/rmf/dependency/RMF/src/exceptions.cpp +++ b/modules/rmf/dependency/RMF/src/exceptions.cpp @@ -19,7 +19,7 @@ RMF_ENABLE_WARNINGS namespace RMF { Exception::Exception() {} -const char* Exception::what() const throw() { +const char* Exception::what() const RMF_NOEXCEPT { try { if (message_.empty()) { message_ = get_message(*this); @@ -30,7 +30,7 @@ const char* Exception::what() const throw() { return message_.c_str(); } -Exception::~Exception() throw() {} +Exception::~Exception() RMF_NOEXCEPT {} std::string get_message(const Exception& e) { using namespace RMF::internal::ErrorInfo; try { @@ -95,16 +95,16 @@ std::string get_message(const Exception& e) { } } UsageException::UsageException() : Exception() {} -UsageException::~UsageException() throw() {} +UsageException::~UsageException() RMF_NOEXCEPT {} IOException::IOException() : Exception() {} -IOException::~IOException() throw() {} +IOException::~IOException() RMF_NOEXCEPT {} IndexException::IndexException() : Exception() {} -IndexException::~IndexException() throw() {} +IndexException::~IndexException() RMF_NOEXCEPT {} InternalException::InternalException() : Exception() {} -InternalException::~InternalException() throw() {} +InternalException::~InternalException() RMF_NOEXCEPT {} } /* namespace RMF */ diff --git a/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp b/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp index 908277191c..0f2958ce90 100644 --- a/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp +++ b/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp @@ -84,7 +84,7 @@ unsigned int ConstGroup::get_number_of_children() const { } std::string ConstGroup::get_child_name(unsigned int i) const { int sz = H5Lget_name_by_idx(get_handle(), ".", H5_INDEX_NAME, H5_ITER_NATIVE, - (hsize_t)i, NULL, 0, H5P_DEFAULT); + (hsize_t)i, nullptr, 0, H5P_DEFAULT); boost::scoped_array buf(new char[sz + 1]); RMF_HDF5_CALL(H5Lget_name_by_idx(get_handle(), ".", H5_INDEX_NAME, H5_ITER_NATIVE, (hsize_t)i, buf.get(), @@ -166,7 +166,7 @@ herr_t error_function(hid_t, void*) { // throws RMF::IOException on error File create_file(std::string name) { RMF_HDF5_CALL(H5open()); - RMF_HDF5_CALL(H5Eset_auto2(H5E_DEFAULT, &error_function, NULL)); + RMF_HDF5_CALL(H5Eset_auto2(H5E_DEFAULT, &error_function, nullptr)); RMF_HDF5_HANDLE(plist, get_parameters(), H5Pclose); RMF_HDF5_NEW_HANDLE( h, H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist), &H5Fclose); @@ -175,7 +175,7 @@ File create_file(std::string name) { File open_file(std::string name) { RMF_HDF5_CALL(H5open()); - RMF_HDF5_CALL(H5Eset_auto2(H5E_DEFAULT, &error_function, NULL)); + RMF_HDF5_CALL(H5Eset_auto2(H5E_DEFAULT, &error_function, nullptr)); RMF_HDF5_HANDLE(plist, get_parameters(), H5Pclose); RMF_HDF5_NEW_HANDLE(h, H5Fopen(name.c_str(), H5F_ACC_RDWR, plist), &H5Fclose); return File(h); @@ -183,7 +183,7 @@ File open_file(std::string name) { ConstFile open_file_read_only(std::string name) { RMF_HDF5_CALL(H5open()); - RMF_HDF5_CALL(H5Eset_auto2(H5E_DEFAULT, &error_function, NULL)); + RMF_HDF5_CALL(H5Eset_auto2(H5E_DEFAULT, &error_function, nullptr)); RMF_HDF5_HANDLE(plist, get_parameters(), H5Pclose); RMF_HDF5_NEW_HANDLE(h, H5Fopen(name.c_str(), H5F_ACC_RDONLY, plist), &H5Fclose); @@ -192,7 +192,7 @@ ConstFile open_file_read_only(std::string name) { File open_file_read_only_returning_nonconst(std::string name) { RMF_HDF5_CALL(H5open()); - RMF_HDF5_CALL(H5Eset_auto2(H5E_DEFAULT, &error_function, NULL)); + RMF_HDF5_CALL(H5Eset_auto2(H5E_DEFAULT, &error_function, nullptr)); RMF_HDF5_HANDLE(plist, get_parameters(), H5Pclose); RMF_HDF5_NEW_HANDLE(h, H5Fopen(name.c_str(), H5F_ACC_RDONLY, plist), &H5Fclose); @@ -212,13 +212,13 @@ void File::flush() { RMF_HDF5_CALL(H5Fflush(get_handle(), H5F_SCOPE_LOCAL)); } }*/ std::string ConstFile::get_name() const { - int sz = H5Fget_name(get_handle(), NULL, 0); + int sz = H5Fget_name(get_handle(), nullptr, 0); boost::scoped_array buf(new char[sz + 1]); RMF_HDF5_CALL(H5Fget_name(get_handle(), buf.get(), sz + 1)); return std::string(buf.get()); } std::string File::get_name() const { - int sz = H5Fget_name(get_handle(), NULL, 0); + int sz = H5Fget_name(get_handle(), nullptr, 0); boost::scoped_array buf(new char[sz + 1]); RMF_HDF5_CALL(H5Fget_name(get_handle(), buf.get(), sz + 1)); return std::string(buf.get()); @@ -277,7 +277,7 @@ void StringsTraits::write_value_dataset(hid_t d, hid_t iss, hid_t s, } data.p = buf.get(); } else { - data.p = NULL; + data.p = nullptr; } RMF_HDF5_CALL( H5Dwrite(d, get_hdf5_memory_type(), iss, s, H5P_DEFAULT, &data)); @@ -302,7 +302,7 @@ StringsTraits::Type StringsTraits::read_value_dataset(hid_t d, hid_t iss, } const hvl_t& StringsTraits::get_fill_value() { - static hvl_t ret = {0, NULL}; + static hvl_t ret = {0, nullptr}; return ret; } @@ -340,7 +340,7 @@ void StringTraits::write_value_dataset(hid_t d, hid_t iss, hid_t s, StringTraits::Type StringTraits::read_value_dataset(hid_t d, hid_t iss, hid_t sp) { - char* c = NULL; + char* c = nullptr; RMF_HDF5_HANDLE(mt, internal::create_string_type(), H5Tclose); RMF_HDF5_CALL(H5Dread(d, mt, iss, sp, H5P_DEFAULT, &c)); std::string ret; diff --git a/modules/rmf/dependency/RMF/src/info.cpp b/modules/rmf/dependency/RMF/src/info.cpp index ac804b9736..58947997a6 100644 --- a/modules/rmf/dependency/RMF/src/info.cpp +++ b/modules/rmf/dependency/RMF/src/info.cpp @@ -26,9 +26,9 @@ namespace RMF { template void show_key_info(FileConstHandle rh, Category cat, std::string name, std::ostream& out) { - RMF_FOREACH(ID k, rh.get_keys(cat)) { + for(ID k : rh.get_keys(cat)) { int static_count = 0, frame_count = 0; - RMF_FOREACH(NodeID n, rh.get_node_ids()) { + for(NodeID n : rh.get_node_ids()) { NodeConstHandle nh = rh.get_node(n); if (rh.get_current_frame() != FrameID() && !nh.get_frame_value(k).get_is_null()) { @@ -48,7 +48,7 @@ void show_key_info(FileConstHandle rh, Category cat, std::string name, void show_info(FileConstHandle rh, std::ostream& out) { out << "Nodes: " << rh.get_number_of_nodes() << std::endl; out << "Frames: " << rh.get_number_of_frames() << std::endl; - RMF_FOREACH(Category c, rh.get_categories()) { + for(Category c : rh.get_categories()) { out << rh.get_name(c) << ":" << std::endl; RMF_FOREACH_TYPE(RMF_SHOW_TYPE_DATA_INFO); } diff --git a/modules/rmf/dependency/RMF/src/internal/clone_shared_data.h b/modules/rmf/dependency/RMF/src/internal/clone_shared_data.h index e17906341a..19d9e0e55c 100644 --- a/modules/rmf/dependency/RMF/src/internal/clone_shared_data.h +++ b/modules/rmf/dependency/RMF/src/internal/clone_shared_data.h @@ -60,9 +60,9 @@ void clone_hierarchy(SDA* sda, SDB* sdb) { RMF_LARGE_UNORDERED_MAP parents, deferred_parents; typedef RMF_LARGE_UNORDERED_MAP::value_type NodeIDMapValue; - RMF_FOREACH(NodeID na, get_nodes(sda)) { + for(NodeID na : get_nodes(sda)) { NodeIDs children = sda->get_children(na); - RMF_FOREACH(NodeID c, children) { + for(NodeID c : children) { if (parents.find(c) == parents.end() && c.get_index() >= sdb->get_number_of_nodes()) { parents[c] = na; @@ -73,13 +73,13 @@ void clone_hierarchy(SDA* sda, SDB* sdb) { RMF_LARGE_UNORDERED_SET existing; RMF_LARGE_UNORDERED_MAP > existing_parents; - RMF_FOREACH(NodeID nb, get_nodes(sdb)) { + for(NodeID nb : get_nodes(sdb)) { existing.insert(nb); - RMF_FOREACH(NodeID ch, sdb->get_children(nb)) { + for(NodeID ch : sdb->get_children(nb)) { existing_parents[ch].insert(nb); } } - RMF_FOREACH(NodeID na, get_nodes(sda)) { + for(NodeID na : get_nodes(sda)) { if (existing.find(na) != existing.end()) continue; if (parents.find(na) != parents.end()) { NodeID parent = parents.find(na)->second; @@ -102,13 +102,13 @@ void clone_hierarchy(SDA* sda, SDB* sdb) { RMF_INTERNAL_CHECK(nid == na, "Don't match"); } } - RMF_FOREACH(NodeIDMapValue v, deferred_parents) { + for(NodeIDMapValue v : deferred_parents) { sdb->add_child(v.second, v.first); } - RMF_FOREACH(NodeID na, get_nodes(sda)) { + for(NodeID na : get_nodes(sda)) { NodeIDs children = sda->get_children(na); - RMF_FOREACH(NodeID c, children) { + for(NodeID c : children) { if (parents.find(c) != parents.end() && parents.find(c)->second != na && existing_parents[c].find(na) == existing_parents[c].end()) { sdb->add_child(na, c); @@ -142,9 +142,8 @@ void clone_values_type(SDA* sda, Category cata, SDB* sdb, Category catb, H) { RMF_LARGE_UNORDERED_MAP, ID > keys = get_key_map(sda, cata, sdb, catb); if (keys.empty()) return; - typedef std::pair, ID > KP; - RMF_FOREACH(KP ks, keys) { - RMF_FOREACH(NodeID n, get_nodes(sda)) { + for(const auto &ks : keys) { + for(NodeID n : get_nodes(sda)) { typename TraitsA::ReturnType rt = H::get(sda, n, ks.first); if (!TraitsA::get_is_null_value(rt)) { H::set(sdb, n, ks.second, get_as(rt)); @@ -170,7 +169,7 @@ void clone_values_category(SDA* sda, Category cata, SDB* sdb, Category catb, template void clone_static_data(SDA* sda, SDB* sdb) { - RMF_FOREACH(Category cata, sda->get_categories()) { + for(Category cata : sda->get_categories()) { Category catb = sdb->get_category(sda->get_name(cata)); clone_values_category(sda, cata, sdb, catb, StaticValues()); } @@ -178,7 +177,7 @@ void clone_static_data(SDA* sda, SDB* sdb) { template void clone_loaded_data(SDA* sda, SDB* sdb) { - RMF_FOREACH(Category cata, sda->get_categories()) { + for(Category cata : sda->get_categories()) { Category catb = sdb->get_category(sda->get_name(cata)); clone_values_category(sda, cata, sdb, catb, LoadedValues()); } diff --git a/modules/rmf/dependency/RMF/src/internal/paths.cpp b/modules/rmf/dependency/RMF/src/internal/paths.cpp index e0013fb235..c147bfc153 100644 --- a/modules/rmf/dependency/RMF/src/internal/paths.cpp +++ b/modules/rmf/dependency/RMF/src/internal/paths.cpp @@ -157,7 +157,7 @@ std::string get_unique_path() { boost::filesystem::path temp = boost::filesystem::unique_path(); return temp.string(); #else - return tmpnam(NULL); + return tmpnam(nullptr); #endif } diff --git a/modules/rmf/dependency/RMF/src/internal/shared_data_equality.h b/modules/rmf/dependency/RMF/src/internal/shared_data_equality.h index e79faae13b..baaccddf2b 100644 --- a/modules/rmf/dependency/RMF/src/internal/shared_data_equality.h +++ b/modules/rmf/dependency/RMF/src/internal/shared_data_equality.h @@ -28,9 +28,9 @@ bool get_equal_values_type(SDA* sda, Category cata, SDB* sdb, Category catb, RMF_LARGE_UNORDERED_MAP, ID > keys = get_key_map(sda, cata, sdb, catb); bool ret = true; - RMF_FOREACH(NodeID n, get_nodes(sda)) { + for(NodeID n : get_nodes(sda)) { typedef std::pair, ID > KP; - RMF_FOREACH(KP ks, keys) { + for(KP ks : keys) { typename Traits::ReturnType rta = H::get(sda, n, ks.first); typename Traits::ReturnType rtb = H::get(sdb, n, ks.second); bool ha = !Traits::get_is_null_value(rta); @@ -65,7 +65,7 @@ bool get_equal_current_values_category(SDA* sda, Category cata, SDB* sdb, template bool get_equal_current_values(SDA* sda, SDB* sdb) { - RMF_FOREACH(Category cata, sda->get_categories()) { + for(Category cata : sda->get_categories()) { Category catb = sdb->get_category(sda->get_name(cata)); if (!get_equal_current_values_category(sda, cata, sdb, catb)) return false; } @@ -85,7 +85,7 @@ bool get_equal_static_values_category(SDA* sda, Category cata, SDB* sdb, template bool get_equal_static_values(SDA* sda, SDB* sdb) { - RMF_FOREACH(Category cata, sda->get_categories()) { + for(Category cata : sda->get_categories()) { Category catb = sdb->get_category(sda->get_name(cata)); if (!get_equal_static_values_category(sda, cata, sdb, catb)) return false; } diff --git a/modules/rmf/dependency/RMF/src/internal/shared_data_maps.h b/modules/rmf/dependency/RMF/src/internal/shared_data_maps.h index db86b0ed3a..a45fa37ed4 100644 --- a/modules/rmf/dependency/RMF/src/internal/shared_data_maps.h +++ b/modules/rmf/dependency/RMF/src/internal/shared_data_maps.h @@ -26,7 +26,7 @@ RMF_LARGE_UNORDERED_MAP, ID > get_key_map(SDA* sda, Category catb) { RMF_LARGE_UNORDERED_MAP, ID > ret; std::vector > keysa = sda->get_keys(cata, TraitsA()); - RMF_FOREACH(ID keya, keysa) { + for(ID keya : keysa) { ret[keya] = sdb->get_key(catb, sda->get_name(keya), TraitsB()); RMF_TRACE(sda->get_name(keya) << " maps to " << sdb->get_name(ret[keya])); } diff --git a/modules/rmf/dependency/RMF/src/show_hierarchy.cpp b/modules/rmf/dependency/RMF/src/show_hierarchy.cpp index 3b31816fbc..718875f4ac 100644 --- a/modules/rmf/dependency/RMF/src/show_hierarchy.cpp +++ b/modules/rmf/dependency/RMF/src/show_hierarchy.cpp @@ -46,7 +46,7 @@ void show_data(NodeConstHandle n, std::ostream& out, const std::vector >& ks, std::string prefix) { using std::operator<<; FileConstHandle f = n.get_file(); - RMF_FOREACH(ID k, ks) { + for(ID k : ks) { if (n.get_file().get_current_frame() != FrameID() && !n.get_frame_value(k).get_is_null()) { out << std::endl << prefix << n.get_file().get_name(k) << ": " @@ -81,7 +81,7 @@ void print_tree(std::ostream& out, RMF::NodeConstHandle start, Show show) { { NodeConstHandles alts = ad.get_alternatives(GAUSSIAN_PARTICLE); std::reverse(alts.begin(), alts.end()); - RMF_FOREACH(NodeConstHandle cur, alts) { + for(NodeConstHandle cur : alts) { RMF_INTERNAL_CHECK(cur != n, "Node can't be a gaussian one"); std::ostringstream oss; oss << "[G" << decorator::get_resolution(cur) << "]"; @@ -93,7 +93,7 @@ void print_tree(std::ostream& out, RMF::NodeConstHandle start, Show show) { RMF_INTERNAL_CHECK(alts.front() == n, "The node itself is not in front"); std::reverse(alts.begin(), alts.end()); - RMF_FOREACH(NodeConstHandle cur, alts) { + for(NodeConstHandle cur : alts) { if (cur == n) continue; std::ostringstream oss; oss << "[" << decorator::get_resolution(cur) << "]"; @@ -138,7 +138,7 @@ void show_frames_impl(FileConstHandle fh, FrameID root, std::string prefix, out << " + "; } out << fh.get_name(root) << " [" << fh.get_type(root) << "]" << std::endl; - RMF_FOREACH(FrameID id, ch) { show_frames_impl(fh, id, prefix + " ", out); } + for(FrameID id : ch) { show_frames_impl(fh, id, prefix + " ", out); } } void simple_show_node(NodeConstHandle n, std::string /*prefix*/, @@ -372,7 +372,7 @@ void show_hierarchy_with_decorators(NodeConstHandle root, bool, } void show_frames(FileConstHandle fh, std::ostream& out) { - RMF_FOREACH(FrameID fr, fh.get_root_frames()) { + for(FrameID fr : fh.get_root_frames()) { show_frames_impl(fh, fr, std::string(), out); } } diff --git a/modules/rmf/dependency/RMF/src/signature.cpp b/modules/rmf/dependency/RMF/src/signature.cpp index 5b4435cdd8..6107b7270d 100644 --- a/modules/rmf/dependency/RMF/src/signature.cpp +++ b/modules/rmf/dependency/RMF/src/signature.cpp @@ -43,17 +43,17 @@ std::string get_static_signature( decorator::ScaleFactory scalecf) { std::ostringstream ret; ret << "hierarchy [\n"; - RMF_FOREACH(NodeID n, file.get_node_ids()) { + for(NodeID n : file.get_node_ids()) { NodeConstHandle nh = file.get_node(n); ret << n << ":"; - RMF_FOREACH(NodeConstHandle c, nh.get_children()) { + for(NodeConstHandle c : nh.get_children()) { ret << " " << c.get_id(); } ret << "\n"; } ret << "]\n"; ret << "static [\n"; - RMF_FOREACH(NodeID n, file.get_node_ids()) { + for(NodeID n : file.get_node_ids()) { NodeConstHandle nh = file.get_node(n); ret << n << ":"; if (bdcf.get_is_static(nh)) ret << " bond"; @@ -96,7 +96,7 @@ std::string get_frame_signature( decorator::ScaleFactory scalecf) { std::ostringstream ret; ret << file.get_current_frame() << " [\n"; - RMF_FOREACH(NodeID n, file.get_node_ids()) { + for(NodeID n : file.get_node_ids()) { NodeConstHandle nh = file.get_node(n); ret << n << ":"; if (bdcf.get_is(nh)) ret << " bond"; @@ -150,7 +150,7 @@ std::string get_signature_string(FileConstHandle file) { bcf, cycf, segcf, rcf, acf, chaincf, fragcf, copycf, diffusercf, typedcf, refcf, scalecf); - RMF_FOREACH(FrameID frame, file.get_frames()) { + for(FrameID frame : file.get_frames()) { file.set_current_frame(frame); ret += std::string("\n") + get_frame_signature(file, bdf, ccf, pcf, ipcf, rpcf, scf, bcf, cycf, segcf, diff --git a/modules/rmf/dependency/RMF/src/utility.cpp b/modules/rmf/dependency/RMF/src/utility.cpp index 97af6de835..95ad996da2 100644 --- a/modules/rmf/dependency/RMF/src/utility.cpp +++ b/modules/rmf/dependency/RMF/src/utility.cpp @@ -139,12 +139,12 @@ void get_bounding_box_impl(NodeConstHandle root, CoordinateTransformer tr, bb); } if (sf.get_is(root)) { - RMF_FOREACH(const Vector3 & v, sf.get(root).get_coordinates_list()) { + for(const Vector3 &v : sf.get(root).get_coordinates_list()) { handle_vector(tr, v, cf.get_is(root) ? cf.get(root).get_radius() : 0.0f, bb); } } - RMF_FOREACH(NodeConstHandle ch, root.get_children()) { + for(NodeConstHandle ch : root.get_children()) { get_bounding_box_impl(ch, tr, ipf, bf, sf, cf, gpf, rff, bb); } } diff --git a/modules/rmf/dependency/RMF/src/validate.cpp b/modules/rmf/dependency/RMF/src/validate.cpp index 4c273e45bb..8c16dc186e 100644 --- a/modules/rmf/dependency/RMF/src/validate.cpp +++ b/modules/rmf/dependency/RMF/src/validate.cpp @@ -32,7 +32,7 @@ bool validate_impl(NodeConstHandle cur, decorator::ParticleFactory pcf, ret = false; } } - RMF_FOREACH(NodeConstHandle c, ch) { + for(NodeConstHandle c : ch) { ret = ret && validate_impl(c, pcf, rcf, acf); } return ret; diff --git a/modules/rmf/dependency/RMF/test/test_ranges.cpp b/modules/rmf/dependency/RMF/test/test_ranges.cpp index 299fcbfc92..b7b7257d97 100644 --- a/modules/rmf/dependency/RMF/test/test_ranges.cpp +++ b/modules/rmf/dependency/RMF/test/test_ranges.cpp @@ -15,7 +15,7 @@ int main(int, char * []) { fh.add_frame("hi", RMF::FRAME); assert(boost::distance(fh.get_frames()) == 1); int count = 0; - RMF_FOREACH(RMF::NodeID n, fh.get_node_ids()) { + for(RMF::NodeID n : fh.get_node_ids()) { RMF_UNUSED(n); ++count; } From 98aca92c5f822e1ef6e669fb7cd467d7d7b7618f Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 10 Mar 2022 14:38:23 -0800 Subject: [PATCH 081/155] Delete Python 3 cache files on uninstall --- tools/w32/make-package.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/w32/make-package.sh b/tools/w32/make-package.sh index 3dc10130dc..a29567d0b2 100755 --- a/tools/w32/make-package.sh +++ b/tools/w32/make-package.sh @@ -240,5 +240,5 @@ rm -f w32.dlls w32.deps w32.unmet_deps ${TOOLDIR}/gen-w32instlist w32-inst > w32files.tmp || exit 1 sed -e '/\.pyc"$/d' < w32files.tmp > w32files.install || exit 1 -tac w32files.tmp | sed -e 's/File "w32-inst\\/Delete "$INSTDIR\\/' -e 's/^SetOutPath/RMDir/' > w32files.uninstall || exit 1 +tac w32files.tmp | sed -e 's/File "w32-inst\\/Delete "$INSTDIR\\/' -e 's#^SetOutPath "\(.*\)"#RMDir /r "\1\\__pycache__"\nRMDir "\1"#' > w32files.uninstall || exit 1 ${MAKENSIS} -DVERSION=${VER} -NOCD ${TOOLDIR}/w32-install.nsi || exit 1 From ded7a8804def28a6e4ddc453e0b6a2fef731aa73 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 10 Mar 2022 16:59:31 -0800 Subject: [PATCH 082/155] Squashed 'modules/pmi/' changes from 4c3ece6809..8c62bd941f 8c62bd941f Improve docs of basic restraints git-subtree-dir: modules/pmi git-subtree-split: 8c62bd941f0a090f44af762dd0dfac30fb347706 --- modules/pmi/include/MembraneRestraint.h | 6 ++- modules/pmi/pyext/src/restraints/basic.py | 57 +++++++++++------------ 2 files changed, 31 insertions(+), 32 deletions(-) diff --git a/modules/pmi/include/MembraneRestraint.h b/modules/pmi/include/MembraneRestraint.h index e34da1d5a8..0c1d69c3b6 100644 --- a/modules/pmi/include/MembraneRestraint.h +++ b/modules/pmi/include/MembraneRestraint.h @@ -8,13 +8,17 @@ #ifndef IMPPMI_MEMBRANE_RESTRAINT_H #define IMPPMI_MEMBRANE_RESTRAINT_H + #include #include #include IMPPMI_BEGIN_NAMESPACE + //! Membrane Restraint -/** Favors configurations where target is in the membrane +/** Favors configurations where target is in the membrane. + This is the C++ implementation; for most modeling the Python wrapper + is more useful - see IMP.pmi.restraints.basic.MembraneRestraint. */ class IMPPMIEXPORT MembraneRestraint : public isd::ISDRestraint { ParticleIndex z_nuisance_; diff --git a/modules/pmi/pyext/src/restraints/basic.py b/modules/pmi/pyext/src/restraints/basic.py index 7d9ac0fc36..f39cc39cae 100644 --- a/modules/pmi/pyext/src/restraints/basic.py +++ b/modules/pmi/pyext/src/restraints/basic.py @@ -13,18 +13,17 @@ class ExternalBarrier(IMP.pmi.restraints.RestraintBase): - - """Restraint to keep all structures inside sphere.""" + """Keeps all structures inside a sphere.""" def __init__(self, hierarchies, radius=10.0, resolution=10, weight=1.0, center=None, label=None): """Setup external barrier restraint. - @param radius Size of external barrier @param hierarchies Can be one of the following inputs: IMP Hierarchy, PMI System/State/Molecule/TempResidue, or a list/set of them + @param radius Size of external barrier @param resolution Select which resolutions to act upon @param weight Weight of restraint - @param center Center of the external barrier restraint + @param center Center of the external barrier (IMP.algebra.Vector3D object) @param label A unique label to be used in outputs and particle/restraint names. @@ -57,7 +56,6 @@ def __init__(self, hierarchies, radius=10.0, resolution=10, weight=1.0, class DistanceRestraint(IMP.pmi.restraints.RestraintBase): - """A simple distance restraint""" def __init__(self, root_hier, tuple_selection1, tuple_selection2, @@ -77,7 +75,7 @@ def __init__(self, root_hier, tuple_selection1, tuple_selection2, particle/restraint names @param weight Weight of restraint @note Pass the same resnum twice to each tuple_selection. Optionally - add a copy number (PMI2 only) + add a copy number. """ ts1 = IMP.core.HarmonicUpperBound(distancemax, kappa) ts2 = IMP.core.HarmonicLowerBound(distancemin, kappa) @@ -125,22 +123,24 @@ def __init__(self, root_hier, tuple_selection1, tuple_selection2, class CylinderRestraint(IMP.Restraint): - ''' - PMI2 python restraint. Restrains particles within a - Cylinder aligned along the z-axis and - centered in x,y=0,0 - Optionally, one can restrain the cylindrical angle - ''' + """Restrain particles within (or outside) a cylinder. + The cylinder is aligned along the z-axis and with center x=y=0. + Optionally, one can restrain the cylindrical angle + """ import math def __init__(self, m, objects, resolution, radius, mintheta=None, maxtheta=None, repulsive=False, label='None'): ''' - @param objects PMI2 objects + @param objects PMI2 objects to restrain @param resolution the resolution you want the restraint to be applied @param radius the radius of the cylinder @param mintheta minimum cylindrical angle in degrees @param maxtheta maximum cylindrical angle in degrees + @param repulsive If True, restrain the particles to be outside + of the cylinder instead of inside + @param label A unique label to be used in outputs and + particle/restraint names ''' IMP.Restraint.__init__(self, m, "CylinderRestraint %1%") self.radius = radius @@ -201,8 +201,7 @@ def get_output(self): class BiStableDistanceRestraint(IMP.Restraint): - ''' - a python restraint with bistable potential + '''Distance restraint with bistable potential Authors: G. Bouvier, R. Pellarin. Pasteur Institute. ''' import numpy as np @@ -211,7 +210,7 @@ class BiStableDistanceRestraint(IMP.Restraint): def __init__(self, m, p1, p2, dist1, dist2, sigma1, sigma2, weight1, weight2): ''' - input twp oarticles, the two equilibrium distances, their amplitudes, + input two particles, the two equilibrium distances, their amplitudes, and their weights (populations) ''' IMP.Restraint.__init__(self, m, "BiStableDistanceRestraint %1%") @@ -246,8 +245,7 @@ def do_get_inputs(self): class DistanceToPointRestraint(IMP.pmi.restraints.RestraintBase): - - """Restraint for anchoring a particle to a specific coordinate.""" + """Anchor a particle to a specific coordinate.""" def __init__(self, root_hier, tuple_selection, anchor_point=IMP.algebra.Vector3D(0, 0, 0), @@ -260,13 +258,13 @@ def __init__(self, root_hier, tuple_selection, @param anchor_point Point to which to restrain particle (IMP.algebra.Vector3D object) @param radius Size of the tolerance length - @param kappa The harmonic parameter + @param kappa Strength of the harmonic restraint @param resolution For selecting a particle @param weight Weight of restraint @param label A unique label to be used in outputs and particle/restraint names @note Pass the same resnum twice to each tuple_selection. Optionally - add a copy number (PMI2 only) + add a copy number """ model = root_hier.get_model() copy_num1 = 0 @@ -306,13 +304,17 @@ def __init__(self, root_hier, tuple_selection, class MembraneRestraint(IMP.pmi.restraints.RestraintBase): + """Restrain particles to be above, below, or inside a planar membrane. + The membrane is defined to lie on the xy plane with a given z + coordinate and thickness, and particles are restrained (by their + z coordinates) with a simple sigmoid score. + """ + def __init__(self, hier, objects_above=None, objects_inside=None, objects_below=None, center=0.0, thickness=30.0, softness=3.0, plateau=0.0000000001, resolution=1, weight=1.0, label=None): - """ Setup Membrane restraint - - Simple sigmoid score calculated for particles above, + """Setup the restraint. @param objects_inside list or tuples of objects in membrane (e.g. ['p1', (10, 30,'p2')]) @@ -325,8 +327,6 @@ def __init__(self, hier, objects_above=None, objects_inside=None, @param weight Weight of restraint @param label A unique label to be used in outputs and particle/restraint names. - input a list of particles, the slope and theta of the sigmoid potential - theta is the cutoff distance for a protein-protein contact """ self.hier = hier @@ -411,12 +411,7 @@ def _select_from_string(self, obj): return particles def create_membrane_density(self, file_out='membrane_localization.mrc'): - - ''' - Just for visualization purposes. - Writes density of membrane localization - ''' - + """Create an MRC density file to visualize the membrane.""" offset = 5.0 * self.thickness apix = 3.0 resolution = 5.0 From cfe3e420cea2360a9701244d0373b2d962efcb10 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 10 Mar 2022 17:17:17 -0800 Subject: [PATCH 083/155] Code should build with MSVS2012 --- ChangeLog.md | 2 +- doc/manual/installation.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index dd4a893d5f..d3a1c2d0e3 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -6,7 +6,7 @@ ChangeLog {#changelog} functions instead to calculate coarse cross correlation. - IMP now requires a C++11 compiler and SWIG 3 (or later) to build. Most recent compilers should support C++11, such as gcc, clang - or MS Visual Studio 2015 or later. Various IMP macro and header workarounds + or MS Visual Studio 2012 or later. Various IMP macro and header workarounds for pre-C++11 environments are thus no longer needed and are deprecated: `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`, `IMP_FOREACH`, `IMP/nullptr.h`, and `IMP/nullptr_macros.h`. diff --git a/doc/manual/installation.md b/doc/manual/installation.md index 3cb5283315..d98836f9b6 100644 --- a/doc/manual/installation.md +++ b/doc/manual/installation.md @@ -23,7 +23,7 @@ to see if the code is currently stable enough for your purposes. In order to build %IMP from source, you will need: - A C++ compiler that supports the C++11 standard, such as gcc, clang, - or Microsoft Visual Studio 2010 or later. + or Microsoft Visual Studio 2012 or later. - [CMake](https://cmake.org) (2.8.12 or later; 3.14 or later is recommended) - [Boost](https://www.boost.org) (1.53 or later; Boost.Iostreams must be built with its [zlib filter enabled](https://www.boost.org/doc/libs/1_67_0/libs/iostreams/doc/installation.html)) From 4009fc6f57ac55aca7c46944522c8507c9d40d8b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 10 Mar 2022 18:08:51 -0800 Subject: [PATCH 084/155] Squashed 'modules/rmf/dependency/RMF/' changes from 7f8c4cab38..fbbe8657fc fbbe8657fc We should still build with MSVS2012 5922de4866 Prepare for 1.4 release git-subtree-dir: modules/rmf/dependency/RMF git-subtree-split: fbbe8657fce5c4d0d5667a9d6f6861eee9abb5c8 --- modules/rmf/dependency/RMF/CMakeLists.txt | 2 +- modules/rmf/dependency/RMF/ChangeLog.md | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/modules/rmf/dependency/RMF/CMakeLists.txt b/modules/rmf/dependency/RMF/CMakeLists.txt index a60daaca9b..734992b33d 100644 --- a/modules/rmf/dependency/RMF/CMakeLists.txt +++ b/modules/rmf/dependency/RMF/CMakeLists.txt @@ -134,7 +134,7 @@ set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib) # Version information set (RMF_VERSION_MAJOR 1) -set (RMF_VERSION_MINOR 3) +set (RMF_VERSION_MINOR 4) set(RMF_SOVERSION "${RMF_VERSION_MAJOR}.${RMF_VERSION_MINOR}" CACHE INTERNAL "" FORCE) set(RMF_HAS_DEBUG_VECTOR 0 CACHE BOOL "Whether to use a bounds checked vector") diff --git a/modules/rmf/dependency/RMF/ChangeLog.md b/modules/rmf/dependency/RMF/ChangeLog.md index 7f6ca62bd7..c9bd18447f 100644 --- a/modules/rmf/dependency/RMF/ChangeLog.md +++ b/modules/rmf/dependency/RMF/ChangeLog.md @@ -1,12 +1,13 @@ Change Log {#changelog} ========== -# HEAD +# 1.4 - 2022-03-10 # {#changelog_1_4} - RMF now requires a C++11 compiler and SWIG 3 (or later) to build. Most recent compilers should support C++11, such as gcc, clang - or MS Visual Studio 2015 or later. Various macro and header workarounds + or MS Visual Studio 2012 or later. Various macro and header workarounds for pre-C++11 environments are thus no longer needed and are deprecated: - `RMF_FINAL`, `RMF_OVERRIDE`, `RMF_CANEXCEPT`, `RMF_FOREACH`. + `RMF_FINAL`, `RMF_OVERRIDE`, and `RMF_FOREACH`. +- Build fixes for latest log4cxx, in C++17 mode, or with newer versions of gcc. # 1.3.1 - 2021-12-01 # {#changelog_1_3_1} - Various build fixes for newer versions of gcc and clang. From ce24a0108297de7d5b0795621d4fd55b2dbf6746 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 11 Mar 2022 12:39:32 -0800 Subject: [PATCH 085/155] Use 'auto' rather than trying to guess type Depending on the map implementation we use, the iterator may not return a std::pair but instead something that can be converted to one. Use auto to prevent an unnecessary conversion (and creation of a temporary object). --- .../container_templates/container/classnames.cpp | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/tools/build/container_templates/container/classnames.cpp b/tools/build/container_templates/container/classnames.cpp index cf8fb12cec..6ebb900dbf 100644 --- a/tools/build/container_templates/container/classnames.cpp +++ b/tools/build/container_templates/container/classnames.cpp @@ -513,8 +513,7 @@ void PredicateClassnamesRestraint::do_add_score_and_derivatives( // currently ignores all maxima // no longer parallizable update_lists_if_necessary(); - typedef std::pair LP; - for(const LP & lp : lists_) { + for(const auto &lp : lists_) { IMP_LOG_VERBOSE("Evaluating score for predicate value " << lp.first << std::endl); ClassnameScore* score= get_score_for_predicate(lp.first); @@ -533,8 +532,7 @@ ModelObjectsTemp PredicateClassnamesRestraint::do_get_inputs() const { ParticleIndexes all = input_->get_all_possible_indexes(); ret += predicate_->get_inputs(get_model(), all); if(!is_get_inputs_ignores_individual_scores_){ - typedef std::pair > SP; - for(const SP & sp : scores_) { + for(const auto &sp : scores_) { ret += sp.second->get_inputs(get_model(), all); } } @@ -544,8 +542,7 @@ ModelObjectsTemp PredicateClassnamesRestraint::do_get_inputs() const { Restraints PredicateClassnamesRestraint::do_create_current_decomposition() const { Restraints ret; - typedef std::pair LP; - for(const LP & lp : lists_) { + for(const auto &lp : lists_) { if(lists_.size()>0){ ClassnameScore* score= get_score_for_predicate(lp.first); if(IMP_LIKELY(score != nullptr)){ @@ -575,8 +572,7 @@ void PredicateClassnamesRestraint::update_lists_if_necessary() const { lists_it.value().clear(); } #else - typedef std::pair LP; - for(LP & lp : lists_) { + for(auto &lp : lists_) { lp.second.clear(); } #endif From 511befec84e80a74685f9bee9562b48659aad610 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 29 Mar 2022 12:40:49 -0700 Subject: [PATCH 086/155] Get latest bayesianem --- modules/bayesianem | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/bayesianem b/modules/bayesianem index 8cbbde4df6..aeb6c4e01b 160000 --- a/modules/bayesianem +++ b/modules/bayesianem @@ -1 +1 @@ -Subproject commit 8cbbde4df6c4f2e57c193563146f8c55b3417548 +Subproject commit aeb6c4e01b68431cf2fb763c807c68b763eba5c4 From 9c570e5b23192642cc14489206830da8d7e526cc Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 4 Apr 2022 14:52:24 -0700 Subject: [PATCH 087/155] Fix typo --- doc/manual/dependencies.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/manual/dependencies.md b/doc/manual/dependencies.md index 8273dd3aa3..1d4798b68f 100644 --- a/doc/manual/dependencies.md +++ b/doc/manual/dependencies.md @@ -11,7 +11,7 @@ When the graph changes, it must be updated. This is done by simply invalidating - a new IMP::ModelObject is created that has a non-empty IMP::ModelObject::get_outputs(). - when IMP::Model::set_has_dependencies(false) is called to deliberately invalidate all dependencies -Each IMP::ModelObject has a bit for whether it's dependencies are valid (IMP::ModelObject::get_has_dependencies()). Its dependencies will be updated any time they are needed (particularly when its IMP::ModelObject::get_required_score_states() method is called. This occurs by having the IMP::Model create the dependency graph if needed and then for each input +Each IMP::ModelObject has a bit for whether its dependencies are valid (IMP::ModelObject::get_has_dependencies()). Its dependencies will be updated any time they are needed (particularly when its IMP::ModelObject::get_required_score_states() method is called. This occurs by having the IMP::Model create the dependency graph if needed and then for each input - add its IMP::ModelObject::get_required_score_state() to the list - if it is an IMP::ScoreState, add it to the list. From 6397c9712636492f4b30edc3c076690d5bbbfffd Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 4 Apr 2022 14:58:31 -0700 Subject: [PATCH 088/155] Remove IncrementalScoringFunction example We will deprecate IncrementalScoringFunction, so rmeove text pertaining to it from the docs. --- doc/manual/dependencies.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/doc/manual/dependencies.md b/doc/manual/dependencies.md index 1d4798b68f..9c05c09a25 100644 --- a/doc/manual/dependencies.md +++ b/doc/manual/dependencies.md @@ -15,4 +15,7 @@ Each IMP::ModelObject has a bit for whether its dependencies are valid (IMP::Mod - add its IMP::ModelObject::get_required_score_state() to the list - if it is an IMP::ScoreState, add it to the list. -As a special case, the IMP::core::IncrementalScoringFunction has to take action after its dependencies are updated. This is because it keeps track of which restraints depend on which of the IMP::Particle instances that it is keeping track of. To do this, the IMP::ModelObject::do_set_has_dependencies() is called after dependencies are set up. IMP::core::IncrementalScoringFunction uses that function to compute its dependencies. +Code can often be made more efficient by caching any data structures that are +derived from the dependency graph, since this graph rarely changes in many +common workflows. To aid in this, use the IMP::Model::get_dependencies_updated() +method, which returns the model age when the graph was last updated. From 965dc67d64538f055d35b5b1bcf22195cb1293f3 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 4 Apr 2022 15:08:49 -0700 Subject: [PATCH 089/155] Remove obsolete examples These examples are at best misleading as they make heavy use of functionality that is rarely used in most contemporary modeling (e.g. domino, IncrementalScoringFunction, protocols written in C++ instead of Python). --- modules/example/src/complex_assembly.cpp | 171 ----------------------- modules/example/src/optimize_balls.cpp | 118 ---------------- 2 files changed, 289 deletions(-) delete mode 100644 modules/example/src/complex_assembly.cpp delete mode 100644 modules/example/src/optimize_balls.cpp diff --git a/modules/example/src/complex_assembly.cpp b/modules/example/src/complex_assembly.cpp deleted file mode 100644 index e05212f015..0000000000 --- a/modules/example/src/complex_assembly.cpp +++ /dev/null @@ -1,171 +0,0 @@ -/** - * \file complex_assembly.cpp - * \brief A Score on the distance between a pair of particles. - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - */ - -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -IMPEXAMPLE_BEGIN_NAMESPACE - -class AssemblyData { - ParticlesTemp ps_; - boost::unordered_map index_; - Restraints rs_; - ParticlesTemps particles_; - domino::InteractionGraph interactions_; - - int get_degree(unsigned int i, const ParticlesTemp &ps) const { - int ret = 0; - domino::InteractionGraphConstVertexName vm = - boost::get(boost::vertex_name, interactions_); - std::pair be = - boost::adjacent_vertices(i, interactions_); - for (; be.first != be.second; ++be.first) { - if (std::binary_search(ps.begin(), ps.end(), vm[*be.first])) { - ++ret; - } - } - return ret; - } - - public: - AssemblyData(Model *m, ParticleIndexes ps, const RestraintsTemp &rs) - : rs_(rs.begin(), rs.end()) { - ps_ = IMP::get_particles(m, ps); - std::sort(ps_.begin(), ps_.end()); - interactions_ = domino::get_interaction_graph(rs, ps_); - for (unsigned int i = 0; i < rs.size(); ++i) { - ParticlesTemp cur = IMP::get_input_particles(rs[i]->get_inputs()); - std::sort(cur.begin(), cur.end()); - cur.erase(std::unique(cur.begin(), cur.end()), cur.end()); - ParticlesTemp used; - std::set_intersection(cur.begin(), cur.end(), ps_.begin(), ps_.end(), - std::back_inserter(used)); - particles_.push_back(used); - } - } - RestraintsTemp get_restraints(ParticlesTemp ps) const { - std::sort(ps.begin(), ps.end()); - RestraintsTemp ret; - for (unsigned int i = 0; i < rs_.size(); ++i) { - ParticlesTemp used; - std::set_intersection(particles_[i].begin(), particles_[i].end(), - ps.begin(), ps.end(), std::back_inserter(used)); - if (used.size() == particles_[i].size()) { - ret.push_back(rs_[i]); - } - } - return ret; - } - Particle *get_highest_degree_unused_particle(ParticlesTemp ps) - const { - std::sort(ps.begin(), ps.end()); - int md = 0; - int mi = -1; - domino::InteractionGraphConstVertexName vm = - boost::get(boost::vertex_name, interactions_); - for (unsigned int i = 0; i < boost::num_vertices(interactions_); ++i) { - if (std::binary_search(ps.begin(), ps.end(), vm[i])) continue; - int degree = get_degree(i, ps); - if (degree >= md) { - md = degree; - mi = i; - } - } - return vm[mi]; - } -}; - -/** Provide an example of a more involved protocol for assembly a complex. The - protocol adds the particles one at a time based on how well connected they - are to the already added particles (in the interaction graph). After each - addition, the assembly is optimized. The protocol seems to work at - assembling the residues of a protein from a truncated distance matrix. -*/ -void optimize_assembly(Model *m, - const ParticleIndexes &components, - const RestraintsTemp &interactions, - const RestraintsTemp &other_restraints, - const algebra::BoundingBox3D &bb, PairScore *ev, - double cutoff, const PairPredicates &excluded) { - IMP_NEW(core::ConjugateGradients, cg, (m)); - cg->set_log_level(IMP::SILENT); - IMP_NEW(core::MonteCarlo, mc, (m)); - mc->set_log_level(IMP::SILENT); - IMP_NEW(core::IncrementalScoringFunction, isf, - (m, components, other_restraints)); - mc->set_incremental_scoring_function(isf); - AssemblyData ad(m, components, interactions); - ParticlesTemp cur; - IMP_NEW(container::ListSingletonContainer, active, (m)); - // fix distance - IMP_NEW(container::ClosePairContainer, cpc, (active, 0, 4)); - cpc->set_pair_filters(excluded); - IMP_NEW(core::SoftSpherePairScore, ssps, (10)); - Pointer evr = - container::create_restraint(ssps.get(), cpc.get()); - IMP_NEW(core::HarmonicUpperBound, hub, (0, 10)); - IMP_NEW(core::BoundingBox3DSingletonScore, bbss, (hub, bb)); - Pointer bbr = - container::create_restraint(bbss.get(), active.get()); - do { - Particle *add = ad.get_highest_degree_unused_particle(cur); - cur.push_back(add); - core::XYZ(add).set_coordinates(algebra::get_random_vector_in(bb)); - mc->clear_movers(); - mc->add_mover(create_serial_mover(m, IMP::get_indexes(cur))); - isf->clear_close_pair_scores(); - isf->add_close_pair_score(ev, 0, cur, excluded); - RestraintsTemp rs = other_restraints + ad.get_restraints(cur); - IMP_LOG_TERSE("Current restraints are " << rs << " and particles " << cur - << std::endl); - mc->set_scoring_function(rs); - cg->set_scoring_function(rs + RestraintsTemp(1, evr.get()) + - RestraintsTemp(1, bbr.get())); - active->set(IMP::get_indexes(cur)); - double e; - for (int j = 0; j < 5; ++j) { - mc->set_kt(100.0 / (3 * j + 1)); - mc->optimize(cur.size() * (j + 1) * 1000); - e = cg->optimize(10 * cur.size()); - IMP_LOG_PROGRESS("Energy is " << e << std::endl); - } - if (e > cutoff) { - IMP_THROW("Failure to converge", ModelException); - } - } while (cur.size() != components.size()); -} - -IMPEXAMPLE_END_NAMESPACE diff --git a/modules/example/src/optimize_balls.cpp b/modules/example/src/optimize_balls.cpp deleted file mode 100644 index 50a91bf184..0000000000 --- a/modules/example/src/optimize_balls.cpp +++ /dev/null @@ -1,118 +0,0 @@ -/** - * \file optimize_balls.cpp - * \brief A Score on the distance between a pair of particles. - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - */ - -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -/* - \example optimize_balls.cpp - This is a C++ equivalent to the optimize_balls.py python example. -*/ - -IMPEXAMPLE_BEGIN_NAMESPACE - -core::MonteCarloMover *create_serial_mover(Model *m, - const ParticleIndexes &pis) { - core::MonteCarloMovers movers; - for (unsigned int i = 0; i < pis.size(); ++i) { - double scale = core::XYZR(m, pis[i]).get_radius(); - movers.push_back( - new core::BallMover(m, pis[i], scale * 2)); - } - IMP_NEW(core::SerialMover, sm, (get_as(movers))); - return sm.release(); -} - -/** Take a set of core::XYZR particles and relax them relative to a set of - restraints. Excluded volume is handle separately, so don't include it -in the passed list of restraints. */ -void optimize_balls(Model *m, - const ParticleIndexes &pis, - const RestraintsTemp &rs, - const PairPredicates &excluded, - const OptimizerStates &opt_states, LogLevel ll) { - // make sure that errors and log messages are marked as coming from this - // function - IMP_FUNCTION_LOG; - SetLogState sls(ll); - IMP_ALWAYS_CHECK(!pis.empty(), "No Particles passed.", ValueException); - // double scale = core::XYZR(ps[0]).get_radius(); - - IMP_NEW(core::SoftSpherePairScore, ssps, (10)); - IMP_NEW(core::ConjugateGradients, cg, (m)); - cg->set_optimizer_states(opt_states); - { - // set up restraints for cg - IMP_NEW(container::ListSingletonContainer, lsc, (m, pis)); - IMP_NEW(container::ClosePairContainer, cpc, - (lsc, 0, core::XYZR(m, pis[0]).get_radius())); - cpc->add_pair_filters(excluded); - Pointer r = - container::create_restraint(ssps.get(), cpc.get()); - cg->set_scoring_function(rs + RestraintsTemp(1, r.get())); - cg->set_optimizer_states(opt_states); - } - IMP_NEW(core::MonteCarlo, mc, (m)); - mc->set_optimizer_states(opt_states); - IMP_NEW(core::IncrementalScoringFunction, isf, (m, pis, rs)); - { - // set up MC - mc->add_mover(create_serial_mover(m, pis)); - // we are special casing the nbl term for montecarlo, but using all for CG - mc->set_incremental_scoring_function(isf); - // use special incremental support for the non-bonded part - isf->add_close_pair_score(ssps, 0, IMP::get_particles(m, pis), excluded); - // make pointer vector - } - - IMP_LOG_PROGRESS("Performing initial optimization" << std::endl); - { - boost::ptr_vector attrs; - for (unsigned int j = 0; j < attrs.size(); ++j) { - attrs.push_back( - new ScopedSetFloatAttribute(m->get_particle(pis[j]), - core::XYZR::get_radius_key(), 0)); - } - cg->optimize(1000); - } - // shrink each of the particles, relax the configuration, repeat - for (int i = 0; i < 11; ++i) { - boost::ptr_vector attrs; - double factor = .1 * i; - IMP_LOG_PROGRESS("Optimizing with radii at " << factor << " of full" - << std::endl); - for (unsigned int j = 0; j < pis.size(); ++j) { - attrs.push_back( - new ScopedSetFloatAttribute(m->get_particle(pis[j]), - core::XYZR::get_radius_key(), - core::XYZR(m, pis[j]).get_radius() * factor)); - } - // changed all radii - isf->set_moved_particles(isf->get_movable_indexes()); - for (int j = 0; j < 5; ++j) { - mc->set_kt(100.0 / (3 * j + 1)); - mc->optimize(pis.size() * (j + 1) * 100); - double e = cg->optimize(10); - IMP_LOG_PROGRESS("Energy is " << e << std::endl); - if (e < .000001) break; - } - } -} - -IMPEXAMPLE_END_NAMESPACE From d91a0ffe48702d200de3f850055f663922760dd3 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 4 Apr 2022 16:00:46 -0700 Subject: [PATCH 090/155] Replace IncrementalScoringFunction with move-aware --- ...nk_ms.py => test_moved_mc_crosslink_ms.py} | 172 +++++++++--------- 1 file changed, 89 insertions(+), 83 deletions(-) rename modules/isd/test/{test_incremental_mc_crosslink_ms.py => test_moved_mc_crosslink_ms.py} (64%) diff --git a/modules/isd/test/test_incremental_mc_crosslink_ms.py b/modules/isd/test/test_moved_mc_crosslink_ms.py similarity index 64% rename from modules/isd/test/test_incremental_mc_crosslink_ms.py rename to modules/isd/test/test_moved_mc_crosslink_ms.py index 86eda86d6e..b07344d149 100644 --- a/modules/isd/test/test_incremental_mc_crosslink_ms.py +++ b/modules/isd/test/test_moved_mc_crosslink_ms.py @@ -4,9 +4,68 @@ import IMP.isd import IMP.test + +def setup_system(coords): + num_balls = 2 + m = IMP.Model() + bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0), + IMP.algebra.Vector3D(30, 30, 30)) + + psigma=IMP.Particle(m) + s1i=psigma.get_index() + s2i=psigma.get_index() + sigma = IMP.isd.Nuisance.setup_particle(psigma) + sigma.set_lower(0.) + sigma.set_nuisance(10) + sigma.set_nuisance_is_optimized(True) + + ppsi=IMP.Particle(m) + psii=ppsi.get_index() + psi = IMP.isd.Nuisance.setup_particle(ppsi) + psi.set_lower(0.) + psi.set_nuisance(0.05) + psi.set_nuisance_is_optimized(True) + + ps=[] + restraints=[] + for n in range(10): + dr = IMP.isd.CrossLinkMSRestraint(m, 21.0, 0.01) + + p1=IMP.Particle(m) + p1i=p1.get_index() + d = IMP.core.XYZR.setup_particle(p1) + d.set_radius(10) + d.set_coordinates(coords[n*2]) + d.set_coordinates_are_optimized(True) + + p2=IMP.Particle(m) + p2i=p2.get_index() + d = IMP.core.XYZR.setup_particle(p2) + d.set_radius(10) + d.set_coordinates(coords[n*2+1]) + d.set_coordinates_are_optimized(True) + + dr.add_contribution((p1i, p2i), (s1i, s2i), psii) + ps+=[p1,p2] + restraints.append(dr) + + mc = IMP.core.MonteCarlo(m) + sf = IMP.core.RestraintsScoringFunction(restraints) + mc.set_scoring_function(sf) + + mvs = [IMP.core.BallMover(m, [p], 5) for p in ps] + sm = IMP.core.SerialMover(mvs) + mc.add_mover(sm) + # Always reject upwards moves + mc.set_kt(0.) + mc.set_return_best(False) + return m, mc + + class Tests(IMP.test.TestCase): - def test_incremental_sanity(self): - """Test ISD restraints functionality and sanity with incremental MC scoring""" + def test_moved_sanity(self): + """Test ISD restraints functionality and sanity with + move-aware MC scoring""" num_balls = 2 num_mc_steps = 10 m = IMP.Model() @@ -50,85 +109,37 @@ def test_incremental_sanity(self): dr.add_contribution((p1i, p2i), (s1i, s2i), psii) mc = IMP.core.MonteCarlo(m) - isf = IMP.core.IncrementalScoringFunction(m, [p1,p2,psigma,ppsi], [dr]) - mc.set_incremental_scoring_function(isf) + sf = IMP.core.RestraintsScoringFunction([dr]) + mc.set_scoring_function(sf) + mc.set_score_moved(True) mvs = [IMP.core.BallMover(m, [p], 5) for p in [p1,p2]] sm = IMP.core.SerialMover(mvs) mc.add_mover(sm) - initial=isf.evaluate(False) + initial=sf.evaluate(False) after = mc.optimize(num_mc_steps) - def test_incremental_score(self): - """Test ISD restraints with incremental MC scoring score is indentical""" - - num_balls = 2 - num_mc_steps = 10 - m = IMP.Model() - bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0), - IMP.algebra.Vector3D(30, 30, 30)) - - psigma=IMP.Particle(m) - s1i=psigma.get_index() - s2i=psigma.get_index() - sigma = IMP.isd.Nuisance.setup_particle(psigma) - sigma.set_lower(0.) - sigma.set_nuisance(10) - sigma.set_nuisance_is_optimized(True) - - ppsi=IMP.Particle(m) - psii=ppsi.get_index() - psi = IMP.isd.Nuisance.setup_particle(ppsi) - psi.set_lower(0.) - psi.set_nuisance(0.05) - psi.set_nuisance_is_optimized(True) - - - ps=[] - restraints=[] - for n in range(10): - - dr = IMP.isd.CrossLinkMSRestraint( - m, - 21.0, - 0.01) - - p1=IMP.Particle(m) - p1i=p1.get_index() - d = IMP.core.XYZR.setup_particle(p1) - d.set_radius(10) - d.set_coordinates(IMP.algebra.get_random_vector_in(bb)) - d.set_coordinates_are_optimized(True) - - p2=IMP.Particle(m) - p2i=p2.get_index() - d = IMP.core.XYZR.setup_particle(p2) - d.set_radius(10) - d.set_coordinates(IMP.algebra.get_random_vector_in(bb)) - d.set_coordinates_are_optimized(True) + def test_moved_score(self): + """Test ISD restraints with move-aware MC scoring is indentical""" - dr.add_contribution((p1i, p2i), (s1i, s2i), psii) - ps+=[p1,p2] - restraints.append(dr) + bb = IMP.algebra.get_unit_bounding_box_3d() + coords = [IMP.algebra.get_random_vector_in(bb) for _ in range(20)] + m1, mc1 = setup_system(coords) + m2, mc2 = setup_system(coords) + # Same seeed, same system, so we should get identical trajectories + IMP.random_number_generator.seed(99) + mc1_score = mc1.optimize(100) - mc = IMP.core.MonteCarlo(m) - sf = IMP.core.RestraintsScoringFunction(restraints) - isf = IMP.core.IncrementalScoringFunction(m, ps+[psigma,ppsi], - restraints) - mc.set_incremental_scoring_function(isf) + mc2.set_score_moved(True) + IMP.random_number_generator.seed(99) + mc2_score = mc2.optimize(100) - mvs = [IMP.core.BallMover(m, [p], 5) for p in ps] - sm = IMP.core.SerialMover(mvs) - mc.add_mover(sm) + self.assertAlmostEqual(mc1_score, mc2_score, delta=1e-2) - self.assertAlmostEqual(isf.evaluate(False),sf.evaluate(False)) - mc.optimize(num_mc_steps*len(ps)) - self.assertAlmostEqual(isf.evaluate(False),sf.evaluate(False)) - - def test_incremental_score_optimization(self): - """Test ISD restraints with incremental MC score decreases""" + def test_moved_score_optimization(self): + """Test ISD restraints with move-aware MC score decreases""" num_mc_steps = 10 m = IMP.Model() @@ -182,10 +193,9 @@ def test_incremental_score_optimization(self): mc = IMP.core.MonteCarlo(m) - isf = IMP.core.IncrementalScoringFunction(m, ps+[psigma,ppsi], - restraints) - mc.set_incremental_scoring_function(isf) sf = IMP.core.RestraintsScoringFunction(restraints) + mc.set_scoring_function(sf) + mc.set_score_moved(True) mvs = [IMP.core.BallMover(m, [p], 5) for p in ps] sm = IMP.core.SerialMover(mvs) @@ -193,11 +203,10 @@ def test_incremental_score_optimization(self): for i in range(10): mc.optimize(len(ps)) - print(isf.evaluate(False)) - + print(sf.evaluate(False)) - def test_incremental_score_rigid_bodies(self): - """Test ISD restraints with incremental MC score decreases""" + def test_moved_score_rigid_bodies(self): + """Test ISD restraints with score-aware MC score decreases""" import random @@ -260,10 +269,9 @@ def test_incremental_score_rigid_bodies(self): mc = IMP.core.MonteCarlo(m) print(list(set(restraints))) - isf = IMP.core.IncrementalScoringFunction(m, - [rb1.get_particle(),rb2.get_particle()] +ps+[psigma,ppsi], - list(set(restraints))) - mc.set_incremental_scoring_function(isf) + sf = IMP.core.RestraintsScoringFunction(list(set(restraints))) + mc.set_scoring_function(sf) + mc.set_score_moved(True) mvs = [IMP.core.RigidBodyMover(m, rb1, 1.0, 0.03), IMP.core.RigidBodyMover(m, rb2, 1.0, 0.03)] @@ -272,9 +280,7 @@ def test_incremental_score_rigid_bodies(self): for i in range(10): mc.optimize(len(mvs)) - print(isf.evaluate(False)) - - + print(sf.evaluate(False)) if __name__ == '__main__': From 9c41a93a822f55be4436894c8be6d43c928a242a Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 4 Apr 2022 16:27:10 -0700 Subject: [PATCH 091/155] Replace IncrementalScoringFunction Use move-aware MonteCarlo scoring rather than the IncrementalScoringFunction. --- modules/core/examples/optimize_balls.py | 21 ++++++--------------- 1 file changed, 6 insertions(+), 15 deletions(-) diff --git a/modules/core/examples/optimize_balls.py b/modules/core/examples/optimize_balls.py index 0c7d3495ea..7e8e2fb968 100644 --- a/modules/core/examples/optimize_balls.py +++ b/modules/core/examples/optimize_balls.py @@ -1,6 +1,6 @@ ## \example core/optimize_balls.py # This example optimizes a set of a balls to form 100 chains packed into a -# box. It illustrates using Monte Carlo (incremental) and conjugate +# box. It illustrates using Monte Carlo and conjugate # gradients in conjunction in a non-trivial optimization. import IMP.core @@ -84,15 +84,6 @@ mc.set_name("MC") sm = IMP.core.SerialMover(movers) mc.add_mover(sm) -# we are special casing the nbl term -isf = IMP.core.IncrementalScoringFunction(m, aps, restraints) -isf.set_name("I") -# use special incremental support for the non-bonded part -# apply the pair score sps to all touching ball pairs from the list -# of particles aps, using the filters to remove undersired pairs -# this is equivalent to the nbl construction above but optimized for -# incremental -isf.add_close_pair_score(sps, 0, aps, filters) # create a scoring function for conjugate gradients that includes the # ExcludedVolumeRestraint @@ -100,11 +91,11 @@ nbl.set_pair_filters(filters) sf = IMP.core.RestraintsScoringFunction(restraints + [nbl], "RSF") -if True: - mc.set_incremental_scoring_function(isf) -else: - # we could, instead do non-incremental scoring - mc.set_scoring_function(sf) +mc.set_scoring_function(sf) + +# Speed up the optimization by only rescoring terms involving particles +# that moved at each MC step +mc.set_score_moved(True) # first relax the bonds a bit rs = [] From 983cd3492d59301e4f3de18189cf8f0cc2887857 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 4 Apr 2022 16:41:03 -0700 Subject: [PATCH 092/155] Replace IncrementalScoringFunction with move-aware MC --- .../{incremental_mc.py => move_aware_mc.py} | 20 ++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) rename modules/core/examples/{incremental_mc.py => move_aware_mc.py} (69%) diff --git a/modules/core/examples/incremental_mc.py b/modules/core/examples/move_aware_mc.py similarity index 69% rename from modules/core/examples/incremental_mc.py rename to modules/core/examples/move_aware_mc.py index 008e294daf..735869ff86 100644 --- a/modules/core/examples/incremental_mc.py +++ b/modules/core/examples/move_aware_mc.py @@ -1,6 +1,6 @@ -## \example core/incremental_mc.py -# This example shows how to do incremental scoring with Monte Carlo. -# Incremental scoring can be significantly faster than non-incremental +## \example core/move_aware_mc.py +# This example shows how to do move-aware scoring with Monte Carlo. +# Move-aware scoring can be significantly faster than regular # scoring when using moves that only move a few particles at a time. import IMP.core @@ -36,17 +36,23 @@ IMP.core.HarmonicUpperBound(0, 1), bb), psl) mc = IMP.core.MonteCarlo(m) -isf = IMP.core.IncrementalScoringFunction(m, ps, [r, rb]) -mc.set_incremental_scoring_function(isf) +sf = IMP.core.RestraintsScoringFunction([r, rb]) +mc.set_scoring_function(sf) + +# Turn on move-aware scoring. +# At each MC step, only the scoring function terms that involve at least +# one particle moved by a Mover will be rescored; the remaining terms will +# be cached. +mc.set_score_moved(True) mvs = [IMP.core.BallMover(m, p, 5) for p in ps] sm = IMP.core.SerialMover(mvs) mc.add_mover(sm) IMP.set_log_level(IMP.SILENT) -print("initial", isf.evaluate(False)) +print("initial", sf.evaluate(False)) after = mc.optimize(num_mc_steps) print("final", after) -name = IMP.create_temporary_file_name("incremental_mc", ".pym") +name = IMP.create_temporary_file_name("move_aware_mc", ".pym") w = IMP.display.PymolWriter(name) for p in ps: g = IMP.core.XYZRGeometry(p) From b426d49b4ab192f2208e750c2f56e0b76d14da12 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 4 Apr 2022 16:50:21 -0700 Subject: [PATCH 093/155] Replace IncrementalScoringFunction with move-aware MC --- ...mental_mc.cpp => benchmark_move_aware.cpp} | 27 ++++++------------- 1 file changed, 8 insertions(+), 19 deletions(-) rename modules/atom/benchmark/{benchmark_incremental_mc.cpp => benchmark_move_aware.cpp} (84%) diff --git a/modules/atom/benchmark/benchmark_incremental_mc.cpp b/modules/atom/benchmark/benchmark_move_aware.cpp similarity index 84% rename from modules/atom/benchmark/benchmark_incremental_mc.cpp rename to modules/atom/benchmark/benchmark_move_aware.cpp index 5fa358a7b9..342037273a 100644 --- a/modules/atom/benchmark/benchmark_incremental_mc.cpp +++ b/modules/atom/benchmark/benchmark_move_aware.cpp @@ -87,7 +87,7 @@ Restraint *add_DOPE(Model *, atom::Hierarchy h) { } #endif -void benchmark_it(std::string name, bool incr, bool nbl) { +void benchmark_it(std::string name, bool score_moved, bool nbl) { IMP_NEW(Model, m, ()); atom::Hierarchy h = atom::Hierarchy::setup_particle(new Particle(m)); h->set_name("root"); @@ -98,21 +98,13 @@ void benchmark_it(std::string name, bool incr, bool nbl) { } IMP_NEW(MonteCarlo, mc, (m)); Restraints rs; - if (!incr && nbl) { + if (nbl) { rs.push_back(create_excluded_volume(h, rbs, 1.0)); } rs.push_back(create_diameter_restraint(m, rbs, 50.0)); - if (incr) { - IMP_NEW(core::IncrementalScoringFunction, sf, - (m, IMP::internal::get_index(rbs), rs)); - if (nbl) { - sf->add_close_pair_score(create_pair_score(h, rbs, 1.0), 0, rbs); - } - mc->set_incremental_scoring_function(sf); - } else { - IMP_NEW(core::RestraintsScoringFunction, sf, (rs)); - mc->set_scoring_function(sf); - } + IMP_NEW(core::RestraintsScoringFunction, sf, (rs)); + mc->set_scoring_function(sf); + mc->set_score_moved(score_moved); // add_DOPE(m, h); // mc->set_log_level(VERBOSE); mc->set_return_best(false); @@ -136,16 +128,13 @@ void benchmark_it(std::string name, bool incr, bool nbl) { } double runtime, score = 0; IMP_TIME(score += mc->optimize(nsteps), runtime); - // std::cout << "average: " - //<< mc->get_average_number_of_incremental_restraints() << std::endl; IMP::benchmark::report(name + " mc", runtime, score); } } int main(int argc, char *argv[]) { - IMP::setup_from_argv(argc, argv, "Benchmark incremenal evaluation"); - benchmark_it("incremental nbl", true, true); - benchmark_it("non incremental", false, false); - benchmark_it("incremental", true, false); + IMP::setup_from_argv(argc, argv, "Benchmark move-aware MC"); + benchmark_it("move-aware", false, true); + benchmark_it("non-move-aware", true, true); return 0; } From 4acbed43107568bb3cb0fd65ef16c10a125da8e4 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 09:48:51 -0700 Subject: [PATCH 094/155] Get latest npctransport --- modules/npctransport | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/npctransport b/modules/npctransport index 34f49afef9..8281a86b36 160000 --- a/modules/npctransport +++ b/modules/npctransport @@ -1 +1 @@ -Subproject commit 34f49afef95d800c2aafaad6f2918f8d4cd1e542 +Subproject commit 8281a86b366b85408aa304e89c65561546915445 From e2cf6f7d7331fb4dca8c475c957e33f329f1ff89 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 10:03:52 -0700 Subject: [PATCH 095/155] Remove references to removed functions --- modules/example/include/complex_assembly.h | 33 ----------------- modules/example/include/optimizing.h | 41 ---------------------- modules/example/pyext/swig.i-in | 2 -- 3 files changed, 76 deletions(-) delete mode 100644 modules/example/include/complex_assembly.h delete mode 100644 modules/example/include/optimizing.h diff --git a/modules/example/include/complex_assembly.h b/modules/example/include/complex_assembly.h deleted file mode 100644 index 00b197747d..0000000000 --- a/modules/example/include/complex_assembly.h +++ /dev/null @@ -1,33 +0,0 @@ -/** - * \file IMP/example/complex_assembly.h - * \brief A simple unary function. - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - * - */ - -#ifndef IMPEXAMPLE_COMPLEX_ASSEMBLY_H -#define IMPEXAMPLE_COMPLEX_ASSEMBLY_H - -#include -#include -#include - -IMPEXAMPLE_BEGIN_NAMESPACE - -/** Provide an example of a more involved protocol for assembly a complex. The - protocol adds the particles one at a time based on how well connected they - are to the already added particles (in the interaction graph). After each - addition, the assembly is optimized. The protocol seems to work at - assembling the residues of a protein from a truncated distance matrix. -*/ -IMPEXAMPLEEXPORT void optimize_assembly( - Model *m, const ParticleIndexes &components, - const RestraintsTemp &interactions, - const RestraintsTemp &other_restraints, - const algebra::BoundingBox3D &bb, PairScore *ev, double cutoff, - const PairPredicates &excluded = PairPredicates()); - -IMPEXAMPLE_END_NAMESPACE - -#endif /* IMPEXAMPLE_COMPLEX_ASSEMBLY_H */ diff --git a/modules/example/include/optimizing.h b/modules/example/include/optimizing.h deleted file mode 100644 index bd0d836a97..0000000000 --- a/modules/example/include/optimizing.h +++ /dev/null @@ -1,41 +0,0 @@ -/** - * \file IMP/example/optimizing.h - * \brief A simple unary function. - * - * Copyright 2007-2022 IMP Inventors. All rights reserved. - * - */ - -#ifndef IMPEXAMPLE_OPTIMIZING_H -#define IMPEXAMPLE_OPTIMIZING_H - -#include -#include -#include -#include -#include -#include - -IMPEXAMPLE_BEGIN_NAMESPACE -/** Create a serial mover from a list of core::XYZR particles. - */ -IMPEXAMPLEEXPORT core::MonteCarloMover *create_serial_mover(Model *m, - const ParticleIndexes &pis); - -/** Take a set of core::XYZR particles and relax them relative to a set of - restraints. Excluded volume is handle separately, so don't include it - in the passed list of restraints. - - \include optimize_balls.cpp -*/ -IMPEXAMPLEEXPORT void optimize_balls( - Model *m, - const ParticleIndexes &pis, - const RestraintsTemp &rs = RestraintsTemp(), - const PairPredicates &excluded = PairPredicates(), - const OptimizerStates &opt_states = OptimizerStates(), - LogLevel ll = DEFAULT); - -IMPEXAMPLE_END_NAMESPACE - -#endif /* IMPEXAMPLE_OPTIMIZING_H */ diff --git a/modules/example/pyext/swig.i-in b/modules/example/pyext/swig.i-in index fa9579b4c9..3a2a53d9f1 100644 --- a/modules/example/pyext/swig.i-in +++ b/modules/example/pyext/swig.i-in @@ -67,8 +67,6 @@ def create_model_and_particles(): %include "IMP/example/ExampleConstraint.h" %include "IMP/example/randomizing.h" -%include "IMP/example/optimizing.h" -%include "IMP/example/complex_assembly.h" %include "IMP/example/counting.h" %include "IMP/example/creating_restraints.h" From 1a612e4bd5354b34433491cdc8634a13f9743449 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 13:18:55 -0700 Subject: [PATCH 096/155] Show docs for unprotected_evaluate and friends --- modules/kernel/include/Restraint.h | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/modules/kernel/include/Restraint.h b/modules/kernel/include/Restraint.h index 91261ebec8..ee80214e74 100644 --- a/modules/kernel/include/Restraint.h +++ b/modules/kernel/include/Restraint.h @@ -99,6 +99,7 @@ class IMPKERNELEXPORT Restraint : public ModelObject { //! \see Model::evaluate_with_maximum() double evaluate_if_below(bool calc_derivatives, double max) const; +#endif /** \name Evaluation implementation These methods are called in order to perform the actual restraint @@ -119,6 +120,15 @@ class IMPKERNELEXPORT Restraint : public ModelObject { /** By default this just calls regular unprotected_evaluate(), but may be overridden by restraints to be more efficient, e.g. by skipping terms that involve unchanged particles. + + \param da Object to accumulate derivatives, or nullptr. + \param moved_pis Particles that have moved since the last + scoring function evaluation. + \param reset_pis Particles that have moved, but back to the + positions they had at the last-but-one evaluation + (e.g. due to a rejected Monte Carlo move). + + \return Current score. */ virtual double unprotected_evaluate_moved( DerivativeAccumulator *da, const ParticleIndexes &moved_pis, @@ -159,8 +169,6 @@ class IMPKERNELEXPORT Restraint : public ModelObject { /** @} */ -#endif - //! \return static key:value information about this restraint, or null. /** \return a set of key:value pairs that contain static information about this restraint (i.e. information that doesn't change during @@ -187,6 +195,7 @@ class IMPKERNELEXPORT Restraint : public ModelObject { return nullptr; } +#ifndef IMP_DOXYGEN //! Perform the actual restraint scoring. /** The restraints should assume that all appropriate ScoreState objects have been updated and so that the input particles and containers @@ -197,6 +206,7 @@ class IMPKERNELEXPORT Restraint : public ModelObject { void add_score_and_derivatives_moved( ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const; +#endif //! Decompose this restraint into constituent terms /** Given the set of input particles, decompose the restraint into parts From bfeddc783c3f72280dc6c236bf47b260cc3b2270 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 13:37:11 -0700 Subject: [PATCH 097/155] Add doc crosslinks --- modules/core/include/MonteCarlo.h | 2 ++ modules/kernel/include/ScoringFunction.h | 2 ++ 2 files changed, 4 insertions(+) diff --git a/modules/core/include/MonteCarlo.h b/modules/core/include/MonteCarlo.h index f2ddc27730..c7ec23727e 100644 --- a/modules/core/include/MonteCarlo.h +++ b/modules/core/include/MonteCarlo.h @@ -64,6 +64,8 @@ class IMPCOREEXPORT MonteCarlo : public Optimizer { more quickly by caching the scores on parts of the system that don't move. This is still experimental. + \see IMP::ScoringFunction::evaluate_moved + \note Some MonteCarlo subclasses do local optimization after each move, which can move more particles than the Movers touched. In this case the guarantee does not hold and this optimization diff --git a/modules/kernel/include/ScoringFunction.h b/modules/kernel/include/ScoringFunction.h index 91d2adde1f..4f9d2096c3 100644 --- a/modules/kernel/include/ScoringFunction.h +++ b/modules/kernel/include/ScoringFunction.h @@ -104,6 +104,8 @@ class IMPKERNELEXPORT ScoringFunction : public ModelObject { /** This should behave identically to evaluate() but may be more efficient if it can skip restraint terms that involve unchanged particles. + \see IMP::core::MonteCarlo::set_score_moved + \param moved_pis Particles that have moved since the last scoring function evaluation. \param reset_pis Particles that have moved, but back to the From 02572256d2269d4704de0296885eef4e90133eef Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 13:57:32 -0700 Subject: [PATCH 098/155] Deprecate IncrementalScoringFunction --- ChangeLog.md | 2 ++ modules/core/include/IncrementalScoringFunction.h | 3 +++ modules/core/src/IncrementalScoringFunction.cpp | 2 ++ modules/core/test/expensive_test_incremental_mc.py | 6 ++++-- modules/core/test/test_incremental_scoring.py | 14 +++++++++----- 5 files changed, 20 insertions(+), 7 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index d3a1c2d0e3..d18546a990 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -10,6 +10,8 @@ ChangeLog {#changelog} for pre-C++11 environments are thus no longer needed and are deprecated: `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`, `IMP_FOREACH`, `IMP/nullptr.h`, and `IMP/nullptr_macros.h`. +- The IMP::core::IncrementalScoringFunction class is now deprecated. Use + IMP::ScoringFunction::evaluate_moved instead. # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} - OpenCubicSpline now throws a ValueException for out-of-range values, to diff --git a/modules/core/include/IncrementalScoringFunction.h b/modules/core/include/IncrementalScoringFunction.h index caf20b7d8d..d3a4f80c8c 100644 --- a/modules/core/include/IncrementalScoringFunction.h +++ b/modules/core/include/IncrementalScoringFunction.h @@ -35,6 +35,8 @@ class NBLScoring; To ensure proper evaluation, the ScoringFunction is divided into a number of sub scoring functions, one for each possibly moved particle. + + \deprecated_at{2.17} Use IMP::ScoringFunction::evaluate_moved instead. */ class IMPCOREEXPORT IncrementalScoringFunction : public ScoringFunction { struct Data { @@ -87,6 +89,7 @@ class IMPCOREEXPORT IncrementalScoringFunction : public ScoringFunction { can be ignored for most purposes @param name The name template to use for the scoring function. */ + IMPCORE_DEPRECATED_OBJECT_DECL(2.17) IncrementalScoringFunction(Model *m, const ParticleIndexes &to_move, const RestraintsTemp &rs, diff --git a/modules/core/src/IncrementalScoringFunction.cpp b/modules/core/src/IncrementalScoringFunction.cpp index 0eef009ee6..a93d4c86d8 100644 --- a/modules/core/src/IncrementalScoringFunction.cpp +++ b/modules/core/src/IncrementalScoringFunction.cpp @@ -28,6 +28,8 @@ IncrementalScoringFunction::IncrementalScoringFunction( Model *m, const ParticleIndexes &ps, const RestraintsTemp &rs, double weight, double max, std::string name) : ScoringFunction(m, name), weight_(weight), max_(max) { + IMPCORE_DEPRECATED_OBJECT_DEF( + 2.17, "Use IMP::ScoringFunction::evaluate_moved() instead."); IMP_OBJECT_LOG; IMP_LOG_TERSE("Creating IncrementalScoringFunction with particles " << ps << " and restraints " << rs << std::endl); diff --git a/modules/core/test/expensive_test_incremental_mc.py b/modules/core/test/expensive_test_incremental_mc.py index 938e701667..8b33106b25 100644 --- a/modules/core/test/expensive_test_incremental_mc.py +++ b/modules/core/test/expensive_test_incremental_mc.py @@ -28,7 +28,8 @@ def test_incr(self): # hps.set_log_level(IMP.VERBOSE) r = IMP.container.PairsRestraint(hps, cpc) sf = IMP.core.RestraintsScoringFunction([r]) - isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) + with IMP.allow_deprecated(): + isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) isf.set_log_level(IMP.SILENT) mc.set_incremental_scoring_function(isf) ms = [IMP.core.BallMover(m, [x], .1) for x in ps] @@ -70,7 +71,8 @@ def test_incr_nbl(self): r = IMP.container.PairsRestraint(hps, cpc) # r.set_log_level(IMP.VERBOSE) sf = IMP.core.RestraintsScoringFunction([r]) - isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) + with IMP.allow_deprecated(): + isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) mc.set_incremental_scoring_function(isf) ms = [IMP.core.BallMover(m, [x], 2) for x in ps] mv = IMP.core.SerialMover(ms) diff --git a/modules/core/test/test_incremental_scoring.py b/modules/core/test/test_incremental_scoring.py index 52bfacbc6e..7b6b614378 100644 --- a/modules/core/test/test_incremental_scoring.py +++ b/modules/core/test/test_incremental_scoring.py @@ -36,7 +36,8 @@ def test_incr(self): sf = IMP.core.RestraintsScoringFunction([r, rnb]) dsf = IMP.core.RestraintsScoringFunction([r.create_decomposition(), rnb.create_decomposition()]) - isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) + with IMP.allow_deprecated(): + isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) isf.add_close_pair_score(nbps, 0, IMP.get_particles(m, ps), [f]) print("iscore") iscore = isf.evaluate(False) @@ -95,7 +96,8 @@ def test_incr_no_restraints(self): rnb.set_name("NB") sf = IMP.core.RestraintsScoringFunction([rnb]) dsf = IMP.core.RestraintsScoringFunction([rnb.create_decomposition()]) - isf = IMP.core.IncrementalScoringFunction(m, ps, []) + with IMP.allow_deprecated(): + isf = IMP.core.IncrementalScoringFunction(m, ps, []) isf.add_close_pair_score(nbps, 0, IMP.get_particles(m, ps), []) print("iscore") iscore = isf.evaluate(False) @@ -154,7 +156,8 @@ def test_incrnonb(self): r = IMP.container.PairsRestraint(hps, cpc) dsf = IMP.core.RestraintsScoringFunction([r.create_decomposition()]) sf = IMP.core.RestraintsScoringFunction([r]) - isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) + with IMP.allow_deprecated(): + isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) # isf.set_log_level(IMP.VERBOSE) print('initial test') iscore = isf.evaluate(False) @@ -272,8 +275,9 @@ def test_incrigid(self): rnb.create_decomposition()], 1.0, IMP.NO_MAX, "D") - isf = IMP.core.IncrementalScoringFunction( - m, rbs, [r], 1.0, IMP.NO_MAX, "I") + with IMP.allow_deprecated(): + isf = IMP.core.IncrementalScoringFunction( + m, rbs, [r], 1.0, IMP.NO_MAX, "I") isf.add_close_pair_score(nbps, 0, ps, [f]) # isf.set_log_level(IMP.VERBOSE) iscore = isf.evaluate(False) From a1ae77897ced3c4976fffd5195a952b1cb23fd43 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 13:59:08 -0700 Subject: [PATCH 099/155] Use modern unittest method --- modules/core/test/expensive_test_incremental_mc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/core/test/expensive_test_incremental_mc.py b/modules/core/test/expensive_test_incremental_mc.py index 8b33106b25..11949d8ea6 100644 --- a/modules/core/test/expensive_test_incremental_mc.py +++ b/modules/core/test/expensive_test_incremental_mc.py @@ -96,7 +96,7 @@ def test_incr_nbl(self): # g= IMP.core.XYZRGeometry(p) # w.add_geometry(g); print(sf.evaluate(False)) - self.assert_(sf.evaluate(False) < 3) + self.assertLess(sf.evaluate(False), 3) if __name__ == '__main__': From b8ddbf4da7bf048943ee3b8514f81a1b710ae502 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 14:19:32 -0700 Subject: [PATCH 100/155] Deprecate MonteCarlo.set_incremental_scoring_function --- modules/core/include/MonteCarlo.h | 12 ++++++------ modules/core/src/MonteCarlo.cpp | 1 + modules/core/test/expensive_test_incremental_mc.py | 4 ++-- 3 files changed, 9 insertions(+), 8 deletions(-) diff --git a/modules/core/include/MonteCarlo.h b/modules/core/include/MonteCarlo.h index c7ec23727e..4825991654 100644 --- a/modules/core/include/MonteCarlo.h +++ b/modules/core/include/MonteCarlo.h @@ -148,20 +148,20 @@ class IMPCOREEXPORT MonteCarlo : public Optimizer { MonteCarloMovers, {}, {}, {}); /** @} */ - /** \name Incremental - Efficient evaluation of non-bonded list based restraints is - a bit tricky with incremental evaluation. - @{ - */ /** Set whether to use incremental evaluate or evaluate all restraints each time. This cannot be changed during optimization. + + \deprecated_at{2.17} Use set_score_moved() instead */ + IMPCORE_DEPRECATED_METHOD_DECL(2.17) void set_incremental_scoring_function(IncrementalScoringFunction *isf); + bool get_use_incremental_scoring_function() const { return isf_; } + IncrementalScoringFunction *get_incremental_scoring_function() const { return isf_; } - /** @} */ + protected: /** Get all movable particles (those that can be moved by the current movers.*/ diff --git a/modules/core/src/MonteCarlo.cpp b/modules/core/src/MonteCarlo.cpp index c262580577..c15b4a3b30 100644 --- a/modules/core/src/MonteCarlo.cpp +++ b/modules/core/src/MonteCarlo.cpp @@ -201,6 +201,7 @@ double MonteCarlo::do_optimize(unsigned int max_steps) { } void MonteCarlo::set_incremental_scoring_function( IncrementalScoringFunction *isf) { + IMPCORE_DEPRECATED_METHOD_DEF(2.17, "Use set_score_moved() instead.") isf_ = isf; Optimizer::set_scoring_function(isf); } diff --git a/modules/core/test/expensive_test_incremental_mc.py b/modules/core/test/expensive_test_incremental_mc.py index 11949d8ea6..ced4db2a36 100644 --- a/modules/core/test/expensive_test_incremental_mc.py +++ b/modules/core/test/expensive_test_incremental_mc.py @@ -30,8 +30,8 @@ def test_incr(self): sf = IMP.core.RestraintsScoringFunction([r]) with IMP.allow_deprecated(): isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) + mc.set_incremental_scoring_function(isf) isf.set_log_level(IMP.SILENT) - mc.set_incremental_scoring_function(isf) ms = [IMP.core.BallMover(m, [x], .1) for x in ps] mv = IMP.core.SerialMover(ms) mc.add_mover(mv) @@ -73,7 +73,7 @@ def test_incr_nbl(self): sf = IMP.core.RestraintsScoringFunction([r]) with IMP.allow_deprecated(): isf = IMP.core.IncrementalScoringFunction(m, ps, [r]) - mc.set_incremental_scoring_function(isf) + mc.set_incremental_scoring_function(isf) ms = [IMP.core.BallMover(m, [x], 2) for x in ps] mv = IMP.core.SerialMover(ms) mc.add_mover(mv) From a172a014a0830fd77fc2b6a8d380e930b2b1f873 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 14:20:42 -0700 Subject: [PATCH 101/155] Also point to MonteCarlo.set_score_moved() --- ChangeLog.md | 1 + 1 file changed, 1 insertion(+) diff --git a/ChangeLog.md b/ChangeLog.md index d18546a990..9b7b0ebc47 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -11,6 +11,7 @@ ChangeLog {#changelog} `IMP_NULLPTR`, `IMP_NULLPTR_T`, `IMP_OVERRIDE`, `IMP_FINAL`, `IMP_UNIQUE_PTR`, `IMP_FOREACH`, `IMP/nullptr.h`, and `IMP/nullptr_macros.h`. - The IMP::core::IncrementalScoringFunction class is now deprecated. Use + IMP::core::MonteCarlo::set_score_moved or IMP::ScoringFunction::evaluate_moved instead. # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} From d83f162359f0b7810e64940a71944638e83d56d8 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 5 Apr 2022 14:21:17 -0700 Subject: [PATCH 102/155] Squashed 'modules/core/dependency/python-ihm/' changes from 60e3116cae..7b4cbaff72 7b4cbaff72 Prepare for 0.30 release e7fc2aa4c9 Fix issue noted by flake8 c1f5a60179 Add support for _struct.pdbx_model_details 8aa374aee4 Fix issue noted by flake8 247a0127d5 Check that we can handle missing entity.type 7dd27da34f Handle missing entity.type 18f33d6a0a Fix typo 95fe5f6620 Prepare for 0.29 release a962b5fb3e Ligand atoms should be marked HETATM in atom_site 0bbab144e9 Allow tailoring the writer to the system 6d65b49c55 Improve test coverage 1eaea91fc7 Force polymer if entity.type says so 07de00546e We should conform to dictionary version 1.17 e76ff0a046 Add an example nonpolymer model; closes ihmwg/python-ihm#76 34fecd441e Fix typo 9ab4be7177 Add pdbx_nonpoly_scheme.ndb_seq_num 6894cb0586 Add script to check example outputs for validity d677cb9b26 Remove UTF characters from AlphaFold citation. 95b9933165 Quote strings starting with an underscore 0989b68412 Prepare for 0.28 release 5b17d3d25a Add citation for AlphaFold2 5a08e173fd Pin pytest-flake8 to work around Python2 breakage 221d67e485 Allow explicitly denoting the primary citation 13172e21ad Explain ihm.Citation parametrs a bit clearer. c39898276c Treat single-residue entities as non-polymers 173837f317 Allow non-poly components in poly Entities 57d643f38f Fix UniProtSequence.from_accession on Python 2 31bcf38c04 Allow for hyphens in data block name 4c5dc6895f Make sure odd characters are OK for data on read git-subtree-dir: modules/core/dependency/python-ihm git-subtree-split: 7b4cbaff727475744c33126bea6be65116604458 --- .../python-ihm/.github/workflows/testpy.yml | 2 +- .../core/dependency/python-ihm/ChangeLog.rst | 23 +++++ .../core/dependency/python-ihm/MANIFEST.in | 2 +- .../dependency/python-ihm/docs/citations.rst | 4 + .../python-ihm/examples/ligands_water.py | 32 +++++++ .../python-ihm/examples/simple-docking.py | 2 +- .../dependency/python-ihm/ihm/__init__.py | 41 +++++--- .../dependency/python-ihm/ihm/citations.py | 15 +++ .../core/dependency/python-ihm/ihm/dumper.py | 50 +++++++--- .../core/dependency/python-ihm/ihm/format.py | 5 + .../dependency/python-ihm/ihm/format_bcif.py | 4 + .../core/dependency/python-ihm/ihm/reader.py | 10 +- .../dependency/python-ihm/ihm/reference.py | 20 +++- .../dependency/python-ihm/make-release.sh | 1 + modules/core/dependency/python-ihm/setup.py | 2 +- .../dependency/python-ihm/test/test_dumper.py | 94 +++++++++++++++++-- .../python-ihm/test/test_examples.py | 8 +- .../dependency/python-ihm/test/test_format.py | 2 + .../dependency/python-ihm/test/test_main.py | 18 ++++ .../dependency/python-ihm/test/test_reader.py | 53 +++++++++-- .../python-ihm/util/validate-outputs.py | 33 +++++++ 21 files changed, 370 insertions(+), 51 deletions(-) create mode 100755 modules/core/dependency/python-ihm/util/validate-outputs.py diff --git a/modules/core/dependency/python-ihm/.github/workflows/testpy.yml b/modules/core/dependency/python-ihm/.github/workflows/testpy.yml index ed7a840670..38bb0f621f 100644 --- a/modules/core/dependency/python-ihm/.github/workflows/testpy.yml +++ b/modules/core/dependency/python-ihm/.github/workflows/testpy.yml @@ -28,7 +28,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install coverage pytest-cov pytest-flake8 + pip install coverage pytest-cov 'pytest-flake8<1.1' - name: Test run: | # Test with Python tokenizer diff --git a/modules/core/dependency/python-ihm/ChangeLog.rst b/modules/core/dependency/python-ihm/ChangeLog.rst index 3063b2d2c7..18a2823389 100644 --- a/modules/core/dependency/python-ihm/ChangeLog.rst +++ b/modules/core/dependency/python-ihm/ChangeLog.rst @@ -1,3 +1,26 @@ +0.30 - 2022-04-05 +================= + - Add support for a long description of the system (like an abstract) + using struct.pdbx_model_details (#80). + - Bugfix: correctly read mmCIF files with missing entity.type. + +0.29 - 2022-04-01 +================= + - Output mmCIF files containing non-polymers should now validate against + the PDBx dictionary (#76). + - Bugfix: non-polymers that are erroneously marked as polymers in + the input mmCIF can now be read in without causing a Python + exception (#78). + - Bugfix: strings starting with an underscore (e.g. chain names) are now + quoted in mmCIF output to conform to the CIF syntax (#75). + +0.28 - 2022-03-21 +================= + - :class:`ihm.Citation` now takes a ``is_primary`` argument, which can + be used to denote the most pertinent publication for the modeling. + - Improved support for non-standard residues, and for standard amino acids + used as nonpolymers. + 0.27 - 2022-01-27 ================= - Minor documentation improvements. diff --git a/modules/core/dependency/python-ihm/MANIFEST.in b/modules/core/dependency/python-ihm/MANIFEST.in index 235fc020ad..b8c25c9380 100644 --- a/modules/core/dependency/python-ihm/MANIFEST.in +++ b/modules/core/dependency/python-ihm/MANIFEST.in @@ -4,4 +4,4 @@ include examples/* include util/make-mmcif.py include src/ihm_format.h include src/ihm_format.i -include src/ihm_format_wrap_0.27.c +include src/ihm_format_wrap_0.30.c diff --git a/modules/core/dependency/python-ihm/docs/citations.rst b/modules/core/dependency/python-ihm/docs/citations.rst index 853857b1f0..e6762c62ca 100644 --- a/modules/core/dependency/python-ihm/docs/citations.rst +++ b/modules/core/dependency/python-ihm/docs/citations.rst @@ -43,3 +43,7 @@ The :mod:`ihm.citations` Python module .. data:: swiss_model SWISS-MODEL: homology modeling of protein structures and complexes. + +.. data:: alphafold2 + + AlphaFold: ab-initio modeling of protein structures. diff --git a/modules/core/dependency/python-ihm/examples/ligands_water.py b/modules/core/dependency/python-ihm/examples/ligands_water.py index b7619588be..366a9f5fd2 100644 --- a/modules/core/dependency/python-ihm/examples/ligands_water.py +++ b/modules/core/dependency/python-ihm/examples/ligands_water.py @@ -4,6 +4,9 @@ import ihm import ihm.dumper +import ihm.protocol +import ihm.representation +import ihm.model system = ihm.System() @@ -45,6 +48,35 @@ # todo: show handling of multiple waters +# Just as in the simple-docking.py example, we can add models with coordinates. +# Here we define an atomic model containing just the two hemes and the water. +assembly = ihm.Assembly((asym_heme1, asym_heme2, asym_h2o), + name="Modeled assembly") +rep = ihm.representation.Representation( + [ihm.representation.AtomicSegment(asym_heme1, rigid=False), + ihm.representation.AtomicSegment(asym_heme2, rigid=False), + ihm.representation.AtomicSegment(asym_h2o, rigid=False)]) +protocol = ihm.protocol.Protocol(name='Modeling') + + +class MyModel(ihm.model.Model): + def get_atoms(self): + # seq_id only makes sense for polymers; for ligands it should be None + yield ihm.model.Atom(asym_unit=asym_heme1, type_symbol='FE', het=True, + seq_id=None, atom_id='FE', x=0., y=0., z=0.) + yield ihm.model.Atom(asym_unit=asym_heme2, type_symbol='FE', het=True, + seq_id=None, atom_id='FE', x=10., y=10., z=10.) + yield ihm.model.Atom(asym_unit=asym_h2o, type_symbol='O', het=True, + seq_id=None, atom_id='O', x=20., y=20., z=20.) + + +# We have only a single model in a single state: +model = MyModel(assembly=assembly, protocol=protocol, representation=rep, + name='Best model') +model_group = ihm.model.ModelGroup([model], name='All models') +state = ihm.model.State([model_group]) +system.state_groups.append(ihm.model.StateGroup([state])) + # Once the system is complete, we can write it out to an mmCIF file: with open('output.cif', 'w') as fh: ihm.dumper.write(fh, [system]) diff --git a/modules/core/dependency/python-ihm/examples/simple-docking.py b/modules/core/dependency/python-ihm/examples/simple-docking.py index b99a564cc9..9117b40595 100644 --- a/modules/core/dependency/python-ihm/examples/simple-docking.py +++ b/modules/core/dependency/python-ihm/examples/simple-docking.py @@ -103,7 +103,7 @@ # Rather than storing another copy of the coordinates in the IHM library # (which could use a lot of memory), we need to provide a mechanism to -# translate them into the IHM data model. We do this straighforwardly by +# translate them into the IHM data model. We do this straightforwardly by # subclassing the IHM Model class and overriding the get_atoms # and get_spheres methods: class MyModel(ihm.model.Model): diff --git a/modules/core/dependency/python-ihm/ihm/__init__.py b/modules/core/dependency/python-ihm/ihm/__init__.py index 1c5075fc69..b596bfe953 100644 --- a/modules/core/dependency/python-ihm/ihm/__init__.py +++ b/modules/core/dependency/python-ihm/ihm/__init__.py @@ -20,7 +20,7 @@ import json from . import util -__version__ = '0.27' +__version__ = '0.30' class __UnknownValue(object): @@ -72,13 +72,16 @@ class System(object): :param str title: Title (longer text description) of the system. :param str id: Unique identifier for this system in the mmCIF file. + :param str model_details: Detailed description of the system, like an + abstract. """ structure_determination_methodology = "integrative" - def __init__(self, title=None, id='model'): + def __init__(self, title=None, id='model', model_details=None): self.id = id self.title = title + self.model_details = model_details #: List of plain text comments. These will be added to the top of #: the mmCIF file. @@ -631,20 +634,27 @@ class Citation(object): :param str pmid: The PubMed ID. :param str title: Full title of the publication. :param str journal: Abbreviated journal name. - :param int volume: Journal volume number. + :param volume: Journal volume as int for a plain number or str for + journals adding a label to the number (e.g. "46(W1)" for + a web server issue). :param page_range: The page (int) or page range (as a 2-element - int tuple). + int tuple). Using str also works for labelled page numbers. :param int year: Year of publication. :param authors: All authors in order, as a list of strings (last name followed by initials, e.g. "Smith AJ"). :param str doi: Digital Object Identifier of the publication. + :param bool is_primary: Denotes the most pertinent publication for the + modeling itself (as opposed to a method or piece of software used + in the protocol). Only one such publication is allowed, and it + is assigned the ID "primary" in the mmCIF file. """ def __init__(self, pmid, title, journal, volume, page_range, year, authors, - doi): + doi, is_primary=False): self.title, self.journal, self.volume = title, journal, volume self.page_range, self.year = page_range, year self.pmid, self.doi = pmid, doi self.authors = authors if authors is not None else [] + self.is_primary = is_primary @classmethod def from_pubmed_id(cls, pubmed_id): @@ -813,19 +823,22 @@ class RNAChemComp(ChemComp): class NonPolymerChemComp(ChemComp): - """A non-polymer chemical component, such as a ligand - (for crystal waters, use :class:`WaterChemComp`). + """A non-polymer chemical component, such as a ligand or a non-standard + residue (for crystal waters, use :class:`WaterChemComp`). :param str id: A globally unique identifier for this component. + :param str code_canonical: Canonical one-letter identifier. This is + used for non-standard residues and should be the one-letter code + of the closest standard residue (or by default, 'X'). :param str name: A longer human-readable name for the component. :param str formula: The chemical formula. See :class:`ChemComp` for more details. """ type = "non-polymer" - def __init__(self, id, name=None, formula=None): - super(NonPolymerChemComp, self).__init__(id, id, id, name=name, - formula=formula) + def __init__(self, id, code_canonical='X', name=None, formula=None): + super(NonPolymerChemComp, self).__init__(id, id, code_canonical, + name=name, formula=formula) class WaterChemComp(NonPolymerChemComp): @@ -1092,6 +1105,7 @@ class Entity(object): """ # noqa: E501 number_of_molecules = 1 + _force_polymer = None def __get_type(self): if self.is_polymeric(): @@ -1147,8 +1161,11 @@ def __str__(self): def is_polymeric(self): """Return True iff this entity represents a polymer, such as an amino acid sequence or DNA/RNA chain (and not a ligand or water)""" - return len(self.sequence) != 1 or not isinstance(self.sequence[0], - NonPolymerChemComp) + return (self._force_polymer or + len(self.sequence) == 0 or + len(self.sequence) > 1 + and any(isinstance(x, (PeptideChemComp, DNAChemComp, + RNAChemComp)) for x in self.sequence)) def residue(self, seq_id): """Get a :class:`Residue` at the given sequence position""" diff --git a/modules/core/dependency/python-ihm/ihm/citations.py b/modules/core/dependency/python-ihm/ihm/citations.py index e3b542c194..dc5ebc8905 100644 --- a/modules/core/dependency/python-ihm/ihm/citations.py +++ b/modules/core/dependency/python-ihm/ihm/citations.py @@ -89,3 +89,18 @@ 'Tauriello G', 'Gumienny R', 'Heer FT', 'de Beer TAP', 'Rempfer C', 'Bordoli L', 'Lepore R', 'Schwede T'], doi='10.1093/nar/gky427') + + +alphafold2 = ihm.Citation( + pmid='34265844', + title='Highly accurate protein structure prediction with AlphaFold.', + journal='Nature', volume=596, page_range=(583, 589), year=2021, + authors=['Jumper J', 'Evans R', 'Pritzel A', 'Green T', 'Figurnov M', + 'Ronneberger O', 'Tunyasuvunakool K', 'Bates R', 'Zidek A', + 'Potapenko A', 'Bridgland A', 'Meyer C', 'Kohl SAA', 'Ballard AJ', + 'Cowie A', 'Romera-Paredes B', 'Nikolov S', 'Jain R', 'Adler J', + 'Back T', 'Petersen S', 'Reiman D', 'Clancy E', 'Zielinski M', + 'Steinegger M', 'Pacholska M', 'Berghammer T', 'Bodenstein S', + 'Silver D', 'Vinyals O', 'Senior AW', 'Kavukcuoglu K', 'Kohli P', + 'Hassabis D'], + doi='10.1038/s41586-021-03819-2') diff --git a/modules/core/dependency/python-ihm/ihm/dumper.py b/modules/core/dependency/python-ihm/ihm/dumper.py index 013fae7341..c4795f0599 100644 --- a/modules/core/dependency/python-ihm/ihm/dumper.py +++ b/modules/core/dependency/python-ihm/ihm/dumper.py @@ -71,7 +71,7 @@ def _get_transform(rot_matrix, tr_vector): class _EntryDumper(Dumper): def dump(self, system, writer): # Write CIF header (so this dumper should always be first) - writer.start_block(re.subn('[^0-9a-zA-z_]', '', system.id)[0]) + writer.start_block(re.subn('[^0-9a-zA-z_-]', '', system.id)[0]) with writer.category("_entry") as lp: lp.write(id=system.id) @@ -83,8 +83,8 @@ class _AuditConformDumper(Dumper): def dump(self, system, writer): with writer.category("_audit_conform") as lp: # Update to match the version of the IHM dictionary we support: - lp.write(dict_name="ihm-extension.dic", dict_version="1.09", - dict_location=self.URL % "b4fe8af") + lp.write(dict_name="ihm-extension.dic", dict_version="1.17", + dict_location=self.URL % "f15a6bb") class _StructDumper(Dumper): @@ -92,7 +92,8 @@ def dump(self, system, writer): with writer.category("_struct") as lp: mth = system.structure_determination_methodology lp.write(title=system.title, entry_id=system.id, - pdbx_structure_determination_methodology=mth) + pdbx_structure_determination_methodology=mth, + pdbx_model_details=system.model_details) class _CommentDumper(Dumper): @@ -127,13 +128,25 @@ def dump(self, system, writer): class _CitationDumper(Dumper): def finalize(self, system): - for nc, c in enumerate(system._all_citations()): + primaries = [] + non_primaries = [] + for c in system._all_citations(): + (primaries if c.is_primary else non_primaries).append(c) + # Put primary citations first in list + self._all_citations = primaries + non_primaries + for nc, c in enumerate(self._all_citations): c._id = nc + 1 + if primaries: + if len(primaries) > 1: + raise ValueError( + "Multiple Citations with is_primary=True; only one can " + "be primary: %s" % primaries) + else: + primaries[0]._id = 'primary' def dump(self, system, writer): - citations = list(system._all_citations()) - self.dump_citations(citations, writer) - self.dump_authors(citations, writer) + self.dump_citations(self._all_citations, writer) + self.dump_authors(self._all_citations, writer) def dump_citations(self, citations, writer): with writer.loop("_citation", @@ -549,8 +562,11 @@ def dump(self, system, writer): for entity in system.entities: if not entity.is_polymeric(): continue + nstd = any(isinstance(x, ihm.NonPolymerChemComp) + for x in entity.sequence) lp.write(entity_id=entity._id, type=self._get_seq_type(entity), - nstd_linkage='no', nstd_monomer='no', + nstd_linkage='no', + nstd_monomer='yes' if nstd else 'no', pdbx_strand_id=strand.get(entity._id, None), pdbx_seq_one_letter_code=self._get_sequence(entity), pdbx_seq_one_letter_code_can=self._get_canon(entity)) @@ -647,7 +663,7 @@ class _NonPolySchemeDumper(Dumper): For now we assume we're using auth_seq_num==pdb_seq_num.""" def dump(self, system, writer): with writer.loop("_pdbx_nonpoly_scheme", - ["asym_id", "entity_id", "mon_id", + ["asym_id", "entity_id", "mon_id", "ndb_seq_num", "pdb_seq_num", "auth_seq_num", "pdb_mon_id", "auth_mon_id", "pdb_strand_id", "pdb_ins_code"]) as lp: @@ -658,8 +674,13 @@ def dump(self, system, writer): # todo: handle multiple waters for num, comp in enumerate(entity.sequence): auth_seq_num, ins = asym._get_auth_seq_id_ins_code(num + 1) + # ndb_seq_num is described as the "NDB/RCSB residue + # number". We don't have one of those but real PDBs + # usually seem to just count sequentially from 1, so + # we'll do that too. lp.write(asym_id=asym._id, pdb_strand_id=asym.strand_id, entity_id=entity._id, + ndb_seq_num=num + 1, pdb_seq_num=auth_seq_num, auth_seq_num=auth_seq_num, mon_id=comp.id, pdb_mon_id=comp.id, @@ -3120,6 +3141,11 @@ def get_dumpers(self): """ pass + def get_system_writer(self, system, writer_class, writer): + """Get a writer tailored to the given system. + By default, this just returns the ``writer`` unchanged.""" + return writer + class IHMVariant(Variant): """Used to select typical PDBx/IHM file output. See :func:`write`.""" @@ -3179,11 +3205,13 @@ def write(fh, systems, format='mmCIF', dumpers=[], variant=IHMVariant): writer = writer_map[format](fh) for system in systems: + w = variant.get_system_writer(system, writer_map[format], writer) system._before_write() for d in dumpers: d.finalize(system) system._check_after_write() for d in dumpers: - d.dump(system, writer) + d.dump(system, w) + w.end_block() # start_block is called by EntryDumper writer.flush() diff --git a/modules/core/dependency/python-ihm/ihm/format.py b/modules/core/dependency/python-ihm/ihm/format.py index 677677fd50..5787283c21 100644 --- a/modules/core/dependency/python-ihm/ihm/format.py +++ b/modules/core/dependency/python-ihm/ihm/format.py @@ -133,6 +133,10 @@ def start_block(self, name): """Start a new data block in the file with the given name.""" self.fh.write('data_%s\n' % name) + def end_block(self): + # noop - mmCIF has no end-of-block indicator + pass + def category(self, category): """Return a context manager to write a CIF category. A CIF category is a simple list of key:value pairs. @@ -187,6 +191,7 @@ def _repr(self, obj): if isinstance(obj, str) and '"' not in obj \ and "'" not in obj and " " not in obj \ and len(obj) > 0 \ + and not obj.startswith('_') \ and not obj.startswith('data_') \ and not obj.startswith('[') \ and obj not in ('save_', 'loop_', 'stop_', 'global_', '?', '.'): diff --git a/modules/core/dependency/python-ihm/ihm/format_bcif.py b/modules/core/dependency/python-ihm/ihm/format_bcif.py index f96482e1ef..327d755d13 100644 --- a/modules/core/dependency/python-ihm/ihm/format_bcif.py +++ b/modules/core/dependency/python-ihm/ihm/format_bcif.py @@ -577,6 +577,10 @@ def start_block(self, name): self._categories = block[u'categories'] self._blocks.append(block) + def end_block(self): + # noop - end-of-block is handled by start_block() and flush() + pass + def _add_category(self, category, data): row_count = 0 cols = [] diff --git a/modules/core/dependency/python-ihm/ihm/reader.py b/modules/core/dependency/python-ihm/ihm/reader.py index fa954e8d2c..9a12e7be5f 100644 --- a/modules/core/dependency/python-ihm/ihm/reader.py +++ b/modules/core/dependency/python-ihm/ihm/reader.py @@ -873,9 +873,10 @@ def copy_if_present(self, obj, data, keys=[], mapkeys={}): class _StructHandler(Handler): category = '_struct' - def __call__(self, title, entry_id): + def __call__(self, title, entry_id, pdbx_model_details): self.copy_if_present(self.system, locals(), keys=('title',), - mapkeys={'entry_id': 'id'}) + mapkeys={'entry_id': 'id', + 'pdbx_model_details': 'model_details'}) class _AuditConformHandler(Handler): @@ -916,6 +917,7 @@ def __call__(self, id, title, year, pdbx_database_id_pubmed, journal_abbrev, journal_volume, pdbx_database_id_doi, page_first, page_last): s = self.sysr.citations.get_by_id(id) + s.is_primary = (id == 'primary') self.copy_if_present( s, locals(), keys=('title', 'year'), mapkeys={'pdbx_database_id_pubmed': 'pmid', @@ -1008,6 +1010,10 @@ def __call__(self, id, details, type, src_method, formula_weight, source_cls = self.src_map.get(src_method.lower(), None) if source_cls and s.source is None: s.source = source_cls() + # Force polymer if _entity.type says so, even if it doesn't look like + # one (e.g. just a single amino acid) + if type and type.lower() == 'polymer': + s._force_polymer = True class _EntitySrcNatHandler(Handler): diff --git a/modules/core/dependency/python-ihm/ihm/reference.py b/modules/core/dependency/python-ihm/ihm/reference.py index a6507742a3..0b7cecffa5 100644 --- a/modules/core/dependency/python-ihm/ihm/reference.py +++ b/modules/core/dependency/python-ihm/ihm/reference.py @@ -2,9 +2,25 @@ # Handle different naming of urllib in Python 2/3 try: - import urllib.request as urllib2 + import urllib.request as urlreq except ImportError: import urllib2 + import contextlib + + class CompatRequest(object): + pass + + # Python 2's urlopen is not a context manager, so wrap it + @contextlib.contextmanager + def urlopen(*args, **keys): + try: + fh = urllib2.urlopen(*args, **keys) + yield fh + finally: + fh.close() + # Provide Python-3-like urllib.request.urlopen + urlreq = CompatRequest() + urlreq.urlopen = urlopen import sys @@ -91,7 +107,7 @@ def decode(t): def decode(t): return t url = 'https://www.uniprot.org/uniprot/%s.fasta' % accession - with urllib2.urlopen(url) as fh: + with urlreq.urlopen(url) as fh: header = decode(fh.readline()) spl = header.split('|') if len(spl) < 3 or spl[0] not in ('>sp', '>tr'): diff --git a/modules/core/dependency/python-ihm/make-release.sh b/modules/core/dependency/python-ihm/make-release.sh index e7809c0f26..d614c9a49c 100755 --- a/modules/core/dependency/python-ihm/make-release.sh +++ b/modules/core/dependency/python-ihm/make-release.sh @@ -1,6 +1,7 @@ #!/bin/bash -e # First, do +# - Update AuditConformDumper to match latest IHM dictionary if necessary # - Update ChangeLog.rst with the release number # - Update release number in ihm/__init__.py, MANIFEST.in, and setup.py # - Commit, tag, and push diff --git a/modules/core/dependency/python-ihm/setup.py b/modules/core/dependency/python-ihm/setup.py index efa2a8ba6a..3f0d042aa4 100755 --- a/modules/core/dependency/python-ihm/setup.py +++ b/modules/core/dependency/python-ihm/setup.py @@ -7,7 +7,7 @@ import sys import os -VERSION = "0.27" +VERSION = "0.30" copy_args = sys.argv[1:] diff --git a/modules/core/dependency/python-ihm/test/test_dumper.py b/modules/core/dependency/python-ihm/test/test_dumper.py index aeedb2cba5..bad25e953c 100644 --- a/modules/core/dependency/python-ihm/test/test_dumper.py +++ b/modules/core/dependency/python-ihm/test/test_dumper.py @@ -51,7 +51,7 @@ def test_write(self): ihm.dumper.write(fh, [sys1, sys2]) lines = fh.getvalue().split('\n') self.assertEqual(lines[:2], ["data_system1", "_entry.id system1"]) - self.assertEqual(lines[15:17], + self.assertEqual(lines[16:18], ["data_system23", "_entry.id 'system 2+3'"]) def test_write_custom_dumper(self): @@ -96,6 +96,14 @@ def test_entry_dumper(self): out = _get_dumper_output(dumper, system) self.assertEqual(out, "data_test_model\n_entry.id test_model\n") + def test_entry_dumper_data_chars(self): + """Test allowed characters in data_ block with EntryDumper""" + system = ihm.System(id='foo99-bar94_ABC $#% x') + dumper = ihm.dumper._EntryDumper() + out = _get_dumper_output(dumper, system).split('\n')[0] + # Whitespace and special characters (except - _) should be removed + self.assertEqual(out, "data_foo99-bar94_ABCx") + def test_audit_conform_dumper(self): """Test AuditConformDumper""" system = ihm.System() @@ -109,10 +117,11 @@ def test_audit_conform_dumper(self): def test_struct_dumper(self): """Test StructDumper""" - system = ihm.System(title='test model') + system = ihm.System(title='test model', model_details="test details") dumper = ihm.dumper._StructDumper() out = _get_dumper_output(dumper, system) self.assertEqual(out, """_struct.entry_id model +_struct.pdbx_model_details 'test details' _struct.pdbx_structure_determination_methodology integrative _struct.title 'test model' """) @@ -228,9 +237,51 @@ def test_citation(self): # Handle no last page c1.page_range = 'e1637' dumper = ihm.dumper._CitationDumper() + dumper.finalize(system) # Assign IDs out = _get_dumper_output(dumper, system) self.assertIn("'Mol Cell Proteomics' 13 e1637 . 2014 ", out) + def test_citation_primary(self): + """Test CitationDumper with a primary citation""" + system = ihm.System() + c1 = ihm.Citation(pmid='x', title='y', journal='z', year=2014, + authors=[], volume=1, page_range=1, doi='d') + c2 = ihm.Citation(pmid='x2', title='y2', journal='z2', year=2015, + authors=[], volume=1, page_range=1, doi='e', + is_primary=True) + system.citations.extend((c1, c2)) + dumper = ihm.dumper._CitationDumper() + dumper.finalize(system) # Assign IDs + out = _get_dumper_output(dumper, system) + self.assertEqual(out, """# +loop_ +_citation.id +_citation.title +_citation.journal_abbrev +_citation.journal_volume +_citation.page_first +_citation.page_last +_citation.year +_citation.pdbx_database_id_PubMed +_citation.pdbx_database_id_DOI +primary y2 z2 1 1 . 2015 x2 e +2 y z 1 1 . 2014 x d +# +""") + + def test_citation_multiple_primary(self): + """Test CitationDumper with multiple primary citations""" + system = ihm.System() + c1 = ihm.Citation(pmid='x', title='y', journal='z', year=2014, + authors=[], volume=1, page_range=1, doi='d', + is_primary=True) + c2 = ihm.Citation(pmid='x2', title='y2', journal='z2', year=2015, + authors=[], volume=1, page_range=1, doi='e', + is_primary=True) + system.citations.extend((c1, c2)) + dumper = ihm.dumper._CitationDumper() + self.assertRaises(ValueError, dumper.finalize, system) + def test_audit_author_empty(self): """Test AuditAuthorDumper with empty list""" system = ihm.System() @@ -673,7 +724,7 @@ def test_entity_poly_dumper(self): """Test EntityPolyDumper""" system = ihm.System() e1 = ihm.Entity('ACGT') # sequence containing glycine - e2 = ihm.Entity(('A', 'C', 'C', 'MSE')) # no glycine + e2 = ihm.Entity(('A', 'C', 'C', 'UNK', 'MSE')) # no glycine # All D-peptides (with glycine) e3 = ihm.Entity(('DAL', 'DCY', 'G'), alphabet=ihm.DPeptideAlphabet) # All D-peptides (without glycine) @@ -683,7 +734,9 @@ def test_entity_poly_dumper(self): e5 = ihm.Entity(('A', dpep_al['DCY'], 'G')) # Non-polymeric entity e6 = ihm.Entity([ihm.NonPolymerChemComp('HEM')]) - system.entities.extend((e1, e2, e3, e4, e5, e6)) + # Sequence containing a non-standard residue + e7 = ihm.Entity((ihm.NonPolymerChemComp('ACE'), 'C', 'C')) + system.entities.extend((e1, e2, e3, e4, e5, e6, e7)) # One protein entity is modeled (with an asym unit) the other not; # this should be reflected in pdbx_strand_id system.asym_units.append(ihm.AsymUnit(e1, 'foo', strand_id='a')) @@ -710,13 +763,14 @@ def test_entity_poly_dumper(self): _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can 1 polypeptide(L) no no a ACGT ACGT -2 polypeptide(L) no no . ACC(MSE) ACCM +2 polypeptide(L) no no . ACC(UNK)(MSE) ACCXM 3 polypeptide(D) no no . (DAL)(DCY)G ACG 4 polypeptide(D) no no . (DAL)(DCY) AC 5 polypeptide(L) no no . A(DCY)G ACG -7 polyribonucleotide no no . AC AC -8 polydeoxyribonucleotide no no . (DA)(DC) AC -9 'polydeoxyribonucleotide/polyribonucleotide hybrid' no no . AC(DA)(DC) ACAC +7 polypeptide(L) no yes . (ACE)CC XCC +8 polyribonucleotide no no . AC AC +9 polydeoxyribonucleotide no no . (DA)(DC) AC +10 'polydeoxyribonucleotide/polyribonucleotide hybrid' no no . AC(DA)(DC) ACAC # """) @@ -844,14 +898,15 @@ def test_nonpoly_scheme_dumper(self): _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id +_pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code -B 2 HEM 1 1 HEM HEM Q . -C 3 ZN 6 6 ZN ZN C . +B 2 HEM 1 1 1 HEM HEM Q . +C 3 ZN 1 6 6 ZN ZN C . # """) @@ -2198,6 +2253,12 @@ def test_model_dumper_atoms(self): N # """) + # Test dump_atoms with add_ihm=False + fh = StringIO() + writer = ihm.format.CifWriter(fh) + dumper.dump_atoms(system, writer, add_ihm=False) + self.assertNotIn('ihm_model_id', fh.getvalue()) + # With auth_seq_id == seq_id-1 asym.auth_seq_id_map = -1 out = _get_dumper_output(dumper, system) @@ -4190,6 +4251,19 @@ class MockObject(object): # """) + def test_variant_base(self): + """Test Variant base class""" + v = ihm.dumper.Variant() + self.assertIsNone(v.get_dumpers()) + self.assertEqual( + v.get_system_writer('system', 'writer_class', 'writer'), 'writer') + + def test_write_variant(self): + """Test write() function with Variant object""" + sys1 = ihm.System(id='system1') + fh = StringIO() + ihm.dumper.write(fh, [sys1], variant=ihm.dumper.IHMVariant()) + if __name__ == '__main__': unittest.main() diff --git a/modules/core/dependency/python-ihm/test/test_examples.py b/modules/core/dependency/python-ihm/test/test_examples.py index 826d3ef6aa..eb08ef8cef 100644 --- a/modules/core/dependency/python-ihm/test/test_examples.py +++ b/modules/core/dependency/python-ihm/test/test_examples.py @@ -41,7 +41,7 @@ def test_simple_docking_example(self): # can read it with open(os.path.join(tmpdir, 'output.cif')) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 315) + self.assertEqual(len(contents), 316) with open(os.path.join(tmpdir, 'output.cif')) as fh: s, = ihm.reader.read(fh) @@ -55,7 +55,7 @@ def test_locations_example(self): # can read it with open(out) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 69) + self.assertEqual(len(contents), 70) with open(out) as fh: s, = ihm.reader.read(fh) os.unlink(out) @@ -70,7 +70,7 @@ def test_ligands_water_example(self): # can read it with open(out) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 161) + self.assertEqual(len(contents), 252) with open(out) as fh: s, = ihm.reader.read(fh) # Make sure that resulting Python objects are picklable @@ -92,7 +92,7 @@ def test_non_standard_residues_example(self): # can read it with open(out) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 65) + self.assertEqual(len(contents), 66) with open(out) as fh: s, = ihm.reader.read(fh) os.unlink(out) diff --git a/modules/core/dependency/python-ihm/test/test_format.py b/modules/core/dependency/python-ihm/test/test_format.py index 96075ab44a..f3ebedf66a 100644 --- a/modules/core/dependency/python-ihm/test/test_format.py +++ b/modules/core/dependency/python-ihm/test/test_format.py @@ -193,6 +193,8 @@ def test_repr(self): self.assertEqual(w._repr('data_'), "'data_'") # [ is a reserved character and cannot start a nonquoted string self.assertEqual(w._repr('[foo'), "'[foo'") + # _ indicates an identifier and cannot start a nonquoted string + self.assertEqual(w._repr('_foo'), "'_foo'") # Empty string must be quoted self.assertEqual(w._repr(""), "''") # Reserved words must be quoted (but just a prefix is OK) diff --git a/modules/core/dependency/python-ihm/test/test_main.py b/modules/core/dependency/python-ihm/test/test_main.py index 02c50e6c36..45102f640e 100644 --- a/modules/core/dependency/python-ihm/test/test_main.py +++ b/modules/core/dependency/python-ihm/test/test_main.py @@ -84,6 +84,9 @@ def test_non_polymer_chem_comp(self): """Test NonPolymerChemComp class""" cc1 = ihm.NonPolymerChemComp('HEM') self.assertEqual(cc1.type, 'non-polymer') + self.assertEqual(cc1.code_canonical, 'X') + cc2 = ihm.NonPolymerChemComp('HEM', code_canonical='G') + self.assertEqual(cc2.code_canonical, 'G') def test_water_chem_comp(self): """Test WaterChemComp class""" @@ -211,6 +214,21 @@ def test_entity_type(self): self.assertEqual(water.type, 'water') self.assertFalse(water.is_polymeric()) + # A single amino acid should be classified non-polymer + single_aa = ihm.Entity('A') + self.assertEqual(single_aa.type, 'non-polymer') + self.assertFalse(single_aa.is_polymeric()) + + # ... unless forced polymer + single_aa._force_polymer = True + self.assertEqual(single_aa.type, 'polymer') + self.assertTrue(single_aa.is_polymeric()) + + # An entity with no sequence is a polymer + empty = ihm.Entity([]) + self.assertEqual(empty.type, 'polymer') + self.assertTrue(empty.is_polymeric()) + def test_entity_src_method_default(self): """Test default values of Entity.src_method""" protein = ihm.Entity('AHCD') diff --git a/modules/core/dependency/python-ihm/test/test_reader.py b/modules/core/dependency/python-ihm/test/test_reader.py index 18f6183f0c..ed1102973e 100644 --- a/modules/core/dependency/python-ihm/test/test_reader.py +++ b/modules/core/dependency/python-ihm/test/test_reader.py @@ -177,11 +177,16 @@ class MockObject(object): def test_struct_handler(self): """Test StructHandler""" - cif = "_struct.entry_id eid\n_struct.title 'Test title'" + cif = """ +_struct.entry_id eid +_struct.title 'Test title' +_struct.pdbx_model_details 'Test details' +""" for fh in cif_file_handles(cif): s, = ihm.reader.read(fh) self.assertEqual(s.id, 'eid') self.assertEqual(s.title, 'Test title') + self.assertEqual(s.model_details, 'Test details') def test_multiple_systems(self): """Test multiple systems from data blocks""" @@ -192,12 +197,17 @@ def test_multiple_systems(self): _struct.entry_id id2 data_id3 _struct.entry_id id3 +data_long-entry$#<> +_struct.entry_id id4 """ for fh in cif_file_handles(cif): - s1, s2, s3 = ihm.reader.read(fh) + s1, s2, s3, s4 = ihm.reader.read(fh) self.assertEqual(s1.id, 'id1') self.assertEqual(s2.id, 'id2') self.assertEqual(s3.id, 'id3') + # Should not be tripped up by odd characters in data_ block, + # and the system ID should match entry_id + self.assertEqual(s4.id, 'id4') def test_software_handler(self): """Test SoftwareHandler""" @@ -284,7 +294,7 @@ def test_citation_handler(self): _citation.year _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI -2 'Mol Cell Proteomics' 9 2943 . 2014 1234 . +primary 'Mol Cell Proteomics' 9 2943 . 2014 1234 . 3 'Mol Cell Proteomics' 9 2943 2946 2014 1234 1.2.3.4 4 'Mol Cell Proteomics' 9 . . 2014 1234 1.2.3.4 # @@ -301,18 +311,21 @@ def test_citation_handler(self): for fh in cif_file_handles(cif): s, = ihm.reader.read(fh) citation1, citation2, citation3, citation4 = s.citations - self.assertEqual(citation1._id, '2') + self.assertEqual(citation1._id, 'primary') + self.assertTrue(citation1.is_primary) self.assertEqual(citation1.page_range, '2943') self.assertEqual(citation1.authors, []) self.assertEqual(citation1.pmid, '1234') self.assertIsNone(citation1.doi) self.assertEqual(citation2._id, '3') + self.assertFalse(citation2.is_primary) self.assertEqual(citation2.page_range, ('2943', '2946')) self.assertEqual(citation2.authors, ['Foo A', 'Bar C']) self.assertEqual(citation2.doi, '1.2.3.4') self.assertEqual(citation3._id, '4') + self.assertFalse(citation3.is_primary) self.assertEqual(citation3.authors, []) self.assertIsNone(citation3.page_range) @@ -487,6 +500,7 @@ def test_entity_handler(self): s, = ihm.reader.read(fh) e1, e2, e3, e4 = s.entities self.assertEqual(e1.description, 'Nup84') + self.assertTrue(e1._force_polymer) self.assertEqual( e1.number_of_molecules, '2') # todo: coerce to int self.assertEqual(e1.source.src_method, 'nat') @@ -494,6 +508,18 @@ def test_entity_handler(self): self.assertIsNone(e3.source) self.assertIsNone(e4.source) + def test_entity_handler_minimal(self): + """Test EntityHandler with minimal entity category""" + cif = """ +loop_ +_entity.id +1 +""" + for fh in cif_file_handles(cif): + s, = ihm.reader.read(fh) + e1, = s.entities + self.assertIsNone(e1.description) + def test_entity_src_gen_handler(self): """Test EntitySrcGenHandler""" entity = """ @@ -754,7 +780,9 @@ def test_assembly_details_handler(self): _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 ALA +1 2 ALA 2 1 ALA +2 2 ALA # loop_ _ihm_entity_poly_segment.id @@ -763,9 +791,9 @@ def test_assembly_details_handler(self): _ihm_entity_poly_segment.seq_id_end 1 1 1 726 2 2 1 744 -3 1 1 1 +3 1 1 2 4 2 1 50 -5 2 1 1 +5 2 1 2 # loop_ _struct_asym.id @@ -4020,6 +4048,19 @@ def test_flr_fps_mpp_modeling_handler(self): ihm.flr.FPSMPPAtomPositionGroup) self.assertEqual(m.mpp_atom_position_group._id, '5') + def test_variant_base(self): + """Test Variant base class""" + v = ihm.reader.Variant() + self.assertIsNone(v.get_handlers(None)) + self.assertIsNone(v.get_audit_conform_handler(None)) + + def test_write_variant(self): + """Test write() function with Variant object""" + cif = "data_model\n_struct.entry_id testid\n" + for fh in cif_file_handles(cif): + s, = ihm.reader.read(fh, variant=ihm.reader.IHMVariant()) + self.assertEqual(s.id, 'testid') + if __name__ == '__main__': unittest.main() diff --git a/modules/core/dependency/python-ihm/util/validate-outputs.py b/modules/core/dependency/python-ihm/util/validate-outputs.py new file mode 100755 index 0000000000..246d094723 --- /dev/null +++ b/modules/core/dependency/python-ihm/util/validate-outputs.py @@ -0,0 +1,33 @@ +#!/usr/bin/python3 + +"""Check the output of each example for validity against the PDBx + and IHM dictionaries. + + This should be periodically rechecked in case the PDBx and IHM dictionaries + are updated. +""" + +import sys +import os +import subprocess +import ihm.dictionary +import urllib.request + +with urllib.request.urlopen( + 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic') as fh: + d_pdbx = ihm.dictionary.read(fh) +with urllib.request.urlopen( + 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm.dic') as fh: + d_ihm = ihm.dictionary.read(fh) +pdbx_ihm = d_pdbx + d_ihm + +for script in ('simple-docking.py', 'ligands_water.py', + 'non_standard_residues.py'): + print(script) + subprocess.check_call([sys.executable, '../examples/' + script]) + with open('output.cif') as fh: + try: + pdbx_ihm.validate(fh) + except ihm.dictionary.ValidatorError as exc: + print(exc) +os.unlink('output.cif') From c7d24884d4d89158e481a0a5b66497115e4d8e37 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 6 Apr 2022 09:21:31 -0700 Subject: [PATCH 103/155] Use polymer sequences Don't use single-residue sequences in tests. These are treated by mmCIF as nonpolymers, to which different rules apply. --- modules/mmcif/test/test_dumper.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/mmcif/test/test_dumper.py b/modules/mmcif/test/test_dumper.py index 73ace1cc35..b808da2b72 100644 --- a/modules/mmcif/test/test_dumper.py +++ b/modules/mmcif/test/test_dumper.py @@ -654,8 +654,8 @@ def test_em3d_dumper(self): def test_site_dumper_spheres_only(self): """Test SiteDumper, spheres only""" system = IMP.mmcif.System() - h, state = self.make_model(system, [("foo", "A", 'A'), - ("bar", "AA", "B")]) + h, state = self.make_model(system, [("foo", "AA", 'A'), + ("bar", "AAA", "B")]) m = state.model # Add coordinates From 4a2c6b3721d8aa7da6cec21b3e479138f4b17af4 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 6 Apr 2022 10:19:58 -0700 Subject: [PATCH 104/155] Squashed 'modules/pmi/' changes from 8c62bd941f..7e63f0aa17 7e63f0aa17 Work with both stable ihm and that bundled with IMP 85cefee53a Use Python 3 by default e8942b7746 Squashed 'tools/dev_tools/' changes from b7538367..c4337f5b e5709a9e64 Add type of each entity to mmCIF output git-subtree-dir: modules/pmi git-subtree-split: 7e63f0aa179052bc715ad4325f6a81d7e8926912 --- modules/pmi/pyext/src/output.py | 4 ++-- modules/pmi/setup_git.py | 2 +- modules/pmi/test/test_mmcif_pmi2.py | 21 ++++++++++++++----- .../dev_tools/.github/workflows/build.yml | 2 +- .../pmi/tools/dev_tools/check_standards.py | 2 +- modules/pmi/tools/dev_tools/cleanup_code.py | 2 +- modules/pmi/tools/dev_tools/cleanup_pycs.py | 2 +- .../pmi/tools/dev_tools/make_all_header.py | 2 +- modules/pmi/tools/dev_tools/replace.py | 2 +- modules/pmi/tools/dev_tools/setup_cmake.py | 4 ++-- 10 files changed, 27 insertions(+), 16 deletions(-) diff --git a/modules/pmi/pyext/src/output.py b/modules/pmi/pyext/src/output.py index 0a87295b0c..0ad52dcd65 100644 --- a/modules/pmi/pyext/src/output.py +++ b/modules/pmi/pyext/src/output.py @@ -142,9 +142,9 @@ def _write_mmcif_internal(flpdb, particle_infos_for_pdb, geometric_center, with writer.category("_entry") as lp: lp.write(id='model') - with writer.loop("_entity", ["id"]) as lp: + with writer.loop("_entity", ["id", "type"]) as lp: for e in entities: - lp.write(id=e.id) + lp.write(id=e.id, type="polymer") with writer.loop("_entity_poly", ["entity_id", "pdbx_seq_one_letter_code"]) as lp: diff --git a/modules/pmi/setup_git.py b/modules/pmi/setup_git.py index ae9b9edb83..ba39988163 100755 --- a/modules/pmi/setup_git.py +++ b/modules/pmi/setup_git.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#! /usr/bin/env python3 """Call the main setup_git.py. This should be copied to the main directory of your project and named setup_git.py.""" diff --git a/modules/pmi/test/test_mmcif_pmi2.py b/modules/pmi/test/test_mmcif_pmi2.py index c7ddf8e67e..a53511c423 100644 --- a/modules/pmi/test/test_mmcif_pmi2.py +++ b/modules/pmi/test/test_mmcif_pmi2.py @@ -92,11 +92,22 @@ def test_finalize_write_mmcif(self): po.finalize() fh = StringIO() ihm.dumper.write(fh, [po.system]) - self.assertEqual( - fh.getvalue().split('\n')[:5], - ['data_model', '_entry.id model', '_struct.entry_id model', - '_struct.pdbx_structure_determination_methodology integrative', - '_struct.title .']) + val = fh.getvalue() + # Work with both latest stable ihm and that bundled with IMP + if '_struct.pdbx_model_details' in val: + self.assertEqual( + val.split('\n')[:5], + ['data_model', '_entry.id model', '_struct.entry_id model', + '_struct.pdbx_model_details .', + '_struct.pdbx_structure_determination_methodology ' + 'integrative']) + else: + self.assertEqual( + val.split('\n')[:5], + ['data_model', '_entry.id model', '_struct.entry_id model', + '_struct.pdbx_structure_determination_methodology ' + 'integrative', + '_struct.title .']) def test_finalize_write_bcif(self): """Test ProtocolOutput.finalize() and BinaryCIF output""" diff --git a/modules/pmi/tools/dev_tools/.github/workflows/build.yml b/modules/pmi/tools/dev_tools/.github/workflows/build.yml index 8a286104cf..d719007528 100644 --- a/modules/pmi/tools/dev_tools/.github/workflows/build.yml +++ b/modules/pmi/tools/dev_tools/.github/workflows/build.yml @@ -20,7 +20,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - pip install pytest-flake8 pytest-cov + pip install 'pytest-flake8<1.1' pytest-cov - name: Test run: | py.test --cov=. --cov-branch --cov-report=xml -v --flake8 . diff --git a/modules/pmi/tools/dev_tools/check_standards.py b/modules/pmi/tools/dev_tools/check_standards.py index 0fb9fb1ca3..ddda6c0ec2 100755 --- a/modules/pmi/tools/dev_tools/check_standards.py +++ b/modules/pmi/tools/dev_tools/check_standards.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Print out any violations of IMP-specific standards.""" diff --git a/modules/pmi/tools/dev_tools/cleanup_code.py b/modules/pmi/tools/dev_tools/cleanup_code.py index dd664d47c7..57098b8fc2 100755 --- a/modules/pmi/tools/dev_tools/cleanup_code.py +++ b/modules/pmi/tools/dev_tools/cleanup_code.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Use clang-format and autopep8 when available to clean up the listed source files.""" diff --git a/modules/pmi/tools/dev_tools/cleanup_pycs.py b/modules/pmi/tools/dev_tools/cleanup_pycs.py index 4948fb9e49..705b311ca4 100755 --- a/modules/pmi/tools/dev_tools/cleanup_pycs.py +++ b/modules/pmi/tools/dev_tools/cleanup_pycs.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Traverses the directory tree deleting any .pyc's who do not have a source .py. Helpful when switching between revisions with source control.""" diff --git a/modules/pmi/tools/dev_tools/make_all_header.py b/modules/pmi/tools/dev_tools/make_all_header.py index 288c9e1ac0..ec9af48aac 100755 --- a/modules/pmi/tools/dev_tools/make_all_header.py +++ b/modules/pmi/tools/dev_tools/make_all_header.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Make a header that lists other headers. usage: make_all_header.py header_name.h include_prefix headers diff --git a/modules/pmi/tools/dev_tools/replace.py b/modules/pmi/tools/dev_tools/replace.py index b16d017343..d8f76dd691 100755 --- a/modules/pmi/tools/dev_tools/replace.py +++ b/modules/pmi/tools/dev_tools/replace.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Replace all instances of argv[1] with argv[2], only updating the file if changes were made. """ diff --git a/modules/pmi/tools/dev_tools/setup_cmake.py b/modules/pmi/tools/dev_tools/setup_cmake.py index 3dd65368a6..2e33bcacb1 100755 --- a/modules/pmi/tools/dev_tools/setup_cmake.py +++ b/modules/pmi/tools/dev_tools/setup_cmake.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Build Files.cmake listing source files for each src, test, examples, benchmark directory in the subtree.""" @@ -39,7 +39,7 @@ def make_files(d): def search_start(d): for cd in [o for o in os.listdir(d) if os.path.isdir(os.path.join(d, o))]: - if cd.startswith("."): + if cd.startswith(".") or cd == 'components': continue cp = os.path.join(d, cd) if cd in ["bin", "src", "test", "examples", "benchmark", "utility"]: From e29870a073389f4eeec0efd521c02a1c4c3f51f6 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 6 Apr 2022 10:20:10 -0700 Subject: [PATCH 105/155] Use Python 3 by default --- setup_git.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup_git.py b/setup_git.py index 15be3f0ddb..b2546252f1 100755 --- a/setup_git.py +++ b/setup_git.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#! /usr/bin/env python3 """Call the main setup_git.py. This should be copied to the main directory of your project and named setup_git.py.""" From 86896f44853f4990a9892418df5d658dc895a1b3 Mon Sep 17 00:00:00 2001 From: Barak Raveh Date: Fri, 8 Apr 2022 08:28:34 +0300 Subject: [PATCH 106/155] Add a test to simulate dialaning from sequence using the CHARMM heavy atom force field of IMP --- ...est_bd_simulate_dialanine_from_sequence.py | 118 ++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 modules/atom/test/test_bd_simulate_dialanine_from_sequence.py diff --git a/modules/atom/test/test_bd_simulate_dialanine_from_sequence.py b/modules/atom/test/test_bd_simulate_dialanine_from_sequence.py new file mode 100644 index 0000000000..fcff839cc9 --- /dev/null +++ b/modules/atom/test/test_bd_simulate_dialanine_from_sequence.py @@ -0,0 +1,118 @@ +import IMP +import IMP.atom +import IMP.core +import IMP.rmf +import IMP.test +import RMF + +##### CONSTANT #### +N_ALANINES = 2 +# Radii by atomic weight of various elements +radius_by_element_id = { + 1: 1.2, # H + 6: 1.7, # C + 7: 1.55, # N + 8: 1.52, # O +} +BD_STEP_SIZE_FS = 1.0 +RMF_FNAME_PREFIX = "dialanine.rmf" +BD_CYCLES = 100 +RMF_PERIOD = 10 + +##### AUXILIARY FUNCTIOONS #### +def add_poly_ALA_to_fragment(fragment, num): + assert (IMP.atom.Fragment.get_is_setup(fragment)) + m = fragment.get_model() + for i in range(num): + p = IMP.Particle(m) + r = IMP.atom.Residue.setup_particle(p, IMP.atom.ALA) + fragment.add_child(r) + +def create_hierarchy_root(m): + p = IMP.Particle(m) + h = IMP.atom.Hierarchy.setup_particle(p) + return h + +def create_fragment(m, num): + p = IMP.Particle(m) + f = IMP.atom.Fragment.setup_particle(p) + add_poly_ALA_to_fragment(f, num) + f.set_residue_indexes([i+1 for i in range(num)]) + return f + +def get_num_res(t): + return [s.get_number_of_residues() for s in t.get_segments()] + +def create_topology(): + m = IMP.Model() + ff = IMP.atom.get_heavy_atom_CHARMM_parameters() + root = create_hierarchy_root(m) + c1 = IMP.atom.Chain.setup_particle(IMP.Particle(m), "A") + root.add_child(c1) + c1.add_child(create_fragment(m, N_ALANINES)) + t = ff.create_topology(root) +# assert(get_num_res(t) == [N_ALANINES]) + return t + +def get_scoring_function(protein, topology, is_non_bonded=True): + force_field = topology.get_parameters() + restraints = [] + restraints.append(IMP.atom.CHARMMStereochemistryRestraint(protein, topology)) + if is_non_bonded: + force_field.add_radii(protein) + force_field.add_well_depths(protein) + atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE) + container = IMP.container.ListSingletonContainer(m, atoms) + cpc = IMP.container.ClosePairContainer(cont, 4.0) + cpc.add_pair_filter(r.get_pair_filter()) + sf = IMP.atom.ForceSwitch(6.0, 7.0) + ljps = IMP.atom.LennardJonesPairScore(sf) + restraints.append(IMP.container.PairsRestraint(ljps, cpc)) + scoring_function = IMP.core.RestraintsScoringFunction(restraints) + return scoring_function + +##### Tests ##### +class Tests(IMP.test.TestCase): + def _create_dialanine_hierarchy_and_topology(self, model): + topology = create_topology() + protein = topology.create_hierarchy(model) + topology.apply_default_patches() + topology.setup_hierarchy(protein) + topology.add_coordinates (protein) + atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE) + for atom in atoms: + self.assertTrue(IMP.atom.Atom.get_is_setup(atom)) + element_id = IMP.atom.Atom(atom).get_element() + atom_radius = radius_by_element_id[element_id] + xyzr = IMP.core.XYZR.setup_particle(atom) + xyzr.set_radius(atom_radius) + if not IMP.atom.Diffusion.get_is_setup(atom): + IMP.atom.Diffusion.setup_particle(atom) + return protein, topology + + def test_bd_simulate_dialanine_from_sequence(self): + model = IMP.Model() + protein, topology = self._create_dialanine_hierarchy_and_topology(model) + sf = get_scoring_function(protein, topology, False) + bd = IMP.atom.BrownianDynamics(model) + bd.set_maximum_time_step(BD_STEP_SIZE_FS) + bd.set_scoring_function(sf) + rmf_fname = self.get_tmp_file_name(RMF_FNAME_PREFIX) + rmf = RMF.create_rmf_file(rmf_fname) + IMP.rmf.add_hierarchy(rmf, protein.get_children()[0]) + os = IMP.rmf.SaveOptimizerState(model, rmf) + os.set_period(RMF_PERIOD) + bd.add_optimizer_state(os) + self.assertAlmostEqual(sf.evaluate(False), 9.224793596016248) + print("Atoms before optimizing:") + atoms = IMP.atom.get_by_type(protein, IMP.atom.ATOM_TYPE) + print(atoms) + print("Optimizing") + bd.optimize(BD_CYCLES) + print(f"Atoms after optimizing for {BD_CYCLES} cycles:") + print(atoms) + print("Final score = {:.2f}".format(sf.evaluate(False))) + + +if __name__ == '__main__': + IMP.test.main() From f3e539c7ec6e11f57cefcae4b7abe18d7a38c861 Mon Sep 17 00:00:00 2001 From: Barak Raveh Date: Sun, 17 Apr 2022 20:41:12 +0300 Subject: [PATCH 107/155] some macro documentation (generic, boundding sphere/box) --- modules/core/include/BoundingBox3DSingletonScore.h | 4 ++++ modules/core/include/BoundingSphere3DSingletonScore.h | 4 ++++ modules/kernel/include/object_macros.h | 10 ++++++++++ 3 files changed, 18 insertions(+) diff --git a/modules/core/include/BoundingBox3DSingletonScore.h b/modules/core/include/BoundingBox3DSingletonScore.h index 5d4cf17b63..f2c187892d 100644 --- a/modules/core/include/BoundingBox3DSingletonScore.h +++ b/modules/core/include/BoundingBox3DSingletonScore.h @@ -91,6 +91,9 @@ double GenericBoundingBox3DSingletonScore::evaluate_index( #endif +//! Score particles based on how far outside a box they are by +//! applying f to the distance. +//! \see GenericBoundingBox3DSingletonScore IMP_GENERIC_OBJECT(BoundingBox3DSingletonScore, bounding_box_3d_singleton_score, UnaryFunction, (UnaryFunction *f, const algebra::BoundingBoxD<3> &bb), @@ -99,3 +102,4 @@ IMP_GENERIC_OBJECT(BoundingBox3DSingletonScore, bounding_box_3d_singleton_score, IMPCORE_END_NAMESPACE #endif /* IMPCORE_BOUNDING_BOX_3DSINGLETON_SCORE_H */ + diff --git a/modules/core/include/BoundingSphere3DSingletonScore.h b/modules/core/include/BoundingSphere3DSingletonScore.h index 481e03edc0..0c671eb631 100644 --- a/modules/core/include/BoundingSphere3DSingletonScore.h +++ b/modules/core/include/BoundingSphere3DSingletonScore.h @@ -89,6 +89,10 @@ double GenericBoundingSphere3DSingletonScore::evaluate_index( #endif + +//! Score particles based on how far outside a sphere they are by +//! applying f to the distance. +//! \see GenericBoundingSphere3DSingletonScore IMP_GENERIC_OBJECT(BoundingSphere3DSingletonScore, bounding_sphere_3d_singleton_score, UnaryFunction, (UnaryFunction *f, const algebra::Sphere3D &sphere), diff --git a/modules/kernel/include/object_macros.h b/modules/kernel/include/object_macros.h index 1c8726ecc0..58517c00cf 100644 --- a/modules/kernel/include/object_macros.h +++ b/modules/kernel/include/object_macros.h @@ -47,6 +47,16 @@ /** A vector of weak (non reference-counting) pointers to specified objects. \see Name */ \ typedef IMP::Vector > PluralName##Temp; +//! Typedefs a default instantiation for a generic (templated) object +/** + Define type [Name] to be an an instantiation of of Generic[Name] with + template targument, and a function create_[lcname]() that generates a + newly allocated object of type [Name], taking parameters [crguments] + and internally paassing [cparguments] to the constructor. + + @note doxygen documentatio prior to this macro will be applied to the type + definition + */ #define IMP_GENERIC_OBJECT(Name, lcname, targument, carguments, cparguments) \ typedef Generic##Name Name; \ template \ From c3498248facb8c72cdc33ec4329d967b85dc80f3 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 21 Apr 2022 11:36:33 -0700 Subject: [PATCH 108/155] Squashed 'modules/rmf/dependency/RMF/' changes from fbbe8657fc..21ac10919e 21ac10919e Use Python 3 by default b365a78381 Squashed 'tools/dev_tools/' changes from 9c0221d4..626e51c1 01d3a8ed41 Remove old Sublime config git-subtree-dir: modules/rmf/dependency/RMF git-subtree-split: 21ac10919e4c63e8bb8760e186438e335a8f188c --- .../rmf/dependency/RMF/rmf.sublime-project | 8 - .../rmf/dependency/RMF/rmf.sublime-workspace | 470 ------------------ modules/rmf/dependency/RMF/setup_git.py | 2 +- .../dev_tools/.github/workflows/build.yml | 2 +- .../RMF/tools/dev_tools/check_standards.py | 2 +- .../RMF/tools/dev_tools/cleanup_code.py | 2 +- .../RMF/tools/dev_tools/cleanup_pycs.py | 2 +- .../dev_tools/git/bootstrap_setup_git.py | 2 +- .../RMF/tools/dev_tools/git/setup_git.py | 2 +- .../RMF/tools/dev_tools/make_all_header.py | 2 +- .../dependency/RMF/tools/dev_tools/replace.py | 2 +- .../RMF/tools/dev_tools/setup_cmake.py | 2 +- 12 files changed, 10 insertions(+), 488 deletions(-) delete mode 100644 modules/rmf/dependency/RMF/rmf.sublime-project delete mode 100644 modules/rmf/dependency/RMF/rmf.sublime-workspace diff --git a/modules/rmf/dependency/RMF/rmf.sublime-project b/modules/rmf/dependency/RMF/rmf.sublime-project deleted file mode 100644 index 7762a6245e..0000000000 --- a/modules/rmf/dependency/RMF/rmf.sublime-project +++ /dev/null @@ -1,8 +0,0 @@ -{ - "folders": - 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{ - "height": 0.0, - "selected_items": - [ - ], - "width": 0.0 - }, - "select_project": - { - "height": 0.0, - "selected_items": - [ - ], - "width": 0.0 - }, - "show_minimap": true, - "show_open_files": false, - "show_tabs": true, - "side_bar_visible": true, - "side_bar_width": 223.0, - "status_bar_visible": true -} diff --git a/modules/rmf/dependency/RMF/setup_git.py b/modules/rmf/dependency/RMF/setup_git.py index 70704bc928..d2916745b6 100755 --- a/modules/rmf/dependency/RMF/setup_git.py +++ b/modules/rmf/dependency/RMF/setup_git.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Call the main setup_git.py. This should be copied to the main directory of your project and named setup_git.py.""" diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/.github/workflows/build.yml b/modules/rmf/dependency/RMF/tools/dev_tools/.github/workflows/build.yml index 8a286104cf..d719007528 100644 --- a/modules/rmf/dependency/RMF/tools/dev_tools/.github/workflows/build.yml +++ b/modules/rmf/dependency/RMF/tools/dev_tools/.github/workflows/build.yml @@ -20,7 +20,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - pip install pytest-flake8 pytest-cov + pip install 'pytest-flake8<1.1' pytest-cov - name: Test run: | py.test --cov=. --cov-branch --cov-report=xml -v --flake8 . diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/check_standards.py b/modules/rmf/dependency/RMF/tools/dev_tools/check_standards.py index 0fb9fb1ca3..ddda6c0ec2 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/check_standards.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/check_standards.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Print out any violations of IMP-specific standards.""" diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/cleanup_code.py b/modules/rmf/dependency/RMF/tools/dev_tools/cleanup_code.py index dd664d47c7..57098b8fc2 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/cleanup_code.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/cleanup_code.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Use clang-format and autopep8 when available to clean up the listed source files.""" diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/cleanup_pycs.py b/modules/rmf/dependency/RMF/tools/dev_tools/cleanup_pycs.py index 4948fb9e49..705b311ca4 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/cleanup_pycs.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/cleanup_pycs.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Traverses the directory tree deleting any .pyc's who do not have a source .py. Helpful when switching between revisions with source control.""" diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/git/bootstrap_setup_git.py b/modules/rmf/dependency/RMF/tools/dev_tools/git/bootstrap_setup_git.py index 1f1a1fa9f1..cd553ebc23 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/git/bootstrap_setup_git.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/git/bootstrap_setup_git.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Update submodules and then call the main setup_git.py. This should be copied to the main directory of your project and named setup_git.py.""" diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/git/setup_git.py b/modules/rmf/dependency/RMF/tools/dev_tools/git/setup_git.py index 0fbbbea078..ec9451b739 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/git/setup_git.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/git/setup_git.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 import sys import os.path diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py b/modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py index 288c9e1ac0..ec9af48aac 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/make_all_header.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Make a header that lists other headers. usage: make_all_header.py header_name.h include_prefix headers diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/replace.py b/modules/rmf/dependency/RMF/tools/dev_tools/replace.py index b16d017343..d8f76dd691 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/replace.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/replace.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Replace all instances of argv[1] with argv[2], only updating the file if changes were made. """ diff --git a/modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py b/modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py index 7b0b2507bc..2e33bcacb1 100755 --- a/modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py +++ b/modules/rmf/dependency/RMF/tools/dev_tools/setup_cmake.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 """Build Files.cmake listing source files for each src, test, examples, benchmark directory in the subtree.""" From 20cbf0f7148996826c732d16f2f3181fe56461fd Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 21 Apr 2022 11:37:26 -0700 Subject: [PATCH 109/155] Squashed 'modules/pmi/' changes from 7e63f0aa17..419124b729 419124b729 Close file when we're done with it git-subtree-dir: modules/pmi git-subtree-split: 419124b7290bcfb67598e37ecc562cdba6dd76f8 --- modules/pmi/pyext/src/io/crosslink.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/pmi/pyext/src/io/crosslink.py b/modules/pmi/pyext/src/io/crosslink.py index f39fb511b9..580034a28e 100644 --- a/modules/pmi/pyext/src/io/crosslink.py +++ b/modules/pmi/pyext/src/io/crosslink.py @@ -728,14 +728,14 @@ def create_set_from_file(self, file_name, converter=None, ''' new_xl_dict = {} - f = open(file_name, "r") nxl = 0 - for line in f: - xl = FixedFormatParser.get_data(line) - if xl: - xl[self.unique_id_key] = str(nxl+1) - new_xl_dict[str(nxl)] = [xl] - nxl += 1 + with open(file_name, "r") as f: + for line in f: + xl = FixedFormatParser.get_data(line) + if xl: + xl[self.unique_id_key] = str(nxl+1) + new_xl_dict[str(nxl)] = [xl] + nxl += 1 self.data_base = new_xl_dict self.name = file_name From f8d7268575304459fc13e3773695db1e42fba66c Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 21 Apr 2022 11:44:05 -0700 Subject: [PATCH 110/155] Squashed 'modules/core/dependency/python-ihm/' changes from 7b4cbaff72..77992d59ca 77992d59ca Test case where asym points to entity with sequence 8dc1845956 Guess sequence from atom_site if necessary 7dfbae1795 Prepare for 0.31 release 2e85519df7 Make sure examples validate before release 329b281429 Increase test coverage ab227650a4 Add a Variant that excludes certain categories 8a861746f1 Check for duplicate atoms on output 34e87d91d1 Remove _pdbx_nonpoly_scheme.pdb_mon_id git-subtree-dir: modules/core/dependency/python-ihm git-subtree-split: 77992d59caf4deaf60d4d5e94d6f9787d6bf9ca5 --- .../core/dependency/python-ihm/ChangeLog.rst | 10 +++ .../core/dependency/python-ihm/MANIFEST.in | 2 +- .../dependency/python-ihm/docs/dumper.rst | 2 + .../dependency/python-ihm/ihm/__init__.py | 2 +- .../core/dependency/python-ihm/ihm/dumper.py | 84 ++++++++++++++++++- .../core/dependency/python-ihm/ihm/reader.py | 40 ++++++++- .../dependency/python-ihm/make-release.sh | 1 + modules/core/dependency/python-ihm/setup.py | 2 +- .../dependency/python-ihm/test/test_dumper.py | 67 +++++++++++++-- .../python-ihm/test/test_examples.py | 2 +- .../dependency/python-ihm/test/test_reader.py | 67 +++++++++++++++ 11 files changed, 264 insertions(+), 15 deletions(-) diff --git a/modules/core/dependency/python-ihm/ChangeLog.rst b/modules/core/dependency/python-ihm/ChangeLog.rst index 18a2823389..9744ab3134 100644 --- a/modules/core/dependency/python-ihm/ChangeLog.rst +++ b/modules/core/dependency/python-ihm/ChangeLog.rst @@ -1,3 +1,13 @@ +0.31 - 2022-04-14 +================= + - The :class:`ihm.dumper.IgnoreVariant` class can now be used to exclude + selected categories from the mmCIF/BinaryCIF output. + - The _pdbx_nonpoly_scheme CIF table should now fully comply with the + PDBx dictionary. + - Atoms are now checked at file-output time to ensure that a given model + chain does not contain multiple atoms with the same atom_id and + seq_id (#81). + 0.30 - 2022-04-05 ================= - Add support for a long description of the system (like an abstract) diff --git a/modules/core/dependency/python-ihm/MANIFEST.in b/modules/core/dependency/python-ihm/MANIFEST.in index b8c25c9380..8ab08deb82 100644 --- a/modules/core/dependency/python-ihm/MANIFEST.in +++ b/modules/core/dependency/python-ihm/MANIFEST.in @@ -4,4 +4,4 @@ include examples/* include util/make-mmcif.py include src/ihm_format.h include src/ihm_format.i -include src/ihm_format_wrap_0.30.c +include src/ihm_format_wrap_0.31.c diff --git a/modules/core/dependency/python-ihm/docs/dumper.rst b/modules/core/dependency/python-ihm/docs/dumper.rst index 78829e0d1a..883af5a427 100644 --- a/modules/core/dependency/python-ihm/docs/dumper.rst +++ b/modules/core/dependency/python-ihm/docs/dumper.rst @@ -15,4 +15,6 @@ The :mod:`ihm.dumper` Python module .. autoclass:: IHMVariant +.. autoclass:: IgnoreVariant + .. autofunction:: write diff --git a/modules/core/dependency/python-ihm/ihm/__init__.py b/modules/core/dependency/python-ihm/ihm/__init__.py index b596bfe953..86eb21e528 100644 --- a/modules/core/dependency/python-ihm/ihm/__init__.py +++ b/modules/core/dependency/python-ihm/ihm/__init__.py @@ -20,7 +20,7 @@ import json from . import util -__version__ = '0.30' +__version__ = '0.31' class __UnknownValue(object): diff --git a/modules/core/dependency/python-ihm/ihm/dumper.py b/modules/core/dependency/python-ihm/ihm/dumper.py index c4795f0599..5d8724b0b9 100644 --- a/modules/core/dependency/python-ihm/ihm/dumper.py +++ b/modules/core/dependency/python-ihm/ihm/dumper.py @@ -664,7 +664,7 @@ class _NonPolySchemeDumper(Dumper): def dump(self, system, writer): with writer.loop("_pdbx_nonpoly_scheme", ["asym_id", "entity_id", "mon_id", "ndb_seq_num", - "pdb_seq_num", "auth_seq_num", "pdb_mon_id", + "pdb_seq_num", "auth_seq_num", "auth_mon_id", "pdb_strand_id", "pdb_ins_code"]) as lp: for asym in system.asym_units: @@ -683,7 +683,7 @@ def dump(self, system, writer): ndb_seq_num=num + 1, pdb_seq_num=auth_seq_num, auth_seq_num=auth_seq_num, - mon_id=comp.id, pdb_mon_id=comp.id, + mon_id=comp.id, auth_mon_id=comp.id, pdb_ins_code=ins) @@ -1296,6 +1296,7 @@ class _RangeChecker(object): def __init__(self, model): self._setup_representation(model) self._setup_assembly(model) + self._seen_atoms = set() def _setup_representation(self, model): """Make map from asym_id to representation segments for that ID""" @@ -1353,9 +1354,19 @@ def __call__(self, obj): else: type_check = self._type_check_atom seq_id_range = (obj.seq_id, obj.seq_id) + self._check_duplicate_atom(obj) self._check_assembly(obj, asym, seq_id_range) self._check_representation(obj, asym, type_check, seq_id_range) + def _check_duplicate_atom(self, atom): + k = (atom.asym_unit._id, atom.atom_id, atom.seq_id) + if k in self._seen_atoms: + raise ValueError( + "Multiple atoms with same atom_id (%s) and seq_id (%d) " + "found in asym ID %s" + % (atom.atom_id, atom.seq_id, atom.asym_unit._id)) + self._seen_atoms.add(k) + def _check_assembly(self, obj, asym, seq_id_range): # Check last match first last_rng = self._last_asmb_range_matched @@ -3131,6 +3142,54 @@ def dump_mpp_modeling(self, system, writer): _FLRFPSMPPModelingDumper] +class _NullLoopCategoryWriter(object): + """A do-nothing replacement for format._CifLoopWriter + or format._CifCategoryWriter""" + def write(self, *args, **keys): + pass + + def __enter__(self): + return self + + def __exit__(self, exc_type, exc_value, traceback): + pass + + +class _IgnoreWriter(object): + """Utility class which normally just passes through to the default + ``base_writer``, but ignores selected categories.""" + def __init__(self, base_writer, ignores): + self._base_writer = base_writer + # Allow for categories with or without leading underscore + self._ignore_category = frozenset('_' + c.lstrip('_').lower() + for c in ignores) + + def category(self, category): + if category in self._ignore_category: + return _NullLoopCategoryWriter() + else: + return self._base_writer.category(category) + + def loop(self, category, keys): + if category in self._ignore_category: + return _NullLoopCategoryWriter() + else: + return self._base_writer.loop(category, keys) + + # Pass through other methods to base_writer + def flush(self): + return self._base_writer.flush() + + def end_block(self): + return self._base_writer.end_block() + + def start_block(self, name): + return self._base_writer.start_block(name) + + def write_comment(self, comment): + return self._base_writer.write_comment(comment) + + class Variant(object): """Utility class to select the type of file to output by :func:`write`.""" @@ -3170,6 +3229,27 @@ def get_dumpers(self): return [d() for d in self._dumpers + _flr_dumpers] +class IgnoreVariant(IHMVariant): + """Exclude selected CIF categories from output. + + This generates the same PDBx/IHM output as :class:`IHMVariant`, + but explicitly listed CIF categories are discarded, for example:: + + ihm.dumper.write(fh, systems, + variant=IgnoreVariant(['_audit_conform'])) + + This is intended for advanced users that have a working knowledge + of the PDBx and IHM CIF dictionaries. + + :param sequence ignores: A list or tuple of CIF categories to exclude. + """ + def __init__(self, ignores): + self._ignores = ignores + + def get_system_writer(self, system, writer_class, writer): + return _IgnoreWriter(writer, self._ignores) + + def write(fh, systems, format='mmCIF', dumpers=[], variant=IHMVariant): """Write out all `systems` to the file handle `fh`. Files can be written in either the text-based mmCIF format or the diff --git a/modules/core/dependency/python-ihm/ihm/reader.py b/modules/core/dependency/python-ihm/ihm/reader.py index 9a12e7be5f..9e810e9bbe 100644 --- a/modules/core/dependency/python-ihm/ihm/reader.py +++ b/modules/core/dependency/python-ihm/ihm/reader.py @@ -17,6 +17,7 @@ import ihm.flr import inspect import warnings +import collections try: from . import _format except ImportError: @@ -1892,17 +1893,29 @@ def __call__(self, model_id, asym_id, rmsf, seq_id_begin, seq_id_end, class _AtomSiteHandler(Handler): category = '_atom_site' + def __init__(self, *args): + super(_AtomSiteHandler, self).__init__(*args) + self._missing_sequence = collections.defaultdict(dict) + def __call__(self, pdbx_pdb_model_num, label_asym_id, b_iso_or_equiv, label_seq_id, label_atom_id, type_symbol, cartn_x, cartn_y, cartn_z, occupancy, group_pdb, auth_seq_id, - pdbx_pdb_ins_code): + pdbx_pdb_ins_code, auth_asym_id, label_comp_id): + # seq_id can be None for non-polymers (HETATM) + seq_id = self.get_int(label_seq_id) # todo: handle fields other than those output by us model = self.sysr.models.get_by_id(pdbx_pdb_model_num) - asym = self.sysr.asym_units.get_by_id(label_asym_id) + if label_asym_id is None: + # If no asym_id is provided (e.g. minimal PyMOL output) then + # use the author-provided ID instead + asym = self.sysr.asym_units.get_by_id(auth_asym_id) + # Chances are the entity_poly table is missing too, so remember + # the comp_id to help us construct missing sequence info + self._missing_sequence[asym][seq_id] = label_comp_id + else: + asym = self.sysr.asym_units.get_by_id(label_asym_id) biso = self.get_float(b_iso_or_equiv) occupancy = self.get_float(occupancy) - # seq_id can be None for non-polymers (HETATM) - seq_id = self.get_int(label_seq_id) group = 'ATOM' if group_pdb is None else group_pdb a = ihm.model.Atom( asym_unit=asym, seq_id=seq_id, atom_id=label_atom_id, @@ -1920,6 +1933,25 @@ def __call__(self, pdbx_pdb_model_num, label_asym_id, b_iso_or_equiv, asym.auth_seq_id_map = {} asym.auth_seq_id_map[seq_id] = auth_seq_id, pdbx_pdb_ins_code + def finalize(self): + # Fill in missing Entity information from comp_ids + entity_from_seq = {} + for asym, comp_from_seq_id in self._missing_sequence.items(): + if asym.entity is None: + # Fill in gaps in seq_id with UNK residues + seq_len = max(comp_from_seq_id.keys()) + unk = ihm.LPeptideAlphabet()['UNK'] + seq = [unk] * seq_len + for seq_id, comp_id in comp_from_seq_id.items(): + seq[seq_id - 1] = self.sysr.chem_comps.get_by_id(comp_id) + seq = tuple(seq) # Lists are not hashable + if seq in entity_from_seq: + asym.entity = entity_from_seq[seq] + else: + asym.entity = ihm.Entity(seq) + entity_from_seq[seq] = asym.entity + self.system.entities.append(asym.entity) + class _StartingModelCoordHandler(Handler): category = '_ihm_starting_model_coord' diff --git a/modules/core/dependency/python-ihm/make-release.sh b/modules/core/dependency/python-ihm/make-release.sh index d614c9a49c..fa4f192532 100755 --- a/modules/core/dependency/python-ihm/make-release.sh +++ b/modules/core/dependency/python-ihm/make-release.sh @@ -2,6 +2,7 @@ # First, do # - Update AuditConformDumper to match latest IHM dictionary if necessary +# - Run util/validate-outputs.py to make sure all example outputs validate # - Update ChangeLog.rst with the release number # - Update release number in ihm/__init__.py, MANIFEST.in, and setup.py # - Commit, tag, and push diff --git a/modules/core/dependency/python-ihm/setup.py b/modules/core/dependency/python-ihm/setup.py index 3f0d042aa4..98e552cc5a 100755 --- a/modules/core/dependency/python-ihm/setup.py +++ b/modules/core/dependency/python-ihm/setup.py @@ -7,7 +7,7 @@ import sys import os -VERSION = "0.30" +VERSION = "0.31" copy_args = sys.argv[1:] diff --git a/modules/core/dependency/python-ihm/test/test_dumper.py b/modules/core/dependency/python-ihm/test/test_dumper.py index bad25e953c..f35fa63045 100644 --- a/modules/core/dependency/python-ihm/test/test_dumper.py +++ b/modules/core/dependency/python-ihm/test/test_dumper.py @@ -901,12 +901,11 @@ def test_nonpoly_scheme_dumper(self): _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num -_pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code -B 2 HEM 1 1 1 HEM HEM Q . -C 3 ZN 1 6 6 ZN ZN C . +B 2 HEM 1 1 1 HEM Q . +C 3 ZN 1 6 6 ZN C . # """) @@ -1906,7 +1905,9 @@ def test_range_checker_asmb_seq_id(self): # Cache should now be set self.assertEqual(rngcheck._last_asmb_range_matched, (1, 2)) self.assertEqual(rngcheck._last_asmb_asym_matched, 'X') - # 2nd check should use the cache + # 2nd check with same seq_id should use the cache + atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', + type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Sphere is OK (good range) sphere = ihm.model.Sphere(asym_unit=asym, seq_id_range=(1, 2), @@ -1923,6 +1924,25 @@ def test_range_checker_asmb_seq_id(self): x=1.0, y=2.0, z=3.0, radius=4.0) self.assertRaises(ValueError, rngcheck, sphere) + def test_range_checker_duplicate_atoms(self): + """Test RangeChecker class checking duplicate atoms""" + system, model, asym = self._make_test_model() + asmb = ihm.Assembly([asym]) + model.assembly = asmb + + # Everything is represented + s = ihm.representation.AtomicSegment(asym, rigid=True) + model.representation.append(s) + + rngcheck = ihm.dumper._RangeChecker(model) + atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', + type_symbol='C', x=1.0, y=2.0, z=3.0) + rngcheck(atom) + # Error to write another atom with same atom_id to same seq_id + atom = ihm.model.Atom(asym_unit=asym, seq_id=1, atom_id='CA', + type_symbol='C', x=1.0, y=2.0, z=3.0) + self.assertRaises(ValueError, rngcheck, atom) + def test_range_checker_repr_asym(self): """Test RangeChecker class checking representation asym ID match""" system, model, asym = self._make_test_model() @@ -1995,7 +2015,9 @@ def test_range_checker_repr_seq_id(self): # Cache should now be set self.assertEqual( rngcheck._last_repr_segment_matched.asym_unit.seq_id_range, (1, 2)) - # 2nd check should use the cache + # 2nd check with same seq_id should use the cache + atom = ihm.model.Atom(asym_unit=asym2, seq_id=1, atom_id='CA', + type_symbol='C', x=1.0, y=2.0, z=3.0) rngcheck(atom) # Sphere is OK (good range) sphere = ihm.model.Sphere(asym_unit=asym2, seq_id_range=(1, 2), @@ -4264,6 +4286,41 @@ def test_write_variant(self): fh = StringIO() ihm.dumper.write(fh, [sys1], variant=ihm.dumper.IHMVariant()) + def test_ignore_writer(self): + """Test _IgnoreWriter utility class""" + class BaseWriter(object): + def flush(self): + return 'flush called' + + def write_comment(self, comment): + return 'write comment ' + comment + + s = ihm.dumper._IgnoreWriter(BaseWriter(), []) + # These methods are not usually called in ordinary operation, but + # we should provide them for Writer compatibility + self.assertEqual(s.flush(), 'flush called') + self.assertEqual(s.write_comment('foo'), 'write comment foo') + + def test_write_ignore_variant(self): + """Test write() function with IgnoreVariant object""" + sys1 = ihm.System(id='system1') + fh = StringIO() + ihm.dumper.write(fh, [sys1]) + self.assertIn('_ihm_struct_assembly', fh.getvalue()) + # Test exclude of ihm_struct_assembly category + fh = StringIO() + ihm.dumper.write( + fh, [sys1], + variant=ihm.dumper.IgnoreVariant(['_ihm_struct_assembly'])) + self.assertNotIn('_ihm_struct_assembly', fh.getvalue()) + # Should be case-insensitive and tolerant of missing underscore + fh = StringIO() + ihm.dumper.write( + fh, [sys1], + variant=ihm.dumper.IgnoreVariant(['IHM_STRUCT_ASSEMBLY', + 'AUDIT_CONFORM'])) + self.assertNotIn('_ihm_struct_assembly', fh.getvalue()) + if __name__ == '__main__': unittest.main() diff --git a/modules/core/dependency/python-ihm/test/test_examples.py b/modules/core/dependency/python-ihm/test/test_examples.py index eb08ef8cef..14b56cc9c6 100644 --- a/modules/core/dependency/python-ihm/test/test_examples.py +++ b/modules/core/dependency/python-ihm/test/test_examples.py @@ -70,7 +70,7 @@ def test_ligands_water_example(self): # can read it with open(out) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 252) + self.assertEqual(len(contents), 251) with open(out) as fh: s, = ihm.reader.read(fh) # Make sure that resulting Python objects are picklable diff --git a/modules/core/dependency/python-ihm/test/test_reader.py b/modules/core/dependency/python-ihm/test/test_reader.py index ed1102973e..3b4aa67c96 100644 --- a/modules/core/dependency/python-ihm/test/test_reader.py +++ b/modules/core/dependency/python-ihm/test/test_reader.py @@ -1945,6 +1945,73 @@ def test_atom_site_handler_auth_seq_id(self): asym, = s.asym_units self.assertEqual(asym.auth_seq_id_map, {1: (2, 'A'), 2: ('20A', None)}) + def test_atom_site_handler_no_asym_id(self): + """Test AtomSiteHandler with missing asym_id""" + fh = StringIO(""" +loop_ +_entity_poly_seq.entity_id +_entity_poly_seq.num +_entity_poly_seq.mon_id +_entity_poly_seq.hetero +5 1 MET . +5 2 CYS . +5 3 MET . +5 4 SER . +# +loop_ +_struct_asym.id +_struct_asym.entity_id +_struct_asym.details +D 5 foo +# +loop_ +_atom_site.group_PDB +_atom_site.id +_atom_site.type_symbol +_atom_site.label_atom_id +_atom_site.label_alt_id +_atom_site.label_comp_id +_atom_site.label_asym_id +_atom_site.label_entity_id +_atom_site.label_seq_id +_atom_site.pdbx_PDB_ins_code +_atom_site.Cartn_x +_atom_site.Cartn_y +_atom_site.Cartn_z +_atom_site.occupancy +_atom_site.B_iso_or_equiv +_atom_site.pdbx_formal_charge +_atom_site.auth_asym_id +_atom_site.pdbx_PDB_model_num +ATOM 1 C CA . MET . . 1 ? 1.000 1.000 1.000 1.00 2.95 0 A 1 +ATOM 2 C CA . ASP . . 2 ? 2.000 2.000 2.000 1.00 0.95 0 A 1 +ATOM 3 C CA . CYS . . 3 ? 3.000 3.000 3.000 1.00 0.95 0 A 1 +ATOM 4 C CA . MET . . 1 ? 1.000 1.000 1.000 1.00 2.95 0 B 1 +ATOM 5 C CA . ASP . . 2 ? 2.000 2.000 2.000 1.00 0.95 0 B 1 +ATOM 6 C CA . CYS . . 3 ? 3.000 3.000 3.000 1.00 0.95 0 B 1 +ATOM 7 C CA . CYS . . 2 ? 1.000 1.000 1.000 1.00 0.95 0 C 1 +ATOM 8 C CA . CYS . . 5 ? 3.000 3.000 3.000 1.00 0.95 0 C 1 +ATOM 9 C CA . MET . . 1 ? 3.000 3.000 3.000 1.00 0.95 0 D 1 +""") + s, = ihm.reader.read(fh) + # No asym_id, so use auth_asym_id + a1, a2, a3, a4 = s.asym_units + self.assertEqual(a1._id, 'D') + self.assertEqual(a2._id, 'A') + self.assertEqual(a3._id, 'B') + self.assertEqual(a4._id, 'C') + # A and B should have same sequence, thus same entity + self.assertIs(a2.entity, a3.entity) + # Sequence should have been populated from comp_ids + self.assertEqual("".join(c.code for c in a2.entity.sequence), "MDC") + # C has different entity and sequence, with gaps + self.assertEqual("".join(c.code_canonical for c in a4.entity.sequence), + "XCXXC") + # D is defined in struct_asym and entity_poly so should use that + # sequence + self.assertEqual("".join(c.code_canonical for c in a1.entity.sequence), + "MCMS") + def test_derived_distance_restraint_handler(self): """Test DerivedDistanceRestraintHandler""" feats = """ From 8ac7f302e79fe57f0d29101fb12893ed9e70e276 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 22 Apr 2022 10:20:26 -0700 Subject: [PATCH 111/155] Don't require Python >= 3.6 f-strings require Python 3.6. Use old-style format strings so that they work everywhere. --- modules/atom/test/test_bd_simulate_dialanine_from_sequence.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/atom/test/test_bd_simulate_dialanine_from_sequence.py b/modules/atom/test/test_bd_simulate_dialanine_from_sequence.py index fcff839cc9..244485e8d5 100644 --- a/modules/atom/test/test_bd_simulate_dialanine_from_sequence.py +++ b/modules/atom/test/test_bd_simulate_dialanine_from_sequence.py @@ -109,9 +109,9 @@ def test_bd_simulate_dialanine_from_sequence(self): print(atoms) print("Optimizing") bd.optimize(BD_CYCLES) - print(f"Atoms after optimizing for {BD_CYCLES} cycles:") + print("Atoms after optimizing for %d cycles:" % BD_CYCLES) print(atoms) - print("Final score = {:.2f}".format(sf.evaluate(False))) + print("Final score = %.2f" % sf.evaluate(False)) if __name__ == '__main__': From baa7e15bc61dea03f53eecea162f7f2b8660de19 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 4 May 2022 15:41:18 -0700 Subject: [PATCH 112/155] Correct get_threshold_map function description --- modules/em/include/DensityMap.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/em/include/DensityMap.h b/modules/em/include/DensityMap.h index 841db29ebf..cbfcd68ebd 100644 --- a/modules/em/include/DensityMap.h +++ b/modules/em/include/DensityMap.h @@ -607,9 +607,9 @@ IMPEMEXPORT DensityMap *binarize(DensityMap *orig_map, float threshold, bool reverse = false); //! Return a map with 0 for all voxels below the threshold -/** \param[in] orig_map the map to binarize +/** \param[in] orig_map the map to threshold \param[in] threshold values below the threshold are set to 0 and - 1 otherwise + left unchanged otherwise */ IMPEMEXPORT DensityMap *get_threshold_map(const DensityMap *orig_map, float threshold); From 3cef109b8716d702c8dcac33e6864377ccef6609 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 4 May 2022 15:44:45 -0700 Subject: [PATCH 113/155] Squashed 'modules/pmi/' changes from 419124b729..195b5193a3 195b5193a3 Fix typo git-subtree-dir: modules/pmi git-subtree-split: 195b5193a353753413997bf055b0e2c6e409f078 --- modules/pmi/pyext/src/topology/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/pmi/pyext/src/topology/__init__.py b/modules/pmi/pyext/src/topology/__init__.py index dfc7a644c9..33a5c8e81e 100644 --- a/modules/pmi/pyext/src/topology/__init__.py +++ b/modules/pmi/pyext/src/topology/__init__.py @@ -1295,7 +1295,7 @@ class TopologyReader(object): [Chimera names](https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortables.html), (e.g. "red"), or R,G,B values as three comma-separated floating point numbers from 0 to 1 (e.g. "1.0, 0.0, 0.0") or a 6-digit hex string - starting with '#' (e.g. 0xff0000). + starting with '#' (e.g. #ff0000). - `fasta_fn`: Name of FASTA file containing this component. - `fasta_id`: String found in FASTA sequence header line. The sequence read from the file is assumed to be a protein sequence. If it should instead From 4166a9b5377cf628dc284c17b738ae12612f86a9 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 5 May 2022 13:31:20 -0700 Subject: [PATCH 114/155] Remove std::binary_function This has been deprecated in C++11 and was removed in C++17. It is unnecessary as modern compilers should be able to automatically figure out the types used by operator(). --- .../domino/include/internal/maximal_cliques.h | 6 +----- modules/em2d/include/scores2D.h | 18 +++--------------- modules/em2d/src/ProjectionFinder.cpp | 4 +--- 3 files changed, 5 insertions(+), 23 deletions(-) diff --git a/modules/domino/include/internal/maximal_cliques.h b/modules/domino/include/internal/maximal_cliques.h index 53386cfe63..50d9769923 100644 --- a/modules/domino/include/internal/maximal_cliques.h +++ b/modules/domino/include/internal/maximal_cliques.h @@ -28,7 +28,6 @@ // STL #include // storing R, P, X in sorted vectors -#include // binary_function #include // back_insert_iterator #include // sort, binary_search, lower_bound, ... @@ -50,10 +49,7 @@ void GX(const Graph& graph, Vector& P, Vector& X, // Binary Predicate: Degree_less // For std::max_element in GX template -class Degree_less - : public std::binary_function< - typename boost::graph_traits::vertex_descriptor, - typename boost::graph_traits::vertex_descriptor, bool> { +class Degree_less { private: typedef typename boost::graph_traits::vertex_descriptor vertex_descriptor; diff --git a/modules/em2d/include/scores2D.h b/modules/em2d/include/scores2D.h index d07c5abb6c..467f76dc29 100644 --- a/modules/em2d/include/scores2D.h +++ b/modules/em2d/include/scores2D.h @@ -116,11 +116,7 @@ IMP_OBJECTS(MeanAbsoluteDifference, MeanAbsoluteDifferences); //! Comparison by value of the ccc template -class HasHigherCCC -#ifndef SWIG - : public std::binary_function -#endif - { +class HasHigherCCC { public: bool operator()(const T &a, const T &b) const { return a.get_ccc() >= b.get_ccc(); @@ -130,11 +126,7 @@ class HasHigherCCC //! Comparison of pairs by checking the second element template -class LessPairBySecond -#ifndef SWIG - : public std::binary_function -#endif - { +class LessPairBySecond { public: bool operator()(const T &a, const T &b) const { return a.second < b.second; } void show(std::ostream &) const {} @@ -142,11 +134,7 @@ class LessPairBySecond //! Compare two classes that return a score template -class HasLowerScore -#ifndef SWIG - : public std::binary_function -#endif - { +class HasLowerScore { public: bool operator()(const T &a, const T &b) const { return a.get_score() < b.get_score(); diff --git a/modules/em2d/src/ProjectionFinder.cpp b/modules/em2d/src/ProjectionFinder.cpp index c1580db3e4..561ec4fdf3 100644 --- a/modules/em2d/src/ProjectionFinder.cpp +++ b/modules/em2d/src/ProjectionFinder.cpp @@ -31,9 +31,7 @@ IMPEM2D_BEGIN_NAMESPACE namespace { - class HasHigherCCCPointer - : public std::binary_function - { + class HasHigherCCCPointer { HasHigherCCC hhccc_; public: bool operator()(const RegistrationResult *a, From 9b81bd123dfce7ac444fa22d5514fab39ba0a61b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 13 May 2022 16:55:45 -0700 Subject: [PATCH 115/155] Squashed 'modules/pmi/' changes from 195b5193a3..5ba52792d5 5ba52792d5 Make sublist_iterator more efficient git-subtree-dir: modules/pmi git-subtree-split: 5ba52792d59cf31ff165076edd7438362d4e9288 --- modules/pmi/pyext/src/output.py | 2 +- modules/pmi/pyext/src/tools.py | 11 ++++------- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/modules/pmi/pyext/src/output.py b/modules/pmi/pyext/src/output.py index 0ad52dcd65..f0cc6c13af 100644 --- a/modules/pmi/pyext/src/output.py +++ b/modules/pmi/pyext/src/output.py @@ -314,7 +314,7 @@ def write_psf(self, filename, name): # get the index list indexes = [x[0] for x in ls] # get the contiguous pairs - indexes_pairs += list(IMP.pmi.tools.sublist_iterator( + indexes_pairs.extend(IMP.pmi.tools.sublist_iterator( indexes, lmin=2, lmax=2)) nbonds = len(indexes_pairs) flpsf.write(str(nbonds)+" !NBOND: bonds"+"\n") diff --git a/modules/pmi/pyext/src/tools.py b/modules/pmi/pyext/src/tools.py index 011ea9f068..f5e5234200 100644 --- a/modules/pmi/pyext/src/tools.py +++ b/modules/pmi/pyext/src/tools.py @@ -641,19 +641,16 @@ def scatter_and_gather(data): # -def sublist_iterator(ls, lmin=None, lmax=None): +def sublist_iterator(ls, lmin=1, lmax=None): ''' Yield all sublists of length >= lmin and <= lmax ''' - if lmin is None: - lmin = 0 if lmax is None: lmax = len(ls) - n = len(ls) + 1 + n = len(ls) for i in range(n): - for j in range(i + 1, n): - if len(ls[i:j]) <= lmax and len(ls[i:j]) >= lmin: - yield ls[i:j] + for j in range(i + lmin, min(n + 1, i + 1 + lmax)): + yield ls[i:j] def flatten_list(ls): From 67ba18acc89fcd4f82ad870ffecde1eff6024f26 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 13 May 2022 17:57:57 -0700 Subject: [PATCH 116/155] Squashed 'modules/core/dependency/python-ihm/' changes from 77992d59ca..8a9839efec 8a9839efec Don't output entity_src_gen if all fields are blank c510290db5 Synthetic class also uses Details 9f2bac0803 Don't add audit_conform to output mmCIFs git-subtree-dir: modules/core/dependency/python-ihm git-subtree-split: 8a9839efecde85beaf02b41223b49e16a6423047 --- modules/core/dependency/python-ihm/ihm/dumper.py | 3 +++ modules/core/dependency/python-ihm/ihm/source.py | 2 +- modules/core/dependency/python-ihm/test/test_dumper.py | 5 ++++- modules/core/dependency/python-ihm/util/make-mmcif.py | 5 +++-- 4 files changed, 11 insertions(+), 4 deletions(-) diff --git a/modules/core/dependency/python-ihm/ihm/dumper.py b/modules/core/dependency/python-ihm/ihm/dumper.py index 5d8724b0b9..083205aacd 100644 --- a/modules/core/dependency/python-ihm/ihm/dumper.py +++ b/modules/core/dependency/python-ihm/ihm/dumper.py @@ -302,6 +302,9 @@ def dump(self, system, writer): def _dump_source(self, lp, e): s = e.source + # Skip output if all fields are blank + if s.gene is None and s.host is None: + return lp.write(entity_id=e._id, pdbx_src_id=s._id, pdbx_gene_src_ncbi_taxonomy_id=s.gene.ncbi_taxonomy_id if s.gene else None, diff --git a/modules/core/dependency/python-ihm/ihm/source.py b/modules/core/dependency/python-ihm/ihm/source.py index 228a77fbae..ab3f3af3e9 100644 --- a/modules/core/dependency/python-ihm/ihm/source.py +++ b/modules/core/dependency/python-ihm/ihm/source.py @@ -11,7 +11,7 @@ class Source(object): class Details(object): """Identifying information for an entity source. - See :class:`Manipulated` or :class:`Natural`. + See :class:`Manipulated`, :class:`Natural` or :class:`Synthetic`. :param ncbi_taxonomy_id: NCBI taxonomy identifier, e.g. "469008" :param scientific_name: Scientific name, e.g. "Escherichia coli" diff --git a/modules/core/dependency/python-ihm/test/test_dumper.py b/modules/core/dependency/python-ihm/test/test_dumper.py index f35fa63045..222603ee4a 100644 --- a/modules/core/dependency/python-ihm/test/test_dumper.py +++ b/modules/core/dependency/python-ihm/test/test_dumper.py @@ -472,6 +472,9 @@ def test_entity_src_gen_dumper(self): system = ihm.System() system.entities.append(ihm.Entity('AHC', description='foo', source=ihm.source.Natural())) + system.entities.append( + ihm.Entity('AHCG', description='bar', + source=ihm.source.Manipulated(gene=None, host=None))) gene = ihm.source.Details(ncbi_taxonomy_id='1234', scientific_name='Test latin name', common_name='Test common name', @@ -499,7 +502,7 @@ def test_entity_src_gen_dumper(self): _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_strain -2 1 1234 'Test latin name' 'Test common name' 'test strain' 5678 +3 2 1234 'Test latin name' 'Test common name' 'test strain' 5678 'Other latin name' 'Other common name' 'other strain' # """) diff --git a/modules/core/dependency/python-ihm/util/make-mmcif.py b/modules/core/dependency/python-ihm/util/make-mmcif.py index 944e232534..9cf5bfff07 100644 --- a/modules/core/dependency/python-ihm/util/make-mmcif.py +++ b/modules/core/dependency/python-ihm/util/make-mmcif.py @@ -59,5 +59,6 @@ def add_ihm_info(s): with open(fname) as fh: with open('output.cif', 'w') as fhout: - ihm.dumper.write(fhout, - [add_ihm_info(s) for s in ihm.reader.read(fh)]) + ihm.dumper.write( + fhout, [add_ihm_info(s) for s in ihm.reader.read(fh)], + variant=ihm.dumper.IgnoreVariant(['_audit_conform'])) From 9571e54cfee737b78be3976fe899b44814a9ad40 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 17 May 2022 16:18:23 -0700 Subject: [PATCH 117/155] RHEL 9 does not provide a python2 package RHEL 9 dropped support for Python 2 entirely, so don't build IMP-python2 subpackage on this system. --- tools/rpm/IMP.spec.in | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in index d7c4e28721..623768d614 100644 --- a/tools/rpm/IMP.spec.in +++ b/tools/rpm/IMP.spec.in @@ -1,5 +1,6 @@ # On modern Fedora/RHEL, use Python 3 by default (and provide an IMP-python2 -# subpackage). On older systems, the IMP package uses Python 2 only. +# subpackage; on RHEL 9 or later, use Python 3 only). +# On older systems, the IMP package uses Python 2 only. %if 0%{?fedora} > 12 || 0%{?rhel} >= 8 %define with_python3 1 %define cmake_use_python2 off @@ -10,6 +11,12 @@ %define default_python python2 %endif +%if 0%{?rhel} >= 9 +%define with_python2 0 +%else +%define with_python2 1 +%endif + # Old RHEL only has a python-devel package, but RHEL8 only has python2-devel %if 0%{?fedora} || 0%{?rhel} >= 8 %define PYTHON2 python2 @@ -34,11 +41,13 @@ Group: Applications/Engineering Packager: Ben Webb URL: https://integrativemodeling.org/ Source0: imp-%{version}.tar.gz +%if 0%{?with_python2} +BuildRequires: %{PYTHON2}-devel >= 2.6 +%endif %if 0%{?with_python3} BuildRequires: python3-devel, symlinks %endif -BuildRequires: %{PYTHON2}-devel >= 2.6, gcc-c++ -BuildRequires: hdf5-devel >= 1.8 +BuildRequires: gcc-c++, hdf5-devel >= 1.8 %if 0%{?rhel} == 7 # The default SWIG package in RHEL7 is SWIG 2, but SWIG 3 is provided # (in the CentOS Extras repository) @@ -94,7 +103,7 @@ BuildRequires: CGAL-nogui-devel %if 0%{?with_python3} BuildRequires: python3-numpy, python3-scipy Requires: python3-numpy, python3-scipy -%if 0%{?fedora} < 34 || 0%{?rhel} +%if 0%{?with_python2} && (0%{?fedora} < 34 || 0%{?rhel}) BuildRequires: python2-numpy %endif %else @@ -166,7 +175,7 @@ Requires: opencv-devel This package contains the include files for building applications that link against IMP. -%if 0%{?with_python3} +%if 0%{?with_python2} && 0%{?with_python3} %package python2 Group: Applications/Engineering Summary: Python wrappers for Python 2 @@ -322,7 +331,7 @@ module purge cd build make DESTDIR=${RPM_BUILD_ROOT} install -%if 0%{?with_python3} +%if 0%{?with_python2} && 0%{?with_python3} # Build Python 2 wrappers py2_ver=`python2 -c "import sys; print('%d.%d' % sys.version_info[:2])"` py3_ver=`python3 -c "import sys; print('%d.%d' % sys.version_info[:2])"` @@ -438,7 +447,7 @@ find ${RPM_BUILD_ROOT}%{_prefix}/share/IMP/tools -name '*.py' -exec perl -pi -e %exclude %{_libdir}/%{default_python}*/site-packages/IMP/spb %endif -%if 0%{?with_python3} +%if 0%{?with_python2} && 0%{?with_python3} %files python2 %defattr(-,root,root) %{_libdir}/python2*/site-packages/IMP From 75fbde0405d134e682d1e749ded0a9ce6fa44cd8 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 19 May 2022 12:02:26 -0700 Subject: [PATCH 118/155] Don't check hierarchies for validity in Selection Checking a hierarchy for validity is quite expensive, more so than getting the selected particles. Skip this (except in debug mode). Users that may generate invalid hierarchies can still call get_is_valid() on them before using Selection. --- ChangeLog.md | 3 +++ modules/atom/include/Selection.h | 4 ++++ modules/atom/src/Selection.cpp | 10 ++++++---- 3 files changed, 13 insertions(+), 4 deletions(-) diff --git a/ChangeLog.md b/ChangeLog.md index 9b7b0ebc47..f9734506c0 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -2,6 +2,9 @@ ChangeLog {#changelog} ========= # HEAD +- IMP::atom::Selection no longer checks that the passed hierarchies are valid, + as this can be quite computationally expensive. If in doubt, call + IMP::atom::Hierarchy::get_is_valid() on each one first. - The IMP::em::CoarseCC class has been removed. Use similarly-named free functions instead to calculate coarse cross correlation. - IMP now requires a C++11 compiler and SWIG 3 (or later) to build. Most diff --git a/modules/atom/include/Selection.h b/modules/atom/include/Selection.h index 9c1483a480..4549b5d6d5 100644 --- a/modules/atom/include/Selection.h +++ b/modules/atom/include/Selection.h @@ -58,6 +58,10 @@ IMPATOM_BEGIN_NAMESPACE To actually get the selected particles, call get_selected_particle_indexes() or get_selected_particles(). + This class assumes the hierarchies are valid (and if they are not, may not + select the correct particles). If in doubt, call + IMP::atom::Hierarchy::get_is_valid() on each one first to verify this. + \note The highest resolution representation that fits is returned. If you want lower resolution, use the resolution parameter to select the desired resolution (pass a very large diff --git a/modules/atom/src/Selection.cpp b/modules/atom/src/Selection.cpp index d5ef206d4d..99ddd995a0 100644 --- a/modules/atom/src/Selection.cpp +++ b/modules/atom/src/Selection.cpp @@ -320,10 +320,12 @@ void Selection::set_hierarchies(Model *m, const ParticleIndexes &pi) { m_ = m; h_ = pi; - for (unsigned int i = 0; i < pi.size(); ++i) { - Hierarchy h(m_, pi[i]); - IMP_USAGE_CHECK(h.get_is_valid(true), "Hierarchy " << h - << " is not valid."); + IMP_IF_CHECK(USAGE_AND_INTERNAL) { + for (unsigned int i = 0; i < pi.size(); ++i) { + Hierarchy h(m_, pi[i]); + IMP_INTERNAL_CHECK(h.get_is_valid(true), + "Hierarchy " << h << " is not valid."); + } } } From f0b434fd5fdba1321ab277807462a858e91e7c0d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 19 May 2022 12:51:15 -0700 Subject: [PATCH 119/155] Speed up finding residues in Fragment Rather than making a temporary list of all residues in the Fragment, act directly on the residue ranges. --- modules/atom/include/Fragment.h | 4 ++++ modules/atom/src/Fragment.cpp | 13 +++++++++++++ modules/atom/src/Selection.cpp | 6 +----- modules/atom/test/test_fragment.py | 11 +++++++++-- 4 files changed, 27 insertions(+), 7 deletions(-) diff --git a/modules/atom/include/Fragment.h b/modules/atom/include/Fragment.h index e543f25ad6..ea5041a950 100644 --- a/modules/atom/include/Fragment.h +++ b/modules/atom/include/Fragment.h @@ -59,6 +59,10 @@ class IMPATOMEXPORT Fragment : public Hierarchy { /** This could be made more efficient. */ bool get_contains_residue(int rindex) const; + //! Return true if this fragment contains any of the sorted residues + /** The input list of residue indexes must be sorted. */ + bool get_contains_any_sorted_residue(const Ints &rinds) const; + IMP_DECORATOR_METHODS(Fragment, Hierarchy); IMP_DECORATOR_SETUP_0(Fragment); IMP_DECORATOR_SETUP_1(Fragment, Fragment, other); diff --git a/modules/atom/src/Fragment.cpp b/modules/atom/src/Fragment.cpp index b99e78c755..842e9144af 100644 --- a/modules/atom/src/Fragment.cpp +++ b/modules/atom/src/Fragment.cpp @@ -55,6 +55,19 @@ bool Fragment::get_contains_residue(int ri) const { return false; } +bool Fragment::get_contains_any_sorted_residue(const Ints &rinds) const { + IMP_INTERNAL_CHECK(std::is_sorted(rinds.begin(), rinds.end()), + "The residue list is not sorted."); + IntPairs all = get_residue_index_ranges(); + for (const IntPair &p : all) { + if (std::lower_bound(rinds.begin(), rinds.end(), p.first) != + std::lower_bound(rinds.begin(), rinds.end(), p.second)) { + return true; + } + } + return false; +} + IntPairs Fragment::get_residue_index_ranges() const { if (!get_model()->get_has_attribute(get_begins_key(), get_particle_index())) { return IntPairs(); diff --git a/modules/atom/src/Selection.cpp b/modules/atom/src/Selection.cpp index 99ddd995a0..8b736f0baf 100644 --- a/modules/atom/src/Selection.cpp +++ b/modules/atom/src/Selection.cpp @@ -358,11 +358,7 @@ bool get_is_residue_index_match(const Ints &data, Model *m, Residue(m, pi).get_index()); } if (Fragment::get_is_setup(m, pi)) { - Ints cur = Fragment(m, pi).get_residue_indexes(); - Ints si; - std::set_intersection(data.begin(), data.end(), cur.begin(), cur.end(), - std::back_inserter(si)); - return !si.empty(); + return Fragment(m, pi).get_contains_any_sorted_residue(data); } else if (Domain::get_is_setup(m, pi)) { IntRange ir = Domain(m, pi).get_index_range(); return std::lower_bound(data.begin(), data.end(), ir.first) != diff --git a/modules/atom/test/test_fragment.py b/modules/atom/test/test_fragment.py index a5f318d409..c389096cd6 100644 --- a/modules/atom/test/test_fragment.py +++ b/modules/atom/test/test_fragment.py @@ -6,8 +6,8 @@ class Tests(IMP.test.TestCase): - def test_bonded(self): - """Check Fragment """ + def test_fragment(self): + """Check Fragment""" m = IMP.Model() p = IMP.Particle(m) f = IMP.atom.Fragment.setup_particle(p) @@ -19,5 +19,12 @@ def test_bonded(self): self.assertTrue(f.get_contains_residue(6)) self.assertFalse(f.get_contains_residue(5)) + self.assertTrue(f.get_contains_any_sorted_residue([1, 34])) + self.assertTrue(f.get_contains_any_sorted_residue([-5, 2])) + self.assertFalse(f.get_contains_any_sorted_residue([3, 5])) + self.assertFalse(f.get_contains_any_sorted_residue([-2, -1])) + self.assertFalse(f.get_contains_any_sorted_residue([7, 8])) + + if __name__ == '__main__': IMP.test.main() From c581175d2df61ade0e05f292bbe33e332c4f95d5 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 19 May 2022 13:06:12 -0700 Subject: [PATCH 120/155] Avoid creating unnecessary Particle object --- modules/atom/include/Hierarchy.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/atom/include/Hierarchy.h b/modules/atom/include/Hierarchy.h index 6766653b09..f4f406e1cd 100644 --- a/modules/atom/include/Hierarchy.h +++ b/modules/atom/include/Hierarchy.h @@ -253,7 +253,7 @@ class IMPATOMEXPORT Hierarchy : public core::Hierarchy { //! Check if the particle has the needed attributes for a cast to succeed static bool get_is_setup(Model *m, ParticleIndex p) { - return H::get_is_setup(m->get_particle(p), get_traits()); + return H::get_is_setup(m, p, get_traits()); } //! Return true if the hierarchy is valid. From bf29ae8219113f18921205c707282e2f28ff591a Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 19 May 2022 14:45:37 -0700 Subject: [PATCH 121/155] Reduce std::vector usage Speed up Selection::get_particle_indexes() by reducing the number of temporary vectors created during the search. --- modules/atom/src/Selection.cpp | 73 +++++++++++++++------------------- 1 file changed, 32 insertions(+), 41 deletions(-) diff --git a/modules/atom/src/Selection.cpp b/modules/atom/src/Selection.cpp index 8b736f0baf..5411848681 100644 --- a/modules/atom/src/Selection.cpp +++ b/modules/atom/src/Selection.cpp @@ -509,20 +509,17 @@ IMP_ATOM_SELECTION_PRED(Terminus, Int, { } }); -IMP_NAMED_TUPLE_2(ExpandResult, ExpandResults, bool, from_rep, - ParticleIndexes, indexes, ); - -ExpandResult expand_search(Model *m, - ParticleIndex pi, - double resolution, - RepresentationType representation_type) { +void expand_search_representation( + Model *m, ParticleIndex pi, double resolution, + RepresentationType representation_type, bool &from_rep, + ParticleIndexes &idxs) { // to handle representations - ParticleIndexes idxs; - bool from_rep = false; + from_rep = false; + idxs.clear(); if (Representation::get_is_setup(m, pi)) { from_rep = true; if (resolution == ALL_RESOLUTIONS) { - idxs = Representation(m, pi).get_representations(representation_type); + idxs += Representation(m, pi).get_representations(representation_type); } else { Hierarchy tmp = Representation(m, pi).get_representation(resolution, @@ -533,21 +530,8 @@ ExpandResult expand_search(Model *m, else { idxs.push_back(pi); } - return ExpandResult(from_rep,idxs); -} - -ExpandResults expand_children_search(Model *m, - ParticleIndex pi, - double resolution, - RepresentationType representation_type) { - Hierarchy h(m, pi); - ExpandResults ret; - for(Hierarchy c : h.get_children()) { - ExpandResult r = expand_search(m, c, resolution, representation_type); - if (r.get_indexes().size()>0) ret.push_back(r); - } - return ret; } + } Selection::SearchResult Selection::search( @@ -570,23 +554,28 @@ Selection::SearchResult Selection::search( } else return SearchResult(false, ParticleIndexes()); } - Hierarchy cur(m, pi); ParticleIndexes children; - ExpandResults cur_children = - expand_children_search(m, pi, resolution_, representation_type_); bool children_covered = true; bool matched = (val == internal::SelectionPredicate::MATCH_WITH_CHILDREN || val == internal::SelectionPredicate::MATCH_SELF_ONLY); - for(ExpandResult chlist : cur_children) { - found_rep_node |= chlist.get_from_rep(); - for(ParticleIndex ch : chlist.get_indexes()) { - SearchResult curr = search(m, ch, parent, with_representation, found_rep_node); - matched |= curr.get_match(); - if (curr.get_match()) { - if (curr.get_indexes().empty()) { - children_covered = false; - } else { - children += curr.get_indexes(); + ParticleIndexes rep_pis; + bool from_rep; + Hierarchy cur(m, pi); + for (Hierarchy child : cur.get_children()) { + expand_search_representation( + m, child, resolution_, representation_type_, from_rep, rep_pis); + if (rep_pis.size() > 0) { + found_rep_node |= from_rep; + for (ParticleIndex ch : rep_pis) { + SearchResult curr = search(m, ch, parent, with_representation, + found_rep_node); + matched |= curr.get_match(); + if (curr.get_match()) { + if (curr.get_indexes().empty()) { + children_covered = false; + } else { + children += curr.get_indexes(); + } } } } @@ -627,11 +616,13 @@ Selection::get_selected_particle_indexes(bool with_representation) const { IMP_LOG_TERSE("Processing selection on " << h_ << " with predicates " << std::endl); IMP_LOG_WRITE(VERBOSE, show_predicate(predicate_, IMP_STREAM)); + ParticleIndexes rep_pis; + bool from_rep; for(ParticleIndex pi : h_) { - ExpandResult res = expand_search(m_, pi, resolution_, - representation_type_); - for(ParticleIndex rpi : res.get_indexes()) { - ret += search(m_, rpi, base, with_representation, res.get_from_rep()).get_indexes(); + expand_search_representation( + m_, pi, resolution_, representation_type_, from_rep, rep_pis); + for (ParticleIndex rpi : rep_pis) { + ret += search(m_, rpi, base, with_representation, from_rep).get_indexes(); } } return ret; From 840389f980eb5ef10df874a905b08c15767e46aa Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 19 May 2022 15:15:45 -0700 Subject: [PATCH 122/155] Avoid creating unnecessary Hierarchy objects --- modules/atom/src/Selection.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/atom/src/Selection.cpp b/modules/atom/src/Selection.cpp index 5411848681..2c9418a8d2 100644 --- a/modules/atom/src/Selection.cpp +++ b/modules/atom/src/Selection.cpp @@ -561,9 +561,9 @@ Selection::SearchResult Selection::search( ParticleIndexes rep_pis; bool from_rep; Hierarchy cur(m, pi); - for (Hierarchy child : cur.get_children()) { + for (ParticleIndex childpi : cur.get_children_indexes()) { expand_search_representation( - m, child, resolution_, representation_type_, from_rep, rep_pis); + m, childpi, resolution_, representation_type_, from_rep, rep_pis); if (rep_pis.size() > 0) { found_rep_node |= from_rep; for (ParticleIndex ch : rep_pis) { From 5195b0c465ccc92253bd523f09c4e13227451282 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 24 May 2022 17:03:31 -0700 Subject: [PATCH 123/155] Speed up traversal of model dependency graph Speed up any uncached traversal of the model dependency graph by avoiding the creation of temporary vectors. --- modules/kernel/include/Model.h | 28 +++++++++++++++++++ modules/kernel/include/dependency_graph.h | 11 +++----- modules/kernel/src/Model_dependencies.cpp | 24 ++++++++++++++++ modules/kernel/src/dependency_graph.cpp | 18 ++++++------ .../src/internal/moved_particles_cache.cpp | 6 ++-- modules/kernel/test/test_dependency_graph.py | 6 ++-- modules/kernel/test/test_score_state.py | 4 +-- 7 files changed, 73 insertions(+), 24 deletions(-) diff --git a/modules/kernel/include/Model.h b/modules/kernel/include/Model.h index 600fbd4011..34b107d058 100644 --- a/modules/kernel/include/Model.h +++ b/modules/kernel/include/Model.h @@ -139,6 +139,26 @@ class IMPKERNELEXPORT Model : public Object } } + template + void do_get_dependent(ModelObject *mo, MOVector &ret) { + const auto &node = dependency_graph_.find(mo); + IMP_INTERNAL_CHECK(mo->get_has_dependencies(), + "Object " << mo->get_name() + << " does not have dependencies."); + IMP_INTERNAL_CHECK(node != dependency_graph_.end(), + "Node not in dependency_graph."); + MOType *r = dynamic_cast(mo); + if (r) { + ret.push_back(r); + } + for (ModelObject *cur : node->second.get_outputs()) { + do_get_dependent(cur, ret); + } + for (ModelObject *cur : node->second.get_readers()) { + do_get_dependent(cur, ret); + } + } + #if !defined(IMP_DOXYGEN) && !defined(SWIG) // things the evaluate template functions need, can't be bothered with friends public: @@ -222,6 +242,14 @@ class IMPKERNELEXPORT Model : public Object //! Add the passed Undecorator to the particle. void add_undecorator(ParticleIndex pi, Undecorator *d); +#if !defined(IMP_DOXYGEN) + RestraintsTemp get_dependent_restraints_uncached(ParticleIndex pi); + + ParticlesTemp get_dependent_particles_uncached(ParticleIndex pi); + + ScoreStatesTemp get_dependent_score_states_uncached(ParticleIndex pi); +#endif + /** @name States ScoreStates maintain invariants in the Model (see ScoreState diff --git a/modules/kernel/include/dependency_graph.h b/modules/kernel/include/dependency_graph.h index 3968072749..3d6f2f6bd6 100644 --- a/modules/kernel/include/dependency_graph.h +++ b/modules/kernel/include/dependency_graph.h @@ -61,14 +61,12 @@ IMPKERNELEXPORT ParticlesTemp const DependencyGraphVertexIndex &index); #ifndef IMP_DOXYGEN -//! Return all Restraints that depend on this Particle. -/* Model::set_has_all_dependencies() must be called first. - \note The list may contain duplicates. */ + +IMPKERNEL_DEPRECATED_FUNCTION_DECL(2.17) IMPKERNELEXPORT RestraintsTemp get_dependent_restraints(Model *m, ParticleIndex pi); -//! Return all ScoreStates that depend on this Particle. -/** \note The list may contain duplicates. */ +IMPKERNEL_DEPRECATED_FUNCTION_DECL(2.17) IMPKERNELEXPORT ScoreStatesTemp get_dependent_score_states(Model *m, ParticleIndex pi); @@ -77,8 +75,7 @@ IMPKERNELEXPORT ScoreStatesTemp IMPKERNELEXPORT ScoreStatesTemp get_required_score_states(Model *m, ParticleIndex pi); -//! Return all Particles that depend on this Particle. -/** \note The list may contain duplicates. */ +IMPKERNEL_DEPRECATED_FUNCTION_DECL(2.17) IMPKERNELEXPORT ParticlesTemp get_dependent_particles(Model *m, ParticleIndex pi); diff --git a/modules/kernel/src/Model_dependencies.cpp b/modules/kernel/src/Model_dependencies.cpp index c4cc77ffce..5e1d62ac5c 100644 --- a/modules/kernel/src/Model_dependencies.cpp +++ b/modules/kernel/src/Model_dependencies.cpp @@ -402,6 +402,30 @@ ModelObjectsTemp Model::get_dependency_graph_outputs(const ModelObject *mo) dependency_graph_.find(mo)->second.get_readers(); } +RestraintsTemp Model::get_dependent_restraints_uncached(ParticleIndex pi) { + set_has_all_dependencies(true); + ModelObject *cur = get_particle(pi); + RestraintsTemp ret; + do_get_dependent(cur, ret); + return ret; +} + +ScoreStatesTemp Model::get_dependent_score_states_uncached(ParticleIndex pi) { + set_has_all_dependencies(true); + ModelObject *cur = get_particle(pi); + ScoreStatesTemp ret; + do_get_dependent(cur, ret); + return ret; +} + +ParticlesTemp Model::get_dependent_particles_uncached(ParticleIndex pi) { + set_has_all_dependencies(true); + ModelObject *cur = get_particle(pi); + ParticlesTemp ret; + do_get_dependent(cur, ret); + return ret; +} + bool Model::do_get_has_required_score_states(const ModelObject *mo) const { return required_score_states_.find(mo) != required_score_states_.end(); } diff --git a/modules/kernel/src/dependency_graph.cpp b/modules/kernel/src/dependency_graph.cpp index b5793f3df9..a89ea5d8ac 100644 --- a/modules/kernel/src/dependency_graph.cpp +++ b/modules/kernel/src/dependency_graph.cpp @@ -355,15 +355,15 @@ MOVector do_get_dependent(ModelObject *mo) { } RestraintsTemp get_dependent_restraints(Model *m, ParticleIndex pi) { - m->set_has_all_dependencies(true); - ModelObject *cur = m->get_particle(pi); - return do_get_dependent(cur); + IMPKERNEL_DEPRECATED_FUNCTION_DEF( + 2.17, "Use Model::get_dependent_restraints_uncached() instead.") + return m->get_dependent_restraints_uncached(pi); } ScoreStatesTemp get_dependent_score_states(Model *m, ParticleIndex pi) { - m->set_has_all_dependencies(true); - ModelObject *cur = m->get_particle(pi); - return do_get_dependent(cur); + IMPKERNEL_DEPRECATED_FUNCTION_DEF( + 2.17, "Use Model::get_dependent_score_states_uncached() instead.") + return m->get_dependent_score_states_uncached(pi); } ScoreStatesTemp get_required_score_states(Model *m, ParticleIndex pi) { @@ -373,9 +373,9 @@ ScoreStatesTemp get_required_score_states(Model *m, ParticleIndex pi) { } ParticlesTemp get_dependent_particles(Model *m, ParticleIndex pi) { - m->set_has_all_dependencies(true); - ModelObject *cur = m->get_particle(pi); - return do_get_dependent(cur); + IMPKERNEL_DEPRECATED_FUNCTION_DEF( + 2.17, "Use Model::get_dependent_particles_uncached() instead.") + return m->get_dependent_particles_uncached(pi); } IMPKERNEL_END_NAMESPACE diff --git a/modules/kernel/src/internal/moved_particles_cache.cpp b/modules/kernel/src/internal/moved_particles_cache.cpp index c928c7445b..6902eeaa06 100644 --- a/modules/kernel/src/internal/moved_particles_cache.cpp +++ b/modules/kernel/src/internal/moved_particles_cache.cpp @@ -17,7 +17,7 @@ const std::set & MovedParticlesRestraintCache::get_dependent_restraints(ParticleIndex pi) { CacheMap::const_iterator it = cache_.find(pi); if (it == cache_.end()) { - RestraintsTemp rs = IMP::get_dependent_restraints(m_, pi); + RestraintsTemp rs = m_->get_dependent_restraints_uncached(pi); std::set rsset(rs.begin(), rs.end()); cache_[pi] = rsset; it = cache_.find(pi); @@ -29,7 +29,7 @@ const std::set & MovedParticlesParticleCache::get_dependent_particles(ParticleIndex pi) { CacheMap::const_iterator it = cache_.find(pi); if (it == cache_.end()) { - ParticlesTemp ps = IMP::get_dependent_particles(m_, pi); + ParticlesTemp ps = m_->get_dependent_particles_uncached(pi); std::set psset; for (ParticlesTemp::const_iterator pi = ps.begin(); pi != ps.end(); ++pi) { psset.insert((*pi)->get_index()); @@ -44,7 +44,7 @@ const std::set & MovedParticlesScoreStateCache::get_affected_score_states(ParticleIndex pi) { CacheMap::const_iterator it = cache_.find(pi); if (it == cache_.end()) { - ScoreStatesTemp pssin = IMP::get_dependent_score_states(m_, pi); + ScoreStatesTemp pssin = m_->get_dependent_score_states_uncached(pi); // We should not be moving a particle that will just be overwritten by // a ScoreState, but include these anyway to make sure the Model stays // consistent diff --git a/modules/kernel/test/test_dependency_graph.py b/modules/kernel/test/test_dependency_graph.py index 13c3d1e169..8bccf13fbe 100644 --- a/modules/kernel/test/test_dependency_graph.py +++ b/modules/kernel/test/test_dependency_graph.py @@ -49,9 +49,9 @@ def test_get_dependent_particles(self): p1 = IMP.Particle(m) p2 = IMP.Particle(m) s0 = NullConstraint(m, inputs=[p0], outputs=[p1]) - self.assertEqual(IMP.get_dependent_particles(m, p0), [p0, p1]) - self.assertEqual(IMP.get_dependent_particles(m, p1), [p1]) - self.assertEqual(IMP.get_dependent_particles(m, p2), [p2]) + self.assertEqual(m.get_dependent_particles_uncached(p0), [p0, p1]) + self.assertEqual(m.get_dependent_particles_uncached(p1), [p1]) + self.assertEqual(m.get_dependent_particles_uncached(p2), [p2]) def test_dependency_age(self): """Test dependency age counter""" diff --git a/modules/kernel/test/test_score_state.py b/modules/kernel/test/test_score_state.py index c8dc038e9f..90ac8510dd 100644 --- a/modules/kernel/test/test_score_state.py +++ b/modules/kernel/test/test_score_state.py @@ -61,8 +61,8 @@ def test_get_dependent_score_states(self): p1 = IMP.Particle(m) p2 = IMP.Particle(m) ss1 = LoggingScoreState(m, log, inputs=[p1]) - self.assertEqual(IMP.get_dependent_score_states(m, p1), [ss1]) - self.assertEqual(IMP.get_dependent_score_states(m, p2), []) + self.assertEqual(m.get_dependent_score_states_uncached(p1), [ss1]) + self.assertEqual(m.get_dependent_score_states_uncached(p2), []) def test_evaluate_moved(self): """Test score state skipping in evaluate_moved()""" From e56a5062612b5b93de83a635d3536993660aca5e Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 25 May 2022 10:22:20 -0700 Subject: [PATCH 124/155] Add spelling exception --- modules/kernel/test/standards_exceptions | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/kernel/test/standards_exceptions b/modules/kernel/test/standards_exceptions index f8be42eb34..8a55b7c676 100644 --- a/modules/kernel/test/standards_exceptions +++ b/modules/kernel/test/standards_exceptions @@ -45,7 +45,7 @@ value_object_exceptions=['Exception', 'TypeException', 'RestraintBase', 'ScoreStateBase'] spelling_exceptions=["undecorator", "undecorate", "altgraph", "networkx", - "numpy"] + "numpy", "uncached"] doc_spelling_exceptions=["num", "args", "pyext", "src", "py", "docstring", "multifit", "cnmultifit"] From 1e627be873a9b99779c0a6927c227996a800f292 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 25 May 2022 10:22:34 -0700 Subject: [PATCH 125/155] Don't use deprecated function --- modules/core/src/IncrementalScoringFunction.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/core/src/IncrementalScoringFunction.cpp b/modules/core/src/IncrementalScoringFunction.cpp index a93d4c86d8..9e7ab68488 100644 --- a/modules/core/src/IncrementalScoringFunction.cpp +++ b/modules/core/src/IncrementalScoringFunction.cpp @@ -107,7 +107,7 @@ void IncrementalScoringFunction::create_scoring_functions() { Vector crs; for(ParticleIndex pi : all_) { - RestraintsTemp cr = get_dependent_restraints(get_model(), pi); + RestraintsTemp cr = get_model()->get_dependent_restraints_uncached(pi); /* Remove any duplicates in cr (could happen with rigid bodies) */ std::sort(cr.begin(), cr.end()); cr.erase(std::unique(cr.begin(), cr.end()), cr.end()); From 94629e1a1f2bb841df1a6636fa1ab00dd07286a7 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 25 May 2022 15:47:14 -0700 Subject: [PATCH 126/155] Allow save/restore of model dependencies Add methods to Model to save and restore the model dependency graph. These can be used to bookend a code section that only temporarily changes the graph, so that caches dependent on the graph are not invalidated. Use these methods when writing an RMF file, which can create temporary decomposed restraints. --- modules/kernel/include/Model.h | 40 +++++++++++++++ modules/kernel/src/Model.cpp | 2 + modules/kernel/src/Model_dependencies.cpp | 11 ++++ modules/kernel/test/test_model.py | 24 +++++++++ modules/rmf/src/restraint_io.cpp | 62 +++++++++++------------ 5 files changed, 107 insertions(+), 32 deletions(-) diff --git a/modules/kernel/include/Model.h b/modules/kernel/include/Model.h index 34b107d058..18a94d23e6 100644 --- a/modules/kernel/include/Model.h +++ b/modules/kernel/include/Model.h @@ -123,6 +123,12 @@ class IMPKERNELEXPORT Model : public Object Vector trigger_age_; // time when dependencies were last changed, or 0 unsigned dependencies_age_; + + // allow skipping updating dependencies_age_ for temporary ModelObjects + bool dependencies_saved_; + unsigned saved_dependencies_age_; + ModelObjectsTemp mos_added_since_save_, mos_removed_since_save_; + // cache of restraints that are affected by each moved particle, // used for evaluate_moved() and related functions internal::MovedParticlesRestraintCache moved_particles_restraint_cache_; @@ -450,6 +456,40 @@ class IMPKERNELEXPORT Model : public Object help maintain caches that depend on the model's dependency graph. */ unsigned get_dependencies_updated() { return dependencies_age_; } + //! Mark a 'restore point' for ModelObject dependencies. + /** \see restore_dependencies() */ + void save_dependencies() { + dependencies_saved_ = true; + saved_dependencies_age_ = dependencies_age_; + IMP_IF_CHECK(USAGE_AND_INTERNAL) { + mos_added_since_save_.clear(); + mos_removed_since_save_.clear(); + } + } + + //! Restore ModelObject dependencies to previous restore point. + /** This method, when paired with save_dependencies(), can be used to + avoid triggering a model dependency update due to a temporary change + in the model dependency graph, for example due to adding a temporary + restraint, evaluating it, then removing that same restraint. It should + only be called in cases where it is known that the dependency graph + is the same as when save_dependencies() was called (this is only checked + in debug mode). Save/restore call pairs cannot be nested, although it + is OK to skip the call to restore_dependencies(), e.g. if an exception + occurs. + + \see get_dependencies_updated() + \see save_dependencies() + */ + void restore_dependencies() { + if (dependencies_saved_) { + dependencies_saved_ = false; + dependencies_age_ = saved_dependencies_age_; + IMP_INTERNAL_CHECK(mos_added_since_save_ == mos_removed_since_save_, + "ModelObjects added do not match those removed"); + } + } + IMP_OBJECT_METHODS(Model); public: diff --git a/modules/kernel/src/Model.cpp b/modules/kernel/src/Model.cpp index adb1f440d6..f022dd2a64 100644 --- a/modules/kernel/src/Model.cpp +++ b/modules/kernel/src/Model.cpp @@ -21,6 +21,8 @@ Model::Model(std::string name) first_call_ = true; age_counter_ = 1; dependencies_age_ = 0; + saved_dependencies_age_ = 0; + dependencies_saved_ = false; moved_particles_cache_age_ = 0; #if IMP_HAS_CHECKS >= IMP_INTERNAL internal::FloatAttributeTable::set_masks( diff --git a/modules/kernel/src/Model_dependencies.cpp b/modules/kernel/src/Model_dependencies.cpp index 5e1d62ac5c..3b54aeb261 100644 --- a/modules/kernel/src/Model_dependencies.cpp +++ b/modules/kernel/src/Model_dependencies.cpp @@ -469,6 +469,12 @@ void Model::do_set_has_required_score_states(ModelObject *mo, bool tf) { } void Model::do_add_model_object(ModelObject *mo) { + IMP_IF_CHECK(USAGE_AND_INTERNAL) { + if (dependencies_saved_) { + mos_added_since_save_.push_back(mo); + } + } + IMP_LOG_VERBOSE("Adding " << mo->get_name() << " to model." << std::endl); if (dependency_graph_.find(mo) == dependency_graph_.end()) { dependency_graph_[mo] = NodeInfo(); @@ -478,6 +484,11 @@ void Model::do_add_model_object(ModelObject *mo) { } void Model::do_remove_model_object(ModelObject *mo) { + IMP_IF_CHECK(USAGE_AND_INTERNAL) { + if (dependencies_saved_) { + mos_removed_since_save_.push_back(mo); + } + } IMP_OBJECT_LOG; IMP_CHECK_OBJECT(this); IMP_USAGE_CHECK(dependency_graph_.find(mo) != dependency_graph_.end(), diff --git a/modules/kernel/test/test_model.py b/modules/kernel/test/test_model.py index 71c54067d8..28c07f8ec7 100644 --- a/modules/kernel/test/test_model.py +++ b/modules/kernel/test/test_model.py @@ -283,5 +283,29 @@ def test_dependencies(self): for p in ps: p.set_has_required_score_states(True) + def test_save_restore_dependencies(self): + """Test save_dependencies() and restore_dependencies()""" + m = IMP.Model() + # No dependencies yet + self.assertEqual(m.get_dependencies_updated(), 0) + m.save_dependencies() + p2 = IMP.Particle(m) + # Adding p2 should update the dependency graph + self.assertEqual(m.get_dependencies_updated(), 1) + m.remove_particle(p2) + m.restore_dependencies() + # Should be back to "no dependencies" state after restore + self.assertEqual(m.get_dependencies_updated(), 0) + + def test_save_restore_dependencies_bad(self): + """Test save/restore_dependencies() with incorrect state""" + m = IMP.Model() + m.save_dependencies() + p2 = IMP.Particle(m) + # Cannot restore dependencies since graph does not match original + # (as p2 was added) + self.assertRaisesInternalException(m.restore_dependencies) + + if __name__ == '__main__': IMP.test.main() diff --git a/modules/rmf/src/restraint_io.cpp b/modules/rmf/src/restraint_io.cpp index d6ac5f510d..ef204e4c70 100644 --- a/modules/rmf/src/restraint_io.cpp +++ b/modules/rmf/src/restraint_io.cpp @@ -541,43 +541,41 @@ class RestraintSaveLink : public SimpleSaveLink { if (no_terms_.find(o) != no_terms_.end()) { // too big, do nothing } else if (!dynamic_cast(o)) { - // required to set last score - Pointer rd = o->create_current_decomposition(); - // set all child scores to 0 for this frame, we will over - // right below - /*RMF::NodeHandles chs = nh.get_children(); - for (unsigned int i = 0; i < chs.size(); ++i) { - if (chs[i].get_type() == RMF::FEATURE) { - RMF::Score s = sf_.get(chs[i]); - s.set_frame_score(0); - } - }*/ - if (rd && rd != o) { - rd->set_was_used(true); - if (Subset(get_input_particles(rd->get_inputs())) != os) { - RestraintsTemp rs = - get_restraints(RestraintsTemp(1, rd)); - if (rs.size() > max_terms_) { - no_terms_.insert(o); - // delete old children - } else { - for(Restraint * r : rs) { - Subset s(get_input_particles(r->get_inputs())); - double score = r->get_last_score(); - r->set_was_used(true); - if (score != 0) { - IMP_LOG_VERBOSE("Saving subscore for " << r->get_name() - << " of " << score - << std::endl); - RMF::NodeHandle nnh = get_node(s, d, rf_, nh); - RMF::decorator::Score csd = sf_.get(nnh); - csd.set_frame_score(score); - // csd.set_representation(get_node_ids(nh.get_file(), s)); + Model *m = o->get_model(); + // adding the decomposed restraint will update the dependency graph; + // restore this again since the restraint is only temporary + m->save_dependencies(); + // make sure rd goes out of scope before we call restore_dependencies + { + // required to set last score + Pointer rd = o->create_current_decomposition(); + if (rd && rd != o) { + rd->set_was_used(true); + if (Subset(get_input_particles(rd->get_inputs())) != os) { + RestraintsTemp rs = + get_restraints(RestraintsTemp(1, rd)); + if (rs.size() > max_terms_) { + no_terms_.insert(o); + // delete old children + } else { + for(Restraint * r : rs) { + Subset s(get_input_particles(r->get_inputs())); + double score = r->get_last_score(); + r->set_was_used(true); + if (score != 0) { + IMP_LOG_VERBOSE("Saving subscore for " << r->get_name() + << " of " << score + << std::endl); + RMF::NodeHandle nnh = get_node(s, d, rf_, nh); + RMF::decorator::Score csd = sf_.get(nnh); + csd.set_frame_score(score); + } } } } } } + m->restore_dependencies(); } } } From 9dd0e96fd6c32a97bb54df56a374b73a465204bf Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 26 May 2022 12:27:37 -0700 Subject: [PATCH 127/155] Don't check references to ModelObjects --- modules/kernel/include/Model.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/kernel/include/Model.h b/modules/kernel/include/Model.h index 18a94d23e6..b209971239 100644 --- a/modules/kernel/include/Model.h +++ b/modules/kernel/include/Model.h @@ -127,7 +127,9 @@ class IMPKERNELEXPORT Model : public Object // allow skipping updating dependencies_age_ for temporary ModelObjects bool dependencies_saved_; unsigned saved_dependencies_age_; - ModelObjectsTemp mos_added_since_save_, mos_removed_since_save_; + // We don't use ModelObjectsTemp here because these objects might get freed + // under us, which would cause WeakPointer to raise an exception + std::vector mos_added_since_save_, mos_removed_since_save_; // cache of restraints that are affected by each moved particle, // used for evaluate_moved() and related functions From 41ea6652be256331fce14977993d313865a2f197 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 26 May 2022 12:28:39 -0700 Subject: [PATCH 128/155] Add spelling exception --- modules/kernel/test/standards_exceptions | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/kernel/test/standards_exceptions b/modules/kernel/test/standards_exceptions index 8a55b7c676..a435733c86 100644 --- a/modules/kernel/test/standards_exceptions +++ b/modules/kernel/test/standards_exceptions @@ -29,6 +29,7 @@ function_name_exceptions=[ 'ArgumentParser.register', 'ArgumentParser.parse_intermixed_args', 'ArgumentParser.parse_known_intermixed_args', + 'Model.restore_dependencies', ] value_object_exceptions=['Exception', 'TypeException', From 15fd902617c655c2129224fd39cce9928fe054a0 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 26 May 2022 14:14:25 -0700 Subject: [PATCH 129/155] Sort vectors before comparing them There is no guarantee that the ModelObjects were removed from the Model in the same order that they were added, so we need to sort the added/removed vectors before comparing them. --- modules/kernel/include/Model.h | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/modules/kernel/include/Model.h b/modules/kernel/include/Model.h index b209971239..d204c39903 100644 --- a/modules/kernel/include/Model.h +++ b/modules/kernel/include/Model.h @@ -487,8 +487,14 @@ class IMPKERNELEXPORT Model : public Object if (dependencies_saved_) { dependencies_saved_ = false; dependencies_age_ = saved_dependencies_age_; - IMP_INTERNAL_CHECK(mos_added_since_save_ == mos_removed_since_save_, - "ModelObjects added do not match those removed"); + IMP_IF_CHECK(USAGE_AND_INTERNAL) { + // Need to sort pointers since we may not add/remove in the same order + std::sort(mos_added_since_save_.begin(), mos_added_since_save_.end()); + std::sort(mos_removed_since_save_.begin(), + mos_removed_since_save_.end()); + IMP_INTERNAL_CHECK(mos_added_since_save_ == mos_removed_since_save_, + "ModelObjects added do not match those removed"); + } } } From e3f065ef426584fdaa39edb38b31876c4ef5bf32 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 26 May 2022 17:07:09 -0700 Subject: [PATCH 130/155] Replace set with bitset to get container subset Rather than looking up every Particle in our container against a set of particles, look up the particle index in a bitset instead. --- modules/kernel/include/Model.h | 6 ++++++ .../internal/AccumulatorScoreModifier.h | 19 ++++++++++++++++--- 2 files changed, 22 insertions(+), 3 deletions(-) diff --git a/modules/kernel/include/Model.h b/modules/kernel/include/Model.h index d204c39903..ce3120fbc8 100644 --- a/modules/kernel/include/Model.h +++ b/modules/kernel/include/Model.h @@ -498,6 +498,12 @@ class IMPKERNELEXPORT Model : public Object } } + //! Get an upper bound on the number of particles in the Model. + /** This value is guaranteed to be at least the number of particles in + the model (there may be fewer particles if any have been removed) + and every ParticleIndex will be smaller than this value. */ + unsigned get_particles_size() const { return particle_index_.size(); } + IMP_OBJECT_METHODS(Model); public: diff --git a/modules/kernel/include/internal/AccumulatorScoreModifier.h b/modules/kernel/include/internal/AccumulatorScoreModifier.h index be2d58c176..e6c23057cd 100644 --- a/modules/kernel/include/internal/AccumulatorScoreModifier.h +++ b/modules/kernel/include/internal/AccumulatorScoreModifier.h @@ -21,6 +21,7 @@ #include #include #include +#include IMPKERNEL_BEGIN_INTERNAL_NAMESPACE @@ -29,15 +30,21 @@ template inline typename boost::disable_if, std::vector >::type get_container_indexes( + Model *m, const Vector &contents, const std::set &ps) { + boost::dynamic_bitset<> bps(m->get_particles_size()); + for (ParticleIndex pi : ps) { + bps[pi.get_index()] = true; + } + std::vector ret; unsigned i = 0; for (typename Vector::const_iterator cit = contents.begin(); cit != contents.end(); ++cit, ++i) { for (typename Score::IndexArgument::const_iterator pit = cit->begin(); pit != cit->end(); ++pit) { - if (ps.find(*pit) != ps.end()) { + if (bps[pit->get_index()]) { ret.push_back(i); break; } @@ -52,13 +59,19 @@ template inline typename boost::enable_if, std::vector >::type get_container_indexes( + Model *m, const Vector &contents, const std::set &ps) { + boost::dynamic_bitset<> bps(m->get_particles_size()); + for (ParticleIndex pi : ps) { + bps[pi.get_index()] = true; + } + std::vector ret; unsigned i = 0; for (Vector::const_iterator cit = contents.begin(); cit != contents.end(); ++cit, ++i) { - if (ps.find(*cit) != ps.end()) { + if (bps[cit->get_index()]) { ret.push_back(i); } } @@ -85,7 +98,7 @@ class MovedIndexesMap { CacheMap::const_iterator it = cache_.find(pi); if (it == cache_.end()) { cache_[pi] = get_container_indexes( - container_->get_contents(), + m, container_->get_contents(), m->get_dependent_particles(pi)); it = cache_.find(pi); } From 9120bbe8d657ee318c3ab24e8554d7acb5f3e353 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 31 May 2022 17:52:36 -0700 Subject: [PATCH 131/155] Squashed 'modules/pmi/' changes from 5ba52792d5..c90656db10 c90656db10 Don't eval() random Python files 992d795393 Put best.scores.rex.py file in output directory 8deb0b3557 Add documentation de55e7f686 This is a prefix, not a suffix git-subtree-dir: modules/pmi git-subtree-split: c90656db10fc13d5b91e21838371304e14a431a3 --- modules/pmi/pyext/src/macros.py | 6 ++-- modules/pmi/pyext/src/output.py | 52 ++++++++++++++++++++------------- 2 files changed, 35 insertions(+), 23 deletions(-) diff --git a/modules/pmi/pyext/src/macros.py b/modules/pmi/pyext/src/macros.py index f060738644..80685b67f0 100644 --- a/modules/pmi/pyext/src/macros.py +++ b/modules/pmi/pyext/src/macros.py @@ -435,7 +435,8 @@ def execute_macro(self): pdb_dir + "/" + self.vars["best_pdb_name_suffix"], self.root_hier, self.vars["number_of_best_scoring_models"], - replica_exchange=True) + replica_exchange=True, + best_score_file=globaldir + "best.scores.rex.py") output.write_psf( pdb_dir + "/" + "model.psf", pdb_dir + "/" + @@ -448,7 +449,8 @@ def execute_macro(self): self.vars["best_pdb_name_suffix"], self.root_hiers[n], self.vars["number_of_best_scoring_models"], - replica_exchange=True) + replica_exchange=True, + best_score_file=globaldir + "best.scores.rex.py") output.write_psf( pdb_dir + "/" + str(n) + "/" + "model.psf", pdb_dir + "/" + str(n) + "/" + diff --git a/modules/pmi/pyext/src/output.py b/modules/pmi/pyext/src/output.py index f0cc6c13af..737bd85b10 100644 --- a/modules/pmi/pyext/src/output.py +++ b/modules/pmi/pyext/src/output.py @@ -211,7 +211,7 @@ def __init__(self, ascii=True, atomistic=False): self.dictionary_stats2 = {} self.best_score_list = None self.nbestscoring = None - self.suffixes = [] + self.prefixes = [] self.replica_exchange = False self.ascii = ascii self.initoutput = {} @@ -475,17 +475,26 @@ def write_pdbs(self, appendmode=True, mmcif=False): for pdb in self.dictionary_pdbs.keys(): self.write_pdb(pdb, appendmode) - def init_pdb_best_scoring(self, - suffix, - prot, - nbestscoring, - replica_exchange=False, mmcif=False): - # save only the nbestscoring conformations - # create as many pdbs as needed + def init_pdb_best_scoring(self, prefix, prot, nbestscoring, + replica_exchange=False, mmcif=False, + best_score_file='best.scores.rex.py'): + """Prepare for writing best-scoring PDBs (or mmCIFs) for a + sampling run. + + @param prefix Initial part of each PDB filename (e.g. 'model'). + @param prot The top-level Hierarchy to output. + @param nbestscoring The number of best-scoring files to output. + @param replica_exchange Whether to combine best scores from a + replica exchange run. + @param mmcif If True, output models in mmCIF format. If False + (the default) output in legacy PDB format. + @param best_score_file The filename to use for replica + exchange scores. + """ self._pdb_best_scoring_mmcif = mmcif fileext = '.cif' if mmcif else '.pdb' - self.suffixes.append(suffix) + self.prefixes.append(prefix) self.replica_exchange = replica_exchange if not self.replica_exchange: # common usage @@ -495,7 +504,7 @@ def init_pdb_best_scoring(self, else: # otherwise the replicas must communicate # through a common file to know what are the best scores - self.best_score_file_name = "best.scores.rex.py" + self.best_score_file_name = best_score_file self.best_score_list = [] with open(self.best_score_file_name, "w") as best_score_file: best_score_file.write( @@ -503,7 +512,7 @@ def init_pdb_best_scoring(self, self.nbestscoring = nbestscoring for i in range(self.nbestscoring): - name = suffix + "." + str(i) + fileext + name = prefix + "." + str(i) + fileext flpdb = open(name, 'w') flpdb.close() self.dictionary_pdbs[name] = prot @@ -521,21 +530,22 @@ def write_pdb_best_scoring(self, score): if self.replica_exchange: # read the self.best_score_list from the file with open(self.best_score_file_name) as fh: - exec(fh.read()) + self.best_score_list = ast.literal_eval( + fh.read().split('=')[1]) if len(self.best_score_list) < self.nbestscoring: self.best_score_list.append(score) self.best_score_list.sort() index = self.best_score_list.index(score) - for suffix in self.suffixes: + for prefix in self.prefixes: for i in range(len(self.best_score_list) - 2, index - 1, -1): - oldname = suffix + "." + str(i) + fileext - newname = suffix + "." + str(i + 1) + fileext + oldname = prefix + "." + str(i) + fileext + newname = prefix + "." + str(i + 1) + fileext # rename on Windows fails if newname already exists if os.path.exists(newname): os.unlink(newname) os.rename(oldname, newname) - filetoadd = suffix + "." + str(index) + fileext + filetoadd = prefix + "." + str(index) + fileext self.write_pdb(filetoadd, appendmode=False) else: @@ -544,16 +554,16 @@ def write_pdb_best_scoring(self, score): self.best_score_list.sort() self.best_score_list.pop(-1) index = self.best_score_list.index(score) - for suffix in self.suffixes: + for prefix in self.prefixes: for i in range(len(self.best_score_list) - 1, index - 1, -1): - oldname = suffix + "." + str(i) + fileext - newname = suffix + "." + str(i + 1) + fileext + oldname = prefix + "." + str(i) + fileext + newname = prefix + "." + str(i + 1) + fileext os.rename(oldname, newname) - filenametoremove = suffix + \ + filenametoremove = prefix + \ "." + str(self.nbestscoring) + fileext os.remove(filenametoremove) - filetoadd = suffix + "." + str(index) + fileext + filetoadd = prefix + "." + str(index) + fileext self.write_pdb(filetoadd, appendmode=False) if self.replica_exchange: From 7649e812a13b36f5821ba84a14cd3aae56257f0d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Tue, 31 May 2022 17:52:49 -0700 Subject: [PATCH 132/155] Squashed 'modules/core/dependency/python-ihm/' changes from 8a9839efec..c76f93944e c76f93944e Prepare for 0.32 release d9c006dd6f Add recent changes 70d159a877 Add all chains to _entity_poly.pdbx_strand_id ab9811feb8 Fix typo 532f12a94f Strip whitespace from reference sequence 24be083f3e Support _ihm_modeling_protocol_details.ensemble_flag git-subtree-dir: modules/core/dependency/python-ihm git-subtree-split: c76f93944ed1550f2992e0cf1f35c3468d8a56a7 --- .../core/dependency/python-ihm/ChangeLog.rst | 11 +++++++++++ modules/core/dependency/python-ihm/MANIFEST.in | 2 +- .../core/dependency/python-ihm/ihm/__init__.py | 2 +- .../core/dependency/python-ihm/ihm/dumper.py | 18 ++++++++++++------ .../core/dependency/python-ihm/ihm/protocol.py | 6 +++++- .../core/dependency/python-ihm/ihm/reader.py | 17 +++++++++-------- modules/core/dependency/python-ihm/setup.py | 2 +- .../dependency/python-ihm/test/test_dumper.py | 13 +++++++------ .../python-ihm/test/test_examples.py | 2 +- .../dependency/python-ihm/test/test_reader.py | 11 +++++++---- 10 files changed, 55 insertions(+), 29 deletions(-) diff --git a/modules/core/dependency/python-ihm/ChangeLog.rst b/modules/core/dependency/python-ihm/ChangeLog.rst index 9744ab3134..28cbb5da26 100644 --- a/modules/core/dependency/python-ihm/ChangeLog.rst +++ b/modules/core/dependency/python-ihm/ChangeLog.rst @@ -1,3 +1,14 @@ +0.32 - 2022-05-31 +================= + - :class:`ihm.protocol.Step` now takes an ``ensemble`` flag, to indicate + whether the modeling involved an ensemble, and which defaults to True if + the system contains at least one :class:`ihm.model.Ensemble` (#83). + - When reading an incomplete mmCIF file, such as that generated by some + versions of PyMOL, python-ihm will now fill in missing entity-related + information by guessing the sequence from the atom_site table (#67). + - Bugfix: :class:`ihm.flr.RefMeasurementGroup` objects are now read + from mmCIF files correctly. + 0.31 - 2022-04-14 ================= - The :class:`ihm.dumper.IgnoreVariant` class can now be used to exclude diff --git a/modules/core/dependency/python-ihm/MANIFEST.in b/modules/core/dependency/python-ihm/MANIFEST.in index 8ab08deb82..ef0786f3bb 100644 --- a/modules/core/dependency/python-ihm/MANIFEST.in +++ b/modules/core/dependency/python-ihm/MANIFEST.in @@ -4,4 +4,4 @@ include examples/* include util/make-mmcif.py include src/ihm_format.h include src/ihm_format.i -include src/ihm_format_wrap_0.31.c +include src/ihm_format_wrap_0.32.c diff --git a/modules/core/dependency/python-ihm/ihm/__init__.py b/modules/core/dependency/python-ihm/ihm/__init__.py index 86eb21e528..7606ea9bb2 100644 --- a/modules/core/dependency/python-ihm/ihm/__init__.py +++ b/modules/core/dependency/python-ihm/ihm/__init__.py @@ -20,7 +20,7 @@ import json from . import util -__version__ = '0.31' +__version__ = '0.32' class __UnknownValue(object): diff --git a/modules/core/dependency/python-ihm/ihm/dumper.py b/modules/core/dependency/python-ihm/ihm/dumper.py index 083205aacd..ba4f30a2c4 100644 --- a/modules/core/dependency/python-ihm/ihm/dumper.py +++ b/modules/core/dependency/python-ihm/ihm/dumper.py @@ -2,6 +2,7 @@ import re import os +import collections import operator import itertools import ihm.format @@ -552,11 +553,10 @@ def _get_seq_type(self, entity): return self._seq_type_map.get(all_types, 'other') def dump(self, system, writer): - # Get the first asym unit (if any) for each entity - strand = {} + # Get all asym units (if any) for each entity + strands = collections.defaultdict(list) for asym in system.asym_units: - if asym.entity._id not in strand: - strand[asym.entity._id] = asym.strand_id + strands[asym.entity._id].append(asym.strand_id) with writer.loop("_entity_poly", ["entity_id", "type", "nstd_linkage", "nstd_monomer", "pdbx_strand_id", @@ -567,10 +567,11 @@ def dump(self, system, writer): continue nstd = any(isinstance(x, ihm.NonPolymerChemComp) for x in entity.sequence) + sids = strands[entity._id] lp.write(entity_id=entity._id, type=self._get_seq_type(entity), nstd_linkage='no', nstd_monomer='yes' if nstd else 'no', - pdbx_strand_id=strand.get(entity._id, None), + pdbx_strand_id=",".join(sids) if sids else None, pdbx_seq_one_letter_code=self._get_sequence(entity), pdbx_seq_one_letter_code_can=self._get_canon(entity)) @@ -1230,10 +1231,14 @@ def dump_details(self, system, writer): "step_name", "step_method", "num_models_begin", "num_models_end", "multi_scale_flag", "multi_state_flag", "ordered_flag", - "software_id", "script_file_id", + "ensemble_flag", "software_id", "script_file_id", "description"]) as lp: for p in system._all_protocols(): for s in p.steps: + if s.ensemble == 'default': + ensemble = len(system.ensembles) > 0 + else: + ensemble = s.ensemble lp.write( id=next(ordinal), protocol_id=p._id, step_id=s._id, @@ -1246,6 +1251,7 @@ def dump_details(self, system, writer): multi_state_flag=s.multi_state, ordered_flag=s.ordered, multi_scale_flag=s.multi_scale, + ensemble_flag=ensemble, software_id=s.software._id if s.software else None, script_file_id=s.script_file._id if s.script_file else None, diff --git a/modules/core/dependency/python-ihm/ihm/protocol.py b/modules/core/dependency/python-ihm/ihm/protocol.py index 2c66d92318..7359419f6b 100644 --- a/modules/core/dependency/python-ihm/ihm/protocol.py +++ b/modules/core/dependency/python-ihm/ihm/protocol.py @@ -23,12 +23,15 @@ class Step(object): :param bool multi_scale: Indicates if the modeling is multi-scale :param bool multi_state: Indicates if the modeling is multi-state :param bool ordered: Indicates if the modeling is ordered + :param bool ensemble: Indicates if the modeling involves an ensemble; + the default if unspecified is True iff the system contains + at least one :class:`~ihm.model.Ensemble`. :param str description: Additional text describing the step """ def __init__(self, assembly, dataset_group, method, num_models_begin=None, num_models_end=None, software=None, script_file=None, multi_scale=False, multi_state=False, ordered=False, - name=None, description=None): + ensemble='default', name=None, description=None): self.assembly = assembly self.dataset_group = dataset_group self.method = method @@ -36,6 +39,7 @@ def __init__(self, assembly, dataset_group, method, num_models_begin=None, self.num_models_end = num_models_end self.multi_scale, self.multi_state = multi_scale, multi_state self.software, self.ordered, self.name = software, ordered, name + self.ensemble = ensemble self.script_file = script_file self.description = description diff --git a/modules/core/dependency/python-ihm/ihm/reader.py b/modules/core/dependency/python-ihm/ihm/reader.py index 9e810e9bbe..9939de3c2e 100644 --- a/modules/core/dependency/python-ihm/ihm/reader.py +++ b/modules/core/dependency/python-ihm/ihm/reader.py @@ -1063,10 +1063,10 @@ def __call__(self, id, entity_id, db_name, db_code, pdbx_db_accession, e = self.sysr.entities.get_by_id(entity_id) typ = self.type_map.get(db_name.lower()) ref = self.sysr.references.get_by_id(id, typ) - # Strip newlines if code is split over multiple lines + # Strip newlines and whitespace from code if pdbx_seq_one_letter_code not in (None, ihm.unknown): pdbx_seq_one_letter_code \ - = pdbx_seq_one_letter_code.replace('\n', '') + = pdbx_seq_one_letter_code.replace('\n', '').replace(' ', '') self.copy_if_present( ref, locals(), keys=('db_name', 'db_code', 'details'), mapkeys={'pdbx_db_accession': 'accession', @@ -1562,14 +1562,15 @@ class _ProtocolDetailsHandler(Handler): def __call__(self, protocol_id, step_id, num_models_begin, num_models_end, multi_scale_flag, multi_state_flag, - ordered_flag, struct_assembly_id, dataset_group_id, - software_id, script_file_id, step_name, step_method, - description): + ordered_flag, ensemble_flag, struct_assembly_id, + dataset_group_id, software_id, script_file_id, step_name, + step_method, description): p = self.sysr.protocols.get_by_id(protocol_id) nbegin = self.get_int(num_models_begin) nend = self.get_int(num_models_end) mscale = self.get_bool(multi_scale_flag) mstate = self.get_bool(multi_state_flag) + ensemble = self.get_bool(ensemble_flag) ordered = self.get_bool(ordered_flag) assembly = self.sysr.assemblies.get_by_id_or_none( struct_assembly_id) @@ -1580,8 +1581,8 @@ def __call__(self, protocol_id, step_id, num_models_begin, method=None, num_models_begin=nbegin, num_models_end=nend, multi_scale=mscale, multi_state=mstate, ordered=ordered, - software=software, script_file=script, - description=description) + ensemble=ensemble, software=software, + script_file=script, description=description) s._id = step_id self.copy_if_present( s, locals(), @@ -2847,7 +2848,7 @@ def __call__(self, ordinal_id, analysis_id, details): f = self.sysr.flr_fret_analyses.get_by_id(analysis_id) f.type = 'lifetime-based' - f.reference_measurement_group \ + f.ref_measurement_group \ = self.sysr.flr_ref_measurement_groups.get_by_id( reference_measurement_group_id) f.lifetime_fit_model = self.sysr.flr_lifetime_fit_models.get_by_id( diff --git a/modules/core/dependency/python-ihm/setup.py b/modules/core/dependency/python-ihm/setup.py index 98e552cc5a..9a1e7f4a51 100755 --- a/modules/core/dependency/python-ihm/setup.py +++ b/modules/core/dependency/python-ihm/setup.py @@ -7,7 +7,7 @@ import sys import os -VERSION = "0.31" +VERSION = "0.32" copy_args = sys.argv[1:] diff --git a/modules/core/dependency/python-ihm/test/test_dumper.py b/modules/core/dependency/python-ihm/test/test_dumper.py index 222603ee4a..6d4db1165f 100644 --- a/modules/core/dependency/python-ihm/test/test_dumper.py +++ b/modules/core/dependency/python-ihm/test/test_dumper.py @@ -765,7 +765,7 @@ def test_entity_poly_dumper(self): _entity_poly.pdbx_strand_id _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can -1 polypeptide(L) no no a ACGT ACGT +1 polypeptide(L) no no a,b ACGT ACGT 2 polypeptide(L) no no . ACC(UNK)(MSE) ACCXM 3 polypeptide(D) no no . (DAL)(DCY)G ACG 4 polypeptide(D) no no . (DAL)(DCY) AC @@ -1646,11 +1646,11 @@ class MockObject(object): p1.steps.append(ihm.protocol.Step( assembly=assembly, dataset_group=dsg, method='Monte Carlo', num_models_begin=0, - num_models_end=500, multi_scale=True, name='s1')) + num_models_end=500, multi_scale=True, ensemble=True, name='s1')) p1.steps.append(ihm.protocol.Step( assembly=assembly, dataset_group=dsg, method='Replica exchange', num_models_begin=500, - num_models_end=2000, multi_scale=True)) + num_models_end=2000, multi_scale=True, ensemble=False)) system.orphan_protocols.append(p1) p2 = ihm.protocol.Protocol('sampling') @@ -1687,12 +1687,13 @@ class MockObject(object): _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.ordered_flag +_ihm_modeling_protocol_details.ensemble_flag _ihm_modeling_protocol_details.software_id _ihm_modeling_protocol_details.script_file_id _ihm_modeling_protocol_details.description -1 1 1 42 99 s1 'Monte Carlo' 0 500 YES NO NO . . . -2 1 2 42 99 . 'Replica exchange' 500 2000 YES NO NO . . . -3 2 1 42 101 . 'Replica exchange' 2000 1000 YES NO NO 80 90 'test step' +1 1 1 42 99 s1 'Monte Carlo' 0 500 YES NO NO YES . . . +2 1 2 42 99 . 'Replica exchange' 500 2000 YES NO NO NO . . . +3 2 1 42 101 . 'Replica exchange' 2000 1000 YES NO NO NO 80 90 'test step' # """) diff --git a/modules/core/dependency/python-ihm/test/test_examples.py b/modules/core/dependency/python-ihm/test/test_examples.py index 14b56cc9c6..96eee59ee3 100644 --- a/modules/core/dependency/python-ihm/test/test_examples.py +++ b/modules/core/dependency/python-ihm/test/test_examples.py @@ -41,7 +41,7 @@ def test_simple_docking_example(self): # can read it with open(os.path.join(tmpdir, 'output.cif')) as fh: contents = fh.readlines() - self.assertEqual(len(contents), 316) + self.assertEqual(len(contents), 317) with open(os.path.join(tmpdir, 'output.cif')) as fh: s, = ihm.reader.read(fh) diff --git a/modules/core/dependency/python-ihm/test/test_reader.py b/modules/core/dependency/python-ihm/test/test_reader.py index 3b4aa67c96..35d07138a5 100644 --- a/modules/core/dependency/python-ihm/test/test_reader.py +++ b/modules/core/dependency/python-ihm/test/test_reader.py @@ -1265,11 +1265,12 @@ def test_protocol_details_handler(self): _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.ordered_flag +_ihm_modeling_protocol_details.ensemble_flag _ihm_modeling_protocol_details.software_id _ihm_modeling_protocol_details.script_file_id _ihm_modeling_protocol_details.description -1 1 1 1 1 . Sampling 'Monte Carlo' 0 500 YES NO NO . . . -2 1 2 1 2 . Sampling 'Monte Carlo' 500 5000 YES . NO 401 501 'test step' +1 1 1 1 1 . Sampling 'Monte Carlo' 0 500 YES NO NO NO . . . +2 1 2 1 2 . Sampling 'Monte Carlo' 500 5000 YES . NO YES 401 501 'test step' """ for fh in cif_file_handles(cif): s, = ihm.reader.read(fh) @@ -1285,6 +1286,7 @@ def test_protocol_details_handler(self): self.assertEqual(p1.steps[0].multi_scale, True) self.assertEqual(p1.steps[0].multi_state, False) self.assertEqual(p1.steps[0].ordered, False) + self.assertEqual(p1.steps[0].ensemble, False) self.assertIsNone(p1.steps[0].software) self.assertIsNone(p1.steps[0].script_file) self.assertIsNone(p1.steps[0].description) @@ -1292,6 +1294,7 @@ def test_protocol_details_handler(self): self.assertEqual(p1.steps[1].multi_scale, True) self.assertIsNone(p1.steps[1].multi_state) self.assertEqual(p1.steps[1].ordered, False) + self.assertEqual(p1.steps[1].ensemble, True) self.assertEqual(p1.steps[1].software._id, '401') self.assertEqual(p1.steps[1].script_file._id, '501') self.assertEqual(p1.steps[1].description, 'test step') @@ -3635,9 +3638,9 @@ def test_flr_fret_analysis_lifetime_handler(self): flr, = s.flr_data a = flr._collection_flr_fret_analysis['2'] self.assertEqual(a.type, 'lifetime-based') - self.assertIsInstance(a.reference_measurement_group, + self.assertIsInstance(a.ref_measurement_group, ihm.flr.RefMeasurementGroup) - self.assertEqual(a.reference_measurement_group._id, '19') + self.assertEqual(a.ref_measurement_group._id, '19') self.assertIsInstance(a.lifetime_fit_model, ihm.flr.LifetimeFitModel) self.assertEqual(a.lifetime_fit_model._id, '23') self.assertAlmostEqual(a.donor_only_fraction, 0.3, delta=0.1) From 4cf2d8eacf14c59cc55cfd7e480ec0f255603ca1 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 1 Jun 2022 11:21:36 -0700 Subject: [PATCH 133/155] Match latest python-ihm --- modules/mmcif/test/test_dumper.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/modules/mmcif/test/test_dumper.py b/modules/mmcif/test/test_dumper.py index b808da2b72..ab6bd37864 100644 --- a/modules/mmcif/test/test_dumper.py +++ b/modules/mmcif/test/test_dumper.py @@ -503,12 +503,13 @@ def test_modeling_protocol(self): _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.ordered_flag +_ihm_modeling_protocol_details.ensemble_flag _ihm_modeling_protocol_details.software_id _ihm_modeling_protocol_details.script_file_id _ihm_modeling_protocol_details.description -1 1 1 2 . Sampling 'Monte Carlo' 0 500 YES NO NO . . . -2 2 1 2 . Sampling 'Replica exchange Molecular Dynamics' 400 2000 YES NO NO . . -. +1 1 1 2 . Sampling 'Monte Carlo' 0 500 YES NO NO YES . . . +2 2 1 2 . Sampling 'Replica exchange Molecular Dynamics' 400 2000 YES NO NO YES +. . . # """) From 90e3b2dd7e37529915ac438e20d5f0b347a28fa1 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 1 Jun 2022 14:02:05 -0700 Subject: [PATCH 134/155] Squashed 'modules/pmi/' changes from c90656db10..57c6eaa9b9 57c6eaa9b9 flake8 fixes 8a1b493588 Update to match latest python-ihm git-subtree-dir: modules/pmi git-subtree-split: 57c6eaa9b90408a5b064bb4634b87e5202a129da --- modules/pmi/pyext/src/mmcif.py | 5 +- modules/pmi/test/test_mmcif.py | 171 ++++++++++++++++++--------------- 2 files changed, 97 insertions(+), 79 deletions(-) diff --git a/modules/pmi/pyext/src/mmcif.py b/modules/pmi/pyext/src/mmcif.py index c4f955d81e..6a3b98afe4 100644 --- a/modules/pmi/pyext/src/mmcif.py +++ b/modules/pmi/pyext/src/mmcif.py @@ -574,7 +574,7 @@ def __init__(self, state, rex): method=method, name='Sampling', num_models_begin=None, # filled in by add_step() num_models_end=rex.vars["number_of_frames"], - multi_scale=True, multi_state=False, ordered=False) + multi_scale=True, multi_state=False, ordered=False, ensemble=True) class _ReplicaExchangeProtocolDumper(ihm.dumper.Dumper): @@ -628,7 +628,8 @@ def __init__(self, state, num_models_end, method): method=method, name='Sampling', num_models_begin=None, # filled in by add_step() num_models_end=num_models_end, - multi_scale=True, multi_state=False, ordered=False) + multi_scale=True, multi_state=False, ordered=False, + ensemble=True) class _Chain(object): diff --git a/modules/pmi/test/test_mmcif.py b/modules/pmi/test/test_mmcif.py index 32983dea12..d2b69d32d6 100644 --- a/modules/pmi/test/test_mmcif.py +++ b/modules/pmi/test/test_mmcif.py @@ -7,7 +7,6 @@ import IMP.pmi.macros import sys import os -import io import ihm.format import ihm.location import ihm.dataset @@ -16,23 +15,28 @@ else: from io import BytesIO as StringIO + class DummyState(object): short_name = None long_name = None + class DummyRepr(object): def __init__(self, short_name, long_name): self.state = DummyState() self.state.short_name = short_name self.state.long_name = long_name + class EmptyObject(object): state = DummyState() + def get_all_models_group(simo, po): state = simo._protocol_output[0][1] return state.add_model_group(ihm.model.ModelGroup(name="All models")) + class Tests(IMP.test.TestCase): def test_assign_id(self): @@ -40,16 +44,18 @@ def test_assign_id(self): class DummyObj(object): def __init__(self, hashval): self.hashval = hashval + def __eq__(self, other): return self.hashval == other.hashval + def __hash__(self): return self.hashval seen_objs = {} obj_by_id = [] - obj1a = DummyObj(42) # obj1a and 1b are identical + obj1a = DummyObj(42) # obj1a and 1b are identical obj1b = DummyObj(42) obj2 = DummyObj(34) - obj3 = DummyObj(23) # obj3 already has an id + obj3 = DummyObj(23) # obj3 already has an id obj3.id = 'foo' for obj in (obj1a, obj1b, obj2, obj3): IMP.pmi.mmcif._assign_id(obj, seen_objs, obj_by_id) @@ -201,7 +207,7 @@ def test_entity_creation(self): """Test creation of Entity objects""" m = IMP.Model() simo = IMP.pmi.topology.System(m) - st = simo.create_state() + simo.create_state() po = IMP.pmi.mmcif.ProtocolOutput() simo.add_protocol_output(po) po.add_component_sequence(po._last_state, 'foo.1@12', 'ACGT') @@ -230,7 +236,7 @@ def test_asym_id_mapper(self): nup85_2 = st2.create_molecule("Nup85", "SELM", "Z") nup85_2.add_representation(resolutions=[1]) - hier = s.build() + _ = s.build() self.assertEqual(len(po.system.asym_units), 2) po.system.asym_units[0]._id = 'A' @@ -265,7 +271,7 @@ def test_rna_dna(self): alphabet=IMP.pmi.alphabets.dna) dna.add_representation(resolutions=[1]) - hier = s.build() + _ = s.build() self.assertEqual(len(po.system.entities), 2) self.assertEqual(len(po.system.entities[0].sequence), 4) for r in po.system.entities[0].sequence: @@ -321,19 +327,19 @@ def test_all_datasets_all_group(self): alld = IMP.pmi.mmcif._AllDatasets(s) - l = ihm.location.InputFileLocation(repo='foo', path='baz') - ds1 = ihm.dataset.EM2DClassDataset(l) - l = ihm.location.InputFileLocation(repo='foo', path='bar') - ds2 = ihm.dataset.CXMSDataset(l) - l = ihm.location.PDBLocation('1abc', '1.0', 'test details') - ds3 = ihm.dataset.PDBDataset(l) + loc = ihm.location.InputFileLocation(repo='foo', path='baz') + ds1 = ihm.dataset.EM2DClassDataset(loc) + loc = ihm.location.InputFileLocation(repo='foo', path='bar') + ds2 = ihm.dataset.CXMSDataset(loc) + loc = ihm.location.PDBLocation('1abc', '1.0', 'test details') + ds3 = ihm.dataset.PDBDataset(loc) g1 = alld.get_all_group(state1) alld.add(state1, ds1) alld.add(state1, ds2) g2 = alld.get_all_group(state1) - g3 = alld.get_all_group(state1) + _ = alld.get_all_group(state1) alld.add(state1, ds3) g4 = alld.get_all_group(state1) @@ -442,8 +448,8 @@ def test_model_dumper_atom(self): asym = po.asym_units['Nup84.0'] assembly = ihm.Assembly([asym]) assembly._id = 42 - s1 = ihm.representation.AtomicSegment(asym(1,2), True) - s2 = ihm.representation.FeatureSegment(asym(3,4), True, + s1 = ihm.representation.AtomicSegment(asym(1, 2), True) + s2 = ihm.representation.FeatureSegment(asym(3, 4), True, primitive='sphere', count=1) representation = ihm.representation.Representation([s1, s2]) representation._id = 99 @@ -555,8 +561,9 @@ def test_model_dumper_sphere_rmsf(self): model.name = 'foo' model.parse_rmsf_file(self.get_input_file_name('test.nup84.rmsf'), 'Nup84.0') - self.assertAlmostEqual(model.get_rmsf('Nup84.0', (1,)), 4.5, delta=1e-4) - self.assertRaises(ValueError, model.get_rmsf, 'Nup84.0', (1,2)) + self.assertAlmostEqual(model.get_rmsf('Nup84.0', (1,)), 4.5, + delta=1e-4) + self.assertRaises(ValueError, model.get_rmsf, 'Nup84.0', (1, 2)) self.assign_entity_asym_ids(po.system) fh = StringIO() w = ihm.format.CifWriter(fh) @@ -644,9 +651,9 @@ def test_starting_model_dumper(self): nup85 = st2.create_molecule("Nup85", "SELM", "B") nup85.add_structure(self.get_input_file_name('test.nup85.pdb'), 'A', - res_range=(8,9), offset=-7) + res_range=(8, 9), offset=-7) nup85.add_representation(resolutions=[1]) - hier = s.build() + _ = s.build() self.assign_entity_asym_ids(po.system) @@ -741,15 +748,13 @@ def test_protocol_dumper(self): dof = IMP.pmi.dof.DegreesOfFreedom(m) dof.create_rigid_body(nup84) - mc1 = IMP.pmi.macros.ReplicaExchange0(m, root_hier=hier, - monte_carlo_sample_objects=dof.get_movers(), - output_objects=[], - test_mode=True) + mc1 = IMP.pmi.macros.ReplicaExchange0( + m, root_hier=hier, monte_carlo_sample_objects=dof.get_movers(), + output_objects=[], test_mode=True) mc1.execute_macro() - mc2 = IMP.pmi.macros.ReplicaExchange0(m, root_hier=hier, - monte_carlo_sample_objects=dof.get_movers(), - output_objects=[], - test_mode=True) + mc2 = IMP.pmi.macros.ReplicaExchange0( + m, root_hier=hier, monte_carlo_sample_objects=dof.get_movers(), + output_objects=[], test_mode=True) mc2.execute_macro() fh = StringIO() w = ihm.format.CifWriter(fh) @@ -782,11 +787,12 @@ def test_protocol_dumper(self): _ihm_modeling_protocol_details.multi_scale_flag _ihm_modeling_protocol_details.multi_state_flag _ihm_modeling_protocol_details.ordered_flag +_ihm_modeling_protocol_details.ensemble_flag _ihm_modeling_protocol_details.software_id _ihm_modeling_protocol_details.script_file_id _ihm_modeling_protocol_details.description -1 1 1 2 1 Sampling 'Replica exchange monte carlo' 0 1000 YES NO NO 1 . . -2 1 2 2 1 Sampling 'Replica exchange monte carlo' 1000 1000 YES NO NO 1 . . +1 1 1 2 1 Sampling 'Replica exchange monte carlo' 0 1000 YES NO NO YES 1 . . +2 1 2 2 1 Sampling 'Replica exchange monte carlo' 1000 1000 YES NO NO YES 1 . . # """) @@ -804,18 +810,16 @@ def test_rex_protocol_dumper(self): dof = IMP.pmi.dof.DegreesOfFreedom(m) dof.create_rigid_body(nup84) - mc1 = IMP.pmi.macros.ReplicaExchange0(m, root_hier=hier, - monte_carlo_sample_objects=dof.get_movers(), - output_objects=[], - test_mode=True, - monte_carlo_temperature=42.0, - replica_exchange_minimum_temperature=100., - replica_exchange_maximum_temperature=200.) + mc1 = IMP.pmi.macros.ReplicaExchange0( + m, root_hier=hier, monte_carlo_sample_objects=dof.get_movers(), + output_objects=[], test_mode=True, monte_carlo_temperature=42.0, + replica_exchange_minimum_temperature=100., + replica_exchange_maximum_temperature=200.) mc1.execute_macro() fh = StringIO() w = ihm.format.CifWriter(fh) self.assign_entity_asym_ids(po.system) - ihm.dumper._ProtocolDumper().finalize(po.system) # assign step IDs + ihm.dumper._ProtocolDumper().finalize(po.system) # assign step IDs d = IMP.pmi.mmcif._ReplicaExchangeProtocolDumper() d.dump(po.system, w) out = fh.getvalue() @@ -946,7 +950,7 @@ def test_simple_ensemble(self): nup84.add_representation(resolutions=[1]) nup85 = st1.create_molecule("Nup85", "SELM", "Y") nup85.add_representation(resolutions=[1]) - hier = s.build() + _ = s.build() densities = {'Nup84.0': "foo.mrc"} pp = None @@ -979,19 +983,24 @@ def test_rex_ensemble(self): class DummyModel(object): def parse_rmsf_file(self, fname, comp): self.comp = comp + class DummyRepresentation(object): def set_coordinates_from_rmf(self, comp, fname, frame, force_rigid_update): pass + class DummySimo(object): all_modeled_components = ['Nup84', 'Nup85'] + class DummyState(object): all_modeled_components = ['Nup84', 'Nup85'] + class DummyRex(object): _number_of_clusters = 1 + class DummyGroup(object): name = 'dgroup' - comp_to_asym = {'Nup84':None} + comp_to_asym = {'Nup84': None} with IMP.test.temporary_directory() as tmpdir: d = DummyRex() d._outputdir = tmpdir @@ -1036,11 +1045,13 @@ class DummyGroup(object): po = IMP.pmi.mmcif.ProtocolOutput() r = DummyRepr('dummy', 'none') state = po._add_state(r) - e.load_localization_density(state, 'Nup84', ['Nup84'], comp_to_asym) + e.load_localization_density(state, 'Nup84', ['Nup84'], + comp_to_asym) self.assertEqual(e.densities[0].file.path, os.path.join(tmpdir, 'cluster.0', 'Nup84.mrc')) - self.assertEqual(e.densities[0].file.details, - 'Localization density for Nup84 dgroup') + self.assertEqual( + e.densities[0].file.details, + 'Localization density for Nup84 dgroup') # No precision available self.assertEqual(e._get_precision(), ihm.unknown) self.assertEqual(e.precision, ihm.unknown) @@ -1061,6 +1072,7 @@ def test_add_rex(self): """Test add_replica_exchange_analysis""" class DummyProtocolStep(object): pass + class DummyRex(object): _number_of_clusters = 1 m = IMP.Model() @@ -1071,7 +1083,7 @@ class DummyRex(object): po = IMP.pmi.mmcif.ProtocolOutput() s.add_protocol_output(po) po_state = st._protocol_output[0][1] - hier = s.build() + _ = s.build() with IMP.test.temporary_directory() as tmpdir: rex = DummyRex() @@ -1095,14 +1107,14 @@ class DummyPostProcess(object): s = IMP.pmi.topology.System(m) po = IMP.pmi.mmcif.ProtocolOutput() s.add_protocol_output(po) - st1 = s.create_state() + s.create_state() pp = DummyPostProcess() pp._id = 99 - e1 = po._add_simple_ensemble(pp, 'Ensemble 1', 5, 0.1, 1, - {}, None) - e2 = po._add_simple_ensemble(pp, 'Ensemble 2', 5, 0.1, 1, - {}, None) + po._add_simple_ensemble(pp, 'Ensemble 1', 5, 0.1, 1, + {}, None) + po._add_simple_ensemble(pp, 'Ensemble 2', 5, 0.1, 1, + {}, None) loc = ihm.location.InputFileLocation(repo='foo', path='bar') po.set_ensemble_file(1, loc) loc._id = 42 @@ -1145,14 +1157,14 @@ class DummyEnsemble(object): st1 = s.create_state() nup84 = st1.create_molecule("Nup84", "MELS", "X") nup84.add_representation(resolutions=[1]) - hier = s.build() + _ = s.build() ensemble = DummyEnsemble() ensemble._id = 42 loc = ihm.location.OutputFileLocation(repo='foo', path='bar') loc._id = 97 - den = ihm.model.LocalizationDensity(file=loc, - asym_unit=po.asym_units['Nup84.0']) + den = ihm.model.LocalizationDensity( + file=loc, asym_unit=po.asym_units['Nup84.0']) ensemble.densities = [den] po.system.ensembles.append(ensemble) @@ -1180,6 +1192,7 @@ def test_cross_link_dumper(self): """Test the CrossLinkDumper""" class DummyDataset(object): pass + class DummyRestraint(object): label = 'foo' m = IMP.Model() @@ -1201,8 +1214,8 @@ class DummyRestraint(object): xl_group = po.get_cross_link_group(r) ex_xl = po.add_experimental_cross_link(1, 'Nup84', 2, 'Nup84', xl_group) - ex_xl2 = po.add_experimental_cross_link(1, 'Nup84', - 3, 'Nup84', xl_group) + _ = po.add_experimental_cross_link(1, 'Nup84', + 3, 'Nup84', xl_group) # Duplicates should be ignored po.add_experimental_cross_link(1, 'Nup84', 3, 'Nup84', xl_group) # Non-modeled component should be ignored @@ -1224,7 +1237,7 @@ class DummyRestraint(object): fh = StringIO() self.assign_entity_asym_ids(po.system) d = ihm.dumper._ChemDescriptorDumper() - d.finalize(po.system) # Assign chemical descriptor IDs + d.finalize(po.system) # Assign chemical descriptor IDs w = ihm.format.CifWriter(fh) d = ihm.dumper._CrossLinkDumper() d.finalize(po.system) @@ -1286,10 +1299,11 @@ def test_add_em2d_restraint(self): state = st1._protocol_output[0][1] nup84 = st1.create_molecule("Nup84", "MELS", "X") nup84.add_representation(resolutions=[1]) - hier = s.build() + _ = s.build() class DummyRestraint(object): label = 'foo' + class DummyProtocolStep(object): pass pr = DummyRestraint() @@ -1301,8 +1315,8 @@ class DummyProtocolStep(object): micrographs_number=50) lp = ihm.location.InputFileLocation(repo='foo', path='baz') dp = ihm.dataset.EMMicrographsDataset(lp) - l = ihm.location.InputFileLocation(repo='foo', path='bar') - d = ihm.dataset.EM2DClassDataset(l) + loc = ihm.location.InputFileLocation(repo='foo', path='bar') + d = ihm.dataset.EM2DClassDataset(loc) d._id = 4 d.parents.append(dp) pr.datasets[0] = d @@ -1673,17 +1687,17 @@ class DummyModel(object): po = IMP.pmi.mmcif.ProtocolOutput() s.add_protocol_output(po) st1 = s.create_state() - state = st1._protocol_output[0][1] + # state = st1._protocol_output[0][1] nup84 = st1.create_molecule("Nup84", "MELS", "X") nup84.add_representation(resolutions=[1]) - hier = s.build() + _ = s.build() lp = ihm.location.InputFileLocation(repo='foo', path='baz') d = ihm.dataset.SASDataset(lp) d._id = 4 model = DummyModel() model._id = 42 - po._add_foxs_restraint(model, 'Nup84.0', (2,3), d, 3.4, 1.2, 'test') + po._add_foxs_restraint(model, 'Nup84.0', (2, 3), d, 3.4, 1.2, 'test') fh = StringIO() w = ihm.format.CifWriter(fh) @@ -1723,8 +1737,10 @@ def test_add_em3d_restraint(self): hier = s.build() p = IMP.atom.get_by_type(hier, IMP.atom.FRAGMENT_TYPE)[0] + class DummyRestraint(object): label = 'foo' + class DummyProtocolStep(object): assembly = None pr = DummyRestraint() @@ -1732,8 +1748,8 @@ class DummyProtocolStep(object): po.add_em3d_restraint(state, pmi_restraint=pr, target_ps=[None, None], densities=[p]) - l = ihm.location.InputFileLocation(repo='foo', path='bar') - d = ihm.dataset.EMDensityDataset(l) + loc = ihm.location.InputFileLocation(repo='foo', path='bar') + d = ihm.dataset.EMDensityDataset(loc) d._id = 4 pr.dataset = d @@ -1781,7 +1797,7 @@ def test_dump_atoms_restype_mismatch(self): nup84 = st1.create_molecule("Nup84", "MELS", "X") nup84.add_structure(self.get_input_file_name('test.nup84.pdb'), 'A') nup84.add_representation(resolutions=[1]) - hier = s.build() + _ = s.build() # Create sequence mismatch po.system.entities[0].sequence = po.system.entities[0].sequence[1:] @@ -1790,7 +1806,7 @@ def test_dump_atoms_restype_mismatch(self): fh = StringIO() w = ihm.format.CifWriter(fh) d.finalize(po.system) - d.dump_coords(po.system, w) # Needed to populate _seq_dif + d.dump_coords(po.system, w) # Needed to populate _seq_dif fh = StringIO() w = ihm.format.CifWriter(fh) d.dump_seq_dif(po.system, w) @@ -1853,7 +1869,6 @@ def get_seq_dif(self): def test_beads_fragment(self): """Test _BeadsFragment class""" - system = ihm.System() e = ihm.Entity('A' * 40) asym = ihm.AsymUnit(e) m = None @@ -1880,7 +1895,6 @@ def test_beads_fragment(self): def test_model_repr_dump_add_frag(self): """Test ModelRepresentationDumper.add_fragment()""" m = None - system = ihm.System() e = ihm.Entity('A' * 40) asym = ihm.AsymUnit(e) state1 = 'state1' @@ -1925,7 +1939,7 @@ def test_model_repr_dump(self): nup84 = state.create_molecule("Nup84", "ME", "A") nup84.add_structure(self.get_input_file_name('test.nup84.pdb'), 'A') nup84.add_representation(nup84, resolutions=[1]) - hier = s.build() + _ = s.build() fh = StringIO() w = ihm.format.CifWriter(fh) @@ -1937,7 +1951,7 @@ def test_model_repr_dump(self): d.finalize(po.system) d.dump(po.system, w) r, = po.system.orphan_representations - self.assertEqual([f.asym_unit.seq_id_range for f in r], [(1,2)]) + self.assertEqual([f.asym_unit.seq_id_range for f in r], [(1, 2)]) out = fh.getvalue() self.assertEqual(out, """# loop_ @@ -1976,7 +1990,7 @@ def test_model_repr_dump_rigid(self): nup84.add_representation(nup84.get_atomic_residues(), resolutions=[1]) nup84.add_representation(nup84.get_non_atomic_residues(), resolutions=[10]) - hier = s.build() + _ = s.build() dof = IMP.pmi.dof.DegreesOfFreedom(m) dof.create_rigid_body(nup84.get_atomic_residues()) fh = StringIO() @@ -1989,7 +2003,8 @@ def test_model_repr_dump_rigid(self): d.finalize(po.system) d.dump(po.system, w) r, = po.system.orphan_representations - self.assertEqual([f.asym_unit.seq_id_range for f in r], [(1,2), (3,4)]) + self.assertEqual([f.asym_unit.seq_id_range for f in r], + [(1, 2), (3, 4)]) out = fh.getvalue() self.assertEqual(out, """# loop_ @@ -2125,21 +2140,23 @@ def test_gaussian_em_restraint(self): s = IMP.pmi.topology.System(m) s.add_protocol_output(po) st1 = s.create_state() - m1 = st1.create_molecule("Prot1",sequence="QEALVVKDLL") + m1 = st1.create_molecule("Prot1", sequence="QEALVVKDLL") atomic_res = m1.add_structure(self.get_input_file_name('prot.pdb'), - chain_id='A', res_range=(55,63), + chain_id='A', res_range=(55, 63), offset=-54) fname = self.get_input_file_name("test_gmm.txt") - m1.add_representation(atomic_res,resolutions=[1,10], + m1.add_representation(atomic_res, resolutions=[1, 10], density_residues_per_component=2, density_voxel_size=3.0, density_prefix=fname[:-4]) hier = s.build() - densities = IMP.atom.Selection(hier, - representation_type=IMP.atom.DENSITIES).get_selected_particles() + densities = IMP.atom.Selection( + hier, + representation_type=IMP.atom.DENSITIES).get_selected_particles() self.assertEqual(len(densities), 4) - gem = IMP.pmi.restraints.em.GaussianEMRestraint(densities, - target_fn=self.get_input_file_name('prot_gmm.mrc.1.txt')) + gem = IMP.pmi.restraints.em.GaussianEMRestraint( + densities, + target_fn=self.get_input_file_name('prot_gmm.mrc.1.txt')) gem.add_to_model() em3d, = po.system.restraints From 15116cf3c5ebd6feaf9c1bfdf07dd60667f67eeb Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 1 Jun 2022 14:02:56 -0700 Subject: [PATCH 135/155] Get latest pmi1 --- modules/pmi1 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/pmi1 b/modules/pmi1 index f5f17e5b29..95f867a1e9 160000 --- a/modules/pmi1 +++ b/modules/pmi1 @@ -1 +1 @@ -Subproject commit f5f17e5b298316599a68c71183ac7ccc3139643d +Subproject commit 95f867a1e9a1c582f70b15532ecd49626e5d6a07 From c6df9556f403bd00faad74eac0bf829101b5d63c Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 1 Jun 2022 09:46:32 -0700 Subject: [PATCH 136/155] Note that .exe installer no longer supports Python 2 --- ChangeLog.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/ChangeLog.md b/ChangeLog.md index f9734506c0..03953f89e2 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -7,6 +7,8 @@ ChangeLog {#changelog} IMP::atom::Hierarchy::get_is_valid() on each one first. - The IMP::em::CoarseCC class has been removed. Use similarly-named free functions instead to calculate coarse cross correlation. +- The Windows .exe installer no longer supports Python 2 (it works with + Python 3.6 through 3.10). - IMP now requires a C++11 compiler and SWIG 3 (or later) to build. Most recent compilers should support C++11, such as gcc, clang or MS Visual Studio 2012 or later. Various IMP macro and header workarounds From 5a7af4b395928fa9538a2a77a8e397d7ca93f65b Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 2 Jun 2022 12:32:42 -0700 Subject: [PATCH 137/155] Put moved particles in a vector, not a set Since we only use moved particles to populate a bitset, we don't need to sort them, so we can use a vector rather than a set, which is both faster to populate and faster to enumerate. --- modules/kernel/include/Model.h | 2 +- .../kernel/include/internal/AccumulatorScoreModifier.h | 4 ++-- modules/kernel/include/internal/moved_particles_cache.h | 4 ++-- modules/kernel/src/internal/moved_particles_cache.cpp | 8 ++++---- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/modules/kernel/include/Model.h b/modules/kernel/include/Model.h index ce3120fbc8..4de56fa650 100644 --- a/modules/kernel/include/Model.h +++ b/modules/kernel/include/Model.h @@ -182,7 +182,7 @@ class IMPKERNELEXPORT Model : public Object } //! Get all particles that depend on the given particle - const std::set &get_dependent_particles(ParticleIndex pi) { + const ParticleIndexes &get_dependent_particles(ParticleIndex pi) { return moved_particles_particle_cache_.get_dependent_particles(pi); } diff --git a/modules/kernel/include/internal/AccumulatorScoreModifier.h b/modules/kernel/include/internal/AccumulatorScoreModifier.h index e6c23057cd..d3cae2eeb9 100644 --- a/modules/kernel/include/internal/AccumulatorScoreModifier.h +++ b/modules/kernel/include/internal/AccumulatorScoreModifier.h @@ -32,7 +32,7 @@ typename boost::disable_if, get_container_indexes( Model *m, const Vector &contents, - const std::set &ps) { + const ParticleIndexes &ps) { boost::dynamic_bitset<> bps(m->get_particles_size()); for (ParticleIndex pi : ps) { bps[pi.get_index()] = true; @@ -61,7 +61,7 @@ typename boost::enable_if, get_container_indexes( Model *m, const Vector &contents, - const std::set &ps) { + const ParticleIndexes &ps) { boost::dynamic_bitset<> bps(m->get_particles_size()); for (ParticleIndex pi : ps) { bps[pi.get_index()] = true; diff --git a/modules/kernel/include/internal/moved_particles_cache.h b/modules/kernel/include/internal/moved_particles_cache.h index ca7a19d137..f867de0bb1 100644 --- a/modules/kernel/include/internal/moved_particles_cache.h +++ b/modules/kernel/include/internal/moved_particles_cache.h @@ -41,7 +41,7 @@ class MovedParticlesRestraintCache { //! Cache Particles that change when a Particle moves class MovedParticlesParticleCache { Model *m_; - typedef std::map > CacheMap; + typedef std::map CacheMap; CacheMap cache_; public: @@ -51,7 +51,7 @@ class MovedParticlesParticleCache { /** The result is cached; the cache should be cleared whenever the dependency graph changes. */ - const std::set &get_dependent_particles(ParticleIndex pi); + const ParticleIndexes &get_dependent_particles(ParticleIndex pi); // clear when dependency graph changes, and/or // particles/restraints added/removed diff --git a/modules/kernel/src/internal/moved_particles_cache.cpp b/modules/kernel/src/internal/moved_particles_cache.cpp index 6902eeaa06..88c0e539a3 100644 --- a/modules/kernel/src/internal/moved_particles_cache.cpp +++ b/modules/kernel/src/internal/moved_particles_cache.cpp @@ -25,16 +25,16 @@ MovedParticlesRestraintCache::get_dependent_restraints(ParticleIndex pi) { return it->second; } -const std::set & +const ParticleIndexes & MovedParticlesParticleCache::get_dependent_particles(ParticleIndex pi) { CacheMap::const_iterator it = cache_.find(pi); if (it == cache_.end()) { ParticlesTemp ps = m_->get_dependent_particles_uncached(pi); - std::set psset; + ParticleIndexes pis; for (ParticlesTemp::const_iterator pi = ps.begin(); pi != ps.end(); ++pi) { - psset.insert((*pi)->get_index()); + pis.push_back((*pi)->get_index()); } - cache_[pi] = psset; + cache_[pi] = pis; it = cache_.find(pi); } return it->second; From bbde109b923ed290cf2639ce04c084033416cd5d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 2 Jun 2022 15:26:50 -0700 Subject: [PATCH 138/155] Bundle a copy of pathlib for Python 2 Include a copy of the pathlib module backported to Python 2, so that we can use pathlib throughout IMP for path manipulation. Closes #1061. --- modules/kernel/pyext/src/_compat_pathlib.py | 1280 +++++++++++++++++++ 1 file changed, 1280 insertions(+) create mode 100644 modules/kernel/pyext/src/_compat_pathlib.py diff --git a/modules/kernel/pyext/src/_compat_pathlib.py b/modules/kernel/pyext/src/_compat_pathlib.py new file mode 100644 index 0000000000..9ab0e703d1 --- /dev/null +++ b/modules/kernel/pyext/src/_compat_pathlib.py @@ -0,0 +1,1280 @@ +import fnmatch +import functools +import io +import ntpath +import os +import posixpath +import re +import sys +import time +from collections import Sequence +from contextlib import contextmanager +from errno import EINVAL, ENOENT +from operator import attrgetter +from stat import S_ISDIR, S_ISLNK, S_ISREG, S_ISSOCK, S_ISBLK, S_ISCHR, S_ISFIFO +try: + from urllib import quote as urlquote, quote as urlquote_from_bytes +except ImportError: + from urllib.parse import quote as urlquote, quote_from_bytes as urlquote_from_bytes + + +try: + intern = intern +except NameError: + intern = sys.intern +try: + basestring = basestring +except NameError: + basestring = str + +supports_symlinks = True +try: + import nt +except ImportError: + nt = None +else: + if sys.getwindowsversion()[:2] >= (6, 0) and sys.version_info >= (3, 2): + from nt import _getfinalpathname + else: + supports_symlinks = False + _getfinalpathname = None + + +__all__ = [ + "PurePath", "PurePosixPath", "PureWindowsPath", + "Path", "PosixPath", "WindowsPath", + ] + +# +# Internals +# + +_py2 = sys.version_info < (3,) +_py2_fs_encoding = 'ascii' + +def _py2_fsencode(parts): + # py2 => minimal unicode support + return [part.encode(_py2_fs_encoding) if isinstance(part, unicode) + else part for part in parts] + +def _is_wildcard_pattern(pat): + # Whether this pattern needs actual matching using fnmatch, or can + # be looked up directly as a file. + return "*" in pat or "?" in pat or "[" in pat + + +class _Flavour(object): + """A flavour implements a particular (platform-specific) set of path + semantics.""" + + def __init__(self): + self.join = self.sep.join + + def parse_parts(self, parts): + if _py2: + parts = _py2_fsencode(parts) + parsed = [] + sep = self.sep + altsep = self.altsep + drv = root = '' + it = reversed(parts) + for part in it: + if not part: + continue + if altsep: + part = part.replace(altsep, sep) + drv, root, rel = self.splitroot(part) + if sep in rel: + for x in reversed(rel.split(sep)): + if x and x != '.': + parsed.append(intern(x)) + else: + if rel and rel != '.': + parsed.append(intern(rel)) + if drv or root: + if not drv: + # If no drive is present, try to find one in the previous + # parts. This makes the result of parsing e.g. + # ("C:", "/", "a") reasonably intuitive. + for part in it: + drv = self.splitroot(part)[0] + if drv: + break + break + if drv or root: + parsed.append(drv + root) + parsed.reverse() + return drv, root, parsed + + def join_parsed_parts(self, drv, root, parts, drv2, root2, parts2): + """ + Join the two paths represented by the respective + (drive, root, parts) tuples. Return a new (drive, root, parts) tuple. + """ + if root2: + if not drv2 and drv: + return drv, root2, [drv + root2] + parts2[1:] + elif drv2: + if drv2 == drv or self.casefold(drv2) == self.casefold(drv): + # Same drive => second path is relative to the first + return drv, root, parts + parts2[1:] + else: + # Second path is non-anchored (common case) + return drv, root, parts + parts2 + return drv2, root2, parts2 + + +class _WindowsFlavour(_Flavour): + # Reference for Windows paths can be found at + # http://msdn.microsoft.com/en-us/library/aa365247%28v=vs.85%29.aspx + + sep = '\\' + altsep = '/' + has_drv = True + pathmod = ntpath + + is_supported = (nt is not None) + + drive_letters = ( + set(chr(x) for x in range(ord('a'), ord('z') + 1)) | + set(chr(x) for x in range(ord('A'), ord('Z') + 1)) + ) + ext_namespace_prefix = '\\\\?\\' + + reserved_names = ( + set(['CON', 'PRN', 'AUX', 'NUL']) | + set(['COM%d' % i for i in range(1, 10)]) | + set(['LPT%d' % i for i in range(1, 10)]) + ) + + # Interesting findings about extended paths: + # - '\\?\c:\a', '//?/c:\a' and '//?/c:/a' are all supported + # but '\\?\c:/a' is not + # - extended paths are always absolute; "relative" extended paths will + # fail. + + def splitroot(self, part, sep=sep): + first = part[0:1] + second = part[1:2] + if (second == sep and first == sep): + # XXX extended paths should also disable the collapsing of "." + # components (according to MSDN docs). + prefix, part = self._split_extended_path(part) + first = part[0:1] + second = part[1:2] + else: + prefix = '' + third = part[2:3] + if (second == sep and first == sep and third != sep): + # is a UNC path: + # vvvvvvvvvvvvvvvvvvvvv root + # \\machine\mountpoint\directory\etc\... + # directory ^^^^^^^^^^^^^^ + index = part.find(sep, 2) + if index != -1: + index2 = part.find(sep, index + 1) + # a UNC path can't have two slashes in a row + # (after the initial two) + if index2 != index + 1: + if index2 == -1: + index2 = len(part) + if prefix: + return prefix + part[1:index2], sep, part[index2+1:] + else: + return part[:index2], sep, part[index2+1:] + drv = root = '' + if second == ':' and first in self.drive_letters: + drv = part[:2] + part = part[2:] + first = third + if first == sep: + root = first + part = part.lstrip(sep) + return prefix + drv, root, part + + def casefold(self, s): + return s.lower() + + def casefold_parts(self, parts): + return [p.lower() for p in parts] + + def resolve(self, path): + s = str(path) + if not s: + return os.getcwd() + if _getfinalpathname is not None: + return self._ext_to_normal(_getfinalpathname(s)) + # Means fallback on absolute + return None + + def _split_extended_path(self, s, ext_prefix=ext_namespace_prefix): + prefix = '' + if s.startswith(ext_prefix): + prefix = s[:4] + s = s[4:] + if s.startswith('UNC\\'): + prefix += s[:3] + s = '\\' + s[3:] + return prefix, s + + def _ext_to_normal(self, s): + # Turn back an extended path into a normal DOS-like path + return self._split_extended_path(s)[1] + + def is_reserved(self, parts): + # NOTE: the rules for reserved names seem somewhat complicated + # (e.g. r"..\NUL" is reserved but not r"foo\NUL"). + # We err on the side of caution and return True for paths which are + # not considered reserved by Windows. + if not parts: + return False + if parts[0].startswith('\\\\'): + # UNC paths are never reserved + return False + return parts[-1].partition('.')[0].upper() in self.reserved_names + + def make_uri(self, path): + # Under Windows, file URIs use the UTF-8 encoding. + drive = path.drive + if len(drive) == 2 and drive[1] == ':': + # It's a path on a local drive => 'file:///c:/a/b' + rest = path.as_posix()[2:].lstrip('/') + return 'file:///%s/%s' % ( + drive, urlquote_from_bytes(rest.encode('utf-8'))) + else: + # It's a path on a network drive => 'file://host/share/a/b' + return 'file:' + urlquote_from_bytes(path.as_posix().encode('utf-8')) + + +class _PosixFlavour(_Flavour): + sep = '/' + altsep = '' + has_drv = False + pathmod = posixpath + + is_supported = (os.name != 'nt') + + def splitroot(self, part, sep=sep): + if part and part[0] == sep: + stripped_part = part.lstrip(sep) + # According to POSIX path resolution: + # http://pubs.opengroup.org/onlinepubs/009695399/basedefs/xbd_chap04.html#tag_04_11 + # "A pathname that begins with two successive slashes may be + # interpreted in an implementation-defined manner, although more + # than two leading slashes shall be treated as a single slash". + if len(part) - len(stripped_part) == 2: + return '', sep * 2, stripped_part + else: + return '', sep, stripped_part + else: + return '', '', part + + def casefold(self, s): + return s + + def casefold_parts(self, parts): + return parts + + def resolve(self, path): + sep = self.sep + accessor = path._accessor + seen = {} + def _resolve(path, rest): + if rest.startswith(sep): + path = '' + + for name in rest.split(sep): + if not name or name == '.': + # current dir + continue + if name == '..': + # parent dir + path, _, _ = path.rpartition(sep) + continue + newpath = path + sep + name + if newpath in seen: + # Already seen this path + path = seen[newpath] + if path is not None: + # use cached value + continue + # The symlink is not resolved, so we must have a symlink loop. + raise RuntimeError("Symlink loop from %r" % newpath) + # Resolve the symbolic link + try: + target = accessor.readlink(newpath) + except OSError as e: + if e.errno != EINVAL: + raise + # Not a symlink + path = newpath + else: + seen[newpath] = None # not resolved symlink + path = _resolve(path, target) + seen[newpath] = path # resolved symlink + + return path + # NOTE: according to POSIX, getcwd() cannot contain path components + # which are symlinks. + base = '' if path.is_absolute() else os.getcwd() + return _resolve(base, str(path)) or sep + + def is_reserved(self, parts): + return False + + def make_uri(self, path): + # We represent the path using the local filesystem encoding, + # for portability to other applications. + bpath = bytes(path) + return 'file://' + urlquote_from_bytes(bpath) + + +_windows_flavour = _WindowsFlavour() +_posix_flavour = _PosixFlavour() + + +class _Accessor: + """An accessor implements a particular (system-specific or not) way of + accessing paths on the filesystem.""" + + +class _NormalAccessor(_Accessor): + + def _wrap_strfunc(strfunc): + @functools.wraps(strfunc) + def wrapped(pathobj, *args): + return strfunc(str(pathobj), *args) + return staticmethod(wrapped) + + def _wrap_binary_strfunc(strfunc): + @functools.wraps(strfunc) + def wrapped(pathobjA, pathobjB, *args): + return strfunc(str(pathobjA), str(pathobjB), *args) + return staticmethod(wrapped) + + stat = _wrap_strfunc(os.stat) + + lstat = _wrap_strfunc(os.lstat) + + open = _wrap_strfunc(os.open) + + listdir = _wrap_strfunc(os.listdir) + + chmod = _wrap_strfunc(os.chmod) + + if hasattr(os, "lchmod"): + lchmod = _wrap_strfunc(os.lchmod) + else: + def lchmod(self, pathobj, mode): + raise NotImplementedError("lchmod() not available on this system") + + mkdir = _wrap_strfunc(os.mkdir) + + unlink = _wrap_strfunc(os.unlink) + + rmdir = _wrap_strfunc(os.rmdir) + + rename = _wrap_binary_strfunc(os.rename) + + if sys.version_info >= (3, 3): + replace = _wrap_binary_strfunc(os.replace) + + if nt: + if supports_symlinks: + symlink = _wrap_binary_strfunc(os.symlink) + else: + def symlink(a, b, target_is_directory): + raise NotImplementedError("symlink() not available on this system") + else: + # Under POSIX, os.symlink() takes two args + @staticmethod + def symlink(a, b, target_is_directory): + return os.symlink(str(a), str(b)) + + utime = _wrap_strfunc(os.utime) + + # Helper for resolve() + def readlink(self, path): + return os.readlink(path) + + +_normal_accessor = _NormalAccessor() + + +# +# Globbing helpers +# + +@contextmanager +def _cached(func): + try: + func.__cached__ + yield func + except AttributeError: + cache = {} + def wrapper(*args): + try: + return cache[args] + except KeyError: + value = cache[args] = func(*args) + return value + wrapper.__cached__ = True + try: + yield wrapper + finally: + cache.clear() + +def _make_selector(pattern_parts): + pat = pattern_parts[0] + child_parts = pattern_parts[1:] + if pat == '**': + cls = _RecursiveWildcardSelector + elif '**' in pat: + raise ValueError("Invalid pattern: '**' can only be an entire path component") + elif _is_wildcard_pattern(pat): + cls = _WildcardSelector + else: + cls = _PreciseSelector + return cls(pat, child_parts) + +if hasattr(functools, "lru_cache"): + _make_selector = functools.lru_cache()(_make_selector) + + +class _Selector: + """A selector matches a specific glob pattern part against the children + of a given path.""" + + def __init__(self, child_parts): + self.child_parts = child_parts + if child_parts: + self.successor = _make_selector(child_parts) + else: + self.successor = _TerminatingSelector() + + def select_from(self, parent_path): + """Iterate over all child paths of `parent_path` matched by this + selector. This can contain parent_path itself.""" + path_cls = type(parent_path) + is_dir = path_cls.is_dir + exists = path_cls.exists + listdir = parent_path._accessor.listdir + return self._select_from(parent_path, is_dir, exists, listdir) + + +class _TerminatingSelector: + + def _select_from(self, parent_path, is_dir, exists, listdir): + yield parent_path + + +class _PreciseSelector(_Selector): + + def __init__(self, name, child_parts): + self.name = name + _Selector.__init__(self, child_parts) + + def _select_from(self, parent_path, is_dir, exists, listdir): + if not is_dir(parent_path): + return + path = parent_path._make_child_relpath(self.name) + if exists(path): + for p in self.successor._select_from(path, is_dir, exists, listdir): + yield p + + +class _WildcardSelector(_Selector): + + def __init__(self, pat, child_parts): + self.pat = re.compile(fnmatch.translate(pat)) + _Selector.__init__(self, child_parts) + + def _select_from(self, parent_path, is_dir, exists, listdir): + if not is_dir(parent_path): + return + cf = parent_path._flavour.casefold + for name in listdir(parent_path): + casefolded = cf(name) + if self.pat.match(casefolded): + path = parent_path._make_child_relpath(name) + for p in self.successor._select_from(path, is_dir, exists, listdir): + yield p + + +class _RecursiveWildcardSelector(_Selector): + + def __init__(self, pat, child_parts): + _Selector.__init__(self, child_parts) + + def _iterate_directories(self, parent_path, is_dir, listdir): + yield parent_path + for name in listdir(parent_path): + path = parent_path._make_child_relpath(name) + if is_dir(path): + for p in self._iterate_directories(path, is_dir, listdir): + yield p + + def _select_from(self, parent_path, is_dir, exists, listdir): + if not is_dir(parent_path): + return + with _cached(listdir) as listdir: + yielded = set() + try: + successor_select = self.successor._select_from + for starting_point in self._iterate_directories(parent_path, is_dir, listdir): + for p in successor_select(starting_point, is_dir, exists, listdir): + if p not in yielded: + yield p + yielded.add(p) + finally: + yielded.clear() + + +# +# Public API +# + +class _PathParents(Sequence): + """This object provides sequence-like access to the logical ancestors + of a path. Don't try to construct it yourself.""" + __slots__ = ('_pathcls', '_drv', '_root', '_parts') + + def __init__(self, path): + # We don't store the instance to avoid reference cycles + self._pathcls = type(path) + self._drv = path._drv + self._root = path._root + self._parts = path._parts + + def __len__(self): + if self._drv or self._root: + return len(self._parts) - 1 + else: + return len(self._parts) + + def __getitem__(self, idx): + if idx < 0 or idx >= len(self): + raise IndexError(idx) + return self._pathcls._from_parsed_parts(self._drv, self._root, + self._parts[:-idx - 1]) + + def __repr__(self): + return "<{0}.parents>".format(self._pathcls.__name__) + + +class PurePath(object): + """PurePath represents a filesystem path and offers operations which + don't imply any actual filesystem I/O. Depending on your system, + instantiating a PurePath will return either a PurePosixPath or a + PureWindowsPath object. You can also instantiate either of these classes + directly, regardless of your system. + """ + __slots__ = ( + '_drv', '_root', '_parts', + '_str', '_hash', '_pparts', '_cached_cparts', + ) + + def __new__(cls, *args): + """Construct a PurePath from one or several strings and or existing + PurePath objects. The strings and path objects are combined so as + to yield a canonicalized path, which is incorporated into the + new PurePath object. + """ + if cls is PurePath: + cls = PureWindowsPath if os.name == 'nt' else PurePosixPath + return cls._from_parts(args) + + def __reduce__(self): + # Using the parts tuple helps share interned path parts + # when pickling related paths. + return (self.__class__, tuple(self._parts)) + + @classmethod + def _parse_args(cls, args): + # This is useful when you don't want to create an instance, just + # canonicalize some constructor arguments. + parts = [] + for a in args: + if isinstance(a, PurePath): + parts += a._parts + elif isinstance(a, basestring): + parts.append(a) + else: + raise TypeError( + "argument should be a path or str object, not %r" + % type(a)) + return cls._flavour.parse_parts(parts) + + @classmethod + def _from_parts(cls, args, init=True): + # We need to call _parse_args on the instance, so as to get the + # right flavour. + self = object.__new__(cls) + drv, root, parts = self._parse_args(args) + self._drv = drv + self._root = root + self._parts = parts + if init: + self._init() + return self + + @classmethod + def _from_parsed_parts(cls, drv, root, parts, init=True): + self = object.__new__(cls) + self._drv = drv + self._root = root + self._parts = parts + if init: + self._init() + return self + + @classmethod + def _format_parsed_parts(cls, drv, root, parts): + if drv or root: + return drv + root + cls._flavour.join(parts[1:]) + else: + return cls._flavour.join(parts) + + def _init(self): + # Overriden in concrete Path + pass + + def _make_child(self, args): + drv, root, parts = self._parse_args(args) + drv, root, parts = self._flavour.join_parsed_parts( + self._drv, self._root, self._parts, drv, root, parts) + return self._from_parsed_parts(drv, root, parts) + + def __str__(self): + """Return the string representation of the path, suitable for + passing to system calls.""" + try: + return self._str + except AttributeError: + self._str = self._format_parsed_parts(self._drv, self._root, + self._parts) or '.' + return self._str + + def as_posix(self): + """Return the string representation of the path with forward (/) + slashes.""" + f = self._flavour + return str(self).replace(f.sep, '/') + + def __bytes__(self): + """Return the bytes representation of the path. This is only + recommended to use under Unix.""" + if sys.version_info < (3, 2): + raise NotImplementedError("needs Python 3.2 or later") + return os.fsencode(str(self)) + + def __repr__(self): + return "{0}({1!r})".format(self.__class__.__name__, self.as_posix()) + + def as_uri(self): + """Return the path as a 'file' URI.""" + if not self.is_absolute(): + raise ValueError("relative path can't be expressed as a file URI") + return self._flavour.make_uri(self) + + @property + def _cparts(self): + # Cached casefolded parts, for hashing and comparison + try: + return self._cached_cparts + except AttributeError: + self._cached_cparts = self._flavour.casefold_parts(self._parts) + return self._cached_cparts + + def __eq__(self, other): + if not isinstance(other, PurePath): + return NotImplemented + return self._cparts == other._cparts and self._flavour is other._flavour + + def __ne__(self, other): + return not self == other + + def __hash__(self): + try: + return self._hash + except AttributeError: + self._hash = hash(tuple(self._cparts)) + return self._hash + + def __lt__(self, other): + if not isinstance(other, PurePath) or self._flavour is not other._flavour: + return NotImplemented + return self._cparts < other._cparts + + def __le__(self, other): + if not isinstance(other, PurePath) or self._flavour is not other._flavour: + return NotImplemented + return self._cparts <= other._cparts + + def __gt__(self, other): + if not isinstance(other, PurePath) or self._flavour is not other._flavour: + return NotImplemented + return self._cparts > other._cparts + + def __ge__(self, other): + if not isinstance(other, PurePath) or self._flavour is not other._flavour: + return NotImplemented + return self._cparts >= other._cparts + + drive = property(attrgetter('_drv'), + doc="""The drive prefix (letter or UNC path), if any.""") + + root = property(attrgetter('_root'), + doc="""The root of the path, if any.""") + + @property + def anchor(self): + """The concatenation of the drive and root, or ''.""" + anchor = self._drv + self._root + return anchor + + @property + def name(self): + """The final path component, if any.""" + parts = self._parts + if len(parts) == (1 if (self._drv or self._root) else 0): + return '' + return parts[-1] + + @property + def suffix(self): + """The final component's last suffix, if any.""" + name = self.name + i = name.rfind('.') + if 0 < i < len(name) - 1: + return name[i:] + else: + return '' + + @property + def suffixes(self): + """A list of the final component's suffixes, if any.""" + name = self.name + if name.endswith('.'): + return [] + name = name.lstrip('.') + return ['.' + suffix for suffix in name.split('.')[1:]] + + @property + def stem(self): + """The final path component, minus its last suffix.""" + name = self.name + i = name.rfind('.') + if 0 < i < len(name) - 1: + return name[:i] + else: + return name + + def with_name(self, name): + """Return a new path with the file name changed.""" + if not self.name: + raise ValueError("%r has an empty name" % (self,)) + return self._from_parsed_parts(self._drv, self._root, + self._parts[:-1] + [name]) + + def with_suffix(self, suffix): + """Return a new path with the file suffix changed (or added, if none).""" + # XXX if suffix is None, should the current suffix be removed? + drv, root, parts = self._flavour.parse_parts((suffix,)) + if drv or root or len(parts) != 1: + raise ValueError("Invalid suffix %r" % (suffix)) + suffix = parts[0] + if not suffix.startswith('.'): + raise ValueError("Invalid suffix %r" % (suffix)) + name = self.name + if not name: + raise ValueError("%r has an empty name" % (self,)) + old_suffix = self.suffix + if not old_suffix: + name = name + suffix + else: + name = name[:-len(old_suffix)] + suffix + return self._from_parsed_parts(self._drv, self._root, + self._parts[:-1] + [name]) + + def relative_to(self, *other): + """Return the relative path to another path identified by the passed + arguments. If the operation is not possible (because this is not + a subpath of the other path), raise ValueError. + """ + # For the purpose of this method, drive and root are considered + # separate parts, i.e.: + # Path('c:/').relative_to('c:') gives Path('/') + # Path('c:/').relative_to('/') raise ValueError + if not other: + raise TypeError("need at least one argument") + parts = self._parts + drv = self._drv + root = self._root + if root: + abs_parts = [drv, root] + parts[1:] + else: + abs_parts = parts + to_drv, to_root, to_parts = self._parse_args(other) + if to_root: + to_abs_parts = [to_drv, to_root] + to_parts[1:] + else: + to_abs_parts = to_parts + n = len(to_abs_parts) + cf = self._flavour.casefold_parts + if (root or drv) if n == 0 else cf(abs_parts[:n]) != cf(to_abs_parts): + formatted = self._format_parsed_parts(to_drv, to_root, to_parts) + raise ValueError("{!r} does not start with {!r}" + .format(str(self), str(formatted))) + return self._from_parsed_parts('', root if n == 1 else '', + abs_parts[n:]) + + @property + def parts(self): + """An object providing sequence-like access to the + components in the filesystem path.""" + # We cache the tuple to avoid building a new one each time .parts + # is accessed. XXX is this necessary? + try: + return self._pparts + except AttributeError: + self._pparts = tuple(self._parts) + return self._pparts + + def joinpath(self, *args): + """Combine this path with one or several arguments, and return a + new path representing either a subpath (if all arguments are relative + paths) or a totally different path (if one of the arguments is + anchored). + """ + return self._make_child(args) + + def __truediv__(self, key): + return self._make_child((key,)) + + def __rtruediv__(self, key): + return self._from_parts([key] + self._parts) + + if sys.version_info < (3,): + __div__ = __truediv__ + __rdiv__ = __rtruediv__ + + @property + def parent(self): + """The logical parent of the path.""" + drv = self._drv + root = self._root + parts = self._parts + if len(parts) == 1 and (drv or root): + return self + return self._from_parsed_parts(drv, root, parts[:-1]) + + @property + def parents(self): + """A sequence of this path's logical parents.""" + return _PathParents(self) + + def is_absolute(self): + """True if the path is absolute (has both a root and, if applicable, + a drive).""" + if not self._root: + return False + return not self._flavour.has_drv or bool(self._drv) + + def is_reserved(self): + """Return True if the path contains one of the special names reserved + by the system, if any.""" + return self._flavour.is_reserved(self._parts) + + def match(self, path_pattern): + """ + Return True if this path matches the given pattern. + """ + cf = self._flavour.casefold + path_pattern = cf(path_pattern) + drv, root, pat_parts = self._flavour.parse_parts((path_pattern,)) + if not pat_parts: + raise ValueError("empty pattern") + if drv and drv != cf(self._drv): + return False + if root and root != cf(self._root): + return False + parts = self._cparts + if drv or root: + if len(pat_parts) != len(parts): + return False + pat_parts = pat_parts[1:] + elif len(pat_parts) > len(parts): + return False + for part, pat in zip(reversed(parts), reversed(pat_parts)): + if not fnmatch.fnmatchcase(part, pat): + return False + return True + + +class PurePosixPath(PurePath): + _flavour = _posix_flavour + __slots__ = () + + +class PureWindowsPath(PurePath): + _flavour = _windows_flavour + __slots__ = () + + +# Filesystem-accessing classes + + +class Path(PurePath): + __slots__ = ( + '_accessor', + ) + + def __new__(cls, *args, **kwargs): + if cls is Path: + cls = WindowsPath if os.name == 'nt' else PosixPath + self = cls._from_parts(args, init=False) + if not self._flavour.is_supported: + raise NotImplementedError("cannot instantiate %r on your system" + % (cls.__name__,)) + self._init() + return self + + def _init(self, + # Private non-constructor arguments + template=None, + ): + if template is not None: + self._accessor = template._accessor + else: + self._accessor = _normal_accessor + + def _make_child_relpath(self, part): + # This is an optimization used for dir walking. `part` must be + # a single part relative to this path. + parts = self._parts + [part] + return self._from_parsed_parts(self._drv, self._root, parts) + + def _opener(self, name, flags, mode=0o666): + # A stub for the opener argument to built-in open() + return self._accessor.open(self, flags, mode) + + def _raw_open(self, flags, mode=0o777): + """ + Open the file pointed by this path and return a file descriptor, + as os.open() does. + """ + return self._accessor.open(self, flags, mode) + + # Public API + + @classmethod + def cwd(cls): + """Return a new path pointing to the current working directory + (as returned by os.getcwd()). + """ + return cls(os.getcwd()) + + def iterdir(self): + """Iterate over the files in this directory. Does not yield any + result for the special paths '.' and '..'. + """ + for name in self._accessor.listdir(self): + if name in ('.', '..'): + # Yielding a path object for these makes little sense + continue + yield self._make_child_relpath(name) + + def glob(self, pattern): + """Iterate over this subtree and yield all existing files (of any + kind, including directories) matching the given pattern. + """ + pattern = self._flavour.casefold(pattern) + drv, root, pattern_parts = self._flavour.parse_parts((pattern,)) + if drv or root: + raise NotImplementedError("Non-relative patterns are unsupported") + selector = _make_selector(tuple(pattern_parts)) + for p in selector.select_from(self): + yield p + + def rglob(self, pattern): + """Recursively yield all existing files (of any kind, including + directories) matching the given pattern, anywhere in this subtree. + """ + pattern = self._flavour.casefold(pattern) + drv, root, pattern_parts = self._flavour.parse_parts((pattern,)) + if drv or root: + raise NotImplementedError("Non-relative patterns are unsupported") + selector = _make_selector(("**",) + tuple(pattern_parts)) + for p in selector.select_from(self): + yield p + + def absolute(self): + """Return an absolute version of this path. This function works + even if the path doesn't point to anything. + + No normalization is done, i.e. all '.' and '..' will be kept along. + Use resolve() to get the canonical path to a file. + """ + # XXX untested yet! + if self.is_absolute(): + return self + # FIXME this must defer to the specific flavour (and, under Windows, + # use nt._getfullpathname()) + obj = self._from_parts([os.getcwd()] + self._parts, init=False) + obj._init(template=self) + return obj + + def resolve(self): + """ + Make the path absolute, resolving all symlinks on the way and also + normalizing it (for example turning slashes into backslashes under + Windows). + """ + s = self._flavour.resolve(self) + if s is None: + # No symlink resolution => for consistency, raise an error if + # the path doesn't exist or is forbidden + self.stat() + s = str(self.absolute()) + # Now we have no symlinks in the path, it's safe to normalize it. + normed = self._flavour.pathmod.normpath(s) + obj = self._from_parts((normed,), init=False) + obj._init(template=self) + return obj + + def stat(self): + """ + Return the result of the stat() system call on this path, like + os.stat() does. + """ + return self._accessor.stat(self) + + def owner(self): + """ + Return the login name of the file owner. + """ + import pwd + return pwd.getpwuid(self.stat().st_uid).pw_name + + def group(self): + """ + Return the group name of the file gid. + """ + import grp + return grp.getgrgid(self.stat().st_gid).gr_name + + def open(self, mode='r', buffering=-1, encoding=None, + errors=None, newline=None): + """ + Open the file pointed by this path and return a file object, as + the built-in open() function does. + """ + if sys.version_info >= (3, 3): + return io.open(str(self), mode, buffering, encoding, errors, newline, + opener=self._opener) + else: + return io.open(str(self), mode, buffering, encoding, errors, newline) + + def touch(self, mode=0o666, exist_ok=True): + """ + Create this file with the given access mode, if it doesn't exist. + """ + if exist_ok: + # First try to bump modification time + # Implementation note: GNU touch uses the UTIME_NOW option of + # the utimensat() / futimens() functions. + t = time.time() + try: + self._accessor.utime(self, (t, t)) + except OSError: + # Avoid exception chaining + pass + else: + return + flags = os.O_CREAT | os.O_WRONLY + if not exist_ok: + flags |= os.O_EXCL + fd = self._raw_open(flags, mode) + os.close(fd) + + def mkdir(self, mode=0o777, parents=False): + if not parents: + self._accessor.mkdir(self, mode) + else: + try: + self._accessor.mkdir(self, mode) + except OSError as e: + if e.errno != ENOENT: + raise + self.parent.mkdir(parents=True) + self._accessor.mkdir(self, mode) + + def chmod(self, mode): + """ + Change the permissions of the path, like os.chmod(). + """ + self._accessor.chmod(self, mode) + + def lchmod(self, mode): + """ + Like chmod(), except if the path points to a symlink, the symlink's + permissions are changed, rather than its target's. + """ + self._accessor.lchmod(self, mode) + + def unlink(self): + """ + Remove this file or link. + If the path is a directory, use rmdir() instead. + """ + self._accessor.unlink(self) + + def rmdir(self): + """ + Remove this directory. The directory must be empty. + """ + self._accessor.rmdir(self) + + def lstat(self): + """ + Like stat(), except if the path points to a symlink, the symlink's + status information is returned, rather than its target's. + """ + return self._accessor.lstat(self) + + def rename(self, target): + """ + Rename this path to the given path. + """ + self._accessor.rename(self, target) + + def replace(self, target): + """ + Rename this path to the given path, clobbering the existing + destination if it exists. + """ + if sys.version_info < (3, 3): + raise NotImplementedError("replace() is only available " + "with Python 3.3 and later") + self._accessor.replace(self, target) + + def symlink_to(self, target, target_is_directory=False): + """ + Make this path a symlink pointing to the given path. + Note the order of arguments (self, target) is the reverse of os.symlink's. + """ + self._accessor.symlink(target, self, target_is_directory) + + # Convenience functions for querying the stat results + + def exists(self): + """ + Whether this path exists. + """ + try: + self.stat() + except OSError as e: + if e.errno != ENOENT: + raise + return False + return True + + def is_dir(self): + """ + Whether this path is a directory. + """ + try: + return S_ISDIR(self.stat().st_mode) + except OSError as e: + if e.errno != ENOENT: + raise + # Path doesn't exist or is a broken symlink + # (see https://bitbucket.org/pitrou/pathlib/issue/12/) + return False + + def is_file(self): + """ + Whether this path is a regular file (also True for symlinks pointing + to regular files). + """ + try: + return S_ISREG(self.stat().st_mode) + except OSError as e: + if e.errno != ENOENT: + raise + # Path doesn't exist or is a broken symlink + # (see https://bitbucket.org/pitrou/pathlib/issue/12/) + return False + + def is_symlink(self): + """ + Whether this path is a symbolic link. + """ + try: + return S_ISLNK(self.lstat().st_mode) + except OSError as e: + if e.errno != ENOENT: + raise + # Path doesn't exist + return False + + def is_block_device(self): + """ + Whether this path is a block device. + """ + try: + return S_ISBLK(self.stat().st_mode) + except OSError as e: + if e.errno != ENOENT: + raise + # Path doesn't exist or is a broken symlink + # (see https://bitbucket.org/pitrou/pathlib/issue/12/) + return False + + def is_char_device(self): + """ + Whether this path is a character device. + """ + try: + return S_ISCHR(self.stat().st_mode) + except OSError as e: + if e.errno != ENOENT: + raise + # Path doesn't exist or is a broken symlink + # (see https://bitbucket.org/pitrou/pathlib/issue/12/) + return False + + def is_fifo(self): + """ + Whether this path is a FIFO. + """ + try: + return S_ISFIFO(self.stat().st_mode) + except OSError as e: + if e.errno != ENOENT: + raise + # Path doesn't exist or is a broken symlink + # (see https://bitbucket.org/pitrou/pathlib/issue/12/) + return False + + def is_socket(self): + """ + Whether this path is a socket. + """ + try: + return S_ISSOCK(self.stat().st_mode) + except OSError as e: + if e.errno != ENOENT: + raise + # Path doesn't exist or is a broken symlink + # (see https://bitbucket.org/pitrou/pathlib/issue/12/) + return False + + +class PosixPath(Path, PurePosixPath): + __slots__ = () + +class WindowsPath(Path, PureWindowsPath): + __slots__ = () + From c12cbf59ebc64223c9e97eb04cda1b710b95117c Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 2 Jun 2022 15:28:19 -0700 Subject: [PATCH 139/155] Use pathlib in IMP.test Start using pathlib for some path manipulation in the IMP.test module. --- modules/test/pyext/src/__init__.py | 37 +++++++++++++++++------------- 1 file changed, 21 insertions(+), 16 deletions(-) diff --git a/modules/test/pyext/src/__init__.py b/modules/test/pyext/src/__init__.py index 7142825226..c2bdf8ec27 100644 --- a/modules/test/pyext/src/__init__.py +++ b/modules/test/pyext/src/__init__.py @@ -21,6 +21,11 @@ import pickle import contextlib import subprocess +try: + from pathlib import Path +except ImportError: # Use bundled pathlib on Python 2 without pathlib + from IMP._compat_pathlib import Path + # Expose some unittest decorators for convenience expectedFailure = unittest.expectedFailure @@ -143,7 +148,7 @@ class TestCase(unittest.TestCase): def __init__(self, *args, **keys): unittest.TestCase.__init__(self, *args, **keys) - self._progname = os.path.abspath(sys.argv[0]) + self._progname = Path(sys.argv[0]).absolute() def setUp(self): self.__check_level = IMP.get_check_level() @@ -163,17 +168,17 @@ def tearDown(self): def get_input_file_name(self, filename): """Get the full name of an input file in the top-level test directory.""" - testdir = os.path.dirname(self._progname) - if self.__module__ != '__main__': - testdir = os.path.dirname(sys.modules[self.__module__].__file__) - dirs = testdir.split(os.path.sep) - for i in range(len(dirs), 0, -1): - input = os.path.sep.join(dirs[:i] + ['input']) - if os.path.isdir(input): - ret = os.path.join(input, filename) - if not os.path.exists(ret): - raise IOError("Test input file "+ret+" does not exist") - return ret + if self.__module__ == '__main__': + testdir = self._progname + else: + testdir = Path(sys.modules[self.__module__].__file__) + for p in testdir.parents: + input = p / "input" + if input.is_dir(): + ret = input / filename + if not ret.exists(): + raise IOError("Test input file %s does not exist" % ret) + return str(ret) raise IOError("No test input directory found") def open_input_file(self, filename, mode='rb'): @@ -187,7 +192,7 @@ def get_tmp_file_name(self, filename): if not hasattr(self, '_tmpdir'): self._tmpdir = _TempDir(os.environ.get('IMP_TMP_DIR')) tmpdir = self._tmpdir.tmpdir - return os.path.join(tmpdir, filename) + return str(Path(tmpdir) / filename) def get_magnitude(self, vector): """Get the magnitude of a list of floats""" @@ -785,9 +790,9 @@ def __init__(self, stream=None, descriptions=None, verbosity=None): def stopTestRun(self): if 'IMP_TEST_DETAIL_DIR' in os.environ: - fname = os.path.join(os.environ['IMP_TEST_DETAIL_DIR'], - os.path.basename(sys.argv[0])) - with open(fname, 'wb') as fh: + fname = (Path(os.environ['IMP_TEST_DETAIL_DIR']) + / Path(sys.argv[0]).name) + with open(str(fname), 'wb') as fh: pickle.dump(self.all_tests, fh, -1) super(_TestResult, self).stopTestRun() From 236ed33c9345b2541fc8beb3b2cb45df584e7e25 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 2 Jun 2022 18:15:58 -0700 Subject: [PATCH 140/155] Note that we now support Ubuntu 22.04 --- ChangeLog.md | 1 + 1 file changed, 1 insertion(+) diff --git a/ChangeLog.md b/ChangeLog.md index 03953f89e2..7de9c3380f 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -9,6 +9,7 @@ ChangeLog {#changelog} functions instead to calculate coarse cross correlation. - The Windows .exe installer no longer supports Python 2 (it works with Python 3.6 through 3.10). +- A binary package is now provided for Ubuntu 22.04 LTS, Jammy Jellyfish. - IMP now requires a C++11 compiler and SWIG 3 (or later) to build. Most recent compilers should support C++11, such as gcc, clang or MS Visual Studio 2012 or later. Various IMP macro and header workarounds From 9721e20de816a6116d7c7496986027f5b36ded25 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 3 Jun 2022 10:40:51 -0700 Subject: [PATCH 141/155] Don't complain about Path attributes --- modules/test/test/standards_exceptions | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/modules/test/test/standards_exceptions b/modules/test/test/standards_exceptions index 72bde5c5e5..6392b47df2 100644 --- a/modules/test/test/standards_exceptions +++ b/modules/test/test/standards_exceptions @@ -16,7 +16,15 @@ standard_unittest_attributes = [ 'setUp', 'setUpClass', 'shortDescription', 'skipTest', 'tearDown', 'tearDownClass', 'assertLogs', 'subTest', 'addClassCleanup', 'doClassCleanups', 'assertNoLogs' ] -exceptions = ["TestCase." + x for x in standard_unittest_attributes] \ +path_attributes = [ + 'absolute', 'as_posix', 'as_uri', 'chmod', 'cwd', 'exists', 'glob', 'group', + 'is_absolute', 'is_block_device', 'is_char_device', 'is_dir', 'is_fifo', + 'is_file', 'is_reserved', 'is_socket', 'is_symlink', 'iterdir', 'joinpath', + 'lchmod', 'lstat', 'match', 'mkdir', 'open', 'owner', 'relative_to', + 'rename', 'replace', 'resolve', 'rglob', 'rmdir', 'stat', 'symlink_to', + 'touch', 'unlink', 'with_name', 'with_suffix' ] +exceptions = ["Path." + x for x in path_attributes] \ + + ["TestCase." + x for x in standard_unittest_attributes] \ + ["ApplicationTestCase." + x for x in standard_unittest_attributes] exceptions.extend([ From 67b0965755848237b2267992386dd8a0cfcda3ed Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 3 Jun 2022 10:45:55 -0700 Subject: [PATCH 142/155] Get latest PMI1 --- modules/pmi1 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/pmi1 b/modules/pmi1 index 95f867a1e9..09a252823a 160000 --- a/modules/pmi1 +++ b/modules/pmi1 @@ -1 +1 @@ -Subproject commit 95f867a1e9a1c582f70b15532ecd49626e5d6a07 +Subproject commit 09a252823af3595ea8f695790e99eeba720fa473 From 69e164a8a983f695777bc77802054ea10552632d Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 3 Jun 2022 11:23:46 -0700 Subject: [PATCH 143/155] Add explicit Decorator==Decorator method Add an operator== overload to compare two Decorator objects. The previous code fails to build with C++20, as there is no direct match for this comparison and the Decorator==Object* and Decorator==Particle* overloads are considered ambiguous. --- modules/kernel/include/Decorator.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/kernel/include/Decorator.h b/modules/kernel/include/Decorator.h index 0df1dc1b3c..429895a15c 100644 --- a/modules/kernel/include/Decorator.h +++ b/modules/kernel/include/Decorator.h @@ -151,6 +151,8 @@ class IMPKERNELEXPORT Decorator : public Value { bool __ge__(Object* o) const { return operator>=(o); } bool __le__(Object* o) const { return operator<=(o); } #ifndef SWIG + bool operator==(Decorator d) const { return (compare(d) == 0); } + bool operator==(Object* o) const { return (compare(o) == 0); } bool operator!=(Object* o) const { return (compare(o) != 0); } bool operator<(Object* o) const { return (compare(o) < 0); } From b44a9bbc526250439deeff529729809c503ee586 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 3 Jun 2022 12:52:46 -0700 Subject: [PATCH 144/155] Work around opencv missing on RHEL 9 RHEL 7 and 8 have OpenCV, but RHEL 9 does not, so build by default without it, or allow bundling our own copy. --- tools/rpm/IMP.spec.in | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in index 623768d614..cf4ca5e0ab 100644 --- a/tools/rpm/IMP.spec.in +++ b/tools/rpm/IMP.spec.in @@ -79,19 +79,30 @@ BuildRequires: cmake >= 2.8 BuildRequires: boost-devel >= 1.53 # RHEL doesn't have a CGAL package, so build without CGAL on RHEL. +# RHEL 7 and 8 have OpenCV, but it was dropped in RHEL 9, so disable the em2d +# module. %if 0%{?fedora} BuildRequires: CGAL-devel %endif +%if 0%{?fedora} || (0%{?rhel} >= 7 && 0%{?rhel} <= 8) BuildRequires: opencv-devel +%endif # If building in the Sali lab, pass '-D "RHEL_SALI_LAB 1"' to your rpmbuild -# invocation. This will pull in our custom CGAL package +# invocation. This will pull in our custom CGAL and OpenCV packages # and bundle the libraries with IMP. # If building outside of the lab and you still want these packages, get them # from https://integrativemodeling.org/build-extras/ %if 0%{?rhel} && 0%{?RHEL_SALI_LAB} +%if 0%{?rhel} == 9 +BuildRequires: opencv-nogui-devel +%endif BuildRequires: CGAL-nogui-devel +%if 0%{?rhel} == 9 +%define bundled libcv\\.so\\|libcxcore\\.so\\|libhighgui.so\\|libTAU\\.so\\|libCGAL\\.so +%else %define bundled libTAU\\.so\\|libCGAL\\.so +%endif %else %define bundled libTAU\\.so %endif @@ -169,7 +180,9 @@ Requires: %{PYTHON2}-devel %if 0%{?fedora} Requires: CGAL-devel %endif +%if 0%{?fedora} || (0%{?rhel} >= 7 && 0%{?rhel} <= 8) Requires: opencv-devel +%endif %description devel This package contains the include files for building applications that link @@ -404,7 +417,13 @@ mkdir ${RPM_BUILD_ROOT}%{_libdir}/IMP cp /usr/%{_lib}/libTAU.so.1 ${RPM_BUILD_ROOT}%{_libdir}/IMP/ %if 0%{?rhel} && 0%{?RHEL_SALI_LAB} -# Bundle CGAL libraries +# Bundle CGAL (and potentially OpenCV) libraries +%if 0%{?rhel} == 9 +for cvlib in cv cxcore highgui; do + cp /usr/%{_lib}/lib${cvlib}.so.2.1 ${RPM_BUILD_ROOT}%{_libdir}/IMP/ +done +%endif + %if 0%{?rhel} == 8 cp /usr/%{_lib}/libCGAL.so.13 ${RPM_BUILD_ROOT}%{_libdir}/IMP/ %else From a06038d0cc80bc335cb46e74a93ad1a4a0bbc5ea Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 3 Jun 2022 17:21:53 -0700 Subject: [PATCH 145/155] Use newer opencv-nogui on RHEL 9 --- tools/rpm/IMP.spec.in | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in index cf4ca5e0ab..ca63719d16 100644 --- a/tools/rpm/IMP.spec.in +++ b/tools/rpm/IMP.spec.in @@ -419,12 +419,12 @@ cp /usr/%{_lib}/libTAU.so.1 ${RPM_BUILD_ROOT}%{_libdir}/IMP/ %if 0%{?rhel} && 0%{?RHEL_SALI_LAB} # Bundle CGAL (and potentially OpenCV) libraries %if 0%{?rhel} == 9 -for cvlib in cv cxcore highgui; do - cp /usr/%{_lib}/lib${cvlib}.so.2.1 ${RPM_BUILD_ROOT}%{_libdir}/IMP/ +for cvlib in core imgproc highgui imgcodecs; do + cp /usr/%{_lib}/libopencv_${cvlib}.so.4.5 ${RPM_BUILD_ROOT}%{_libdir}/IMP/ done %endif -%if 0%{?rhel} == 8 +%if 0%{?rhel} >= 8 cp /usr/%{_lib}/libCGAL.so.13 ${RPM_BUILD_ROOT}%{_libdir}/IMP/ %else cp /usr/%{_lib}/libCGAL.so.10 ${RPM_BUILD_ROOT}%{_libdir}/IMP/ From a388cbc2bce1b7c8c549aff57a9bfc652f44efbc Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 3 Jun 2022 18:37:00 -0700 Subject: [PATCH 146/155] Use same req/proprog for IMP & IMP-devel packages --- tools/rpm/IMP.spec.in | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in index ca63719d16..6af5ad6f5f 100644 --- a/tools/rpm/IMP.spec.in +++ b/tools/rpm/IMP.spec.in @@ -277,8 +277,8 @@ Development files for IMP.mpi module (and dependents) with openmpi. %global __requires_exclude ^libTAU\\.so.*$ %endif %else -%define reqprog %{_builddir}/find-requires-%{name} -%define proprog %{_builddir}/find-provides-%{name} +%define reqprog %{_builddir}/find-requires-IMP +%define proprog %{_builddir}/find-provides-IMP cat < %{reqprog} #!/bin/bash From 3b4bfaa9c1cea4518cd3e109146a931017270caa Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 3 Jun 2022 23:38:09 -0700 Subject: [PATCH 147/155] RHEL9 includes python3 protobuf, so pull it in --- tools/rpm/IMP.spec.in | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in index 6af5ad6f5f..4577a68b71 100644 --- a/tools/rpm/IMP.spec.in +++ b/tools/rpm/IMP.spec.in @@ -67,10 +67,10 @@ BuildRequires: libTAU-devel # Need for npctransport module BuildRequires: protobuf-devel -%if 0%{?fedora} +# No Python protobuf package in RHEL8 +%if 0%{?fedora} || 0%{?rhel} == 9 Requires: python3-protobuf %endif -# No Python protobuf package in RHEL8 %if 0%{?rhel} == 7 Requires: protobuf-python %endif From 3afc2a2be1e1108725c80391c5f55adce1cf4b36 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Fri, 3 Jun 2022 23:38:29 -0700 Subject: [PATCH 148/155] Add tests for IMP RPMs built on RHEL9 --- tools/nightly-tests/test-install/test_mock.py | 5 +++-- tools/nightly-tests/test-install/test_mpi.py | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/tools/nightly-tests/test-install/test_mock.py b/tools/nightly-tests/test-install/test_mock.py index 2fa23a1025..82162c8f18 100644 --- a/tools/nightly-tests/test-install/test_mock.py +++ b/tools/nightly-tests/test-install/test_mock.py @@ -23,11 +23,12 @@ def test_modules_installed(self): import IMP.npctransport # Ubuntu only supports protobuf with Python 3 in 18.04 or later; # our Windows protobuf install is Python 2 only; - # for RHEL8, Fedora and Ubuntu 22.04 or later we only have Python 3 + # for RHEL8/9, Fedora and Ubuntu 22.04 or later we only have Python 3 # protobuf wrappers. py2only_pb = frozenset(('ubuntu-trusty', 'ubuntu-xenial', 'w32', 'w64')) - py3only_pb = frozenset(('epel-8-x86_64', 'ubuntu-jammy')) + py3only_pb = frozenset(('epel-8-x86_64', 'ubuntu-jammy', + 'epel-9-x86_64')) if ((sys.version_info[0] == 3 and mock_config not in py2only_pb) or (sys.version_info[0] == 2 and mock_config not in py3only_pb and not mock_config.startswith('fedora'))): diff --git a/tools/nightly-tests/test-install/test_mpi.py b/tools/nightly-tests/test-install/test_mpi.py index d968a9432e..df2a748da6 100644 --- a/tools/nightly-tests/test-install/test_mpi.py +++ b/tools/nightly-tests/test-install/test_mpi.py @@ -11,9 +11,10 @@ class Tests(unittest.TestCase): def test_modules_installed(self): """Check MPI-dependent Python modules""" - # Fedora and RHEL 8 only have a Python 3 MPI module; other systems + # Fedora and RHEL 8/9 only have a Python 3 MPI module; other systems # only have Python 2 - if 'fedora' in mock_config or 'epel-8' in mock_config: + if ('fedora' in mock_config or 'epel-8' in mock_config + or 'epel-9' in mock_config): if sys.version_info[0] == 2: self.skipTest("No Python2 support for MPI") elif sys.version_info[0] >= 3: From 34351849b70cd3c0762a655235e19af93c15c493 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Sat, 4 Jun 2022 15:29:12 -0700 Subject: [PATCH 149/155] Exclude more Path attributes --- modules/test/test/standards_exceptions | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/test/test/standards_exceptions b/modules/test/test/standards_exceptions index 6392b47df2..0a3465edc9 100644 --- a/modules/test/test/standards_exceptions +++ b/modules/test/test/standards_exceptions @@ -22,7 +22,8 @@ path_attributes = [ 'is_file', 'is_reserved', 'is_socket', 'is_symlink', 'iterdir', 'joinpath', 'lchmod', 'lstat', 'match', 'mkdir', 'open', 'owner', 'relative_to', 'rename', 'replace', 'resolve', 'rglob', 'rmdir', 'stat', 'symlink_to', - 'touch', 'unlink', 'with_name', 'with_suffix' ] + 'touch', 'unlink', 'with_name', 'with_suffix', 'expanduser', 'hardlink_to', + 'home', 'is_mount', 'is_relative_to', 'readlink', 'samefile', 'with_stem' ] exceptions = ["Path." + x for x in path_attributes] \ + ["TestCase." + x for x in standard_unittest_attributes] \ + ["ApplicationTestCase." + x for x in standard_unittest_attributes] From ecc86814b591eea5ffba48033b4513dd4f1eebde Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Mon, 6 Jun 2022 17:05:54 -0700 Subject: [PATCH 150/155] Set initial size for Mac disk image hdiutil recently started failing with "create failed - error -5341". This seems to be related to running out of space; request more space to try to fix this. --- tools/mac/make-package.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/mac/make-package.sh b/tools/mac/make-package.sh index 8d9400d057..08e1202350 100755 --- a/tools/mac/make-package.sh +++ b/tools/mac/make-package.sh @@ -304,6 +304,7 @@ rm -f Info.plist.$$ Description.plist.$$ echo "Making disk image (.dmg)..." hdiutil create -fs HFS+ -volname "IMP ${VER} for OS X ${TARGET_OSX_VER}" \ + -megabytes 300 \ -srcfolder imp-${VER}-package IMP-${VER}-${TARGET_OSX_VER}.dmg \ || exit 1 hdiutil internet-enable -yes IMP-${VER}-${TARGET_OSX_VER}.dmg || exit 1 From e641b782343e03b343d5c2de25a5197636816c99 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 9 Jun 2022 11:17:57 -0700 Subject: [PATCH 151/155] Link to nbspike repo --- ChangeLog.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/ChangeLog.md b/ChangeLog.md index 7de9c3380f..51fc01fdac 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -19,6 +19,8 @@ ChangeLog {#changelog} - The IMP::core::IncrementalScoringFunction class is now deprecated. Use IMP::core::MonteCarlo::set_score_moved or IMP::ScoringFunction::evaluate_moved instead. +- A new application of IMP is now available: + - [Integrative modeling of nanobody binding modes to the SARS-CoV-2 Spike protein](https://integrativemodeling.org/systems/nbspike) # 2.16.0 - 2021-12-16 # {#changelog_2_16_0} - OpenCubicSpline now throws a ValueException for out-of-range values, to From bdb54f9b94b34a4ffb2d6cb3afbf3a01d0abc0df Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 9 Jun 2022 16:28:55 -0700 Subject: [PATCH 152/155] Squashed 'modules/pmi/' changes from 57c6eaa9b9..56c07d58fd 56c07d58fd Document best-scoring options f03729b5ae Allow writing best-scoring files in mmCIF format 60d342b7a0 Handle tuple/list mismatch 2905c4ee76 Suppress flake8 warning 3c2720f1ca Coerce Path to string 906d9a6fad Don't use Path.open() 8f56236811 Start using pathlib for path manipulation git-subtree-dir: modules/pmi git-subtree-split: 56c07d58fd95f8b00f0f1fe930ffd95a25e14129 --- modules/pmi/pyext/src/macros.py | 26 ++++++++++++--- modules/pmi/pyext/src/mmcif.py | 50 +++++++++++++++------------- modules/pmi/pyext/src/output.py | 4 ++- modules/pmi/test/test_mmcif.py | 46 +++++++++++++------------ modules/pmi/test/test_pdb_writing.py | 30 +++++++++++++++++ 5 files changed, 104 insertions(+), 52 deletions(-) diff --git a/modules/pmi/pyext/src/macros.py b/modules/pmi/pyext/src/macros.py index 80685b67f0..6da459b4a9 100644 --- a/modules/pmi/pyext/src/macros.py +++ b/modules/pmi/pyext/src/macros.py @@ -14,6 +14,10 @@ import IMP.isd import IMP.pmi.dof import os +try: + from pathlib import Path +except ImportError: # Use bundled pathlib on Python 2 without pathlib + from IMP._compat_pathlib import Path import glob from operator import itemgetter from collections import defaultdict @@ -90,6 +94,7 @@ def __init__(self, model, root_hier, initial_rmf_name_suffix="initial", stat_file_name_suffix="stat", best_pdb_name_suffix="model", + mmcif=False, do_clean_first=True, do_create_directories=True, global_output_directory="./", @@ -135,8 +140,14 @@ def __init__(self, model, root_hier, @param replica_exchange_swap Boolean, enable disable temperature swap (Default=True) @param num_sample_rounds Number of rounds of MC/MD per cycle - @param number_of_best_scoring_models Number of top-scoring PDB - models to keep around for analysis + @param number_of_best_scoring_models Number of top-scoring PDB/mmCIF + models to keep around for analysis. + @param mmcif If True, write best scoring models in mmCIF format; + if False (the default), write in legacy PDB format. + @param best_pdb_dir The directory under `global_output_directory` + where best-scoring PDB/mmCIF files are written. + @param best_pdb_name_suffix Part of the file name for best-scoring + PDB/mmCIF files. @param monte_carlo_steps Number of MC steps per round @param self_adaptive self adaptive scheme for Monte Carlo movers @param molecular_dynamics_steps Number of MD steps per round @@ -238,6 +249,7 @@ def __init__(self, model, root_hier, self.vars["write_initial_rmf"] = write_initial_rmf self.vars["initial_rmf_name_suffix"] = initial_rmf_name_suffix self.vars["best_pdb_name_suffix"] = best_pdb_name_suffix + self.vars["mmcif"] = mmcif self.vars["stat_file_name_suffix"] = stat_file_name_suffix self.vars["do_clean_first"] = do_clean_first self.vars["do_create_directories"] = do_create_directories @@ -436,11 +448,13 @@ def execute_macro(self): self.root_hier, self.vars["number_of_best_scoring_models"], replica_exchange=True, + mmcif=self.vars['mmcif'], best_score_file=globaldir + "best.scores.rex.py") + pdbext = ".0.cif" if self.vars['mmcif'] else ".0.pdb" output.write_psf( pdb_dir + "/" + "model.psf", pdb_dir + "/" + - self.vars["best_pdb_name_suffix"] + ".0.pdb") + self.vars["best_pdb_name_suffix"] + pdbext) else: if self.vars["number_of_best_scoring_models"] > 0: for n in range(self.vars["number_of_states"]): @@ -450,11 +464,13 @@ def execute_macro(self): self.root_hiers[n], self.vars["number_of_best_scoring_models"], replica_exchange=True, + mmcif=self.vars['mmcif'], best_score_file=globaldir + "best.scores.rex.py") + pdbext = ".0.cif" if self.vars['mmcif'] else ".0.pdb" output.write_psf( pdb_dir + "/" + str(n) + "/" + "model.psf", pdb_dir + "/" + str(n) + "/" + - self.vars["best_pdb_name_suffix"] + ".0.pdb") + self.vars["best_pdb_name_suffix"] + pdbext) # --------------------------------------------- if self.em_object_for_rmf is not None: @@ -1080,7 +1096,7 @@ def clustering(self, """ # Track provenance information to be added to each output model prov = [] - self._outputdir = os.path.abspath(outputdir) + self._outputdir = Path(outputdir).absolute() self._number_of_clusters = number_of_clusters for p, state in self._protocol_output: p.add_replica_exchange_analysis(state, self, density_custom_ranges) diff --git a/modules/pmi/pyext/src/mmcif.py b/modules/pmi/pyext/src/mmcif.py index 6a3b98afe4..15d5851cc4 100644 --- a/modules/pmi/pyext/src/mmcif.py +++ b/modules/pmi/pyext/src/mmcif.py @@ -26,6 +26,10 @@ import ast import sys import os +try: + from pathlib import Path +except ImportError: # Use bundled pathlib on Python 2 without pathlib + from IMP._compat_pathlib import Path # noqa: F401 import weakref import ihm.location import ihm.dataset @@ -761,7 +765,7 @@ def _make_spheres_atoms(self, particle_infos_for_pdb, o, name, simo): def parse_rmsf_file(self, fname, component): self.rmsf[component] = rmsf = {} - with open(fname) as fh: + with open(str(fname)) as fh: for line in fh: resnum, blocknum, val = line.split() rmsf[int(resnum)] = (int(blocknum), float(val)) @@ -936,15 +940,14 @@ def __init__(self, rex, num_models_begin): self.rex = rex num_models_end = 0 for fname in self.get_all_stat_files(): - with open(fname) as fh: + with open(str(fname)) as fh: num_models_end += len(fh.readlines()) super(_ReplicaExchangeAnalysisPostProcess, self).__init__( feature='RMSD', num_models_begin=num_models_begin, num_models_end=num_models_end) def get_stat_file(self, cluster_num): - return os.path.join(self.rex._outputdir, "cluster.%d" % cluster_num, - 'stat.out') + return self.rex._outputdir / ("cluster.%d" % cluster_num) / 'stat.out' def get_all_stat_files(self): for i in range(self.rex._number_of_clusters): @@ -957,7 +960,7 @@ class _ReplicaExchangeAnalysisEnsemble(ihm.model.Ensemble): num_models_deposited = None # Override base class property def __init__(self, pp, cluster_num, model_group, num_deposit): - with open(pp.get_stat_file(cluster_num)) as fh: + with open(str(pp.get_stat_file(cluster_num))) as fh: num_models = len(fh.readlines()) super(_ReplicaExchangeAnalysisEnsemble, self).__init__( num_models=num_models, @@ -968,27 +971,27 @@ def __init__(self, pp, cluster_num, model_group, num_deposit): self.num_models_deposited = num_deposit def get_rmsf_file(self, component): - return os.path.join(self.post_process.rex._outputdir, - 'cluster.%d' % self.cluster_num, - 'rmsf.%s.dat' % component) + return (self.post_process.rex._outputdir + / ('cluster.%d' % self.cluster_num) + / ('rmsf.%s.dat' % component)) def load_rmsf(self, model, component): fname = self.get_rmsf_file(component) - if os.path.exists(fname): + if fname.exists(): model.parse_rmsf_file(fname, component) def get_localization_density_file(self, fname): - return os.path.join(self.post_process.rex._outputdir, - 'cluster.%d' % self.cluster_num, - '%s.mrc' % fname) + return (self.post_process.rex._outputdir + / ('cluster.%d' % self.cluster_num) + / ('%s.mrc' % fname)) def load_localization_density(self, state, fname, select_tuple, asym_units): fullpath = self.get_localization_density_file(fname) - if os.path.exists(fullpath): + if fullpath.exists(): details = "Localization density for %s %s" \ % (fname, self.model_group.name) - local_file = ihm.location.OutputFileLocation(fullpath, + local_file = ihm.location.OutputFileLocation(str(fullpath), details=details) for s in select_tuple: if isinstance(s, tuple) and len(s) == 3: @@ -1002,14 +1005,13 @@ def load_localization_density(self, state, fname, select_tuple, def load_all_models(self, simo, state): stat_fname = self.post_process.get_stat_file(self.cluster_num) model_num = 0 - with open(stat_fname) as fh: + with open(str(stat_fname)) as fh: stats = ast.literal_eval(fh.readline()) # Correct path - rmf_file = os.path.join(os.path.dirname(stat_fname), - "%d.rmf3" % model_num) + rmf_file = stat_fname.parent / ("%d.rmf3" % model_num) # todo: test with real PMI2 systems - if os.path.exists(rmf_file): - rh = RMF.open_rmf_file_read_only(rmf_file) + if rmf_file.exists(): + rh = RMF.open_rmf_file_read_only(str(rmf_file)) system = state._pmi_object.system IMP.rmf.link_hierarchies(rh, [system.hier]) IMP.rmf.load_frame(fh, RMF.FrameID(0)) @@ -1021,16 +1023,16 @@ def load_all_models(self, simo, state): # todo: also support dRMS precision def _get_precision(self): - precfile = os.path.join(self.post_process.rex._outputdir, - "precision.%d.%d.out" % (self.cluster_num, - self.cluster_num)) - if not os.path.exists(precfile): + precfile = (self.post_process.rex._outputdir / + ("precision.%d.%d.out" % (self.cluster_num, + self.cluster_num))) + if not precfile.exists(): return ihm.unknown # Fail if the precision.x.x.out file doesn't match the cluster r = re.compile( r'All .*/cluster.%d/ average centroid distance ([\d\.]+)' % self.cluster_num) - with open(precfile) as fh: + with open(str(precfile)) as fh: for line in fh: m = r.match(line) if m: diff --git a/modules/pmi/pyext/src/output.py b/modules/pmi/pyext/src/output.py index 737bd85b10..6c24bebafb 100644 --- a/modules/pmi/pyext/src/output.py +++ b/modules/pmi/pyext/src/output.py @@ -171,7 +171,9 @@ def _write_mmcif_internal(flpdb, particle_infos_for_pdb, geometric_center, ci = chain_info[chain_id] if atom_type is None: atom_type = IMP.atom.AT_CA - c = xyz - geometric_center + c = (xyz[0] - geometric_center[0], + xyz[1] - geometric_center[1], + xyz[2] - geometric_center[2]) if write_all_residues_per_bead and all_indexes is not None: for residue_number in all_indexes: lp.write(group_PDB='ATOM', diff --git a/modules/pmi/test/test_mmcif.py b/modules/pmi/test/test_mmcif.py index d2b69d32d6..7a240fb016 100644 --- a/modules/pmi/test/test_mmcif.py +++ b/modules/pmi/test/test_mmcif.py @@ -6,7 +6,10 @@ import IMP.pmi.topology import IMP.pmi.macros import sys -import os +try: + from pathlib import Path +except ImportError: # Use bundled pathlib on Python 2 without pathlib + from IMP._compat_pathlib import Path import ihm.format import ihm.location import ihm.dataset @@ -559,8 +562,8 @@ def test_model_dumper_sphere_rmsf(self): representation) group.append(model) model.name = 'foo' - model.parse_rmsf_file(self.get_input_file_name('test.nup84.rmsf'), - 'Nup84.0') + model.parse_rmsf_file( + Path(self.get_input_file_name('test.nup84.rmsf')), 'Nup84.0') self.assertAlmostEqual(model.get_rmsf('Nup84.0', (1,)), 4.5, delta=1e-4) self.assertRaises(ValueError, model.get_rmsf, 'Nup84.0', (1, 2)) @@ -965,11 +968,11 @@ class DummyRex(object): _number_of_clusters = 2 d = DummyRex() with IMP.test.temporary_directory() as tmpdir: - d._outputdir = tmpdir + d._outputdir = Path(tmpdir) for i in range(d._number_of_clusters): - subdir = os.path.join(tmpdir, 'cluster.%d' % i) - os.mkdir(subdir) - with open(os.path.join(subdir, 'stat.out'), 'w') as fh: + subdir = Path(tmpdir) / ('cluster.%d' % i) + subdir.mkdir() + with open(str(subdir / 'stat.out'), 'w') as fh: # 1 model for first cluster, 2 for second cluster for line in range(i + 1): fh.write('#\n') @@ -1003,18 +1006,18 @@ class DummyGroup(object): comp_to_asym = {'Nup84': None} with IMP.test.temporary_directory() as tmpdir: d = DummyRex() - d._outputdir = tmpdir - subdir = os.path.join(tmpdir, 'cluster.0') - os.mkdir(subdir) + d._outputdir = Path(tmpdir) + subdir = Path(tmpdir) / 'cluster.0' + subdir.mkdir() # Two models - with open(os.path.join(subdir, 'stat.out'), 'w') as fh: + with open(str(subdir / 'stat.out'), 'w') as fh: fh.write("{'modelnum': 0}\n") fh.write("{'modelnum': 1}\n") # Mock localization density file - with open(os.path.join(subdir, 'Nup84.mrc'), 'w') as fh: + with open(str(subdir / 'Nup84.mrc'), 'w') as fh: pass # Mock RMSF file - with open(os.path.join(subdir, 'rmsf.Nup84.dat'), 'w') as fh: + with open(str(subdir / 'rmsf.Nup84.dat'), 'w') as fh: pass pp = IMP.pmi.mmcif._ReplicaExchangeAnalysisPostProcess(d, 45) mg = DummyGroup() @@ -1027,8 +1030,7 @@ class DummyGroup(object): self.assertEqual(e.clustering_feature, 'RMSD') self.assertEqual(e.name, 'dgroup') self.assertEqual(e.get_rmsf_file('Nup84'), - os.path.join(tmpdir, 'cluster.0', - 'rmsf.Nup84.dat')) + Path(tmpdir) / 'cluster.0' / 'rmsf.Nup84.dat') # RMSF that doesn't exist e.load_rmsf(None, 'normsf') # RMSF that does exist @@ -1036,7 +1038,7 @@ class DummyGroup(object): e.load_rmsf(dm, 'Nup84') self.assertEqual(dm.comp, 'Nup84') self.assertEqual(e.get_localization_density_file('Nup84'), - os.path.join(tmpdir, 'cluster.0', 'Nup84.mrc')) + Path(tmpdir) / 'cluster.0' / 'Nup84.mrc') self.assertEqual(len(e.densities), 0) # Density that doesn't exist e.load_localization_density(None, 'noden', [], comp_to_asym) @@ -1048,7 +1050,7 @@ class DummyGroup(object): e.load_localization_density(state, 'Nup84', ['Nup84'], comp_to_asym) self.assertEqual(e.densities[0].file.path, - os.path.join(tmpdir, 'cluster.0', 'Nup84.mrc')) + str(Path(tmpdir) / 'cluster.0' / 'Nup84.mrc')) self.assertEqual( e.densities[0].file.details, 'Localization density for Nup84 dgroup') @@ -1056,7 +1058,7 @@ class DummyGroup(object): self.assertEqual(e._get_precision(), ihm.unknown) self.assertEqual(e.precision, ihm.unknown) # Make precision available - with open(os.path.join(tmpdir, 'precision.0.0.out'), 'w') as fh: + with open(str(Path(tmpdir) / 'precision.0.0.out'), 'w') as fh: fh.write(""" All kmeans_weight_500_2/cluster.0/ average centroid distance 24.3744728893 All kmeans_weight_500_2/cluster.0/ centroid index 49 @@ -1087,11 +1089,11 @@ class DummyRex(object): with IMP.test.temporary_directory() as tmpdir: rex = DummyRex() - rex._outputdir = tmpdir - subdir = os.path.join(tmpdir, 'cluster.0') - os.mkdir(subdir) + rex._outputdir = Path(tmpdir) + subdir = Path(tmpdir) / 'cluster.0' + subdir.mkdir() # Two models - with open(os.path.join(subdir, 'stat.out'), 'w') as fh: + with open(str(subdir / 'stat.out'), 'w') as fh: fh.write("{'modelnum': 0}\n") fh.write("{'modelnum': 1}\n") prot = DummyProtocolStep() diff --git a/modules/pmi/test/test_pdb_writing.py b/modules/pmi/test/test_pdb_writing.py index 0cc1f1a15a..63f4762ef7 100644 --- a/modules/pmi/test/test_pdb_writing.py +++ b/modules/pmi/test/test_pdb_writing.py @@ -204,6 +204,19 @@ def test_pdb_from_rex(self): self.assertEqual(len(IMP.core.get_leaves(mhtest)),17) shutil.rmtree("pdb_test/") + rex = IMP.pmi.macros.ReplicaExchange0( + mdl, root_hier=root_hier, + monte_carlo_sample_objects=dof.get_movers(), number_of_frames=3, + monte_carlo_steps=10, number_of_best_scoring_models=3, + global_output_directory='mmcif_test/', mmcif=True, + replica_exchange_object=rem) + rex.execute_macro() + for i in range(3): + self.assertTrue(os.path.isfile('mmcif_test/pdbs/model.%i.cif' % i)) + mhtest = IMP.atom.read_mmcif('mmcif_test/pdbs/model.0.cif', mdl) + self.assertEqual(len(IMP.core.get_leaves(mhtest)), 17) + shutil.rmtree("mmcif_test/") + def test_pdb_multistate(self): """Test PDB writing in PMI2 from replica exchange""" mdl = IMP.Model() @@ -246,5 +259,22 @@ def test_pdb_multistate(self): self.assertEqual(len(IMP.core.get_leaves(testB)),8) shutil.rmtree("pdb_test/") + rex = IMP.pmi.macros.ReplicaExchange0( + mdl, root_hier=root_hier, + monte_carlo_sample_objects=dof.get_movers(), number_of_frames=3, + monte_carlo_steps=10, number_of_best_scoring_models=3, + global_output_directory='mmcif_test/', mmcif=True, + replica_exchange_object=rem) + rex.execute_macro() + for i in range(3): + self.assertTrue(os.path.isfile('mmcif_test/pdbs/0/model.%i.cif'%i)) + self.assertTrue(os.path.isfile('mmcif_test/pdbs/1/model.%i.cif'%i)) + testA = IMP.atom.read_mmcif('mmcif_test/pdbs/0/model.0.cif', mdl) + self.assertEqual(len(IMP.core.get_leaves(testA)), 53) + testB = IMP.atom.read_mmcif('mmcif_test/pdbs/1/model.0.cif', mdl) + self.assertEqual(len(IMP.core.get_leaves(testB)), 8) + shutil.rmtree("mmcif_test/") + + if __name__ == '__main__': IMP.test.main() From b7c8dc7fe64292bf328b6cffb26cf2de1b431640 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 9 Jun 2022 17:28:50 -0700 Subject: [PATCH 153/155] Note that we build for RHEL9 now --- ChangeLog.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/ChangeLog.md b/ChangeLog.md index 51fc01fdac..471332e411 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -9,7 +9,8 @@ ChangeLog {#changelog} functions instead to calculate coarse cross correlation. - The Windows .exe installer no longer supports Python 2 (it works with Python 3.6 through 3.10). -- A binary package is now provided for Ubuntu 22.04 LTS, Jammy Jellyfish. +- Binary packages are now provided for Ubuntu 22.04 LTS, Jammy Jellyfish + and RedHat Enterprise Linux 9 (and variants, such as Rocky or Alma). - IMP now requires a C++11 compiler and SWIG 3 (or later) to build. Most recent compilers should support C++11, such as gcc, clang or MS Visual Studio 2012 or later. Various IMP macro and header workarounds From ad3ca918cbdb03b867be6e6c67af446455b3ac81 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 9 Jun 2022 17:30:58 -0700 Subject: [PATCH 154/155] Prepare for 2.17.0 release --- ChangeLog.md | 2 +- tools/rpm/IMP.spec.in | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/ChangeLog.md b/ChangeLog.md index 471332e411..c567b5236f 100644 --- a/ChangeLog.md +++ b/ChangeLog.md @@ -1,7 +1,7 @@ ChangeLog {#changelog} ========= -# HEAD +# 2.17.0 - 2022-06-23 # {#changelog_2_17_0} - IMP::atom::Selection no longer checks that the passed hierarchies are valid, as this can be quite computationally expensive. If in doubt, call IMP::atom::Hierarchy::get_is_valid() on each one first. diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in index 4577a68b71..2552dcbe1a 100644 --- a/tools/rpm/IMP.spec.in +++ b/tools/rpm/IMP.spec.in @@ -532,6 +532,9 @@ find ${RPM_BUILD_ROOT}%{_prefix}/share/IMP/tools -name '*.py' -exec perl -pi -e %endif %changelog +* Thu Jun 23 2022 Ben Webb 2.17.0-1 +- 2.17.0 release. + * Thu Dec 16 2021 Ben Webb 2.16.0-1 - 2.16.0 release. From a25a47b3152f246cdcd05609ae2894618708a322 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Thu, 9 Jun 2022 17:38:04 -0700 Subject: [PATCH 155/155] Add version for 2.17.0 release --- VERSION | 1 + 1 file changed, 1 insertion(+) create mode 100644 VERSION diff --git a/VERSION b/VERSION new file mode 100644 index 0000000000..d76bd2ba3e --- /dev/null +++ b/VERSION @@ -0,0 +1 @@ +2.17.0