From 2e04017a02c18f91c07add96e45a1729c9d4ebb4 Mon Sep 17 00:00:00 2001 From: Niccolo Date: Tue, 14 May 2024 14:17:37 -0700 Subject: [PATCH] Fixed error in importing cosolvkit with python3.9 --- README.md | 2 +- cosolvkit/cosolvent_system.py | 39 +-- cosolvkit_env.yml | 462 ---------------------------------- setup.py | 2 +- 4 files changed, 22 insertions(+), 483 deletions(-) delete mode 100644 cosolvkit_env.yml diff --git a/README.md b/README.md index b6fe2ee..5b1a4ee 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) [![License: LGPL v2.1](https://img.shields.io/badge/License-LGPL_v2.1-green.svg)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html) [![PyPI - Version](https://img.shields.io/pypi/v/cosolvkit)](https://pypi.org/project/cosolvkit/0.4.4/) [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/) +[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) [![License: LGPL v2.1](https://img.shields.io/badge/License-LGPL_v2.1-green.svg)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html) [![PyPI - Version](https://img.shields.io/pypi/v/cosolvkit)](https://pypi.org/project/cosolvkit/0.4.5/) [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/) [![Documentation Status](https://readthedocs.org/projects/cosolvkit/badge/?version=latest)](https://cosolvkit.readthedocs.io/en/latest/?badge=latest) diff --git a/cosolvkit/cosolvent_system.py b/cosolvkit/cosolvent_system.py index 56598ac..b310c52 100644 --- a/cosolvkit/cosolvent_system.py +++ b/cosolvkit/cosolvent_system.py @@ -3,6 +3,7 @@ import sys import io from collections import defaultdict +from typing import Union import numpy as np from scipy import spatial from scipy.stats import qmc @@ -635,8 +636,8 @@ def _create_system(self, forcefield: app.forcefield, topology: app.Topology) -> def add_cosolvents(self, cosolvents: dict, vectors: tuple[Vec3, Vec3, Vec3], - lowerBound: openmmunit.Quantity | Vec3, - upperBound: openmmunit.Quantity | Vec3, + lowerBound: Union[openmmunit.Quantity, Vec3], + upperBound: Union[openmmunit.Quantity, Vec3], receptor_positions: list) -> dict: """This function adds the desired number of cosolvent molecules using the halton sequence to generate random uniformly distributed points inside the grid where to place the cosolvent molecules. @@ -648,9 +649,9 @@ def add_cosolvents(self, :param vectors: vectors defining the simulation box :type vectors: tuple[openmm.Vec3, openmm.Vec3, openmm.Vec3] :param lowerBound: lower bound of the simulation box - :type lowerBound: openmm.unit.Quantity | Vec3 + :type lowerBound: Union[openmm.unit.Quantity, Vec3] :param upperBound: upper bound of the simulation box - :type upperBound: openmm.unit.Quantity | Vec3 + :type upperBound: [openmm.unit.Quantity, Vec3] :param receptor_positions: list of 3D coordinates of the receptor :type receptor_positions: list :return: keys are cosolvent molecules and values are 3D coordinates of the newly added cosolvent molecules @@ -758,8 +759,8 @@ def accept_reject(self, halton: list, kdtree: spatial.cKDTree, valid_ids: list, - lowerBound: openmmunit.Quantity | Vec3, - upperBound: openmmunit.Quantity | Vec3, + lowerBound: Union[openmmunit.Quantity, Vec3], + upperBound: Union[openmmunit.Quantity, Vec3], protein_kdtree: spatial.cKDTree) -> tuple[np.ndarray, list]: """Accepts or reject the halton move. A random halton point is selected and checked, if accepted the cosolvent is placed there, otherwise a local search is performed in the neighbors of the point @@ -776,9 +777,9 @@ def accept_reject(self, :param valid_ids: valid halton indices :type valid_ids: list :param lowerBound: lower bound of the box - :type lowerBound: openmm.unit.Quantity | Vec3 + :type lowerBound: Union[openmm.unit.Quantity, Vec3] :param upperBound: upper bound of the box - :type upperBound: openmm.unit.Quantity | Vec3 + :type upperBound: Union[openmm.unit.Quantity, Vec3] :param protein_kdtree: tree of the protein's positions :type protein_kdtree: spatial.cKDTree :return: accepted coordinates for the cosolvent and the used halton ids @@ -812,16 +813,16 @@ def accept_reject(self, def is_in_box(self, xyzs: np.ndarray, - lowerBound: openmmunit.Quantity | Vec3, - upperBound: openmmunit.Quantity | Vec3) -> bool: + lowerBound: Union[openmmunit.Quantity, Vec3], + upperBound: Union[openmmunit.Quantity, Vec3]) -> bool: """Checks if the coordinates are in the box or not :param xyzs: coordinates to check :type xyzs: np.ndarray :param lowerBound: lower bound of the box - :type lowerBound: openmmunit.Quantity | Vec3 + :type lowerBound: Union[openmmunit.Quantity, Vec3] :param upperBound: upper bound of the box - :type upperBound: openmmunit.Quantity | Vec3 + :type upperBound: Union[openmmunit.Quantity, Vec3] :return: True if all the coordinates are in the box, Flase otherwise :rtype: bool """ @@ -902,13 +903,13 @@ def calculate_mol_volume(self, mol_positions: np.ndarray) -> float: points = np.unique(np.hstack(query)).astype(int) return round(len(points)*mesh_step**3, 2) - def fitting_checks(self) -> float | None: + def fitting_checks(self) -> Union[float, None]: """Checks if the required cosolvents can fit in the box and do not exceed the 50% of the available fillable volume (volume not occupied by the receptor, if present). :return: available volume if the cosolvents can fit, None otherwise - :rtype: float | None + :rtype: Union[float, None] """ prot_volume = 0 if self.receptor: @@ -928,11 +929,11 @@ def fitting_checks(self) -> float | None: return None return empty_available_volume - def liters_to_cubic_nanometers(self, liters: float | openmmunit.Quantity) -> float: + def liters_to_cubic_nanometers(self, liters: Union[float, openmmunit.Quantity]) -> float: """Converts liters in cubic nanometers :param liters: volume to convert - :type liters: float | openmm.unit.Quantity + :type liters: Union[float, openmm.unit.Quantity] :return: converted volume :rtype: float """ @@ -1006,8 +1007,8 @@ def _build_box(self, padding: openmmunit.Quantity, radius: openmmunit.Quantity = None) -> tuple[tuple[Vec3, Vec3, Vec3], Vec3, - openmmunit.Quantity | Vec3, - openmmunit.Quantity | Vec3]: + Union[openmmunit.Quantity, Vec3], + Union[openmmunit.Quantity, Vec3]]: """Builds the simulation box. If a receptor is passed it is used alongside with the padding parameter to build the box automatically, otherwise a radius has to be passed. If no receptor the box is centered on the point [0, 0, 0]. @@ -1021,7 +1022,7 @@ def _build_box(self, :return: The first element returned is a tuple containing the three vectors describing the simulation box. The second element is the box itself. Third and fourth elements are the lower and upper bound of the simulation box. - :rtype: tuple[tuple[Vec3, Vec3, Vec3], Vec3, openmmunit.Quantity | Vec3, openmmunit.Quantity | Vec3] + :rtype: tuple[tuple[Vec3, Vec3, Vec3], Vec3, Union[openmmunit.Quantity, Vec3], Union[openmmunit.Quantity, Vec3]] """ padding = padding.value_in_unit(openmmunit.nanometer) if positions is not None: diff --git a/cosolvkit_env.yml b/cosolvkit_env.yml deleted file mode 100644 index 3dfb386..0000000 --- a/cosolvkit_env.yml +++ /dev/null @@ -1,462 +0,0 @@ -name: cosolvkit -channels: - - conda-forge -dependencies: - - _libgcc_mutex=0.1=conda_forge - - _openmp_mutex=4.5=2_gnu - - absl-py=2.1.0=pyhd8ed1ab_0 - - aiohttp=3.9.5=py310h2372a71_0 - - aiosignal=1.3.1=pyhd8ed1ab_0 - - alsa-lib=1.2.11=hd590300_1 - - ambertools=22.5=py310hd182041_0 - - anyio=4.3.0=pyhd8ed1ab_0 - - argon2-cffi=23.1.0=pyhd8ed1ab_0 - - argon2-cffi-bindings=21.2.0=py310h2372a71_4 - - arpack=3.7.0=hdefa2d7_2 - - arrow=1.3.0=pyhd8ed1ab_0 - - asttokens=2.4.1=pyhd8ed1ab_0 - 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- libgrpc=1.54.3=hb20ce57_0 - - libiconv=1.17=hd590300_2 - - libjpeg-turbo=3.0.0=hd590300_1 - - liblapack=3.9.0=22_linux64_openblas - - liblapacke=3.9.0=22_linux64_openblas - - libllvm15=15.0.7=hb3ce162_4 - - libllvm18=18.1.4=h2448989_0 - - libnetcdf=4.9.2=nompi_h9612171_113 - - libnghttp2=1.58.0=h47da74e_1 - - libnsl=2.0.1=hd590300_0 - - libnuma=2.0.18=hd590300_0 - - libogg=1.3.4=h7f98852_1 - - libopenblas=0.3.27=pthreads_h413a1c8_0 - - libopus=1.3.1=h7f98852_1 - - libpng=1.6.43=h2797004_0 - - libpq=16.2=h33b98f1_1 - - libprotobuf=3.21.12=hfc55251_2 - - libsndfile=1.2.2=hc60ed4a_1 - - libsodium=1.0.18=h36c2ea0_1 - - libsqlite=3.45.3=h2797004_0 - - libssh2=1.11.0=h0841786_0 - - libstdcxx-ng=13.2.0=h95c4c6d_6 - - libsystemd0=255=h3516f8a_1 - - libthrift=0.18.1=h8fd135c_2 - - libtiff=4.6.0=h1dd3fc0_3 - - libutf8proc=2.8.0=h166bdaf_0 - - libuuid=2.38.1=h0b41bf4_0 - - libuv=1.48.0=hd590300_0 - - libvorbis=1.3.7=h9c3ff4c_0 - - libwebp-base=1.4.0=hd590300_0 - - libxcb=1.15=h0b41bf4_0 - - libxcrypt=4.4.36=hd590300_1 - - libxkbcommon=1.7.0=h662e7e4_0 - - libxml2=2.12.6=h232c23b_2 - - libxslt=1.1.39=h76b75d6_0 - - libzip=1.10.1=h2629f0a_3 - - libzlib=1.2.13=hd590300_5 - - lxml=5.2.1=py310h6a33d3d_0 - - lz4-c=1.9.4=hcb278e6_0 - - lzo=2.10=hd590300_1001 - - markdown=3.6=pyhd8ed1ab_0 - - markupsafe=2.1.5=py310h2372a71_0 - - matplotlib-base=3.8.4=py310h62c0568_0 - - matplotlib-inline=0.1.7=pyhd8ed1ab_0 - - mda-xdrlib=0.2.0=pyhd8ed1ab_0 - - mdanalysis=2.7.0=py310hcc13569_1 - - mdtraj=1.9.9=py310h523e8d7_1 - - metis=5.1.1=h59595ed_2 - - mistune=3.0.2=pyhd8ed1ab_0 - - ml_dtypes=0.2.0=py310hcc13569_2 - - mmtf-python=1.1.3=pyhd8ed1ab_0 - - mpc=1.3.1=hfe3b2da_0 - - mpfr=4.2.1=h9458935_1 - - mpg123=1.32.6=h59595ed_0 - - mpmath=1.3.0=pyhd8ed1ab_0 - - mrcfile=1.5.0=pyhd8ed1ab_0 - - msgpack-python=1.0.7=py310hd41b1e2_0 - - multidict=6.0.5=py310h2372a71_0 - - munkres=1.1.4=pyh9f0ad1d_0 - - mysql-common=8.3.0=hf1915f5_4 - - mysql-libs=8.3.0=hca2cd23_4 - - nbclient=0.10.0=pyhd8ed1ab_0 - - nbconvert-core=7.16.3=pyhd8ed1ab_1 - - nbformat=5.10.4=pyhd8ed1ab_0 - - nccl=2.21.5.1=h6103f9b_0 - - ncurses=6.4.20240210=h59595ed_0 - - nest-asyncio=1.6.0=pyhd8ed1ab_0 - - netcdf-fortran=4.6.1=nompi_hacb5139_103 - - netcdf4=1.6.5=nompi_py310hba70d50_100 - - networkx=3.3=pyhd8ed1ab_1 - - nglview=3.1.2=pyh15ce09e_0 - - nomkl=1.0=h5ca1d4c_0 - - notebook=7.1.3=pyhd8ed1ab_0 - - notebook-shim=0.2.4=pyhd8ed1ab_0 - - nspr=4.35=h27087fc_0 - - nss=3.98=h1d7d5a4_0 - - numexpr=2.9.0=py310hc2d3c2e_100 - - numpy=1.26.4=py310hb13e2d6_0 - - oauthlib=3.2.2=pyhd8ed1ab_0 - - ocl-icd=2.3.2=hd590300_1 - - ocl-icd-system=1.0.0=1 - - openff-amber-ff-ports=0.0.4=pyhca7485f_0 - - openff-forcefields=2024.04.0=pyhca7485f_0 - - openff-interchange=0.3.18=pyhd8ed1ab_0 - - openff-interchange-base=0.3.18=pyhd8ed1ab_0 - - openff-models=0.1.2=pyhca7485f_0 - - openff-toolkit=0.14.5=pyhd8ed1ab_1 - - openff-toolkit-base=0.14.5=pyhd8ed1ab_1 - - openff-units=0.2.2=pyhca7485f_0 - - openff-utilities=0.1.12=pyhd8ed1ab_0 - - openjpeg=2.5.2=h488ebb8_0 - - openmm=8.1.1=py310h43b6314_1 - - openmmforcefields=0.12.0=pyhd8ed1ab_0 - - openssl=3.2.1=hd590300_1 - - opt_einsum=3.3.0=pyhc1e730c_2 - - orc=1.9.0=h2f23424_1 - - overrides=7.7.0=pyhd8ed1ab_0 - - packaging=24.0=pyhd8ed1ab_0 - - packmol=20.010=h86c2bf4_0 - - pandas=1.4.4=py310h769672d_0 - - pandocfilters=1.5.0=pyhd8ed1ab_0 - - panedr=0.8.0=pyhd8ed1ab_0 - - parmed=4.2.2=py310hc6cd4ac_1 - - parso=0.8.4=pyhd8ed1ab_0 - - patsy=0.5.6=pyhd8ed1ab_0 - - pcre2=10.43=hcad00b1_0 - - pdbfixer=1.9=pyh1a96a4e_0 - - perl=5.32.1=7_hd590300_perl5 - - pexpect=4.9.0=pyhd8ed1ab_0 - - pickleshare=0.7.5=py_1003 - - pillow=10.3.0=py310hf73ecf8_0 - - pint=0.23=pyhd8ed1ab_0 - - pip=24.0=pyhd8ed1ab_0 - - pixman=0.43.2=h59595ed_0 - - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1 - - platformdirs=4.2.1=pyhd8ed1ab_0 - - plotly=5.21.0=pyhd8ed1ab_0 - - ply=3.11=pyhd8ed1ab_2 - - pmw=2.0.1=py310hff52083_1008 - - prometheus_client=0.20.0=pyhd8ed1ab_0 - - prompt-toolkit=3.0.42=pyha770c72_0 - - protobuf=4.21.12=py310heca2aa9_0 - - psutil=5.9.8=py310h2372a71_0 - - pthread-stubs=0.4=h36c2ea0_1001 - - ptyprocess=0.7.0=pyhd3deb0d_0 - - pulseaudio-client=17.0=hb77b528_0 - - pure_eval=0.2.2=pyhd8ed1ab_0 - - py-cpuinfo=9.0.0=pyhd8ed1ab_0 - - pyarrow=12.0.1=py310h0576679_8_cpu - - pyasn1=0.6.0=pyhd8ed1ab_0 - - pyasn1-modules=0.4.0=pyhd8ed1ab_0 - - pycairo=1.26.0=py310hda9f760_0 - - pycparser=2.22=pyhd8ed1ab_0 - - pydantic=1.10.14=py310h2372a71_0 - - pyedr=0.8.0=pyhd8ed1ab_0 - - pygments=2.17.2=pyhd8ed1ab_0 - - pyjwt=2.8.0=pyhd8ed1ab_1 - - pymol-open-source=3.0.0=py310h530ea78_7 - - pyopenssl=24.0.0=pyhd8ed1ab_0 - - pyparsing=3.1.2=pyhd8ed1ab_0 - - pyqt=5.15.9=py310h04931ad_5 - - pyqt5-sip=12.12.2=py310hc6cd4ac_5 - - pysocks=1.7.1=pyha2e5f31_6 - - pytables=3.9.2=py310hd76cd5d_2 - - python=3.10.14=hd12c33a_0_cpython - - python-constraint=1.4.0=py_0 - - python-dateutil=2.9.0=pyhd8ed1ab_0 - - python-fastjsonschema=2.19.1=pyhd8ed1ab_0 - - python-flatbuffers=24.3.25=pyh59ac667_0 - - python-json-logger=2.0.7=pyhd8ed1ab_0 - - python_abi=3.10=4_cp310 - - pytng=0.3.1=py310h7d11597_1 - - pytorch=2.0.0=cpu_generic_py310h7ffd2bf_1 - - pytz=2024.1=pyhd8ed1ab_0 - - pyu2f=0.1.5=pyhd8ed1ab_0 - - pyyaml=6.0.1=py310h2372a71_1 - - pyzmq=26.0.2=py310h6883aea_0 - - qcelemental=0.27.1=pyhd8ed1ab_0 - - qcportal=0.15.8=pyhd8ed1ab_1 - - qt-main=5.15.8=hc9dc06e_21 - - rdkit=2023.03.3=py310h399bcf7_0 - - rdma-core=28.9=h59595ed_1 - - re2=2023.03.02=h8c504da_0 - - readline=8.2=h8228510_1 - - referencing=0.35.0=pyhd8ed1ab_0 - - reportlab=4.1.0=py310h2372a71_0 - - requests=2.31.0=pyhd8ed1ab_0 - - requests-oauthlib=2.0.0=pyhd8ed1ab_0 - - rfc3339-validator=0.1.4=pyhd8ed1ab_0 - - rfc3986-validator=0.1.1=pyh9f0ad1d_0 - - rlpycairo=0.2.0=pyhd8ed1ab_0 - - rpds-py=0.18.0=py310hcb5633a_0 - - rsa=4.9=pyhd8ed1ab_0 - - s2n=1.3.49=h06160fa_0 - - scikit-learn=1.4.2=py310h1fdf081_0 - - scipy=1.13.0=py310hb13e2d6_0 - - seaborn=0.13.2=hd8ed1ab_0 - - seaborn-base=0.13.2=pyhd8ed1ab_0 - - send2trash=1.8.3=pyh0d859eb_0 - - setuptools=69.5.1=pyhd8ed1ab_0 - - sip=6.7.12=py310hc6cd4ac_0 - - six=1.16.0=pyh6c4a22f_0 - - sleef=3.5.1=h9b69904_2 - - smirnoff99frosst=1.1.0=pyh44b312d_0 - - snappy=1.1.10=hdb0a2a9_1 - - sniffio=1.3.1=pyhd8ed1ab_0 - - soupsieve=2.5=pyhd8ed1ab_1 - - sphinx - - sphinx_rtd_theme - - sqlalchemy=2.0.29=py310h2372a71_0 - - stack_data=0.6.2=pyhd8ed1ab_0 - - statsmodels=0.14.1=py310h1f7b6fc_0 - - sympy=1.12=pypyh9d50eac_103 - - tenacity=8.2.3=pyhd8ed1ab_0 - - tensorboard=2.14.1=pyhd8ed1ab_0 - - tensorboard-data-server=0.7.0=py310h75e40e8_1 - - tensorflow=2.14.0=cuda118py310h148f8e3_0 - - tensorflow-base=2.14.0=cuda118py310h2e5981e_0 - - tensorflow-estimator=2.14.0=cuda118py310ha99e61b_0 - - termcolor=2.4.0=pyhd8ed1ab_0 - - terminado=0.18.1=pyh0d859eb_0 - - threadpoolctl=3.5.0=pyhc1e730c_0 - - tidynamics=1.1.2=pyhd8ed1ab_0 - - tinycss2=1.3.0=pyhd8ed1ab_0 - - tinydb=4.8.0=pyhd8ed1ab_0 - - tk=8.6.13=noxft_h4845f30_101 - - toml=0.10.2=pyhd8ed1ab_0 - - tomli=2.0.1=pyhd8ed1ab_0 - - tornado=6.4=py310h2372a71_0 - - tqdm=4.66.2=pyhd8ed1ab_0 - - traitlets=5.14.3=pyhd8ed1ab_0 - - types-python-dateutil=2.9.0.20240316=pyhd8ed1ab_0 - - typing-extensions=4.11.0=hd8ed1ab_0 - - typing_extensions=4.11.0=pyha770c72_0 - - typing_utils=0.1.0=pyhd8ed1ab_0 - - tzdata=2024a=h0c530f3_0 - - ucx=1.14.1=h64cca9d_5 - - unicodedata2=15.1.0=py310h2372a71_0 - - uri-template=1.3.0=pyhd8ed1ab_0 - - urllib3=2.2.1=pyhd8ed1ab_0 - - validators=0.28.1=pyhd8ed1ab_0 - - wcwidth=0.2.13=pyhd8ed1ab_0 - - webcolors=1.13=pyhd8ed1ab_0 - - webencodings=0.5.1=pyhd8ed1ab_2 - - websocket-client=1.8.0=pyhd8ed1ab_0 - - werkzeug=3.0.2=pyhd8ed1ab_0 - - wheel=0.43.0=pyhd8ed1ab_1 - - widgetsnbextension=4.0.10=pyhd8ed1ab_0 - - wrapt=1.14.1=py310h5764c6d_1 - - xcb-util=0.4.0=hd590300_1 - - xcb-util-image=0.4.0=h8ee46fc_1 - - xcb-util-keysyms=0.4.0=h8ee46fc_1 - - xcb-util-renderutil=0.3.9=hd590300_1 - - xcb-util-wm=0.4.1=h8ee46fc_1 - - xkeyboard-config=2.41=hd590300_0 - - xmltodict=0.13.0=pyhd8ed1ab_0 - - xorg-kbproto=1.0.7=h7f98852_1002 - - xorg-libice=1.1.1=hd590300_0 - - xorg-libsm=1.2.4=h7391055_0 - - xorg-libx11=1.8.9=h8ee46fc_0 - - xorg-libxau=1.0.11=hd590300_0 - - xorg-libxdmcp=1.1.3=h7f98852_0 - - xorg-libxext=1.3.4=h0b41bf4_2 - - xorg-libxrender=0.9.11=hd590300_0 - - xorg-libxt=1.3.0=hd590300_1 - - xorg-renderproto=0.11.1=h7f98852_1002 - - xorg-xextproto=7.3.0=h0b41bf4_1003 - - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002 - - xorg-xproto=7.0.31=h7f98852_1007 - - xz=5.2.6=h166bdaf_0 - - yaml=0.2.5=h7f98852_2 - - yarl=1.9.4=py310h2372a71_0 - - zeromq=4.3.5=h59595ed_1 - - zipp=3.17.0=pyhd8ed1ab_0 - - zlib=1.2.13=hd590300_5 - - zlib-ng=2.0.7=h0b41bf4_0 - - zstd=1.5.5=hfc55251_0 - - pip: - - amberlite==22.0 - - amberutils==21.0 - - mmpbsa-py==16.0 - - packmol-memgen==1.2.3rc0 - - pdb4amber==22.0 - - pytraj==2.0.6 - - sander==22.0 \ No newline at end of file diff --git a/setup.py b/setup.py index 94b93e5..9ea14ec 100644 --- a/setup.py +++ b/setup.py @@ -18,7 +18,7 @@ def find_files(directory): setup(name="cosolvkit", - version='0.4.4', + version='0.4.5', description="CosolvKit", author="Niccolo Bruciaferri, Jerome Eberhardt", author_email="forli@scripps.edu",