From 7bc5bc07c6d3a50fc1a734177ee67b7a0435db74 Mon Sep 17 00:00:00 2001 From: DLS Jenkins Date: Thu, 14 Nov 2024 16:46:44 +0000 Subject: [PATCH] htdocs update (master) --- _sources/about.rst.txt | 16 ++++++++++++ _sources/index.rst.txt | 11 ++++++++ _sources/publications.rst.txt | 8 ++++++ about.html | 14 ++++++++++ index.html | 8 ++++++ publications.html | 48 +++++++++++++++++++++++++++++++++++ searchindex.js | 2 +- 7 files changed, 106 insertions(+), 1 deletion(-) diff --git a/_sources/about.rst.txt b/_sources/about.rst.txt index 1b5e03b0..8d9d3a12 100644 --- a/_sources/about.rst.txt +++ b/_sources/about.rst.txt @@ -2,6 +2,22 @@ About +++++ +Atomic structures are vital for scientific research. From understanding +the mechanisms of biology to the design of new materials for industrial applications, +knowing the placement of atoms in a molecule assists in the control of disease progression, +drug design, the development of therapies such as vaccines, building new compounds +for better batteries, and finding new methods of carbon sequestration. + +Crystallography is one of the prime technologies used to generate high quality structures, +generated from crystallographic data collected at large facilities like synchrotrons and +X-ray free electron lasers, on large micro electron diffraction instruments, at neutron +sources, or at home in a lab. At these facilities and instruments, crystals are either +rotated in a beam of photons, neutrons, or electrons, or are exposed one at a time in a +serial experiment, and diffraction data from detectors are collected and stored in image +files. The DIALS software package (Diffraction Integration for Advanced Light Sources) is +used throughout the world for processing crystallographic data in automated pipelines or +through graphical user interfaces. + The DIALS software is developed in a fully open-source, collaborative environment. The main development teams are based at `Diamond Light Source`_ and `CCP4`_, in the UK, and at `Lawrence Berkeley National Laboratory`_, USA. diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt index dd9febd1..30df6a5c 100644 --- a/_sources/index.rst.txt +++ b/_sources/index.rst.txt @@ -42,6 +42,17 @@ For feature requests, bug reports or any other information, please contact the DIALS developers at dials-support@lists.sourceforge.net, or post an `issue`_. +Citing DIALS +============ + +Researchers using DIALS to process their data should cite the DIALS publication: + +**DIALS: implementation and evaluation of a new integration package**. +Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G (2018). +Acta Crystallogr D Struct Biol 74, 85-97 + +To acknowledge direct support from the :ref:`DIALS Resource`, such as when Resource staff assist with data collection or processing, or to acknowledge DIALS software integration at a facility or instrument, please acknowledge NiH grant R24GM154040. + Funding ======= diff --git a/_sources/publications.rst.txt b/_sources/publications.rst.txt index b3ab62d7..63348bc7 100644 --- a/_sources/publications.rst.txt +++ b/_sources/publications.rst.txt @@ -10,6 +10,7 @@ DIALS Journal Articles * .. pubmed:: 35647922 xia2.multiplex * .. pubmed:: 34747533 DIALS as a toolkit * .. pubmed:: 32254063 dials.scale +* .. pubmed:: 31692470 XFEL error modeling * .. pubmed:: 30950396 How best to use photons * .. pubmed:: 30198898 Serial crystallography * .. pubmed:: 29872002 Electron diffraction @@ -29,7 +30,14 @@ DIALS Journal Articles DIALS Application to XFEL Crystallography ----------------------------------------- +* .. pubmed:: 37797025 ribonucleotide reductase R2 protein radical +* .. pubmed:: 37138085 PSII O2 formation * .. pubmed:: 35046599 Chemical Crystallography at XFELs +* .. pubmed:: 30405241 PSII Kok cycle +* .. pubmed:: 28835537 M2 proton channel +* .. pubmed:: 27871088 PSII RT +* .. pubmed:: 27680699 De novo phasing +* .. pubmed:: 26422513 Multitemperature dynamics * .. pubmed:: 26352473 synuclein * .. pubmed:: 26280336 synaptotagmin-SNARE * .. pubmed:: 26057680 Ginn 2015b diff --git a/about.html b/about.html index f8069184..8337ab2c 100644 --- a/about.html +++ b/about.html @@ -47,6 +47,20 @@

About

+

Atomic structures are vital for scientific research. From understanding +the mechanisms of biology to the design of new materials for industrial applications, +knowing the placement of atoms in a molecule assists in the control of disease progression, +drug design, the development of therapies such as vaccines, building new compounds +for better batteries, and finding new methods of carbon sequestration.

+

Crystallography is one of the prime technologies used to generate high quality structures, +generated from crystallographic data collected at large facilities like synchrotrons and +X-ray free electron lasers, on large micro electron diffraction instruments, at neutron +sources, or at home in a lab. At these facilities and instruments, crystals are either +rotated in a beam of photons, neutrons, or electrons, or are exposed one at a time in a +serial experiment, and diffraction data from detectors are collected and stored in image +files. The DIALS software package (Diffraction Integration for Advanced Light Sources) is +used throughout the world for processing crystallographic data in automated pipelines or +through graphical user interfaces.

The DIALS software is developed in a fully open-source, collaborative environment. The main development teams are based at Diamond Light Source and CCP4, in the UK, and at Lawrence Berkeley National Laboratory, USA. diff --git a/index.html b/index.html index 50c24137..4aca1a10 100644 --- a/index.html +++ b/index.html @@ -67,6 +67,14 @@

Contact¶ the DIALS developers at dials-support@lists.sourceforge.net, or post an issue.

+
+

Citing DIALS

+

Researchers using DIALS to process their data should cite the DIALS publication:

+

DIALS: implementation and evaluation of a new integration package. +Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G (2018). +Acta Crystallogr D Struct Biol 74, 85-97

+

To acknowledge direct support from the DIALS Resource, such as when Resource staff assist with data collection or processing, or to acknowledge DIALS software integration at a facility or instrument, please acknowledge NiH grant R24GM154040.

+

Funding

DIALS development at Diamond Light Source is performed by employees of diff --git a/publications.html b/publications.html index ba22041b..3c6f2f2e 100644 --- a/publications.html +++ b/publications.html @@ -75,6 +75,12 @@

DIALS Journal Articles
  • +
    SAD phasing of XFEL data depends critically on the error model
    +
    Brewster AS, Bhowmick A, Bolotovsky R, Mendez D, Zwart PH, Sauter NK.
    +
    Acta Crystallogr D Struct Biol 75, 959-968 (01 Nov 2019). [PMID:31692470] [PMC reprint: PMC6834081]
    +
    +
    • +
  • How best to use photons
    Winter G, Gildea RJ, Paterson NG, Beale J, Gerstel M, Axford D, Vollmar M, McAuley KE, Owen RL, Flaig R, Ashton AW, Hall DR.
    Acta Crystallogr D Struct Biol 75, 242-261 (01 Mar 2019). [PMID:30950396] [PMC reprint: PMC6450062]
    @@ -159,12 +165,54 @@

    DIALS Journal ArticlesDIALS Application to XFEL Crystallography

    • +
      Structure of a ribonucleotide reductase R2 protein radical
      +
      Lebrette H, Srinivas V, John J, Aurelius O, Kumar R, Lundin D, Brewster AS, Bhowmick A, Sirohiwal A, Kim IS, Gul S, Pham C, Sutherlin KD, Simon P, Butryn A, Aller P, Orville AM, Fuller FD, Alonso-Mori R, Batyuk A, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Sjöberg BM, Kern J, Roos K, Högbom M.
      +
      Science 382, 109-113 (06 Oct 2023). [PMID:37797025] [PMC reprint: PMC7615503]
      +
      +
      • +
    • +
      Structural evidence for intermediates during O2 formation in photosystem II
      +
      Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK.
      +
      Nature 617, 629-636 (1 May 2023). [PMID:37138085] [PMC reprint: PMC10191843]
      +
      +
      • +
    • Chemical crystallography by serial femtosecond X-ray diffraction
      Schriber EA, Paley DW, Bolotovsky R, Rosenberg DJ, Sierra RG, Aquila A, Mendez D, Poitevin F, Blaschke JP, Bhowmick A, Kelly RP, Hunter M, Hayes B, Popple DC, Yeung M, Pareja-Rivera C, Lisova S, Tono K, Sugahara M, Owada S, Kuykendall T, Yao K, Schuck PJ, Solis-Ibarra D, Sauter NK, Brewster AS, Hohman JN.
      Nature 601, 360-365 (1 Jan 2022). [PMID:35046599] [PMC reprint: PMC8770144]
    • +
      Structures of the intermediates of Kok's photosynthetic water oxidation clock
      +
      Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK.
      +
      Nature 563, 421-425 (1 Nov 2018). [PMID:30405241] [PMC reprint: PMC6485242]
      +
      +
      • +
    • +
      XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction
      +
      Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF.
      +
      Proc Natl Acad Sci U S A 114, 13357-13362 (19 Dec 2017). [PMID:28835537] [PMC reprint: PMC5754760]
      +
      +
      • +
    • +
      Structure of photosystem II and substrate binding at room temperature
      +
      Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J.
      +
      Nature 540, 453-457 (15 Dec 2016). [PMID:27871088] [PMC reprint: PMC5201176]
      +
      +
      • +
    • +
      De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure
      +
      Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS.
      +
      Nature 539, 43-47 (03 Nov 2016). [PMID:27680699] [PMC reprint: PMC5161637]
      +
      +
      • +
    • +
      Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography
      +
      Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS.
      +
      Elife 4 (30 Sep 2015). [PMID:26422513] [PMC reprint: PMC4721965]
      +
      +
      • +
    • Structure of the toxic core of α-synuclein from invisible crystals
      Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS.
      Nature 525, 486-90 (24 Sep 2015). [PMID:26352473] [PMC reprint: PMC4791177]
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"dials.algorithms.refinement.engine.AdaptLbfgs.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_diag() (dials.algorithms.refinement.engine.lbfgscurvs method)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs.compute_functional_gradients_diag", false]], "compute_functional_gradients_diag() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_gradients_diag", false]], "compute_functional_score_for_dimension_assessment() 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false]], "dials.algorithms.indexing": [[11, "module-dials.algorithms.indexing", false]], "dials.algorithms.indexing.assign_indices": [[11, "module-dials.algorithms.indexing.assign_indices", false]], "dials.algorithms.indexing.basis_vector_search": [[11, "module-dials.algorithms.indexing.basis_vector_search", false]], "dials.algorithms.indexing.basis_vector_search.combinations": [[11, "module-dials.algorithms.indexing.basis_vector_search.combinations", false]], "dials.algorithms.indexing.basis_vector_search.optimise": [[11, "module-dials.algorithms.indexing.basis_vector_search.optimise", false]], "dials.algorithms.indexing.compare_orientation_matrices": [[11, "module-dials.algorithms.indexing.compare_orientation_matrices", false]], "dials.algorithms.indexing.indexer": [[11, "module-dials.algorithms.indexing.indexer", false]], "dials.algorithms.indexing.lattice_search": [[11, "module-dials.algorithms.indexing.lattice_search", false]], "dials.algorithms.indexing.max_cell": [[11, "module-dials.algorithms.indexing.max_cell", false]], "dials.algorithms.indexing.model_evaluation": [[11, "module-dials.algorithms.indexing.model_evaluation", false]], "dials.algorithms.indexing.nearest_neighbor": [[11, "module-dials.algorithms.indexing.nearest_neighbor", false]], "dials.algorithms.indexing.refinement": [[11, "module-dials.algorithms.indexing.refinement", false]], "dials.algorithms.indexing.stills_indexer": [[11, "module-dials.algorithms.indexing.stills_indexer", false]], "dials.algorithms.indexing.symmetry": [[11, "module-dials.algorithms.indexing.symmetry", false]], "dials.algorithms.integration.integrator": [[12, "module-dials.algorithms.integration.integrator", false]], "dials.algorithms.profile_model": [[13, "module-dials.algorithms.profile_model", false]], "dials.algorithms.refinement.engine": [[14, "module-dials.algorithms.refinement.engine", false]], "dials.algorithms.refinement.refiner": [[14, "module-dials.algorithms.refinement.refiner", false]], "dials.algorithms.refinement.reflection_manager": [[14, "module-dials.algorithms.refinement.reflection_manager", false]], "dials.algorithms.refinement.target": [[14, "module-dials.algorithms.refinement.target", false]], "dials.algorithms.refinement.target_stills": [[14, "module-dials.algorithms.refinement.target_stills", false]], "dials.algorithms.refinement.weighting_strategies": [[14, "module-dials.algorithms.refinement.weighting_strategies", false]], "dials.algorithms.scaling": [[15, "module-dials.algorithms.scaling", false]], "dials.algorithms.scaling.model.model": [[15, "module-dials.algorithms.scaling.model.model", false]], "dials.algorithms.scaling.outlier_rejection": [[15, "module-dials.algorithms.scaling.outlier_rejection", false]], "dials.algorithms.spot_finding.factory": [[16, "module-dials.algorithms.spot_finding.factory", false]], "dials.algorithms.spot_finding.finder": [[16, "module-dials.algorithms.spot_finding.finder", false]], "dials.algorithms.spot_prediction.reflection_predictor": [[17, "module-dials.algorithms.spot_prediction.reflection_predictor", false]], "dials.algorithms.symmetry": [[18, "module-dials.algorithms.symmetry", false]], "dials.algorithms.symmetry.cosym": [[18, "module-dials.algorithms.symmetry.cosym", false]], "dials.algorithms.symmetry.cosym.engine": [[18, "module-dials.algorithms.symmetry.cosym.engine", false]], "dials.algorithms.symmetry.cosym.target": [[18, "module-dials.algorithms.symmetry.cosym.target", false]], "dials.algorithms.symmetry.laue_group": [[18, "module-dials.algorithms.symmetry.laue_group", false]], "dials.algorithms.symmetry.reindex_to_reference": [[18, "module-dials.algorithms.symmetry.reindex_to_reference", false]], "dials.array_family.flex": [[20, "module-dials.array_family.flex", false]], "dials.extensions.dispersion_spotfinder_threshold_ext": [[31, "module-dials.extensions.dispersion_spotfinder_threshold_ext", false]], "dials.extensions.gaussian_rs_profile_model_ext": [[31, "module-dials.extensions.gaussian_rs_profile_model_ext", false]], "dials.extensions.null_background_ext": [[31, "module-dials.extensions.null_background_ext", false]], "dials.extensions.simple_background_ext": [[31, "module-dials.extensions.simple_background_ext", false]], "dials.extensions.simple_centroid_ext": [[31, "module-dials.extensions.simple_centroid_ext", false]], "dials.util.command_line": [[33, "module-dials.util.command_line", false]], "dials.util.export_mtz": [[33, "module-dials.util.export_mtz", false]], "dials.util.export_text": [[33, "module-dials.util.export_text", false]], "dials.util.image": [[33, "module-dials.util.image", false]], "dials.util.installer": [[33, "module-dials.util.installer", false]], "dials.util.ioutil": [[33, "module-dials.util.ioutil", false]], "dials.util.nexus": [[33, "module-dials.util.nexus", false]], "dials.util.options": [[33, "module-dials.util.options", false]], "dialsindexerror": [[11, "dials.algorithms.indexing.DialsIndexError", false]], "dialsindexrefineerror": [[11, "dials.algorithms.indexing.DialsIndexRefineError", false]], "diff_phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.diff_phil", false]], "diff_phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.diff_phil", false]], "difference_rotation_matrix_axis_angle() (in module dials.algorithms.indexing.compare_orientation_matrices)": [[11, "dials.algorithms.indexing.compare_orientation_matrices.difference_rotation_matrix_axis_angle", false]], "dim (dials.algorithms.refinement.target.target property)": [[14, "dials.algorithms.refinement.target.Target.dim", false]], "dim (dials.algorithms.symmetry.cosym.target.target attribute)": [[18, "dials.algorithms.symmetry.cosym.target.Target.dim", false]], "disablempmixin (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.DisableMPmixin", false]], "dispersionspotfinderthresholdext (class in dials.extensions.dispersion_spotfinder_threshold_ext)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt", false]], "dosedecay (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.DoseDecay", false]], "dump() (in module dials.util.nexus)": [[33, "dials.util.nexus.dump", false]], "dx (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.dx", false]], "dxtbx.imageset": [[26, "module-dxtbx.imageset", false]], "dxtbx.model.beam": [[21, "module-dxtbx.model.beam", false]], "dxtbx.model.crystal": [[22, "module-dxtbx.model.crystal", false]], "dxtbx.model.detector": [[23, "module-dxtbx.model.detector", false]], "dxtbx.model.experiment_list": [[24, "module-dxtbx.model.experiment_list", false]], "dxtbx.model.goniometer": [[25, "module-dxtbx.model.goniometer", false]], "dxtbx.model.profile": [[28, "module-dxtbx.model.profile", false]], "dxtbx.model.scan": [[29, "module-dxtbx.model.scan", false]], "dxtbx.serialize.imageset": [[30, "module-dxtbx.serialize.imageset", false]], "dxtbx.serialize.load": [[30, "module-dxtbx.serialize.load", false]], "dxtbx.serialize.xds": [[30, "module-dxtbx.serialize.xds", false]], "dy (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.dy", false]], "e_refine() (in module dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.e_refine", false]], "empty() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.empty", false]], "end() (dials.util.command_line.command class method)": [[33, "dials.util.command_line.Command.end", false]], "error_model (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.error_model", false]], "estimate_global_threshold() (in module dials.extensions.dispersion_spotfinder_threshold_ext)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.estimate_global_threshold", false]], "evaluate() (dials.algorithms.indexing.model_evaluation.modelevaluation method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelEvaluation.evaluate", false]], "evaluate() (dials.algorithms.indexing.model_evaluation.strategy method)": [[11, "dials.algorithms.indexing.model_evaluation.Strategy.evaluate", false]], "exception (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.exception", false]], "executor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Executor", false]], "exp_nos (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.exp_nos", false]], "experiment_list() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.experiment_list", false]], "experiment_list_for_crystal() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.experiment_list_for_crystal", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.lauereflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager.experiment_type", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.reflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.experiment_type", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager.experiment_type", false]], "experimentlist (class in dxtbx.model)": [[24, "dxtbx.model.ExperimentList", false]], "experimentlistfactory (class in dxtbx.model.experiment_list)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory", false]], "export_as_json() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.export_as_json", false]], "export_mtz() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.export_mtz", false]], "export_reflections() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.export_reflections", false]], "export_text() (in module dials.util.export_text)": [[33, "dials.util.export_text.export_text", false]], "extend() (dials.algorithms.indexing.model_evaluation.modelrank method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRank.extend", false]], "extend() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.extend", false]], "extend() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.extend", false]], "external_lookup (dxtbx.imageset.imageset property)": [[26, "dxtbx.imageset.ImageSet.external_lookup", false]], "external_lookup (dxtbx.imageset.imagesetdata property)": [[26, "dxtbx.imageset.ImageSetData.external_lookup", false]], "externaldelpsiweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy", false]], "externallookup (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookup", false]], "externallookupitembool (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookupItemBool", false]], "externallookupitemdouble (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookupItemDouble", false]], "extract_reference_intensities() (in module dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.extract_reference_intensities", false]], "extractpixelsfromimage (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractPixelsFromImage", false]], "extractpixelsfromimage2dnoshoeboxes (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractPixelsFromImage2DNoShoeboxes", false]], "extractspots (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractSpots", false]], "extractspotsparalleltask (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractSpotsParallelTask", false]], "fft1d (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D", false]], "fft3d (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D", false]], "filename (dxtbx.imageset.externallookupitembool property)": [[26, "dxtbx.imageset.ExternalLookupItemBool.filename", false]], "filename (dxtbx.imageset.externallookupitemdouble property)": [[26, "dxtbx.imageset.ExternalLookupItemDouble.filename", false]], "filename_or_none() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.filename_or_none", false]], "filename_to_absolute() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.filename_to_absolute", false]], "filter_by_likelihood() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_likelihood", false]], "filter_by_n_indexed() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_n_indexed", false]], "filter_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_volume", false]], "filter_doubled_cell() (in module dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.filter_doubled_cell", false]], "filter_known_symmetry() (in module dials.algorithms.indexing.basis_vector_search.combinations)": [[11, "dials.algorithms.indexing.basis_vector_search.combinations.filter_known_symmetry", false]], "filter_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.filter_obs", false]], "filter_similar_orientations() (in module dials.algorithms.indexing.basis_vector_search.combinations)": [[11, "dials.algorithms.indexing.basis_vector_search.combinations.filter_similar_orientations", false]], "filterrunner (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.FilterRunner", false]], "final_outlier_arrays (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase attribute)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.final_outlier_arrays", false]], "finalise() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.finalise", false]], "finalise() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.finalise", false]], "finalize() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.finalize", false]], "finalize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.finalize", false]], "finalize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.finalize", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)": [[12, "dials.algorithms.integration.integrator.Integrator2D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)": [[12, "dials.algorithms.integration.integrator.Integrator3D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.finalize_reflections", false]], "find() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.find", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft1d method)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft3d method)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.strategy method)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.find_basis_vectors", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.lowresspotmatch method)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.find_crystal_models", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.pinkindexer method)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.find_crystal_models", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.strategy method)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.find_crystal_models", false]], "find_lattices() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.find_lattices", false]], "find_matching_symmetry() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.find_matching_symmetry", false]], "find_max_cell() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.find_max_cell", false]], "find_max_cell() (in module dials.algorithms.indexing.max_cell)": [[11, "dials.algorithms.indexing.max_cell.find_max_cell", false]], "find_spots() (dials.algorithms.spot_finding.finder.spotfinder method)": [[16, "dials.algorithms.spot_finding.finder.SpotFinder.find_spots", false]], "finished() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.finished", false]], "finished() (dials.util.command_line.progressbar method)": [[33, "dials.util.command_line.ProgressBar.finished", false]], "fit_profiles() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.fit_profiles", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.fix_initial_parameter", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.fix_initial_parameter", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.fix_initial_parameter", false]], "fixed_components (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, 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"dxtbx.model.experiment_list.ExperimentListFactory.from_args", false]], "from_data() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.dosedecay class method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.kbscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.physicalscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.scalingmodelbase class method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.from_data", false]], "from_dict() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)": [[15, 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"dxtbx.model.beam.BeamFactory.from_dict", false]], "from_dict() (dxtbx.model.crystal static method)": [[22, "dxtbx.model.Crystal.from_dict", false]], "from_dict() (dxtbx.model.crystal.crystalfactory static method)": [[22, "dxtbx.model.crystal.CrystalFactory.from_dict", false]], "from_dict() (dxtbx.model.detector static method)": [[23, "dxtbx.model.Detector.from_dict", false]], "from_dict() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.from_dict", false]], "from_dict() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_dict", false]], "from_dict() (dxtbx.model.goniometer.goniometer static method)": [[25, "dxtbx.model.goniometer.Goniometer.from_dict", false]], "from_dict() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.from_dict", false]], "from_dict() (dxtbx.model.goniometer.multiaxisgoniometer static method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.from_dict", false]], "from_dict() (dxtbx.model.mosaiccrystalkabsch2010 class method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.from_dict", false]], "from_dict() (dxtbx.model.mosaiccrystalsauter2014 class method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.from_dict", false]], "from_dict() (dxtbx.model.profile.profilemodelfactory static method)": [[28, "dxtbx.model.profile.ProfileModelFactory.from_dict", false]], "from_dict() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.from_dict", false]], "from_file() (dxtbx.model.experimentlist static method)": [[24, "dxtbx.model.ExperimentList.from_file", false]], "from_filenames() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_filenames", false]], "from_imageset() (dxtbx.imageset.imagegrid static method)": [[26, "dxtbx.imageset.ImageGrid.from_imageset", false]], "from_imageset_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_imageset_and_crystal", false]], "from_json() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_json", false]], "from_json_file() (dials.algorithms.refinement.engine.journal class method)": [[14, "dials.algorithms.refinement.engine.Journal.from_json_file", false]], "from_json_file() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_json_file", false]], "from_mosflm_matrix() (dxtbx.model.crystal.crystalfactory static method)": [[22, "dxtbx.model.crystal.CrystalFactory.from_mosflm_matrix", false]], "from_parameters() (dials.algorithms.indexing.indexer.indexer static method)": [[11, "dials.algorithms.indexing.indexer.Indexer.from_parameters", false]], "from_parameters() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.from_parameters", false]], "from_parameters_and_experiments() (dials.algorithms.refinement.target.targetfactory static method)": [[14, "dials.algorithms.refinement.target.TargetFactory.from_parameters_and_experiments", false]], "from_parameters_data_experiments() (dials.algorithms.refinement.refiner.refinerfactory class method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.from_parameters_data_experiments", false]], "from_parameters_reflections_experiments() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.from_parameters_reflections_experiments", false]], "from_phil() (dials.algorithms.integration.integrator.parameters static method)": [[12, "dials.algorithms.integration.integrator.Parameters.from_phil", false]], "from_phil() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.from_phil", false]], "from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.from_phil", false]], "from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.from_phil", false]], "from_phil() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.from_phil", false]], "from_pickle_file() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_pickle_file", false]], "from_sequence_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_sequence_and_crystal", false]], "from_serialized_format() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_serialized_format", false]], "from_stills_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_stills_and_crystal", false]], "from_template() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.from_template", false]], "from_templates() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_templates", false]], "from_templates() (dxtbx.model.experimentlist static method)": [[24, "dxtbx.model.ExperimentList.from_templates", false]], "from_xds() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_xds", false]], "gain (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.gain", false]], "gaussianrsprofilemodelext (class in dials.extensions.gaussian_rs_profile_model_ext)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt", false]], "gaussnewtoniterations (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations", false]], "generate_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.generate_from_phil", false]], "generate_phil_scope() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.generate_phil_scope", false]], "generate_phil_scope() (in module dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.generate_phil_scope", false]], "get_a_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_A_as_sqr", false]], "get_a_inverse_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_A_inverse_as_sqr", false]], "get_accepted_refs_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_accepted_refs_size", false]], "get_alpha_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_alpha_angle", false]], "get_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_angles", false]], "get_array_range() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_array_range", false]], "get_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_axes", false]], "get_beam() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_beam", false]], "get_beam() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_beam", false]], "get_beam() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_beam", false]], "get_beam() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_beam", false]], "get_beam() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_beam", false]], "get_centroid_analyser() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_centroid_analyser", false]], "get_corrected_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_corrected_data", false]], "get_corrected_data() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_corrected_data", false]], "get_correlation_matrix_for_step() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.get_correlation_matrix_for_step", false]], "get_crystal_symmetry() (dxtbx.model.crystal method)": [[22, "dxtbx.model.Crystal.get_crystal_symmetry", false]], "get_data() (dials.util.image.reader method)": [[33, "dials.util.image.reader.get_data", false]], "get_data() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_data", false]], "get_detector() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_detector", false]], "get_detector() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_detector", false]], "get_detector() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_detector", false]], "get_detector() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_detector", false]], "get_detector() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_detector", false]], "get_detectorbase() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_detectorbase", false]], "get_direction() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_direction", false]], "get_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_domain_size_ang", false]], "get_elapsed_time() (dials.util.command_line.progressbartimer method)": [[33, "dials.util.command_line.ProgressBarTimer.get_elapsed_time", false]], "get_entry() (in module dials.util.nexus)": [[33, "dials.util.nexus.get_entry", false]], "get_experiments() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_experiments", false]], "get_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_fixed_rotation", false]], "get_format_class() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_format_class", false]], "get_format_class() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_format_class", false]], "get_free_reflections() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_free_reflections", false]], "get_free_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_free_reflections", false]], "get_gain() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_gain", false]], "get_gain() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_gain", false]], "get_goniometer() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_goniometer", false]], "get_goniometer() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_goniometer", false]], "get_grid_size() (dxtbx.imageset.imagegrid method)": [[26, "dxtbx.imageset.ImageGrid.get_grid_size", false]], "get_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_half_mosaicity_deg", false]], "get_image_identifier() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_image_identifier", false]], "get_image_identifier() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_image_identifier", false]], "get_indexed() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_indexed", false]], "get_inverse_ub_matrix_from_xparm() (in module dials.util.ioutil)": [[33, "dials.util.ioutil.get_inverse_ub_matrix_from_xparm", false]], "get_kappa_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_angle", false]], "get_kappa_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_axis", false]], "get_mask() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_mask", false]], "get_mask() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_mask", false]], "get_master_path() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_master_path", false]], "get_matches() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_matches", false]], "get_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_matches", false]], "get_max_inscribed_resolution() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_max_inscribed_resolution", false]], "get_max_resolution() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_max_resolution", false]], "get_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.get_mosaicity", false]], "get_names() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_names", false]], "get_names() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_names", false]], "get_nrows() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.get_nrows", false]], "get_num_matches() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches", false]], "get_num_matches_for_experiment() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches_for_experiment", false]], "get_num_matches_for_panel() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches_for_panel", false]], "get_num_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_num_scan_points", false]], "get_num_steps() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.get_num_steps", false]], "get_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_obs", false]], "get_omega_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_omega_angle", false]], "get_omega_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_omega_axis", false]], "get_panel_intersection() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_panel_intersection", false]], "get_param_reporter() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_param_reporter", false]], "get_parameter_correlation_matrix() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_parameter_correlation_matrix", false]], "get_params() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_params", false]], "get_path() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_path", false]], "get_path() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_path", false]], "get_pedestal() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_pedestal", false]], "get_phi_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_phi_angle", false]], "get_phi_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_phi_axis", false]], "get_raw_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_raw_data", false]], "get_ray_intersection() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_ray_intersection", false]], "get_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_rotation_axis", false]], "get_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_rotation_axis_datum", false]], "get_sample_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_sample_size", false]], "get_scan() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_scan", false]], "get_scan() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_scan", false]], "get_scan() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_scan", false]], "get_scan() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_scan", false]], "get_scan() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_scan", false]], "get_scan_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_scan_axis", false]], "get_scan_axis() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_scan_axis", false]], "get_setting_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation", false]], "get_setting_rotation_at_scan_point() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_point", false]], "get_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_points", false]], "get_shared_components() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.get_shared_components", false]], "get_shared_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.get_shared_components", false]], "get_shared_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.get_shared_components", false]], "get_space_group_type_from_xparm() (in module dials.util.ioutil)": [[33, "dials.util.ioutil.get_space_group_type_from_xparm", false]], "get_spectrum() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_spectrum", false]], "get_template() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_template", false]], "get_template() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_template", false]], "get_template() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_template", false]], "get_vendor() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_vendor", false]], "get_vendortype() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_vendortype", false]], "get_weighting_strategy_override() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.get_weighting_strategy_override", false]], "goniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.Goniometer", false]], "goniometercomparison (class in dxtbx.model.experiment_list)": [[24, "dxtbx.model.experiment_list.GoniometerComparison", false]], "goniometerfactory (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.GoniometerFactory", false]], "goniometers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.goniometers", false]], "gradient_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.gradient_threshold", false]], "groups_cache() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.groups_cache", false]], "has_dynamic_mask() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.has_dynamic_mask", false]], "has_projection_2d() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.has_projection_2d", false]], "has_single_file_reader() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.has_single_file_reader", false]], "heading() (in module dials.util.command_line)": [[33, "dials.util.command_line.heading", false]], "hierarchy() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.hierarchy", false]], "hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.hist", false]], "history (dials.algorithms.refinement.refiner.refiner property)": [[14, "dials.algorithms.refinement.refiner.Refiner.history", false]], "hkl_offset (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.hkl_offset", false]], "id_ (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.dosedecay attribute)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.id_", false]], "id_ (dials.algorithms.scaling.model.model.kbscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.scalingmodelbase attribute)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.id_", false]], "identifiers (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.identifiers", false]], "identifiers() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.identifiers", false]], "identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.identifiers", false]], "identify_outliers() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.identify_outliers", false]], "imagegrid (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageGrid", false]], "imagesequence (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSequence", false]], "imagesequence_from_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imagesequence_from_dict", false]], "imagesequence_to_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imagesequence_to_dict", false]], "imageset (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSet", false]], "imageset() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.imageset", false]], "imageset_from_anyset() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.imageset_from_anyset", false]], "imageset_from_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imageset_from_dict", false]], "imageset_to_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imageset_to_dict", false]], "imagesetdata (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetData", false]], "imagesetfactory (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetFactory", false]], "imagesetlazy (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetLazy", false]], "imagesets() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.imagesets", false]], "imgcif() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.imgCIF", false]], "imgcif() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.imgCIF", false]], "imgcif() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.imgCIF", false]], "imgcif() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.imgCIF", false]], "imgcif_h() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.imgCIF_H", false]], "importer (class in dials.util.options)": [[33, "dials.util.options.Importer", false]], "include_gui_packages (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.include_gui_packages", false]], "indent (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.indent", false]], "index() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.index", false]], "index() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.index", false]], "index_reflections() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.index_reflections", false]], "indexer (class in dials.algorithms.indexing.indexer)": [[11, "dials.algorithms.indexing.indexer.Indexer", false]], "indices() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.indices", false]], "indices() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.indices", false]], "initialise() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.initialise", false]], "initialise_smooth_input() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.initialise_smooth_input", false]], "initialize() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.initialize", false]], "initialize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.initialize", false]], "initialize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.initialize", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)": [[12, "dials.algorithms.integration.integrator.Integrator2D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)": [[12, "dials.algorithms.integration.integrator.Integrator3D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.initialize_reflections", false]], "installer (class in dials.util.installer)": [[33, "dials.util.installer.installer", false]], "installer_dir (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.installer_dir", false]], "integrate() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.integrate", false]], "integrate() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.integrate", false]], "integrator (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator", false]], "integrator2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator2D", false]], "integrator3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator3D", false]], "integrator3dthreaded (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded", false]], "integratorexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor", false]], "integratorflat3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D", false]], "integratorsingle2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D", false]], "integratorstills (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorStills", false]], "inv_d2() (dials.algorithms.background.radialaverage method)": [[10, "dials.algorithms.background.RadialAverage.inv_d2", false]], "invalidphilerror": [[33, "dials.util.options.InvalidPhilError", false]], "is_consistent() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.is_consistent", false]], "is_marked_for_rejection() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.is_marked_for_rejection", false]], "is_marked_for_rejection() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.is_marked_for_rejection", false]], "is_scaled (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.is_scaled", false]], "is_similar_to() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.is_similar_to", false]], "is_similar_to() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.is_similar_to", false]], "is_similar_to() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.is_similar_to", false]], "is_similar_to() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.is_similar_to", false]], "is_single_file_reader() (dxtbx.imageset.memreader static method)": [[26, "dxtbx.imageset.MemReader.is_single_file_reader", false]], "iter_levelorder() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_levelorder", false]], "iter_panels() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_panels", false]], "iter_preorder() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_preorder", false]], "jacobian_condition_number() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.jacobian_condition_number", false]], "job() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.job", false]], "joblist (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.JobList", false]], "journal (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.Journal", false]], "kappa() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.kappa", false]], "kappagoniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.KappaGoniometer", false]], "kbscalingmodel (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel", false]], "kernel_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.kernel_normalisation", false]], "known_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.known_axis", false]], "laue_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.laue_manager", false]], "lauegroupanalysis (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.LaueGroupAnalysis", false]], "laueleastsquaresresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff", false]], "lauemixedweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy", false]], "lauereflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager", false]], "lauestatisticalweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy", false]], "lbfgs_with_curvs (class in dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs", false]], "lbfgscurvs (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs", false]], "leastsquarespositionalresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff", false]], "leastsquarespositionalresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoffSparse", false]], "leastsquaresstillsresidualwithrmsdcutoff (class in dials.algorithms.refinement.target_stills)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff", false]], "leastsquaresstillsresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target_stills)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoffSparse", false]], "levenbergmarquardtiterations (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations", false]], "limit_image_range() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.limit_image_range", false]], "load() (in module dials.util.nexus)": [[33, "dials.util.nexus.load", false]], "load_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.load_error_model", false]], "load_image() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.load_image", false]], "log_summary() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.log_summary", false]], "lowresspotmatch (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch", false]], "madmergedmtzwriter (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MADMergedMTZWriter", false]], "make_apps (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.make_apps", false]], "make_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_beam", false]], "make_combined_plots() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.make_combined_plots", false]], "make_detector() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.make_detector", false]], "make_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_goniometer", false]], "make_imageset() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.make_imageset", false]], "make_kappa_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_kappa_goniometer", false]], "make_multi_axis_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_multi_axis_goniometer", false]], "make_polarized_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_polarized_beam", false]], "make_polychromatic_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_polychromatic_beam", false]], "make_scan() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.make_scan", false]], "make_scan_from_properties() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.make_scan_from_properties", false]], "make_sequence() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.make_sequence", false]], "mark_for_rejection() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.mark_for_rejection", false]], "mark_for_rejection() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.mark_for_rejection", false]], "mask (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.mask", false]], "masker() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.masker", false]], "masker() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.masker", false]], "master_path() (dxtbx.imageset.memreader static method)": [[26, "dxtbx.imageset.MemReader.master_path", false]], "match_wavelengths() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.match_wavelengths", false]], "max_length (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.max_length", false]], "max_possible_wl (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.max_possible_wl", false]], "max_shift_over_esd (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.max_shift_over_esd", false]], "mean() (dials.algorithms.background.radialaverage method)": [[10, "dials.algorithms.background.RadialAverage.mean", false]], "median_unit_cell() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.median_unit_cell", false]], "memreader (class in dxtbx.imageset)": [[26, "dxtbx.imageset.MemReader", false]], "merge_panel_scope_extracts_by_id() (in module dxtbx.model.detector)": [[23, "dxtbx.model.detector.merge_panel_scope_extracts_by_id", false]], "mergedmtzwriter (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MergedMTZWriter", false]], "message (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.message", false]], "metric_supergroup() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.metric_supergroup", false]], "min_wl (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.min_wl", false]], "minimize_scipy() (in module dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.minimize_scipy", false]], "minimize_scitbx_lbfgs() (in module dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.minimize_scitbx_lbfgs", false]], "ml_aniso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.ml_aniso_normalisation", false]], "ml_iso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.ml_iso_normalisation", false]], "model_likelihood (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.model_likelihood", false]], "modelevaluation (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelEvaluation", false]], "modelrank (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRank", false]], "modelrankfilter (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter", false]], "modelrankweighted (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted", false]], "module": [[10, "module-dials.algorithms.background", false], [11, "module-dials.algorithms.indexing", false], [11, "module-dials.algorithms.indexing.assign_indices", false], [11, "module-dials.algorithms.indexing.basis_vector_search", false], [11, "module-dials.algorithms.indexing.basis_vector_search.combinations", false], [11, "module-dials.algorithms.indexing.basis_vector_search.optimise", false], [11, "module-dials.algorithms.indexing.compare_orientation_matrices", false], [11, "module-dials.algorithms.indexing.indexer", false], [11, "module-dials.algorithms.indexing.lattice_search", false], [11, "module-dials.algorithms.indexing.max_cell", false], [11, "module-dials.algorithms.indexing.model_evaluation", false], [11, "module-dials.algorithms.indexing.nearest_neighbor", false], [11, "module-dials.algorithms.indexing.refinement", false], [11, "module-dials.algorithms.indexing.stills_indexer", false], [11, "module-dials.algorithms.indexing.symmetry", false], [12, "module-dials.algorithms.integration.integrator", false], [13, "module-dials.algorithms.profile_model", false], [14, "module-dials.algorithms.refinement.engine", false], [14, "module-dials.algorithms.refinement.refiner", false], [14, "module-dials.algorithms.refinement.reflection_manager", false], [14, "module-dials.algorithms.refinement.target", false], [14, "module-dials.algorithms.refinement.target_stills", false], [14, "module-dials.algorithms.refinement.weighting_strategies", false], [15, "module-dials.algorithms.scaling", false], [15, "module-dials.algorithms.scaling.model.model", false], [15, "module-dials.algorithms.scaling.outlier_rejection", false], [16, "module-dials.algorithms.spot_finding.factory", false], [16, "module-dials.algorithms.spot_finding.finder", false], [17, "module-dials.algorithms.spot_prediction.reflection_predictor", false], [18, "module-dials.algorithms.symmetry", false], [18, "module-dials.algorithms.symmetry.cosym", false], [18, "module-dials.algorithms.symmetry.cosym.engine", false], [18, "module-dials.algorithms.symmetry.cosym.target", false], [18, "module-dials.algorithms.symmetry.laue_group", false], [18, "module-dials.algorithms.symmetry.reindex_to_reference", false], [20, "module-dials.array_family.flex", false], [21, "module-dxtbx.model.beam", false], [22, "module-dxtbx.model.crystal", false], [23, "module-dxtbx.model.detector", false], [24, "module-dxtbx.model.experiment_list", false], [25, "module-dxtbx.model.goniometer", false], [26, "module-dxtbx.imageset", false], [28, "module-dxtbx.model.profile", false], [29, "module-dxtbx.model.scan", false], [30, "module-dxtbx.serialize.imageset", false], [30, "module-dxtbx.serialize.load", false], [30, "module-dxtbx.serialize.xds", false], [31, "module-dials.extensions.dispersion_spotfinder_threshold_ext", false], [31, "module-dials.extensions.gaussian_rs_profile_model_ext", false], [31, "module-dials.extensions.null_background_ext", false], [31, "module-dials.extensions.simple_background_ext", false], [31, "module-dials.extensions.simple_centroid_ext", false], [33, "module-dials.util.command_line", false], [33, "module-dials.util.export_mtz", false], [33, "module-dials.util.export_text", false], [33, "module-dials.util.image", false], [33, "module-dials.util.installer", false], [33, "module-dials.util.ioutil", false], [33, "module-dials.util.nexus", false], [33, "module-dials.util.options", false]], "mosaiccrystalkabsch2010 (class in dxtbx.model)": [[22, "dxtbx.model.MosaicCrystalKabsch2010", false]], "mosaiccrystalsauter2014 (class in dxtbx.model)": [[22, "dxtbx.model.MosaicCrystalSauter2014", false]], "mtzwriterbase (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MTZWriterBase", false]], "mu (dials.algorithms.refinement.engine.levenbergmarquardtiterations property)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.mu", false]], "multi_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.multi_axis", false]], "multi_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.multi_axis_goniometer_from_phil", false]], "multiaxisgoniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer", false]], "n() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.n", false]], "n_indexed (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.n_indexed", false]], "n_params (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.n_params", false]], "name (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext attribute)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.name", false]], "name (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext attribute)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.name", false]], "name (dials.extensions.null_background_ext.nullbackgroundext attribute)": [[31, "dials.extensions.null_background_ext.NullBackgroundExt.name", false]], "name (dials.extensions.simple_background_ext.simplebackgroundext attribute)": [[31, "dials.extensions.simple_background_ext.SimpleBackgroundExt.name", false]], "name (dials.extensions.simple_centroid_ext.simplecentroidext attribute)": [[31, "dials.extensions.simple_centroid_ext.SimpleCentroidExt.name", false]], "name (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.name", false]], "neighboranalysis (class in dials.algorithms.indexing.nearest_neighbor)": [[11, "dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis", false]], "new() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.new", false]], "nframes_hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.nframes_hist", false]], "normdevoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.NormDevOutlierRejection", false]], "nullbackgroundext (class in dials.extensions.null_background_ext)": [[31, "dials.extensions.null_background_ext.NullBackgroundExt", false]], "nullify_all_single_file_reader_format_instances() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.nullify_all_single_file_reader_format_instances", false]], "num_reflections() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.num_reflections", false]], "num_scan_points (dxtbx.model.goniometer.goniometer property)": [[25, "dxtbx.model.goniometer.Goniometer.num_scan_points", false]], "numerator() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.numerator", false]], "optimise_basis_vectors() (in module dials.algorithms.indexing.basis_vector_search.optimise)": [[11, "dials.algorithms.indexing.basis_vector_search.optimise.optimise_basis_vectors", false]], "optionparser (class in dials.util.options)": [[33, "dials.util.options.OptionParser", false]], "outlierrejectionbase (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase", false]], "overwrite_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.overwrite_from_phil", false]], "p_cc_given_not_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_not_s", false]], "p_cc_given_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_s", false]], "p_s_given_cc (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_s_given_cc", false]], "parameter_vector_norm() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.parameter_vector_norm", false]], "parameters (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters", false]], "parameters.filter (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Filter", false]], "parameters.profile (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Profile", false]], "parameters.profile.validation (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Profile.Validation", false]], "params() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.params", false]], "parse_args() (dials.util.options.argumentparser method)": [[33, "dials.util.options.ArgumentParser.parse_args", false]], "parse_args() (dials.util.options.philcommandparser method)": [[33, "dials.util.options.PhilCommandParser.parse_args", false]], "parse_known_args() (dials.util.options.argumentparserbase method)": [[33, "dials.util.options.ArgumentParserBase.parse_known_args", false]], "partial_data() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.partial_data", false]], "partial_set() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.partial_set", false]], "partial_set() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.partial_set", false]], "paths() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.paths", false]], "paths() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.paths", false]], "peakcentroiddistancefilter (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter", false]], "pedestal (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.pedestal", false]], "per_image() (dials.algorithms.refinement.reflection_manager.blockcalculator method)": [[14, "dials.algorithms.refinement.reflection_manager.BlockCalculator.per_image", false]], "per_width() (dials.algorithms.refinement.reflection_manager.blockcalculator method)": [[14, "dials.algorithms.refinement.reflection_manager.BlockCalculator.per_width", false]], "phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.phil", false]], "phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.phil", false]], "phil() (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext static method)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.phil", false]], "phil() (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext static method)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.phil", false]], "phil() (dials.extensions.simple_background_ext.simplebackgroundext static method)": [[31, "dials.extensions.simple_background_ext.SimpleBackgroundExt.phil", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.fft1d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.fft3d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.strategy attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.pinkindexer attribute)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.strategy attribute)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.phil_help", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.fft1d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.fft3d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.strategy attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.pinkindexer attribute)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.strategy attribute)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.dosedecay attribute)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.kbscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.phil_scope", false]], "philcommandparser (class in dials.util.options)": [[33, "dials.util.options.PhilCommandParser", false]], "physicalscalingmodel (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel", false]], "pinkindexer (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer", false]], "pixel_list_to_reflection_table() (in module dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.pixel_list_to_reflection_table", false]], "pixel_list_to_shoeboxes() (in module dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.pixel_list_to_shoeboxes", false]], "plot_displacements() (in module dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.plot_displacements", false]], "plot_histogram() (dials.algorithms.indexing.nearest_neighbor.neighboranalysis method)": [[11, "dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis.plot_histogram", false]], "plot_model_components() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.plot_model_components", false]], "plot_scaling_models() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.plot_scaling_models", false]], "predict() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict", false]], "predict_for_free_reflections() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict_for_free_reflections", false]], "predict_for_indexed() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.predict_for_indexed", false]], "predict_for_reflection_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.predict_for_reflection_table", false]], "predict_for_reflection_table() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict_for_reflection_table", false]], "predict_for_reflection_table() (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff method)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.predict_for_reflection_table", false]], "predictor() (dials.algorithms.spot_prediction.reflection_predictor.reflectionpredictor method)": [[17, "dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor.predictor", false]], "prepare_for_step() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.prepare_for_step", false]], "print_exp_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_exp_rmsd_table", false]], "print_out_of_sample_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_out_of_sample_rmsd_table", false]], "print_panel_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_panel_rmsd_table", false]], "print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.lauereflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager.print_stats_on_matches", false]], "print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.print_stats_on_matches", false]], "print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager.print_stats_on_matches", false]], "print_step_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_step_table", false]], "print_time (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.print_time", false]], "process() (dials.algorithms.integration.integrator.executor method)": [[12, "dials.algorithms.integration.integrator.Executor.process", false]], "process() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.process", false]], "process() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.process", false]], "process() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.process", false]], "processor2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Processor2D", false]], "processor3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Processor3D", false]], "processorclass (dials.algorithms.integration.integrator.integrator2d attribute)": [[12, "dials.algorithms.integration.integrator.Integrator2D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integrator3d attribute)": [[12, "dials.algorithms.integration.integrator.Integrator3D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorflat3d attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorsingle2d attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorstills attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.ProcessorClass", false]], "processorflat3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorFlat3D", false]], "processorsingle2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorSingle2D", false]], "processorstills (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorStills", false]], "product_name (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.product_name", false]], "product_specific_finalize_install() (dials.util.installer.installer method)": [[33, "dials.util.installer.installer.product_specific_finalize_install", false]], "profilemodelfactory (class in dxtbx.model.profile)": [[28, "dxtbx.model.profile.ProfileModelFactory", false]], "profilemodellerexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor", false]], "profiles() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.profiles", false]], "profilevalidatorexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor", false]], "progressbar (class in dials.util.command_line)": [[33, "dials.util.command_line.ProgressBar", false]], "progressbartimer (class in dials.util.command_line)": [[33, "dials.util.command_line.ProgressBarTimer", false]], "radialaverage (class in dials.algorithms.background)": [[10, "dials.algorithms.background.RadialAverage", false]], "read() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.read", false]], "read_file() (dials.util.image.reader method)": [[33, "dials.util.image.reader.read_file", false]], "reader (class in dials.util.image)": [[33, "dials.util.image.reader", false]], "reader() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.reader", false]], "reader() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.reader", false]], "realspacegridsearch (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch", false]], "reason_for_termination (dials.algorithms.refinement.engine.journal attribute)": [[14, "dials.algorithms.refinement.engine.Journal.reason_for_termination", false]], "record_intensity_combination_imid() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.record_intensity_combination_Imid", false]], "refine() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.refine", false]], "refine() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.refine", false]], "refine() (in module dials.algorithms.indexing.refinement)": [[11, "dials.algorithms.indexing.refinement.refine", false]], "refiner (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.Refiner", false]], "refinerfactory (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory", false]], "refinery (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.Refinery", false]], "reflectionmanager (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ReflectionManager", false]], "reflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager", false]], "reflectionmanagerfactory (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory", false]], "reflectionpredictor (class in dials.algorithms.spot_prediction.reflection_predictor)": [[17, "dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor", false]], "reflections_after_outlier_rejection() (dials.algorithms.refinement.refiner.refinerfactory class method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.reflections_after_outlier_rejection", false]], "reflections_and_experiments_from_files() (in module dials.util.options)": [[33, "dials.util.options.reflections_and_experiments_from_files", false]], "reject_outliers() (in module dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.reject_outliers", false]], "remove_on_experiment_identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.remove_on_experiment_identifiers", false]], "remove_sources_default (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.remove_sources_default", false]], "replace() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.replace", false]], "report() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.report", false]], "report() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.report", false]], "report_progress() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.report_progress", false]], "reset_accepted_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.reset_accepted_reflections", false]], "reset_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.reset_scan_points", false]], "resolution_filter_from_array() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.resolution_filter_from_array", false]], "resolution_filter_from_reflections_experiments() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.resolution_filter_from_reflections_experiments", false]], "restart() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.restart", false]], "result (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.Result", false]], "rmsd_names (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_units (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_units", false]], "rmsds (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.rmsds", false]], "rmsds() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.rmsds", false]], "rmsds() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds", false]], "rmsds_for_experiment() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds_for_experiment", false]], 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"dials.algorithms.indexing.compare_orientation_matrices.rotation_matrix_differences", false]], "rotation_scan_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.rotation_scan_manager", false]], "run() (dials.algorithms.refinement.engine.gaussnewtoniterations method)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.run", false]], "run() (dials.algorithms.refinement.engine.lbfgscurvs method)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs.run", false]], "run() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.run", false]], "run() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.run", false]], "run() (dials.algorithms.refinement.engine.simplelbfgs method)": [[14, "dials.algorithms.refinement.engine.SimpleLBFGS.run", false]], "run() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.run", false]], "run() (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase method)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.run", false]], "run() (dials.algorithms.spot_finding.factory.backgroundgradientfilter method)": [[16, "dials.algorithms.spot_finding.factory.BackgroundGradientFilter.run", false]], "run() (dials.algorithms.spot_finding.factory.peakcentroiddistancefilter method)": [[16, "dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter.run", false]], "run() (dials.algorithms.spot_finding.factory.spotdensityfilter method)": [[16, "dials.algorithms.spot_finding.factory.SpotDensityFilter.run", false]], "run() (dials.algorithms.symmetry.cosym.cosymanalysis method)": [[18, "dials.algorithms.symmetry.cosym.CosymAnalysis.run", false]], "run_lbfgs() 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dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.ScoreSymmetryElement", false]], "scoresymmetryelement (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.ScoreSymmetryElement", false]], "search() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.search", false]], "search_directions (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_directions", false]], "search_vectors (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_vectors", false]], "select_on_experiment_identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.select_on_experiment_identifiers", false]], "selection_used_for_refinement() (dials.algorithms.refinement.refiner.refiner method)": 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"dials.algorithms.scaling.outlier_rejection.SimpleNormDevOutlierRejection", false]], "single_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.single_axis", false]], "single_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.single_axis_goniometer_from_phil", false]], "single_axis_reverse() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.single_axis_reverse", false]], "single_file() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.single_file", false]], "size() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.size", false]], "source_packages (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.source_packages", false]], "sparsegradientsmixin (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.SparseGradientsMixin", false]], "split() (dials.algorithms.integration.integrator.joblist method)": [[12, "dials.algorithms.integration.integrator.JobList.split", false]], "split() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.split", false]], "split_jacobian_into_blocks() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.split_jacobian_into_blocks", false]], "split_matches_into_blocks() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.split_matches_into_blocks", false]], "spotdensityfilter (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.SpotDensityFilter", false]], "spotfinder (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.SpotFinder", false]], "spotfinderfactory (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory", false]], "stars (dials.algorithms.symmetry.cosym.scoresubgroup property)": [[18, "dials.algorithms.symmetry.cosym.ScoreSubGroup.stars", false]], "stars (dials.algorithms.symmetry.cosym.scoresymmetryelement property)": [[18, "dials.algorithms.symmetry.cosym.ScoreSymmetryElement.stars", false]], "start() (dials.util.command_line.command class method)": [[33, "dials.util.command_line.Command.start", false]], "statisticalweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.StatisticalWeightingStrategy", false]], "step_backward() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.step_backward", false]], "step_forward() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.step_forward", false]], "step_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.step_threshold", false]], "stills_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.stills_manager", false]], "stillsindexer (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer", false]], "stillsindexerbasisvectorsearch (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerBasisVectorSearch", false]], "stillsindexerknownorientation (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerKnownOrientation", false]], "stillsindexerlatticesearch (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerLatticeSearch", false]], "stillsreflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager", false]], "stillsweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy", false]], "strategy (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy", false]], "strategy (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.Strategy", false]], "strategy (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.Strategy", false]], "subgroups_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)": [[18, 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dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.SymmetryHandler", false]], "system_phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.system_phil", false]], "system_phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.system_phil", false]], "target (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.Target", false]], "target (class in dials.algorithms.symmetry.cosym.target)": [[18, "dials.algorithms.symmetry.cosym.target.Target", false]], "targetedoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.TargetedOutlierRejection", false]], "targetfactory (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.TargetFactory", false]], "tau (dials.algorithms.refinement.engine.levenbergmarquardtiterations attribute)": [[14, 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"dials.algorithms.refinement.engine.AdaptLbfgs.compute_functional_and_gradients", false]], "compute_functional_and_gradients() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_and_gradients", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.refinement.engine.adaptlbfgs method)": [[14, "dials.algorithms.refinement.engine.AdaptLbfgs.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_and_curvatures() (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs.compute_functional_gradients_and_curvatures", false]], "compute_functional_gradients_diag() 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false]], "configure_threshold() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.configure_threshold", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.arrayscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.dosedecay property)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.kbscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.consecutive_refinement_order", false]], "consecutive_refinement_order (dials.algorithms.scaling.model.model.physicalscalingmodel property)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.consecutive_refinement_order", false]], 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dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.CosymAnalysis", false]], "crystal (class in dxtbx.model)": [[22, "dxtbx.model.Crystal", false]], "crystal (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.crystal", false]], "crystal() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.crystal", false]], "crystalfactory (class in dxtbx.model.crystal)": [[22, "dxtbx.model.crystal.CrystalFactory", false]], "crystals() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.crystals", false]], "curvatures() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.curvatures", false]], "curvatures_fd() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.curvatures_fd", false]], "damping_value (dials.algorithms.refinement.engine.gaussnewtoniterations 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false]], "data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.data", false]], "default (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext attribute)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.default", false]], "default (dials.extensions.simple_centroid_ext.simplecentroidext attribute)": [[31, "dials.extensions.simple_centroid_ext.SimpleCentroidExt.default", false]], "del_last_row() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.del_last_row", false]], "denominator() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.denominator", false]], "dest_dir_prefix (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.dest_dir_prefix", false]], "detector (class in dxtbx.model)": [[23, "dxtbx.model.Detector", false]], 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"module-dials.algorithms.indexing.indexer", false]], "dials.algorithms.indexing.lattice_search": [[11, "module-dials.algorithms.indexing.lattice_search", false]], "dials.algorithms.indexing.max_cell": [[11, "module-dials.algorithms.indexing.max_cell", false]], "dials.algorithms.indexing.model_evaluation": [[11, "module-dials.algorithms.indexing.model_evaluation", false]], "dials.algorithms.indexing.nearest_neighbor": [[11, "module-dials.algorithms.indexing.nearest_neighbor", false]], "dials.algorithms.indexing.refinement": [[11, "module-dials.algorithms.indexing.refinement", false]], "dials.algorithms.indexing.stills_indexer": [[11, "module-dials.algorithms.indexing.stills_indexer", false]], "dials.algorithms.indexing.symmetry": [[11, "module-dials.algorithms.indexing.symmetry", false]], "dials.algorithms.integration.integrator": [[12, "module-dials.algorithms.integration.integrator", false]], "dials.algorithms.profile_model": [[13, "module-dials.algorithms.profile_model", false]], 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"module-dials.algorithms.spot_finding.factory", false]], "dials.algorithms.spot_finding.finder": [[16, "module-dials.algorithms.spot_finding.finder", false]], "dials.algorithms.spot_prediction.reflection_predictor": [[17, "module-dials.algorithms.spot_prediction.reflection_predictor", false]], "dials.algorithms.symmetry": [[18, "module-dials.algorithms.symmetry", false]], "dials.algorithms.symmetry.cosym": [[18, "module-dials.algorithms.symmetry.cosym", false]], "dials.algorithms.symmetry.cosym.engine": [[18, "module-dials.algorithms.symmetry.cosym.engine", false]], "dials.algorithms.symmetry.cosym.target": [[18, "module-dials.algorithms.symmetry.cosym.target", false]], "dials.algorithms.symmetry.laue_group": [[18, "module-dials.algorithms.symmetry.laue_group", false]], "dials.algorithms.symmetry.reindex_to_reference": [[18, "module-dials.algorithms.symmetry.reindex_to_reference", false]], "dials.array_family.flex": [[20, "module-dials.array_family.flex", false]], "dials.extensions.dispersion_spotfinder_threshold_ext": [[31, "module-dials.extensions.dispersion_spotfinder_threshold_ext", false]], "dials.extensions.gaussian_rs_profile_model_ext": [[31, "module-dials.extensions.gaussian_rs_profile_model_ext", false]], "dials.extensions.null_background_ext": [[31, "module-dials.extensions.null_background_ext", false]], "dials.extensions.simple_background_ext": [[31, "module-dials.extensions.simple_background_ext", false]], "dials.extensions.simple_centroid_ext": [[31, "module-dials.extensions.simple_centroid_ext", false]], "dials.util.command_line": [[33, "module-dials.util.command_line", false]], "dials.util.export_mtz": [[33, "module-dials.util.export_mtz", false]], "dials.util.export_text": [[33, "module-dials.util.export_text", false]], "dials.util.image": [[33, "module-dials.util.image", false]], "dials.util.installer": [[33, "module-dials.util.installer", false]], "dials.util.ioutil": [[33, "module-dials.util.ioutil", false]], "dials.util.nexus": [[33, "module-dials.util.nexus", false]], "dials.util.options": [[33, "module-dials.util.options", false]], "dialsindexerror": [[11, "dials.algorithms.indexing.DialsIndexError", false]], "dialsindexrefineerror": [[11, "dials.algorithms.indexing.DialsIndexRefineError", false]], "diff_phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.diff_phil", false]], "diff_phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.diff_phil", false]], "difference_rotation_matrix_axis_angle() (in module dials.algorithms.indexing.compare_orientation_matrices)": [[11, "dials.algorithms.indexing.compare_orientation_matrices.difference_rotation_matrix_axis_angle", false]], "dim (dials.algorithms.refinement.target.target property)": [[14, "dials.algorithms.refinement.target.Target.dim", false]], "dim (dials.algorithms.symmetry.cosym.target.target attribute)": [[18, "dials.algorithms.symmetry.cosym.target.Target.dim", false]], "disablempmixin (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.DisableMPmixin", false]], "dispersionspotfinderthresholdext (class in dials.extensions.dispersion_spotfinder_threshold_ext)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt", false]], "dosedecay (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.DoseDecay", false]], "dump() (in module dials.util.nexus)": [[33, "dials.util.nexus.dump", false]], "dx (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.dx", false]], "dxtbx.imageset": [[26, "module-dxtbx.imageset", false]], "dxtbx.model.beam": [[21, "module-dxtbx.model.beam", false]], "dxtbx.model.crystal": [[22, "module-dxtbx.model.crystal", false]], "dxtbx.model.detector": [[23, "module-dxtbx.model.detector", false]], "dxtbx.model.experiment_list": [[24, "module-dxtbx.model.experiment_list", false]], "dxtbx.model.goniometer": [[25, "module-dxtbx.model.goniometer", false]], "dxtbx.model.profile": [[28, "module-dxtbx.model.profile", false]], "dxtbx.model.scan": [[29, "module-dxtbx.model.scan", false]], "dxtbx.serialize.imageset": [[30, "module-dxtbx.serialize.imageset", false]], "dxtbx.serialize.load": [[30, "module-dxtbx.serialize.load", false]], "dxtbx.serialize.xds": [[30, "module-dxtbx.serialize.xds", false]], "dy (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.dy", false]], "e_refine() (in module dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.e_refine", false]], "empty() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.empty", false]], "end() (dials.util.command_line.command class method)": [[33, "dials.util.command_line.Command.end", false]], "error_model (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.error_model", false]], "estimate_global_threshold() (in module dials.extensions.dispersion_spotfinder_threshold_ext)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.estimate_global_threshold", false]], "evaluate() (dials.algorithms.indexing.model_evaluation.modelevaluation method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelEvaluation.evaluate", false]], "evaluate() (dials.algorithms.indexing.model_evaluation.strategy method)": [[11, "dials.algorithms.indexing.model_evaluation.Strategy.evaluate", false]], "exception (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.exception", false]], "executor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Executor", false]], "exp_nos (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.exp_nos", false]], "experiment_list() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.experiment_list", false]], "experiment_list_for_crystal() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.experiment_list_for_crystal", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.lauereflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager.experiment_type", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.reflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.experiment_type", false]], "experiment_type (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager attribute)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager.experiment_type", false]], "experimentlist (class in dxtbx.model)": [[24, "dxtbx.model.ExperimentList", false]], 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method)": [[24, "dxtbx.model.ExperimentList.extend", false]], "external_lookup (dxtbx.imageset.imageset property)": [[26, "dxtbx.imageset.ImageSet.external_lookup", false]], "external_lookup (dxtbx.imageset.imagesetdata property)": [[26, "dxtbx.imageset.ImageSetData.external_lookup", false]], "externaldelpsiweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy", false]], "externallookup (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookup", false]], "externallookupitembool (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookupItemBool", false]], "externallookupitemdouble (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ExternalLookupItemDouble", false]], "extract_reference_intensities() (in module dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.extract_reference_intensities", false]], "extractpixelsfromimage (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractPixelsFromImage", false]], "extractpixelsfromimage2dnoshoeboxes (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractPixelsFromImage2DNoShoeboxes", false]], "extractspots (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractSpots", false]], "extractspotsparalleltask (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.ExtractSpotsParallelTask", false]], "fft1d (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D", false]], "fft3d (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D", false]], "filename (dxtbx.imageset.externallookupitembool property)": [[26, "dxtbx.imageset.ExternalLookupItemBool.filename", false]], "filename (dxtbx.imageset.externallookupitemdouble property)": [[26, "dxtbx.imageset.ExternalLookupItemDouble.filename", false]], "filename_or_none() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.filename_or_none", false]], "filename_to_absolute() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.filename_to_absolute", false]], "filter_by_likelihood() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_likelihood", false]], "filter_by_n_indexed() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_n_indexed", false]], "filter_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.filter_by_volume", false]], "filter_doubled_cell() (in module dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.filter_doubled_cell", false]], "filter_known_symmetry() (in module dials.algorithms.indexing.basis_vector_search.combinations)": [[11, "dials.algorithms.indexing.basis_vector_search.combinations.filter_known_symmetry", false]], "filter_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.filter_obs", false]], "filter_similar_orientations() (in module dials.algorithms.indexing.basis_vector_search.combinations)": [[11, "dials.algorithms.indexing.basis_vector_search.combinations.filter_similar_orientations", false]], "filterrunner (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.FilterRunner", false]], "final_outlier_arrays (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase attribute)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.final_outlier_arrays", false]], "finalise() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.finalise", false]], "finalise() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.finalise", false]], "finalize() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.finalize", false]], "finalize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.finalize", false]], "finalize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.finalize", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)": [[12, "dials.algorithms.integration.integrator.Integrator2D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)": [[12, "dials.algorithms.integration.integrator.Integrator3D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.finalize_reflections", false]], "finalize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.finalize_reflections", false]], "find() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.find", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft1d method)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.fft3d method)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.find_basis_vectors", false]], "find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.strategy method)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.find_basis_vectors", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.lowresspotmatch method)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.find_crystal_models", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.pinkindexer method)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.find_crystal_models", false]], "find_crystal_models() (dials.algorithms.indexing.lattice_search.strategy method)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.find_crystal_models", false]], "find_lattices() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.find_lattices", false]], "find_matching_symmetry() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.find_matching_symmetry", false]], "find_max_cell() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.find_max_cell", false]], "find_max_cell() (in module dials.algorithms.indexing.max_cell)": [[11, "dials.algorithms.indexing.max_cell.find_max_cell", false]], "find_spots() (dials.algorithms.spot_finding.finder.spotfinder method)": [[16, "dials.algorithms.spot_finding.finder.SpotFinder.find_spots", false]], "finished() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.finished", false]], "finished() (dials.util.command_line.progressbar method)": [[33, "dials.util.command_line.ProgressBar.finished", false]], "fit_profiles() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.fit_profiles", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.fix_initial_parameter", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.fix_initial_parameter", false]], "fix_initial_parameter() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, 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"dials.algorithms.integration.integrator.frame_hist", false]], "from_args() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_args", false]], "from_data() (dials.algorithms.scaling.model.model.arrayscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.dosedecay class method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.kbscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.physicalscalingmodel class method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.from_data", false]], "from_data() (dials.algorithms.scaling.model.model.scalingmodelbase class method)": [[15, 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"dxtbx.model.experiment_list.ExperimentListFactory.from_filenames", false]], "from_imageset() (dxtbx.imageset.imagegrid static method)": [[26, "dxtbx.imageset.ImageGrid.from_imageset", false]], "from_imageset_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_imageset_and_crystal", false]], "from_json() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_json", false]], "from_json_file() (dials.algorithms.refinement.engine.journal class method)": [[14, "dials.algorithms.refinement.engine.Journal.from_json_file", false]], "from_json_file() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_json_file", false]], "from_mosflm_matrix() (dxtbx.model.crystal.crystalfactory static method)": [[22, "dxtbx.model.crystal.CrystalFactory.from_mosflm_matrix", false]], "from_parameters() (dials.algorithms.indexing.indexer.indexer static method)": [[11, "dials.algorithms.indexing.indexer.Indexer.from_parameters", false]], "from_parameters() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.from_parameters", false]], "from_parameters_and_experiments() (dials.algorithms.refinement.target.targetfactory static method)": [[14, "dials.algorithms.refinement.target.TargetFactory.from_parameters_and_experiments", false]], "from_parameters_data_experiments() (dials.algorithms.refinement.refiner.refinerfactory class method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.from_parameters_data_experiments", false]], "from_parameters_reflections_experiments() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.from_parameters_reflections_experiments", false]], "from_phil() (dials.algorithms.integration.integrator.parameters static method)": [[12, "dials.algorithms.integration.integrator.Parameters.from_phil", false]], "from_phil() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.from_phil", false]], "from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.from_phil", false]], "from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.from_phil", false]], "from_phil() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.from_phil", false]], "from_pickle_file() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_pickle_file", false]], "from_sequence_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_sequence_and_crystal", false]], "from_serialized_format() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_serialized_format", false]], "from_stills_and_crystal() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_stills_and_crystal", false]], "from_template() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.from_template", false]], "from_templates() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_templates", false]], "from_templates() (dxtbx.model.experimentlist static method)": [[24, "dxtbx.model.ExperimentList.from_templates", false]], "from_xds() (dxtbx.model.experiment_list.experimentlistfactory static method)": [[24, "dxtbx.model.experiment_list.ExperimentListFactory.from_xds", false]], "gain (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.gain", false]], "gaussianrsprofilemodelext (class in dials.extensions.gaussian_rs_profile_model_ext)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt", false]], "gaussnewtoniterations (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations", false]], "generate_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.generate_from_phil", false]], "generate_phil_scope() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.generate_phil_scope", false]], "generate_phil_scope() (in module dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.generate_phil_scope", false]], "get_a_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_A_as_sqr", false]], "get_a_inverse_as_sqr() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_A_inverse_as_sqr", false]], "get_accepted_refs_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_accepted_refs_size", false]], "get_alpha_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_alpha_angle", false]], "get_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_angles", false]], "get_array_range() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_array_range", false]], "get_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_axes", false]], "get_beam() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_beam", false]], "get_beam() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_beam", false]], "get_beam() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_beam", false]], "get_beam() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_beam", false]], "get_beam() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_beam", false]], "get_centroid_analyser() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_centroid_analyser", false]], "get_corrected_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_corrected_data", false]], "get_corrected_data() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_corrected_data", false]], "get_correlation_matrix_for_step() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.get_correlation_matrix_for_step", false]], "get_crystal_symmetry() (dxtbx.model.crystal method)": [[22, "dxtbx.model.Crystal.get_crystal_symmetry", false]], "get_data() (dials.util.image.reader method)": [[33, "dials.util.image.reader.get_data", false]], "get_data() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_data", false]], "get_detector() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_detector", false]], "get_detector() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_detector", false]], "get_detector() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_detector", false]], "get_detector() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_detector", false]], "get_detector() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_detector", false]], "get_detectorbase() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_detectorbase", false]], "get_direction() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_direction", false]], "get_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_domain_size_ang", false]], "get_elapsed_time() (dials.util.command_line.progressbartimer method)": [[33, "dials.util.command_line.ProgressBarTimer.get_elapsed_time", false]], "get_entry() (in module dials.util.nexus)": [[33, "dials.util.nexus.get_entry", false]], "get_experiments() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_experiments", false]], "get_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_fixed_rotation", false]], "get_format_class() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_format_class", false]], "get_format_class() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_format_class", false]], "get_free_reflections() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_free_reflections", false]], "get_free_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_free_reflections", false]], "get_gain() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_gain", false]], "get_gain() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_gain", false]], "get_goniometer() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_goniometer", false]], "get_goniometer() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_goniometer", false]], "get_goniometer() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_goniometer", false]], "get_grid_size() (dxtbx.imageset.imagegrid method)": [[26, "dxtbx.imageset.ImageGrid.get_grid_size", false]], "get_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.get_half_mosaicity_deg", false]], "get_image_identifier() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_image_identifier", false]], "get_image_identifier() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_image_identifier", false]], "get_indexed() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_indexed", false]], "get_inverse_ub_matrix_from_xparm() (in module dials.util.ioutil)": [[33, "dials.util.ioutil.get_inverse_ub_matrix_from_xparm", false]], "get_kappa_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_angle", false]], "get_kappa_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_kappa_axis", false]], "get_mask() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_mask", false]], "get_mask() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_mask", false]], "get_master_path() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_master_path", false]], "get_matches() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_matches", false]], "get_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_matches", false]], "get_max_inscribed_resolution() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_max_inscribed_resolution", false]], "get_max_resolution() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_max_resolution", false]], "get_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.get_mosaicity", false]], "get_names() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_names", false]], "get_names() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_names", false]], "get_nrows() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.get_nrows", false]], "get_num_matches() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches", false]], "get_num_matches_for_experiment() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches_for_experiment", false]], "get_num_matches_for_panel() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.get_num_matches_for_panel", false]], "get_num_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_num_scan_points", false]], "get_num_steps() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.get_num_steps", false]], "get_obs() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_obs", false]], "get_omega_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_omega_angle", false]], "get_omega_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_omega_axis", false]], "get_panel_intersection() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_panel_intersection", false]], "get_param_reporter() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_param_reporter", false]], "get_parameter_correlation_matrix() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.get_parameter_correlation_matrix", false]], "get_params() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_params", false]], "get_path() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_path", false]], "get_path() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_path", false]], "get_pedestal() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_pedestal", false]], "get_phi_angle() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_phi_angle", false]], "get_phi_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_phi_axis", false]], "get_raw_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_raw_data", false]], "get_ray_intersection() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.get_ray_intersection", false]], "get_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_rotation_axis", false]], "get_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_rotation_axis_datum", false]], "get_sample_size() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.get_sample_size", false]], "get_scan() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_scan", false]], "get_scan() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_scan", false]], "get_scan() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_scan", false]], "get_scan() (dxtbx.imageset.imagesetlazy method)": [[26, "dxtbx.imageset.ImageSetLazy.get_scan", false]], "get_scan() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_scan", false]], "get_scan_axis() (dxtbx.model.goniometer.kappagoniometer method)": [[25, "dxtbx.model.goniometer.KappaGoniometer.get_scan_axis", false]], "get_scan_axis() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.get_scan_axis", false]], "get_setting_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation", false]], "get_setting_rotation_at_scan_point() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_point", false]], "get_setting_rotation_at_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.get_setting_rotation_at_scan_points", false]], "get_shared_components() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.get_shared_components", false]], "get_shared_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.get_shared_components", false]], "get_shared_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.get_shared_components", false]], "get_space_group_type_from_xparm() (in module dials.util.ioutil)": [[33, "dials.util.ioutil.get_space_group_type_from_xparm", false]], "get_spectrum() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_spectrum", false]], "get_template() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.get_template", false]], "get_template() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_template", false]], "get_template() (dxtbx.serialize.xds.to_xds method)": [[30, "dxtbx.serialize.xds.to_xds.get_template", false]], "get_vendor() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.get_vendor", false]], "get_vendortype() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.get_vendortype", false]], "get_weighting_strategy_override() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.get_weighting_strategy_override", false]], "goniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.Goniometer", false]], "goniometercomparison (class in dxtbx.model.experiment_list)": [[24, "dxtbx.model.experiment_list.GoniometerComparison", false]], "goniometerfactory (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.GoniometerFactory", false]], "goniometers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.goniometers", false]], "gradient_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.gradient_threshold", false]], "groups_cache() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.groups_cache", false]], "has_dynamic_mask() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.has_dynamic_mask", false]], "has_projection_2d() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.has_projection_2d", false]], "has_single_file_reader() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.has_single_file_reader", false]], "heading() (in module dials.util.command_line)": [[33, "dials.util.command_line.heading", false]], "hierarchy() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.hierarchy", false]], "hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.hist", false]], "history (dials.algorithms.refinement.refiner.refiner property)": [[14, "dials.algorithms.refinement.refiner.Refiner.history", false]], "hkl_offset (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.hkl_offset", false]], "id_ (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.dosedecay attribute)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.id_", false]], "id_ (dials.algorithms.scaling.model.model.kbscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.id_", false]], "id_ (dials.algorithms.scaling.model.model.scalingmodelbase attribute)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.id_", false]], "identifiers (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.identifiers", false]], "identifiers() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.identifiers", false]], "identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.identifiers", false]], "identify_outliers() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.identify_outliers", false]], "imagegrid (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageGrid", false]], "imagesequence (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSequence", false]], "imagesequence_from_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imagesequence_from_dict", false]], "imagesequence_to_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imagesequence_to_dict", false]], "imageset (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSet", false]], "imageset() (in module dxtbx.serialize.load)": [[30, "dxtbx.serialize.load.imageset", false]], "imageset_from_anyset() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.imageset_from_anyset", false]], "imageset_from_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imageset_from_dict", false]], "imageset_to_dict() (in module dxtbx.serialize.imageset)": [[30, "dxtbx.serialize.imageset.imageset_to_dict", false]], "imagesetdata (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetData", false]], "imagesetfactory (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetFactory", false]], "imagesetlazy (class in dxtbx.imageset)": [[26, "dxtbx.imageset.ImageSetLazy", false]], "imagesets() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.imagesets", false]], "imgcif() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.imgCIF", false]], "imgcif() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.imgCIF", false]], "imgcif() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.imgCIF", false]], "imgcif() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.imgCIF", false]], "imgcif_h() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.imgCIF_H", false]], "imgcif_h() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.imgCIF_H", false]], "importer (class in dials.util.options)": [[33, "dials.util.options.Importer", false]], "include_gui_packages (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.include_gui_packages", false]], "indent (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.indent", false]], "index() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.index", false]], "index() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.index", false]], "index_reflections() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.index_reflections", false]], "indexer (class in dials.algorithms.indexing.indexer)": [[11, "dials.algorithms.indexing.indexer.Indexer", false]], "indices() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.indices", false]], "indices() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.indices", false]], "initialise() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.initialise", false]], "initialise_smooth_input() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.initialise_smooth_input", false]], "initialize() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.initialize", false]], "initialize() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.initialize", false]], "initialize() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.initialize", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integrator2d static method)": [[12, "dials.algorithms.integration.integrator.Integrator2D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integrator3d static method)": [[12, "dials.algorithms.integration.integrator.Integrator3D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorflat3d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorsingle2d static method)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.initialize_reflections", false]], "initialize_reflections() (dials.algorithms.integration.integrator.integratorstills static method)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.initialize_reflections", false]], "installer (class in dials.util.installer)": [[33, "dials.util.installer.installer", false]], "installer_dir (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.installer_dir", false]], "integrate() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.integrate", false]], "integrate() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.integrate", false]], "integrator (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator", false]], "integrator2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator2D", false]], "integrator3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator3D", false]], "integrator3dthreaded (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded", false]], "integratorexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor", false]], "integratorflat3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D", false]], "integratorsingle2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D", false]], "integratorstills (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.IntegratorStills", false]], "inv_d2() (dials.algorithms.background.radialaverage method)": [[10, "dials.algorithms.background.RadialAverage.inv_d2", false]], "invalidphilerror": [[33, "dials.util.options.InvalidPhilError", false]], "is_consistent() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.is_consistent", false]], "is_marked_for_rejection() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.is_marked_for_rejection", false]], "is_marked_for_rejection() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.is_marked_for_rejection", false]], "is_scaled (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.is_scaled", false]], "is_similar_to() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.is_similar_to", false]], "is_similar_to() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.is_similar_to", false]], "is_similar_to() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.is_similar_to", false]], "is_similar_to() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.is_similar_to", false]], "is_single_file_reader() (dxtbx.imageset.memreader static method)": [[26, "dxtbx.imageset.MemReader.is_single_file_reader", false]], "iter_levelorder() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_levelorder", false]], "iter_panels() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_panels", false]], "iter_preorder() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.iter_preorder", false]], "jacobian_condition_number() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.jacobian_condition_number", false]], "job() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.job", false]], "joblist (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.JobList", false]], "journal (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.Journal", false]], "kappa() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.kappa", false]], "kappagoniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.KappaGoniometer", false]], "kbscalingmodel (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel", false]], "kernel_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.kernel_normalisation", false]], "known_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.known_axis", false]], "laue_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.laue_manager", false]], "lauegroupanalysis (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.LaueGroupAnalysis", false]], "laueleastsquaresresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff", false]], "lauemixedweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy", false]], "lauereflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager", false]], "lauestatisticalweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy", false]], "lbfgs_with_curvs (class in dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs", false]], "lbfgscurvs (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs", false]], "leastsquarespositionalresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff", false]], "leastsquarespositionalresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoffSparse", false]], "leastsquaresstillsresidualwithrmsdcutoff (class in dials.algorithms.refinement.target_stills)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff", false]], "leastsquaresstillsresidualwithrmsdcutoffsparse (class in dials.algorithms.refinement.target_stills)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoffSparse", false]], "levenbergmarquardtiterations (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations", false]], "limit_image_range() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.limit_image_range", false]], "limit_image_range() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.limit_image_range", false]], "load() (in module dials.util.nexus)": [[33, "dials.util.nexus.load", false]], "load_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.load_error_model", false]], "load_image() (dials.algorithms.spot_finding.factory.spotfinderfactory static method)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory.load_image", false]], "log_summary() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.log_summary", false]], "lowresspotmatch (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch", false]], "madmergedmtzwriter (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MADMergedMTZWriter", false]], "make_apps (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.make_apps", false]], "make_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_beam", false]], "make_combined_plots() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.make_combined_plots", false]], "make_detector() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.make_detector", false]], "make_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_goniometer", false]], "make_imageset() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.make_imageset", false]], "make_kappa_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_kappa_goniometer", false]], "make_multi_axis_goniometer() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.make_multi_axis_goniometer", false]], "make_polarized_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_polarized_beam", false]], "make_polychromatic_beam() (dxtbx.model.beam.beamfactory static method)": [[21, "dxtbx.model.beam.BeamFactory.make_polychromatic_beam", false]], "make_scan() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.make_scan", false]], "make_scan_from_properties() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.make_scan_from_properties", false]], "make_sequence() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.make_sequence", false]], "mark_for_rejection() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.mark_for_rejection", false]], "mark_for_rejection() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.mark_for_rejection", false]], "mask (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.mask", false]], "masker() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.masker", false]], "masker() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.masker", false]], "master_path() (dxtbx.imageset.memreader static method)": [[26, "dxtbx.imageset.MemReader.master_path", false]], "match_wavelengths() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.match_wavelengths", false]], "max_length (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.max_length", false]], "max_possible_wl (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.max_possible_wl", false]], "max_shift_over_esd (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.max_shift_over_esd", false]], "mean() (dials.algorithms.background.radialaverage method)": [[10, "dials.algorithms.background.RadialAverage.mean", false]], "median_unit_cell() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.median_unit_cell", false]], "memreader (class in dxtbx.imageset)": [[26, "dxtbx.imageset.MemReader", false]], "merge_panel_scope_extracts_by_id() (in module dxtbx.model.detector)": [[23, "dxtbx.model.detector.merge_panel_scope_extracts_by_id", false]], "mergedmtzwriter (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MergedMTZWriter", false]], "message (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.message", false]], "metric_supergroup() (in module dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.metric_supergroup", false]], "min_wl (dials.util.export_mtz.wavelengthgroup attribute)": [[33, "dials.util.export_mtz.WavelengthGroup.min_wl", false]], "minimize_scipy() (in module dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.minimize_scipy", false]], "minimize_scitbx_lbfgs() (in module dials.algorithms.symmetry.cosym.engine)": [[18, "dials.algorithms.symmetry.cosym.engine.minimize_scitbx_lbfgs", false]], "ml_aniso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.ml_aniso_normalisation", false]], "ml_iso_normalisation() (dials.algorithms.symmetry.symmetry_base static method)": [[18, "dials.algorithms.symmetry.symmetry_base.ml_iso_normalisation", false]], "model_likelihood (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.model_likelihood", false]], "modelevaluation (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelEvaluation", false]], "modelrank (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRank", false]], "modelrankfilter (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter", false]], "modelrankweighted (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted", false]], "module": [[10, "module-dials.algorithms.background", false], [11, "module-dials.algorithms.indexing", false], [11, "module-dials.algorithms.indexing.assign_indices", false], [11, "module-dials.algorithms.indexing.basis_vector_search", false], [11, "module-dials.algorithms.indexing.basis_vector_search.combinations", false], [11, "module-dials.algorithms.indexing.basis_vector_search.optimise", false], [11, "module-dials.algorithms.indexing.compare_orientation_matrices", false], [11, "module-dials.algorithms.indexing.indexer", false], [11, "module-dials.algorithms.indexing.lattice_search", false], [11, "module-dials.algorithms.indexing.max_cell", false], [11, "module-dials.algorithms.indexing.model_evaluation", false], [11, "module-dials.algorithms.indexing.nearest_neighbor", false], [11, "module-dials.algorithms.indexing.refinement", false], [11, "module-dials.algorithms.indexing.stills_indexer", false], [11, "module-dials.algorithms.indexing.symmetry", false], [12, "module-dials.algorithms.integration.integrator", false], [13, "module-dials.algorithms.profile_model", false], [14, "module-dials.algorithms.refinement.engine", false], [14, "module-dials.algorithms.refinement.refiner", false], [14, "module-dials.algorithms.refinement.reflection_manager", false], [14, "module-dials.algorithms.refinement.target", false], [14, "module-dials.algorithms.refinement.target_stills", false], [14, "module-dials.algorithms.refinement.weighting_strategies", false], [15, "module-dials.algorithms.scaling", false], [15, "module-dials.algorithms.scaling.model.model", false], [15, "module-dials.algorithms.scaling.outlier_rejection", false], [16, "module-dials.algorithms.spot_finding.factory", false], [16, "module-dials.algorithms.spot_finding.finder", false], [17, "module-dials.algorithms.spot_prediction.reflection_predictor", false], [18, "module-dials.algorithms.symmetry", false], [18, "module-dials.algorithms.symmetry.cosym", false], [18, "module-dials.algorithms.symmetry.cosym.engine", false], [18, "module-dials.algorithms.symmetry.cosym.target", false], [18, "module-dials.algorithms.symmetry.laue_group", false], [18, "module-dials.algorithms.symmetry.reindex_to_reference", false], [20, "module-dials.array_family.flex", false], [21, "module-dxtbx.model.beam", false], [22, "module-dxtbx.model.crystal", false], [23, "module-dxtbx.model.detector", false], [24, "module-dxtbx.model.experiment_list", false], [25, "module-dxtbx.model.goniometer", false], [26, "module-dxtbx.imageset", false], [28, "module-dxtbx.model.profile", false], [29, "module-dxtbx.model.scan", false], [30, "module-dxtbx.serialize.imageset", false], [30, "module-dxtbx.serialize.load", false], [30, "module-dxtbx.serialize.xds", false], [31, "module-dials.extensions.dispersion_spotfinder_threshold_ext", false], [31, "module-dials.extensions.gaussian_rs_profile_model_ext", false], [31, "module-dials.extensions.null_background_ext", false], [31, "module-dials.extensions.simple_background_ext", false], [31, "module-dials.extensions.simple_centroid_ext", false], [33, "module-dials.util.command_line", false], [33, "module-dials.util.export_mtz", false], [33, "module-dials.util.export_text", false], [33, "module-dials.util.image", false], [33, "module-dials.util.installer", false], [33, "module-dials.util.ioutil", false], [33, "module-dials.util.nexus", false], [33, "module-dials.util.options", false]], "mosaiccrystalkabsch2010 (class in dxtbx.model)": [[22, "dxtbx.model.MosaicCrystalKabsch2010", false]], "mosaiccrystalsauter2014 (class in dxtbx.model)": [[22, "dxtbx.model.MosaicCrystalSauter2014", false]], "mtzwriterbase (class in dials.util.export_mtz)": [[33, "dials.util.export_mtz.MTZWriterBase", false]], "mu (dials.algorithms.refinement.engine.levenbergmarquardtiterations property)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.mu", false]], "multi_axis() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.multi_axis", false]], "multi_axis_goniometer_from_phil() (dxtbx.model.goniometer.goniometerfactory static method)": [[25, "dxtbx.model.goniometer.GoniometerFactory.multi_axis_goniometer_from_phil", false]], "multiaxisgoniometer (class in dxtbx.model.goniometer)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer", false]], "n() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.n", false]], "n_indexed (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.n_indexed", false]], "n_params (dials.algorithms.scaling.model.model.scalingmodelbase property)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.n_params", false]], "name (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext attribute)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.name", false]], "name (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext attribute)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.name", false]], "name (dials.extensions.null_background_ext.nullbackgroundext attribute)": [[31, "dials.extensions.null_background_ext.NullBackgroundExt.name", false]], "name (dials.extensions.simple_background_ext.simplebackgroundext attribute)": [[31, "dials.extensions.simple_background_ext.SimpleBackgroundExt.name", false]], "name (dials.extensions.simple_centroid_ext.simplecentroidext attribute)": [[31, "dials.extensions.simple_centroid_ext.SimpleCentroidExt.name", false]], "name (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.name", false]], "neighboranalysis (class in dials.algorithms.indexing.nearest_neighbor)": [[11, "dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis", false]], "new() (dxtbx.imageset.imagesetfactory static method)": [[26, "dxtbx.imageset.ImageSetFactory.new", false]], "nframes_hist() (in module dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.nframes_hist", false]], "normdevoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.NormDevOutlierRejection", false]], "nullbackgroundext (class in dials.extensions.null_background_ext)": [[31, "dials.extensions.null_background_ext.NullBackgroundExt", false]], "nullify_all_single_file_reader_format_instances() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.nullify_all_single_file_reader_format_instances", false]], "num_reflections() (dials.algorithms.integration.integrator.reflectionmanager method)": [[12, "dials.algorithms.integration.integrator.ReflectionManager.num_reflections", false]], "num_scan_points (dxtbx.model.goniometer.goniometer property)": [[25, "dxtbx.model.goniometer.Goniometer.num_scan_points", false]], "numerator() (dials.algorithms.symmetry.laue_group.correlationcoefficientaccumulator method)": [[18, "dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator.numerator", false]], "optimise_basis_vectors() (in module dials.algorithms.indexing.basis_vector_search.optimise)": [[11, "dials.algorithms.indexing.basis_vector_search.optimise.optimise_basis_vectors", false]], "optionparser (class in dials.util.options)": [[33, "dials.util.options.OptionParser", false]], "outlierrejectionbase (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase", false]], "overwrite_from_phil() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.overwrite_from_phil", false]], "p_cc_given_not_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_not_s", false]], "p_cc_given_s (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_cc_given_s", false]], "p_s_given_cc (dials.algorithms.symmetry.laue_group.scorecorrelationcoefficient property)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient.p_s_given_cc", false]], "parameter_vector_norm() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.parameter_vector_norm", false]], "parameters (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters", false]], "parameters.filter (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Filter", false]], "parameters.profile (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Profile", false]], "parameters.profile.validation (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Parameters.Profile.Validation", false]], "params() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.params", false]], "parse_args() (dials.util.options.argumentparser method)": [[33, "dials.util.options.ArgumentParser.parse_args", false]], "parse_args() (dials.util.options.philcommandparser method)": [[33, "dials.util.options.PhilCommandParser.parse_args", false]], "parse_known_args() (dials.util.options.argumentparserbase method)": [[33, "dials.util.options.ArgumentParserBase.parse_known_args", false]], "partial_data() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.partial_data", false]], "partial_set() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.partial_set", false]], "partial_set() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.partial_set", false]], "paths() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.paths", false]], "paths() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.paths", false]], "peakcentroiddistancefilter (class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter", false]], "pedestal (dxtbx.imageset.externallookup property)": [[26, "dxtbx.imageset.ExternalLookup.pedestal", false]], "per_image() (dials.algorithms.refinement.reflection_manager.blockcalculator method)": [[14, "dials.algorithms.refinement.reflection_manager.BlockCalculator.per_image", false]], "per_width() (dials.algorithms.refinement.reflection_manager.blockcalculator method)": [[14, "dials.algorithms.refinement.reflection_manager.BlockCalculator.per_width", false]], "phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.phil", false]], "phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.phil", false]], "phil() (dials.extensions.dispersion_spotfinder_threshold_ext.dispersionspotfinderthresholdext static method)": [[31, "dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt.phil", false]], "phil() (dials.extensions.gaussian_rs_profile_model_ext.gaussianrsprofilemodelext static method)": [[31, "dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt.phil", false]], "phil() (dials.extensions.simple_background_ext.simplebackgroundext static method)": [[31, "dials.extensions.simple_background_ext.SimpleBackgroundExt.phil", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.fft1d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.fft3d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_help", false]], "phil_help (dials.algorithms.indexing.basis_vector_search.strategy attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.pinkindexer attribute)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.phil_help", false]], "phil_help (dials.algorithms.indexing.lattice_search.strategy attribute)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.phil_help", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.fft1d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT1D.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.fft3d attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.FFT3D.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.realspacegridsearch attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.phil_scope", false]], "phil_scope (dials.algorithms.indexing.basis_vector_search.strategy attribute)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.lowresspotmatch attribute)": [[11, "dials.algorithms.indexing.lattice_search.LowResSpotMatch.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.pinkindexer attribute)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer.phil_scope", false]], "phil_scope (dials.algorithms.indexing.lattice_search.strategy attribute)": [[11, "dials.algorithms.indexing.lattice_search.Strategy.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.arrayscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.dosedecay attribute)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.kbscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.phil_scope", false]], "phil_scope (dials.algorithms.scaling.model.model.physicalscalingmodel attribute)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.phil_scope", false]], "philcommandparser (class in dials.util.options)": [[33, "dials.util.options.PhilCommandParser", false]], "physicalscalingmodel (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel", false]], "pinkindexer (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.PinkIndexer", false]], "pixel_list_to_reflection_table() (in module dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.pixel_list_to_reflection_table", false]], "pixel_list_to_shoeboxes() (in module dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.pixel_list_to_shoeboxes", false]], "plot_displacements() (in module dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.plot_displacements", false]], "plot_histogram() (dials.algorithms.indexing.nearest_neighbor.neighboranalysis method)": [[11, "dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis.plot_histogram", false]], "plot_model_components() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.plot_model_components", false]], "plot_model_components() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.plot_model_components", false]], "plot_scaling_models() (in module dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.plot_scaling_models", false]], "predict() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict", false]], "predict_for_free_reflections() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict_for_free_reflections", false]], "predict_for_indexed() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.predict_for_indexed", false]], "predict_for_reflection_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.predict_for_reflection_table", false]], "predict_for_reflection_table() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.predict_for_reflection_table", false]], "predict_for_reflection_table() (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff method)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.predict_for_reflection_table", false]], "predictor() (dials.algorithms.spot_prediction.reflection_predictor.reflectionpredictor method)": [[17, "dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor.predictor", false]], "prepare_for_step() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.prepare_for_step", false]], "print_exp_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_exp_rmsd_table", false]], "print_out_of_sample_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_out_of_sample_rmsd_table", false]], "print_panel_rmsd_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_panel_rmsd_table", false]], "print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.lauereflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.LaueReflectionManager.print_stats_on_matches", false]], "print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.print_stats_on_matches", false]], "print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.stillsreflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager.print_stats_on_matches", false]], "print_step_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.print_step_table", false]], "print_time (dials.util.command_line.command attribute)": [[33, "dials.util.command_line.Command.print_time", false]], "process() (dials.algorithms.integration.integrator.executor method)": [[12, "dials.algorithms.integration.integrator.Executor.process", false]], "process() (dials.algorithms.integration.integrator.integratorexecutor method)": [[12, "dials.algorithms.integration.integrator.IntegratorExecutor.process", false]], "process() (dials.algorithms.integration.integrator.profilemodellerexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor.process", false]], "process() (dials.algorithms.integration.integrator.profilevalidatorexecutor method)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor.process", false]], "processor2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Processor2D", false]], "processor3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.Processor3D", false]], "processorclass (dials.algorithms.integration.integrator.integrator2d attribute)": [[12, "dials.algorithms.integration.integrator.Integrator2D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integrator3d attribute)": [[12, "dials.algorithms.integration.integrator.Integrator3D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorflat3d attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorFlat3D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorsingle2d attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorSingle2D.ProcessorClass", false]], "processorclass (dials.algorithms.integration.integrator.integratorstills attribute)": [[12, "dials.algorithms.integration.integrator.IntegratorStills.ProcessorClass", false]], "processorflat3d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorFlat3D", false]], "processorsingle2d (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorSingle2D", false]], "processorstills (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProcessorStills", false]], "product_name (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.product_name", false]], "product_specific_finalize_install() (dials.util.installer.installer method)": [[33, "dials.util.installer.installer.product_specific_finalize_install", false]], "profilemodelfactory (class in dxtbx.model.profile)": [[28, "dxtbx.model.profile.ProfileModelFactory", false]], "profilemodellerexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProfileModellerExecutor", false]], "profiles() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.profiles", false]], "profilevalidatorexecutor (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ProfileValidatorExecutor", false]], "progressbar (class in dials.util.command_line)": [[33, "dials.util.command_line.ProgressBar", false]], "progressbartimer (class in dials.util.command_line)": [[33, "dials.util.command_line.ProgressBarTimer", false]], "radialaverage (class in dials.algorithms.background)": [[10, "dials.algorithms.background.RadialAverage", false]], "read() (dxtbx.imageset.memreader method)": [[26, "dxtbx.imageset.MemReader.read", false]], "read_file() (dials.util.image.reader method)": [[33, "dials.util.image.reader.read_file", false]], "reader (class in dials.util.image)": [[33, "dials.util.image.reader", false]], "reader() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.reader", false]], "reader() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.reader", false]], "realspacegridsearch (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch", false]], "reason_for_termination (dials.algorithms.refinement.engine.journal attribute)": [[14, "dials.algorithms.refinement.engine.Journal.reason_for_termination", false]], "record_intensity_combination_imid() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.record_intensity_combination_Imid", false]], "refine() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.refine", false]], "refine() (dials.algorithms.indexing.stills_indexer.stillsindexer method)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer.refine", false]], "refine() (in module dials.algorithms.indexing.refinement)": [[11, "dials.algorithms.indexing.refinement.refine", false]], "refiner (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.Refiner", false]], "refinerfactory (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory", false]], "refinery (class in dials.algorithms.refinement.engine)": [[14, "dials.algorithms.refinement.engine.Refinery", false]], "reflectionmanager (class in dials.algorithms.integration.integrator)": [[12, "dials.algorithms.integration.integrator.ReflectionManager", false]], "reflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager", false]], "reflectionmanagerfactory (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory", false]], "reflectionpredictor (class in dials.algorithms.spot_prediction.reflection_predictor)": [[17, "dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor", false]], "reflections_after_outlier_rejection() (dials.algorithms.refinement.refiner.refinerfactory class method)": [[14, "dials.algorithms.refinement.refiner.RefinerFactory.reflections_after_outlier_rejection", false]], "reflections_and_experiments_from_files() (in module dials.util.options)": [[33, "dials.util.options.reflections_and_experiments_from_files", false]], "reject_outliers() (in module dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.reject_outliers", false]], "remove_on_experiment_identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.remove_on_experiment_identifiers", false]], "remove_sources_default (dials.util.installer.installer attribute)": [[33, "dials.util.installer.installer.remove_sources_default", false]], "replace() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.replace", false]], "report() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.report", false]], "report() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.report", false]], "report_progress() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.report_progress", false]], "reset_accepted_reflections() (dials.algorithms.refinement.reflection_manager.reflectionmanager method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManager.reset_accepted_reflections", false]], "reset_scan_points() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.reset_scan_points", false]], "resolution_filter_from_array() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.resolution_filter_from_array", false]], "resolution_filter_from_reflections_experiments() (in module dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.resolution_filter_from_reflections_experiments", false]], "restart() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.restart", false]], "result (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.Result", false]], "rmsd_names (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_names (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_names", false]], "rmsd_units (dials.algorithms.refinement.target.laueleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target.target attribute)": [[14, "dials.algorithms.refinement.target.Target.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target.tofleastsquaresresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff.rmsd_units", false]], "rmsd_units (dials.algorithms.refinement.target_stills.leastsquaresstillsresidualwithrmsdcutoff attribute)": [[14, "dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff.rmsd_units", false]], "rmsds (dials.algorithms.indexing.model_evaluation.result attribute)": [[11, "dials.algorithms.indexing.model_evaluation.Result.rmsds", false]], "rmsds() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.rmsds", false]], "rmsds() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds", false]], "rmsds_for_experiment() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds_for_experiment", false]], "rmsds_for_panel() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds_for_panel", false]], "rmsds_for_reflection_table() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.rmsds_for_reflection_table", false]], "rmsds_for_reflection_table() (dials.algorithms.refinement.target.target method)": [[14, "dials.algorithms.refinement.target.Target.rmsds_for_reflection_table", false]], "rotate_around_origin() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.rotate_around_origin", false]], "rotate_around_origin() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.rotate_around_origin", false]], "rotate_crystal() (in module dials.util.export_mtz)": [[33, "dials.util.export_mtz.rotate_crystal", false]], "rotation_matrix_differences() (in module dials.algorithms.indexing.compare_orientation_matrices)": [[11, "dials.algorithms.indexing.compare_orientation_matrices.rotation_matrix_differences", false]], "rotation_scan_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.rotation_scan_manager", false]], "run() (dials.algorithms.refinement.engine.gaussnewtoniterations method)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.run", false]], "run() (dials.algorithms.refinement.engine.lbfgscurvs method)": [[14, "dials.algorithms.refinement.engine.LBFGScurvs.run", false]], "run() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.run", false]], "run() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.run", false]], "run() (dials.algorithms.refinement.engine.simplelbfgs method)": [[14, "dials.algorithms.refinement.engine.SimpleLBFGS.run", false]], "run() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.run", false]], "run() (dials.algorithms.scaling.outlier_rejection.outlierrejectionbase method)": [[15, "dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase.run", false]], "run() (dials.algorithms.spot_finding.factory.backgroundgradientfilter method)": [[16, "dials.algorithms.spot_finding.factory.BackgroundGradientFilter.run", false]], "run() (dials.algorithms.spot_finding.factory.peakcentroiddistancefilter method)": [[16, "dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter.run", false]], "run() (dials.algorithms.spot_finding.factory.spotdensityfilter method)": [[16, "dials.algorithms.spot_finding.factory.SpotDensityFilter.run", false]], "run() (dials.algorithms.symmetry.cosym.cosymanalysis method)": [[18, "dials.algorithms.symmetry.cosym.CosymAnalysis.run", false]], "run_lbfgs() (dials.algorithms.refinement.engine.adaptlbfgs method)": [[14, "dials.algorithms.refinement.engine.AdaptLbfgs.run_lbfgs", false]], "scaling_models() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.scaling_models", false]], "scalingmodelbase (class in dials.algorithms.scaling.model.model)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase", false]], "scanfactory (class in dxtbx.model.scan)": [[29, "dxtbx.model.scan.ScanFactory", false]], "scans() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.scans", false]], "scanvaryingrefiner (class in dials.algorithms.refinement.refiner)": [[14, "dials.algorithms.refinement.refiner.ScanVaryingRefiner", false]], "score_by_fraction_indexed() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_fraction_indexed", false]], "score_by_rmsd_xy() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_rmsd_xy", false]], "score_by_volume() (dials.algorithms.indexing.model_evaluation.modelrankweighted method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankWeighted.score_by_volume", false]], "score_vectors() (dials.algorithms.indexing.basis_vector_search.realspacegridsearch method)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.score_vectors", false]], "scorecorrelationcoefficient (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient", false]], "scoresubgroup (class in dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.ScoreSubGroup", false]], "scoresubgroup (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.ScoreSubGroup", false]], "scoresymmetryelement (class in dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.ScoreSymmetryElement", false]], "scoresymmetryelement (class in dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.ScoreSymmetryElement", false]], "search() (dxtbx.model.scan.scanfactory static method)": [[29, "dxtbx.model.scan.ScanFactory.search", false]], "search_directions (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_directions", false]], "search_vectors (dials.algorithms.indexing.basis_vector_search.realspacegridsearch property)": [[11, "dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch.search_vectors", false]], "select_on_experiment_identifiers() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.select_on_experiment_identifiers", false]], "selection_used_for_refinement() (dials.algorithms.refinement.refiner.refiner method)": [[14, "dials.algorithms.refinement.refiner.Refiner.selection_used_for_refinement", false]], "sensor() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.sensor", false]], "set_angles() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.set_angles", false]], "set_axes() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.set_axes", false]], "set_beam() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_beam", false]], "set_beam() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_beam", false]], "set_beam() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_beam", false]], "set_cholesky_factor() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.set_cholesky_factor", false]], "set_detector() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_detector", false]], "set_detector() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_detector", false]], "set_detector() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_detector", false]], "set_dimensions() (dials.algorithms.symmetry.cosym.target.target method)": [[18, "dials.algorithms.symmetry.cosym.target.Target.set_dimensions", false]], "set_domain_size_ang() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.set_domain_size_ang", false]], "set_error_model() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_error_model", false]], "set_fixed_rotation() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_fixed_rotation", false]], "set_format_class() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_format_class", false]], "set_goniometer() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.set_goniometer", false]], "set_goniometer() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.set_goniometer", false]], "set_goniometer() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_goniometer", false]], "set_half_mosaicity_deg() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.set_half_mosaicity_deg", false]], "set_last_cell() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.set_last_cell", false]], "set_mosaicity() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.set_mosaicity", false]], "set_nproc() (dials.algorithms.refinement.engine.disablempmixin method)": [[14, "dials.algorithms.refinement.engine.DisableMPmixin.set_nproc", false]], "set_nproc() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.set_nproc", false]], "set_params() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_params", false]], "set_rotation_axis() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_rotation_axis", false]], "set_rotation_axis_datum() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.set_rotation_axis_datum", false]], "set_scaling_model_as_scaled() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_scaling_model_as_scaled", false]], "set_scaling_model_as_unscaled() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.set_scaling_model_as_unscaled", false]], "set_scan() (dxtbx.imageset.imagesequence method)": [[26, 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"dials.algorithms.scaling.model.model.ScalingModelBase.set_valid_image_range", false]], "set_vendor() (dxtbx.imageset.imagesetdata method)": [[26, "dxtbx.imageset.ImageSetData.set_vendor", false]], "setup_indexing() (dials.algorithms.indexing.indexer.indexer method)": [[11, "dials.algorithms.indexing.indexer.Indexer.setup_indexing", false]], "setup_mu() (dials.algorithms.refinement.engine.levenbergmarquardtiterations method)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.setup_mu", false]], "shoebox_memory() (dials.algorithms.integration.integrator.joblist method)": [[12, "dials.algorithms.integration.integrator.JobList.shoebox_memory", false]], "shoeboxes_to_reflection_table() (in module dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.shoeboxes_to_reflection_table", false]], "show() (dxtbx.model.crystal method)": [[22, "dxtbx.model.Crystal.show", false]], "show_experiments() (dials.algorithms.indexing.indexer.indexer 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(class in dials.algorithms.spot_finding.factory)": [[16, "dials.algorithms.spot_finding.factory.SpotFinderFactory", false]], "stars (dials.algorithms.symmetry.cosym.scoresubgroup property)": [[18, "dials.algorithms.symmetry.cosym.ScoreSubGroup.stars", false]], "stars (dials.algorithms.symmetry.cosym.scoresymmetryelement property)": [[18, "dials.algorithms.symmetry.cosym.ScoreSymmetryElement.stars", false]], "start() (dials.util.command_line.command class method)": [[33, "dials.util.command_line.Command.start", false]], "statisticalweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.StatisticalWeightingStrategy", false]], "step_backward() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.step_backward", false]], "step_forward() (dials.algorithms.refinement.engine.adaptlstbx method)": [[14, "dials.algorithms.refinement.engine.AdaptLstbx.step_forward", false]], "step_threshold (dials.algorithms.refinement.engine.gaussnewtoniterations attribute)": [[14, "dials.algorithms.refinement.engine.GaussNewtonIterations.step_threshold", false]], "stills_manager() (dials.algorithms.refinement.reflection_manager.reflectionmanagerfactory static method)": [[14, "dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory.stills_manager", false]], "stillsindexer (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexer", false]], "stillsindexerbasisvectorsearch (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerBasisVectorSearch", false]], "stillsindexerknownorientation (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerKnownOrientation", false]], "stillsindexerlatticesearch (class in dials.algorithms.indexing.stills_indexer)": [[11, "dials.algorithms.indexing.stills_indexer.StillsIndexerLatticeSearch", false]], "stillsreflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.StillsReflectionManager", false]], "stillsweightingstrategy (class in dials.algorithms.refinement.weighting_strategies)": [[14, "dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy", false]], "strategy (class in dials.algorithms.indexing.basis_vector_search)": [[11, "dials.algorithms.indexing.basis_vector_search.Strategy", false]], "strategy (class in dials.algorithms.indexing.lattice_search)": [[11, "dials.algorithms.indexing.lattice_search.Strategy", false]], "strategy (class in dials.algorithms.indexing.model_evaluation)": [[11, "dials.algorithms.indexing.model_evaluation.Strategy", false]], "subgroups_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)": [[18, "dials.algorithms.symmetry.cosym.SymmetryAnalysis.subgroups_table", false]], "summary() (dials.algorithms.integration.integrator.integrator method)": [[12, "dials.algorithms.integration.integrator.Integrator.summary", false]], "summary() (dials.algorithms.integration.integrator.integrator3dthreaded method)": [[12, "dials.algorithms.integration.integrator.Integrator3DThreaded.summary", false]], "summary_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)": [[18, "dials.algorithms.symmetry.cosym.SymmetryAnalysis.summary_table", false]], "sym_ops_table() (dials.algorithms.symmetry.cosym.symmetryanalysis static method)": [[18, "dials.algorithms.symmetry.cosym.SymmetryAnalysis.sym_ops_table", false]], "symmetry_base (class in dials.algorithms.symmetry)": [[18, "dials.algorithms.symmetry.symmetry_base", false]], "symmetryanalysis (class in dials.algorithms.symmetry.cosym)": [[18, "dials.algorithms.symmetry.cosym.SymmetryAnalysis", false]], "symmetryhandler (class in dials.algorithms.indexing.symmetry)": [[11, "dials.algorithms.indexing.symmetry.SymmetryHandler", false]], "system_phil (dials.util.options.argumentparser property)": [[33, "dials.util.options.ArgumentParser.system_phil", false]], "system_phil (dials.util.options.philcommandparser property)": [[33, "dials.util.options.PhilCommandParser.system_phil", false]], "target (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.Target", false]], "target (class in dials.algorithms.symmetry.cosym.target)": [[18, "dials.algorithms.symmetry.cosym.target.Target", false]], "targetedoutlierrejection (class in dials.algorithms.scaling.outlier_rejection)": [[15, "dials.algorithms.scaling.outlier_rejection.TargetedOutlierRejection", false]], "targetfactory (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.TargetFactory", false]], "tau (dials.algorithms.refinement.engine.levenbergmarquardtiterations attribute)": [[14, "dials.algorithms.refinement.engine.LevenbergMarquardtIterations.tau", false]], "test_for_termination() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.test_for_termination", false]], "test_objective_increasing_but_not_nref() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.test_objective_increasing_but_not_nref", false]], "test_rmsd_convergence() (dials.algorithms.refinement.engine.refinery method)": [[14, "dials.algorithms.refinement.engine.Refinery.test_rmsd_convergence", false]], "to_crystal() (in module dxtbx.serialize.xds)": [[30, "dxtbx.serialize.xds.to_crystal", false]], "to_dict() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.to_dict", false]], "to_dict() (dxtbx.model.crystal method)": [[22, "dxtbx.model.Crystal.to_dict", false]], "to_dict() (dxtbx.model.detector method)": [[23, "dxtbx.model.Detector.to_dict", false]], "to_dict() (dxtbx.model.experimentlist method)": [[24, "dxtbx.model.ExperimentList.to_dict", false]], "to_dict() (dxtbx.model.goniometer.goniometer method)": [[25, "dxtbx.model.goniometer.Goniometer.to_dict", false]], "to_dict() (dxtbx.model.goniometer.multiaxisgoniometer method)": [[25, "dxtbx.model.goniometer.MultiAxisGoniometer.to_dict", false]], "to_dict() (dxtbx.model.mosaiccrystalkabsch2010 method)": [[22, "dxtbx.model.MosaicCrystalKabsch2010.to_dict", false]], "to_dict() (dxtbx.model.mosaiccrystalsauter2014 method)": [[22, "dxtbx.model.MosaicCrystalSauter2014.to_dict", false]], "to_imageset() (in module dxtbx.serialize.xds)": [[30, "dxtbx.serialize.xds.to_imageset", false]], "to_json_file() (dials.algorithms.refinement.engine.journal method)": [[14, "dials.algorithms.refinement.engine.Journal.to_json_file", false]], "to_xds (class in dxtbx.serialize.xds)": [[30, "dxtbx.serialize.xds.to_xds", false]], "tofleastsquaresresidualwithrmsdcutoff (class in dials.algorithms.refinement.target)": [[14, "dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff", false]], "tofreflectionmanager (class in dials.algorithms.refinement.reflection_manager)": [[14, "dials.algorithms.refinement.reflection_manager.TOFReflectionManager", false]], "tofspotfinder (class in dials.algorithms.spot_finding.finder)": [[16, "dials.algorithms.spot_finding.finder.TOFSpotFinder", false]], "traceback (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.traceback", false]], "trunccauchy_pdf() (in module dials.algorithms.symmetry.laue_group)": [[18, "dials.algorithms.symmetry.laue_group.trunccauchy_pdf", false]], "try_read_experiments() (dials.util.options.importer method)": [[33, "dials.util.options.Importer.try_read_experiments", false]], "try_read_experiments_from_images() (dials.util.options.importer method)": [[33, "dials.util.options.Importer.try_read_experiments_from_images", false]], "try_read_reflections() (dials.util.options.importer method)": [[33, "dials.util.options.Importer.try_read_reflections", false]], "two_theta() (dxtbx.model.detector.detectorfactory static method)": [[23, "dxtbx.model.detector.DetectorFactory.two_theta", false]], "type (dials.util.options.argumenthandlingerrorinfo attribute)": [[33, "dials.util.options.ArgumentHandlingErrorInfo.type", false]], "update() (dials.algorithms.scaling.model.model.arrayscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.ArrayScalingModel.update", false]], "update() (dials.algorithms.scaling.model.model.dosedecay method)": [[15, "dials.algorithms.scaling.model.model.DoseDecay.update", false]], "update() (dials.algorithms.scaling.model.model.kbscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.KBScalingModel.update", false]], "update() (dials.algorithms.scaling.model.model.physicalscalingmodel method)": [[15, "dials.algorithms.scaling.model.model.PhysicalScalingModel.update", false]], "update() (dials.algorithms.scaling.model.model.scalingmodelbase method)": [[15, "dials.algorithms.scaling.model.model.ScalingModelBase.update", false]], "update() (dials.util.command_line.progressbar method)": [[33, "dials.util.command_line.ProgressBar.update", false]], "update() (dials.util.command_line.progressbartimer method)": [[33, "dials.util.command_line.ProgressBarTimer.update", false]], "update_analysis() (dials.algorithms.indexing.model_evaluation.modelrankfilter method)": [[11, "dials.algorithms.indexing.model_evaluation.ModelRankFilter.update_analysis", false]], "update_detector_px_mm_data() (dxtbx.imageset.imagesequence method)": [[26, "dxtbx.imageset.ImageSequence.update_detector_px_mm_data", false]], "update_detector_px_mm_data() (dxtbx.imageset.imageset method)": [[26, "dxtbx.imageset.ImageSet.update_detector_px_mm_data", false]], "update_journal() (dials.algorithms.refinement.engine.refinery 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