Index

_

__init__() (dials.algorithms.background.RadialAverage method) (dials.algorithms.indexing.assign_indices.AssignIndicesGlobal method) (dials.algorithms.indexing.assign_indices.AssignIndicesLocal method) (dials.algorithms.indexing.assign_indices.AssignIndicesStrategy method) (dials.algorithms.indexing.basis_vector_search.FFT1D method) (dials.algorithms.indexing.basis_vector_search.FFT3D method) (dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorMinimiser method) (dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget method) (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch method) (dials.algorithms.indexing.basis_vector_search.Strategy method) (dials.algorithms.indexing.indexer.Indexer method) (dials.algorithms.indexing.lattice_search.LowResSpotMatch method) (dials.algorithms.indexing.lattice_search.PinkIndexer method) (dials.algorithms.indexing.lattice_search.Strategy method) (dials.algorithms.indexing.model_evaluation.ModelEvaluation method) (dials.algorithms.indexing.model_evaluation.ModelRank method) (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) (dials.algorithms.indexing.model_evaluation.ModelRankWeighted method) (dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis method) (dials.algorithms.indexing.stills_indexer.StillsIndexer method) (dials.algorithms.indexing.symmetry.SymmetryHandler method) (dials.algorithms.integration.integrator.Executor method) (dials.algorithms.integration.integrator.Integrator method) (dials.algorithms.integration.integrator.Integrator3DThreaded method) (dials.algorithms.integration.integrator.IntegratorExecutor method) (dials.algorithms.integration.integrator.JobList method) (dials.algorithms.integration.integrator.Parameters method) (dials.algorithms.integration.integrator.Parameters.Filter method) (dials.algorithms.integration.integrator.Parameters.Profile method) (dials.algorithms.integration.integrator.Parameters.Profile.Validation method) (dials.algorithms.integration.integrator.Processor2D method) (dials.algorithms.integration.integrator.Processor3D method) (dials.algorithms.integration.integrator.ProcessorFlat3D method) (dials.algorithms.integration.integrator.ProcessorSingle2D method) (dials.algorithms.integration.integrator.ProcessorStills method) (dials.algorithms.integration.integrator.ProfileModellerExecutor method) (dials.algorithms.integration.integrator.ProfileValidatorExecutor method) (dials.algorithms.integration.integrator.ReflectionManager method) (dials.algorithms.refinement.engine.AdaptLbfgs method) (dials.algorithms.refinement.engine.AdaptLstbx method) (dials.algorithms.refinement.engine.GaussNewtonIterations method) (dials.algorithms.refinement.engine.Refinery method) (dials.algorithms.refinement.refiner.Refiner method) (dials.algorithms.refinement.reflection_manager.BlockCalculator method) (dials.algorithms.refinement.reflection_manager.LaueReflectionManager method) (dials.algorithms.refinement.reflection_manager.ReflectionManager method) (dials.algorithms.refinement.reflection_manager.TOFReflectionManager method) (dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff method) (dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff method) (dials.algorithms.refinement.target.Target method) (dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff method) (dials.algorithms.refinement.weighting_strategies.ConstantWeightingStrategy method) (dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy method) (dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy method) (dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy method) (dials.algorithms.scaling.model.model.ArrayScalingModel method) (dials.algorithms.scaling.model.model.DoseDecay method) (dials.algorithms.scaling.model.model.KBScalingModel method) (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) (dials.algorithms.scaling.outlier_rejection.NormDevOutlierRejection method) (dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase method) (dials.algorithms.scaling.outlier_rejection.SimpleNormDevOutlierRejection method) (dials.algorithms.scaling.outlier_rejection.TargetedOutlierRejection method) (dials.algorithms.spot_finding.factory.BackgroundGradientFilter method) (dials.algorithms.spot_finding.factory.FilterRunner method) (dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter method) (dials.algorithms.spot_finding.factory.SpotDensityFilter method) (dials.algorithms.spot_finding.finder.ExtractPixelsFromImage method) (dials.algorithms.spot_finding.finder.ExtractPixelsFromImage2DNoShoeboxes method) (dials.algorithms.spot_finding.finder.ExtractSpots method) (dials.algorithms.spot_finding.finder.ExtractSpotsParallelTask method) (dials.algorithms.spot_finding.finder.SpotFinder method) (dials.algorithms.spot_finding.finder.TOFSpotFinder method) (dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor method) (dials.algorithms.symmetry.cosym.CosymAnalysis method) (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method) (dials.algorithms.symmetry.cosym.ScoreSubGroup method) (dials.algorithms.symmetry.cosym.ScoreSymmetryElement method) (dials.algorithms.symmetry.cosym.SymmetryAnalysis method) (dials.algorithms.symmetry.cosym.target.Target method) (dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator method) (dials.algorithms.symmetry.laue_group.LaueGroupAnalysis method) (dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient method) (dials.algorithms.symmetry.laue_group.ScoreSubGroup method) (dials.algorithms.symmetry.laue_group.ScoreSymmetryElement method) (dials.algorithms.symmetry.symmetry_base method) (dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt method) (dials.extensions.null_background_ext.NullBackgroundExt method) (dials.extensions.simple_background_ext.SimpleBackgroundExt method) (dials.extensions.simple_centroid_ext.SimpleCentroidExt method) (dials.util.command_line.ProgressBar method) (dials.util.command_line.ProgressBarTimer method) (dials.util.export_mtz.MTZWriterBase method) (dials.util.export_mtz.WavelengthGroup method) (dials.util.options.ArgumentParser method) (dials.util.options.ArgumentParserBase method) (dials.util.options.Importer method) (dials.util.options.OptionParser method) (dials.util.options.PhilCommandParser method) (dxtbx.imageset.ExternalLookup method) (dxtbx.imageset.ExternalLookupItemBool method) (dxtbx.imageset.ExternalLookupItemDouble method) (dxtbx.imageset.ImageGrid method) (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) (dxtbx.imageset.MemReader method) (dxtbx.model.Crystal method) (dxtbx.model.Detector method) (dxtbx.model.experiment_list.BeamComparison method) (dxtbx.model.experiment_list.DetectorComparison method) (dxtbx.model.experiment_list.GoniometerComparison method) (dxtbx.model.ExperimentList method) (dxtbx.model.goniometer.Goniometer method) (dxtbx.model.goniometer.KappaGoniometer method) (dxtbx.model.goniometer.MultiAxisGoniometer method) (dxtbx.model.MosaicCrystalKabsch2010 method) (dxtbx.model.MosaicCrystalSauter2014 method) (dxtbx.serialize.xds.to_xds method)

A

accumulate() (dials.algorithms.integration.integrator.ReflectionManager method) (dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator method) achieved() (dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff method) (dials.algorithms.refinement.target.LeastSquaresPositionalResidualWithRmsdCutoff method) (dials.algorithms.refinement.target.Target method) (dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff method) AdaptLbfgs (class in dials.algorithms.refinement.engine) AdaptLstbx (class in dials.algorithms.refinement.engine) add() (dials.algorithms.background.RadialAverage method) (dials.algorithms.integration.integrator.JobList method) (dxtbx.model.scan.ScanFactory static method) add_batch_list() (in module dials.util.export_mtz) add_column() (dials.algorithms.refinement.engine.Journal method) add_constant_to_diagonal() (dials.algorithms.refinement.engine.LevenbergMarquardtIterations method) add_crystal() (dials.util.export_mtz.MTZWriterBase method) add_dataset() (dials.util.export_mtz.MADMergedMTZWriter method) (dials.util.export_mtz.MergedMTZWriter method) add_empty_dataset() (dials.util.export_mtz.MTZWriterBase method) add_experiment() (dials.util.export_mtz.WavelengthGroup method) add_group() (dxtbx.model.Detector method) add_panel() (dxtbx.model.Detector method) add_row() (dials.algorithms.refinement.engine.Journal method) algorithm() (dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt static method) all_laue() (dxtbx.model.ExperimentList method) all_rotations() (dxtbx.model.ExperimentList method) all_same_type() (dxtbx.model.ExperimentList method) all_sequences() (dxtbx.model.ExperimentList method) all_stills() (dxtbx.model.ExperimentList method)

all_tof() (dxtbx.model.ExperimentList method) append() (dials.algorithms.indexing.model_evaluation.ModelRank method) (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) (dxtbx.model.ExperimentList method) apply_hkl_offset() (in module dials.algorithms.indexing.indexer) apply_symmetry() (dials.algorithms.indexing.symmetry.SymmetryHandler method) ArgumentHandlingErrorInfo (class in dials.util.options) ArgumentParser (class in dials.util.options) ArgumentParserBase (class in dials.util.options) ArrayScalingModel (class in dials.algorithms.scaling.model.model) as_dict() (dials.algorithms.symmetry.cosym.CosymAnalysis method) (dials.algorithms.symmetry.cosym.ScoreSubGroup method) (dials.algorithms.symmetry.cosym.ScoreSymmetryElement method) (dials.algorithms.symmetry.cosym.SymmetryAnalysis method) (dials.algorithms.symmetry.laue_group.LaueGroupAnalysis method) (dials.algorithms.symmetry.laue_group.ScoreSubGroup method) (dials.algorithms.symmetry.laue_group.ScoreSymmetryElement method) as_file() (dxtbx.model.ExperimentList method) as_imageset() (dxtbx.imageset.ImageSet method) as_json() (dials.algorithms.symmetry.cosym.CosymAnalysis method) (dials.algorithms.symmetry.laue_group.LaueGroupAnalysis method) (dxtbx.model.ExperimentList method) as_str() (dxtbx.model.Crystal method) (dxtbx.model.MosaicCrystalKabsch2010 method) (dxtbx.model.MosaicCrystalSauter2014 method) AssignIndicesGlobal (class in dials.algorithms.indexing.assign_indices) AssignIndicesLocal (class in dials.algorithms.indexing.assign_indices) AssignIndicesStrategy (class in dials.algorithms.indexing.assign_indices)

B

BackgroundGradientFilter (class in dials.algorithms.spot_finding.factory) base_package_options (dials.util.installer.installer attribute) basic_imageset_from_dict() (in module dxtbx.serialize.imageset) basic_imageset_to_dict() (in module dxtbx.serialize.imageset) BasisVectorMinimiser (class in dials.algorithms.indexing.basis_vector_search.optimise) BasisVectorTarget (class in dials.algorithms.indexing.basis_vector_search.optimise) BeamComparison (class in dxtbx.model.experiment_list)

BeamFactory (class in dxtbx.model.beam) beams() (dxtbx.model.ExperimentList method) best_model() (dials.algorithms.indexing.model_evaluation.ModelRank method) (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) (dials.algorithms.indexing.model_evaluation.ModelRankWeighted method) BlockCalculator (class in dials.algorithms.refinement.reflection_manager) build_up() (dials.algorithms.refinement.engine.AdaptLstbx method)

C

calc_2D_rmsd_and_displacements() (in module dials.algorithms.indexing.stills_indexer) calc_acentric_subgroups() (in module dials.algorithms.indexing.symmetry) calc_exp_rmsd_table() (dials.algorithms.refinement.refiner.Refiner method) calc_n_param_from_bins() (in module dials.algorithms.scaling.model.model) calculate_esds() (dials.algorithms.refinement.engine.AdaptLstbx method) calculate_gradients() (dials.algorithms.refinement.target.Target method) calculate_new_offset() (in module dials.algorithms.scaling.model.model) calculate_weighted_mean() (dials.util.export_mtz.WavelengthGroup method) calculate_weights() (dials.algorithms.refinement.weighting_strategies.ConstantWeightingStrategy method) (dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy method) (dials.algorithms.refinement.weighting_strategies.LaueMixedWeightingStrategy method) (dials.algorithms.refinement.weighting_strategies.LaueStatisticalWeightingStrategy method) (dials.algorithms.refinement.weighting_strategies.StatisticalWeightingStrategy static method) (dials.algorithms.refinement.weighting_strategies.StillsWeightingStrategy method) callback_after_step() (dials.algorithms.refinement.engine.AdaptLbfgs method) (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method) candidate_orientation_matrices() (in module dials.algorithms.indexing.basis_vector_search.combinations) change_basis() (dxtbx.model.ExperimentList method) change_of_basis_op_to_best_cell() (in module dials.algorithms.symmetry.cosym) check_flags() (dials.algorithms.spot_finding.factory.FilterRunner method) choose_best_orientation_matrix() (dials.algorithms.indexing.stills_indexer.StillsIndexer method) clear() (dxtbx.model.ExperimentList method) clear_cache() (dxtbx.imageset.ImageSet method) coefficient() (dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator method) coloured() (in module dials.util.command_line) combined_scores() (dials.algorithms.indexing.model_evaluation.ModelRankWeighted method) Command (class in dials.util.command_line) complete_set() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) complex() (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.detector.DetectorFactory static method) components (dials.algorithms.scaling.model.model.ScalingModelBase property) compute_background() (dials.extensions.null_background_ext.NullBackgroundExt method) (dials.extensions.simple_background_ext.SimpleBackgroundExt method) compute_centroid() (dials.extensions.simple_centroid_ext.SimpleCentroidExt method) compute_functional() (dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget method) (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch static method) (dials.algorithms.symmetry.cosym.target.Target method) compute_functional_and_gradients() (dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorMinimiser method) (dials.algorithms.indexing.basis_vector_search.optimise.BasisVectorTarget method) (dials.algorithms.refinement.engine.AdaptLbfgs method) (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method) compute_functional_gradients_and_curvatures() (dials.algorithms.refinement.engine.AdaptLbfgs method) (dials.algorithms.refinement.target.Target method) (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method)

compute_functional_gradients_diag() (dials.algorithms.refinement.engine.LBFGScurvs method) (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method) compute_functional_score_for_dimension_assessment() (dials.algorithms.symmetry.cosym.target.Target method) compute_gradients() (dials.algorithms.symmetry.cosym.target.Target method) compute_gradients_fd() (dials.algorithms.symmetry.cosym.target.Target method) compute_residuals() (dials.algorithms.refinement.target.Target method) compute_residuals_and_gradients() (dials.algorithms.refinement.target.Target method) compute_restraints_functional_gradients_and_curvatures() (dials.algorithms.refinement.target.Target method) compute_restraints_residuals_and_gradients() (dials.algorithms.refinement.target.Target method) compute_threshold() (dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt method) config_refinery() (dials.algorithms.refinement.refiner.RefinerFactory static method) config_restraints() (dials.algorithms.refinement.refiner.RefinerFactory static method) config_sparse() (dials.algorithms.refinement.refiner.RefinerFactory static method) config_target() (dials.algorithms.refinement.refiner.RefinerFactory static method) configdict (dials.algorithms.scaling.model.model.ScalingModelBase property) configure_components() (dials.algorithms.scaling.model.model.ArrayScalingModel method) (dials.algorithms.scaling.model.model.DoseDecay method) (dials.algorithms.scaling.model.model.KBScalingModel method) (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) configure_filter() (dials.algorithms.spot_finding.factory.SpotFinderFactory static method) configure_modules (dials.util.installer.installer attribute) configure_threshold() (dials.algorithms.spot_finding.factory.SpotFinderFactory static method) consecutive_refinement_order (dials.algorithms.scaling.model.model.ArrayScalingModel property) (dials.algorithms.scaling.model.model.DoseDecay property) (dials.algorithms.scaling.model.model.KBScalingModel property) (dials.algorithms.scaling.model.model.PhysicalScalingModel property) consecutive_refinement_order() (dials.algorithms.scaling.model.model.ScalingModelBase method) ConstantWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) convergence_as_shift_over_esd (dials.algorithms.refinement.engine.GaussNewtonIterations attribute) convert_to_cambridge() (in module dials.util.export_mtz) copy() (dxtbx.imageset.MemReader method) CorrelationCoefficientAccumulator (class in dials.algorithms.symmetry.laue_group) CosymAnalysis (class in dials.algorithms.symmetry.cosym) Crystal (class in dxtbx.model) crystal (dials.algorithms.indexing.model_evaluation.Result attribute) crystal() (in module dxtbx.serialize.load) CrystalFactory (class in dxtbx.model.crystal) crystals() (dxtbx.model.ExperimentList method) curvatures() (dials.algorithms.symmetry.cosym.target.Target method) curvatures_fd() (dials.algorithms.symmetry.cosym.target.Target method)

D

damping_value (dials.algorithms.refinement.engine.GaussNewtonIterations attribute) data (dxtbx.imageset.ExternalLookupItemBool property) (dxtbx.imageset.ExternalLookupItemDouble property) data() (dials.algorithms.integration.integrator.IntegratorExecutor method) (dials.algorithms.integration.integrator.ProfileModellerExecutor method) (dials.algorithms.integration.integrator.ProfileValidatorExecutor method) (dials.algorithms.integration.integrator.ReflectionManager method) (dxtbx.imageset.ImageSet method) default (dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt attribute) (dials.extensions.simple_centroid_ext.SimpleCentroidExt attribute) del_last_row() (dials.algorithms.refinement.engine.Journal method) denominator() (dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator method) dest_dir_prefix (dials.util.installer.installer attribute) Detector (class in dxtbx.model) DetectorComparison (class in dxtbx.model.experiment_list) DetectorFactory (class in dxtbx.model.detector) detectors() (dxtbx.model.ExperimentList method) determine_auto_absorption_params() (in module dials.algorithms.scaling.model.model) determine_Esq_outlier_index_arrays() (in module dials.algorithms.scaling.outlier_rejection) determine_outlier_index_arrays() (in module dials.algorithms.scaling.outlier_rejection) determine_reindex_operator_against_reference() (in module dials.algorithms.symmetry.reindex_to_reference) dials.algorithms.background module dials.algorithms.indexing module dials.algorithms.indexing.assign_indices module dials.algorithms.indexing.basis_vector_search module dials.algorithms.indexing.basis_vector_search.combinations module dials.algorithms.indexing.basis_vector_search.optimise module dials.algorithms.indexing.compare_orientation_matrices module dials.algorithms.indexing.indexer module dials.algorithms.indexing.lattice_search module dials.algorithms.indexing.max_cell module dials.algorithms.indexing.model_evaluation module dials.algorithms.indexing.nearest_neighbor module dials.algorithms.indexing.refinement module dials.algorithms.indexing.stills_indexer module dials.algorithms.indexing.symmetry module dials.algorithms.integration.integrator module dials.algorithms.profile_model module dials.algorithms.refinement.engine module dials.algorithms.refinement.refiner module dials.algorithms.refinement.reflection_manager module dials.algorithms.refinement.target module dials.algorithms.refinement.target_stills module dials.algorithms.refinement.weighting_strategies module dials.algorithms.scaling module dials.algorithms.scaling.model.model module dials.algorithms.scaling.outlier_rejection module dials.algorithms.spot_finding.factory module dials.algorithms.spot_finding.finder module

dials.algorithms.spot_prediction.reflection_predictor module dials.algorithms.symmetry module dials.algorithms.symmetry.cosym module dials.algorithms.symmetry.cosym.engine module dials.algorithms.symmetry.cosym.target module dials.algorithms.symmetry.laue_group module dials.algorithms.symmetry.reindex_to_reference module dials.array_family.flex module dials.extensions.dispersion_spotfinder_threshold_ext module dials.extensions.gaussian_rs_profile_model_ext module dials.extensions.null_background_ext module dials.extensions.simple_background_ext module dials.extensions.simple_centroid_ext module dials.util.command_line module dials.util.export_mtz module dials.util.export_text module dials.util.image module dials.util.installer module dials.util.ioutil module dials.util.nexus module dials.util.options module DialsIndexError DialsIndexRefineError diff_phil (dials.util.options.ArgumentParser property) (dials.util.options.PhilCommandParser property) difference_rotation_matrix_axis_angle() (in module dials.algorithms.indexing.compare_orientation_matrices) dim (dials.algorithms.refinement.target.Target property) (dials.algorithms.symmetry.cosym.target.Target attribute) DisableMPmixin (class in dials.algorithms.refinement.engine) DispersionSpotFinderThresholdExt (class in dials.extensions.dispersion_spotfinder_threshold_ext) DoseDecay (class in dials.algorithms.scaling.model.model) dump() (in module dials.util.nexus) dx (dxtbx.imageset.ExternalLookup property) dxtbx.imageset module dxtbx.model.beam module dxtbx.model.crystal module dxtbx.model.detector module dxtbx.model.experiment_list module dxtbx.model.goniometer module dxtbx.model.profile module dxtbx.model.scan module dxtbx.serialize.imageset module dxtbx.serialize.load module dxtbx.serialize.xds module dy (dxtbx.imageset.ExternalLookup property)

E

e_refine() (in module dials.algorithms.indexing.stills_indexer) empty() (dxtbx.model.ExperimentList method) end() (dials.util.command_line.Command class method) error_model (dials.algorithms.scaling.model.model.ScalingModelBase property) estimate_global_threshold() (in module dials.extensions.dispersion_spotfinder_threshold_ext) evaluate() (dials.algorithms.indexing.model_evaluation.ModelEvaluation method) (dials.algorithms.indexing.model_evaluation.Strategy method) exception (dials.util.options.ArgumentHandlingErrorInfo attribute) Executor (class in dials.algorithms.integration.integrator) exp_nos (dials.util.export_mtz.WavelengthGroup attribute) experiment_list() (in module dxtbx.serialize.load) experiment_list_for_crystal() (dials.algorithms.indexing.stills_indexer.StillsIndexer method) experiment_type (dials.algorithms.refinement.reflection_manager.LaueReflectionManager attribute) (dials.algorithms.refinement.reflection_manager.ReflectionManager attribute) (dials.algorithms.refinement.reflection_manager.StillsReflectionManager attribute) ExperimentList (class in dxtbx.model) ExperimentListFactory (class in dxtbx.model.experiment_list)

export_as_json() (dials.algorithms.indexing.indexer.Indexer method) export_mtz() (in module dials.util.export_mtz) export_reflections() (dials.algorithms.indexing.indexer.Indexer method) export_text() (in module dials.util.export_text) extend() (dials.algorithms.indexing.model_evaluation.ModelRank method) (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) (dxtbx.model.ExperimentList method) external_lookup (dxtbx.imageset.ImageSet property) (dxtbx.imageset.ImageSetData property) ExternalDelPsiWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) ExternalLookup (class in dxtbx.imageset) ExternalLookupItemBool (class in dxtbx.imageset) ExternalLookupItemDouble (class in dxtbx.imageset) extract_reference_intensities() (in module dials.algorithms.symmetry.cosym) ExtractPixelsFromImage (class in dials.algorithms.spot_finding.finder) ExtractPixelsFromImage2DNoShoeboxes (class in dials.algorithms.spot_finding.finder) ExtractSpots (class in dials.algorithms.spot_finding.finder) ExtractSpotsParallelTask (class in dials.algorithms.spot_finding.finder)

F

FFT1D (class in dials.algorithms.indexing.basis_vector_search) FFT3D (class in dials.algorithms.indexing.basis_vector_search) filename (dxtbx.imageset.ExternalLookupItemBool property) (dxtbx.imageset.ExternalLookupItemDouble property) filename_or_none() (in module dxtbx.serialize.imageset) filename_to_absolute() (in module dxtbx.serialize.imageset) filter_by_likelihood() (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) filter_by_n_indexed() (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) filter_by_volume() (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) filter_doubled_cell() (in module dials.algorithms.indexing.model_evaluation) filter_known_symmetry() (in module dials.algorithms.indexing.basis_vector_search.combinations) filter_obs() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) filter_similar_orientations() (in module dials.algorithms.indexing.basis_vector_search.combinations) FilterRunner (class in dials.algorithms.spot_finding.factory) final_outlier_arrays (dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase attribute) finalise() (dials.algorithms.integration.integrator.Integrator3DThreaded method) (dials.algorithms.refinement.reflection_manager.ReflectionManager method) finalize() (dials.algorithms.integration.integrator.IntegratorExecutor method) (dials.algorithms.integration.integrator.ProfileModellerExecutor method) (dials.algorithms.integration.integrator.ProfileValidatorExecutor method) finalize_reflections() (dials.algorithms.integration.integrator.Integrator2D static method) (dials.algorithms.integration.integrator.Integrator3D static method) (dials.algorithms.integration.integrator.IntegratorFlat3D static method) (dials.algorithms.integration.integrator.IntegratorSingle2D static method) (dials.algorithms.integration.integrator.IntegratorStills static method) find() (dxtbx.model.ExperimentList method) find_basis_vectors() (dials.algorithms.indexing.basis_vector_search.FFT1D method) (dials.algorithms.indexing.basis_vector_search.FFT3D method) (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch method) (dials.algorithms.indexing.basis_vector_search.Strategy method) find_crystal_models() (dials.algorithms.indexing.lattice_search.LowResSpotMatch method) (dials.algorithms.indexing.lattice_search.PinkIndexer method) (dials.algorithms.indexing.lattice_search.Strategy method) find_lattices() (dials.algorithms.indexing.indexer.Indexer method) find_matching_symmetry() (in module dials.algorithms.indexing.symmetry) find_max_cell() (dials.algorithms.indexing.indexer.Indexer method) (in module dials.algorithms.indexing.max_cell) find_spots() (dials.algorithms.spot_finding.finder.SpotFinder method) finished() (dials.algorithms.integration.integrator.ReflectionManager method) (dials.util.command_line.ProgressBar method) fit_profiles() (dials.algorithms.integration.integrator.Integrator method) fix_initial_parameter() (dials.algorithms.scaling.model.model.DoseDecay method) (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) fixed_components (dials.algorithms.scaling.model.model.ScalingModelBase property) flatten_experiments() (in module dials.util.options) flatten_reflections() (in module dials.util.options) format_epilog() (dials.util.options.ArgumentParserBase method) format_help() (dials.util.options.ArgumentParser method) fraction_indexed (dials.algorithms.indexing.model_evaluation.Result attribute) frame_hist() (in module dials.algorithms.integration.integrator)

from_args() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_data() (dials.algorithms.scaling.model.model.ArrayScalingModel class method) (dials.algorithms.scaling.model.model.DoseDecay class method) (dials.algorithms.scaling.model.model.KBScalingModel class method) (dials.algorithms.scaling.model.model.PhysicalScalingModel class method) (dials.algorithms.scaling.model.model.ScalingModelBase class method) from_dict() (dials.algorithms.scaling.model.model.ArrayScalingModel class method) (dials.algorithms.scaling.model.model.DoseDecay class method) (dials.algorithms.scaling.model.model.KBScalingModel class method) (dials.algorithms.scaling.model.model.PhysicalScalingModel class method) (dials.algorithms.scaling.model.model.ScalingModelBase class method) (dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt class method) (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.Crystal static method) (dxtbx.model.crystal.CrystalFactory static method) (dxtbx.model.Detector static method) (dxtbx.model.detector.DetectorFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static method) (dxtbx.model.goniometer.Goniometer static method) (dxtbx.model.goniometer.GoniometerFactory static method) (dxtbx.model.goniometer.MultiAxisGoniometer static method) (dxtbx.model.MosaicCrystalKabsch2010 class method) (dxtbx.model.MosaicCrystalSauter2014 class method) (dxtbx.model.profile.ProfileModelFactory static method) (dxtbx.model.scan.ScanFactory static method) from_file() (dxtbx.model.ExperimentList static method) from_filenames() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_imageset() (dxtbx.imageset.ImageGrid static method) from_imageset_and_crystal() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_json() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_json_file() (dials.algorithms.refinement.engine.Journal class method) (dxtbx.model.experiment_list.ExperimentListFactory static method) from_mosflm_matrix() (dxtbx.model.crystal.CrystalFactory static method) from_parameters() (dials.algorithms.indexing.indexer.Indexer static method) (dials.algorithms.spot_finding.factory.SpotFinderFactory static method) from_parameters_and_experiments() (dials.algorithms.refinement.target.TargetFactory static method) from_parameters_data_experiments() (dials.algorithms.refinement.refiner.RefinerFactory class method) from_parameters_reflections_experiments() (dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory static method) from_phil() (dials.algorithms.integration.integrator.Parameters static method) (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.detector.DetectorFactory static method) (dxtbx.model.goniometer.GoniometerFactory static method) (dxtbx.model.scan.ScanFactory static method) from_pickle_file() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_sequence_and_crystal() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_serialized_format() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_stills_and_crystal() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_template() (dxtbx.imageset.ImageSetFactory static method) from_templates() (dxtbx.model.experiment_list.ExperimentListFactory static method) (dxtbx.model.ExperimentList static method) from_xds() (dxtbx.model.experiment_list.ExperimentListFactory static method)

G

gain (dxtbx.imageset.ExternalLookup property) GaussianRSProfileModelExt (class in dials.extensions.gaussian_rs_profile_model_ext) GaussNewtonIterations (class in dials.algorithms.refinement.engine) generate_from_phil() (dxtbx.model.detector.DetectorFactory static method) generate_phil_scope() (in module dials.algorithms.integration.integrator) (in module dials.algorithms.spot_finding.factory) get_A_as_sqr() (dxtbx.model.MosaicCrystalSauter2014 method) get_A_inverse_as_sqr() (dxtbx.model.MosaicCrystalSauter2014 method) get_accepted_refs_size() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_alpha_angle() (dxtbx.model.goniometer.KappaGoniometer method) get_angles() (dxtbx.model.goniometer.MultiAxisGoniometer method) get_array_range() (dxtbx.imageset.ImageSequence method) get_axes() (dxtbx.model.goniometer.MultiAxisGoniometer method) get_beam() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) (dxtbx.imageset.ImageSetLazy method) (dxtbx.serialize.xds.to_xds method) get_centroid_analyser() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_corrected_data() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetLazy method) get_correlation_matrix_for_step() (dials.algorithms.refinement.engine.Refinery method) get_crystal_symmetry() (dxtbx.model.Crystal method) get_data() (dials.util.image.reader method) (dxtbx.imageset.ImageSetData method) get_detector() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) (dxtbx.imageset.ImageSetLazy method) (dxtbx.serialize.xds.to_xds method) get_detectorbase() (dxtbx.imageset.ImageSet method) get_direction() (dxtbx.model.goniometer.KappaGoniometer method) get_domain_size_ang() (dxtbx.model.MosaicCrystalSauter2014 method) get_elapsed_time() (dials.util.command_line.ProgressBarTimer method) get_entry() (in module dials.util.nexus) get_experiments() (dials.algorithms.refinement.refiner.Refiner method) get_fixed_rotation() (dxtbx.model.goniometer.Goniometer method) get_format_class() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) get_free_reflections() (dials.algorithms.refinement.refiner.Refiner method) (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_gain() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetLazy method) get_goniometer() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) (dxtbx.imageset.ImageSetLazy method) (dxtbx.serialize.xds.to_xds method) get_grid_size() (dxtbx.imageset.ImageGrid method) get_half_mosaicity_deg() (dxtbx.model.MosaicCrystalSauter2014 method) get_image_identifier() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) get_indexed() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_inverse_ub_matrix_from_xparm() (in module dials.util.ioutil) get_kappa_angle() (dxtbx.model.goniometer.KappaGoniometer method) get_kappa_axis() (dxtbx.model.goniometer.KappaGoniometer method) get_mask() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetLazy method)

get_master_path() (dxtbx.imageset.ImageSetData method) get_matches() (dials.algorithms.refinement.refiner.Refiner method) (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_max_inscribed_resolution() (dxtbx.model.Detector method) get_max_resolution() (dxtbx.model.Detector method) get_mosaicity() (dxtbx.model.MosaicCrystalKabsch2010 method) get_names() (dxtbx.model.Detector method) (dxtbx.model.goniometer.MultiAxisGoniometer method) get_nrows() (dials.algorithms.refinement.engine.Journal method) get_num_matches() (dials.algorithms.refinement.target.Target method) get_num_matches_for_experiment() (dials.algorithms.refinement.target.Target method) get_num_matches_for_panel() (dials.algorithms.refinement.target.Target method) get_num_scan_points() (dxtbx.model.goniometer.Goniometer method) get_num_steps() (dials.algorithms.refinement.engine.Refinery method) get_obs() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_omega_angle() (dxtbx.model.goniometer.KappaGoniometer method) get_omega_axis() (dxtbx.model.goniometer.KappaGoniometer method) get_panel_intersection() (dxtbx.model.Detector method) get_param_reporter() (dials.algorithms.refinement.refiner.Refiner method) get_parameter_correlation_matrix() (dials.algorithms.refinement.refiner.Refiner method) get_params() (dxtbx.imageset.ImageSetData method) get_path() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) get_pedestal() (dxtbx.imageset.ImageSet method) get_phi_angle() (dxtbx.model.goniometer.KappaGoniometer method) get_phi_axis() (dxtbx.model.goniometer.KappaGoniometer method) get_raw_data() (dxtbx.imageset.ImageSet method) get_ray_intersection() (dxtbx.model.Detector method) get_rotation_axis() (dxtbx.model.goniometer.Goniometer method) get_rotation_axis_datum() (dxtbx.model.goniometer.Goniometer method) get_sample_size() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_scan() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) (dxtbx.imageset.ImageSetLazy method) (dxtbx.serialize.xds.to_xds method) get_scan_axis() (dxtbx.model.goniometer.KappaGoniometer method) (dxtbx.model.goniometer.MultiAxisGoniometer method) get_setting_rotation() (dxtbx.model.goniometer.Goniometer method) get_setting_rotation_at_scan_point() (dxtbx.model.goniometer.Goniometer method) get_setting_rotation_at_scan_points() (dxtbx.model.goniometer.Goniometer method) get_shared_components() (dials.algorithms.scaling.model.model.DoseDecay method) (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) get_space_group_type_from_xparm() (in module dials.util.ioutil) get_spectrum() (dxtbx.imageset.ImageSet method) get_template() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSetData method) (dxtbx.serialize.xds.to_xds method) get_vendor() (dxtbx.imageset.ImageSetData method) get_vendortype() (dxtbx.imageset.ImageSet method) get_weighting_strategy_override() (dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory static method) Goniometer (class in dxtbx.model.goniometer) GoniometerComparison (class in dxtbx.model.experiment_list) GoniometerFactory (class in dxtbx.model.goniometer) goniometers() (dxtbx.model.ExperimentList method) gradient_threshold (dials.algorithms.refinement.engine.GaussNewtonIterations attribute) groups_cache() (in module dials.algorithms.indexing.symmetry)

H

has_dynamic_mask() (dxtbx.imageset.ImageSet method) has_projection_2d() (dxtbx.model.Detector method) has_single_file_reader() (dxtbx.imageset.ImageSetData method) heading() (in module dials.util.command_line)

hierarchy() (dxtbx.model.Detector method) hist() (in module dials.algorithms.integration.integrator) history (dials.algorithms.refinement.refiner.Refiner property) hkl_offset (dials.algorithms.indexing.model_evaluation.Result attribute)

I

id_ (dials.algorithms.scaling.model.model.ArrayScalingModel attribute) (dials.algorithms.scaling.model.model.DoseDecay attribute) (dials.algorithms.scaling.model.model.KBScalingModel attribute) (dials.algorithms.scaling.model.model.PhysicalScalingModel attribute) (dials.algorithms.scaling.model.model.ScalingModelBase attribute) identifiers (dials.util.export_mtz.WavelengthGroup attribute) identifiers() (dxtbx.imageset.MemReader method) (dxtbx.model.ExperimentList method) identify_outliers() (dials.algorithms.indexing.stills_indexer.StillsIndexer method) ImageGrid (class in dxtbx.imageset) ImageSequence (class in dxtbx.imageset) imagesequence_from_dict() (in module dxtbx.serialize.imageset) imagesequence_to_dict() (in module dxtbx.serialize.imageset) ImageSet (class in dxtbx.imageset) imageset() (in module dxtbx.serialize.load) imageset_from_anyset() (dxtbx.imageset.ImageSetFactory static method) imageset_from_dict() (in module dxtbx.serialize.imageset) imageset_to_dict() (in module dxtbx.serialize.imageset) ImageSetData (class in dxtbx.imageset) ImageSetFactory (class in dxtbx.imageset) ImageSetLazy (class in dxtbx.imageset) imagesets() (dxtbx.model.ExperimentList method) imgCIF() (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.detector.DetectorFactory static method) (dxtbx.model.goniometer.GoniometerFactory static method) (dxtbx.model.scan.ScanFactory static method) imgCIF_H() (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.detector.DetectorFactory static method) (dxtbx.model.goniometer.GoniometerFactory static method) (dxtbx.model.scan.ScanFactory static method) Importer (class in dials.util.options) include_gui_packages (dials.util.installer.installer attribute) indent (dials.util.command_line.Command attribute) index() (dials.algorithms.indexing.indexer.Indexer method) (dials.algorithms.indexing.stills_indexer.StillsIndexer method) index_reflections() (dials.algorithms.indexing.indexer.Indexer method) Indexer (class in dials.algorithms.indexing.indexer)

indices() (dxtbx.imageset.ImageSet method) (dxtbx.model.ExperimentList method) initialise() (dials.algorithms.integration.integrator.Integrator3DThreaded method) initialise_smooth_input() (in module dials.algorithms.scaling.model.model) initialize() (dials.algorithms.integration.integrator.IntegratorExecutor method) (dials.algorithms.integration.integrator.ProfileModellerExecutor method) (dials.algorithms.integration.integrator.ProfileValidatorExecutor method) initialize_reflections() (dials.algorithms.integration.integrator.Integrator2D static method) (dials.algorithms.integration.integrator.Integrator3D static method) (dials.algorithms.integration.integrator.IntegratorFlat3D static method) (dials.algorithms.integration.integrator.IntegratorSingle2D static method) (dials.algorithms.integration.integrator.IntegratorStills static method) installer (class in dials.util.installer) installer_dir (dials.util.installer.installer attribute) integrate() (dials.algorithms.integration.integrator.Integrator method) (dials.algorithms.integration.integrator.Integrator3DThreaded method) Integrator (class in dials.algorithms.integration.integrator) Integrator2D (class in dials.algorithms.integration.integrator) Integrator3D (class in dials.algorithms.integration.integrator) Integrator3DThreaded (class in dials.algorithms.integration.integrator) IntegratorExecutor (class in dials.algorithms.integration.integrator) IntegratorFlat3D (class in dials.algorithms.integration.integrator) IntegratorSingle2D (class in dials.algorithms.integration.integrator) IntegratorStills (class in dials.algorithms.integration.integrator) inv_d2() (dials.algorithms.background.RadialAverage method) InvalidPhilError is_consistent() (dxtbx.model.ExperimentList method) is_marked_for_rejection() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) is_scaled (dials.algorithms.scaling.model.model.ScalingModelBase property) is_similar_to() (dxtbx.model.Detector method) (dxtbx.model.goniometer.Goniometer method) (dxtbx.model.MosaicCrystalKabsch2010 method) (dxtbx.model.MosaicCrystalSauter2014 method) is_single_file_reader() (dxtbx.imageset.MemReader static method) iter_levelorder() (dxtbx.model.Detector method) iter_panels() (dxtbx.model.Detector method) iter_preorder() (dxtbx.model.Detector method)

J

jacobian_condition_number() (dials.algorithms.refinement.engine.Refinery method) job() (dials.algorithms.integration.integrator.ReflectionManager method)

JobList (class in dials.algorithms.integration.integrator) Journal (class in dials.algorithms.refinement.engine)

K

kappa() (dxtbx.model.goniometer.GoniometerFactory static method) KappaGoniometer (class in dxtbx.model.goniometer)

KBScalingModel (class in dials.algorithms.scaling.model.model) kernel_normalisation() (dials.algorithms.symmetry.symmetry_base static method) known_axis() (dxtbx.model.goniometer.GoniometerFactory static method)

L

laue_manager() (dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory static method) LaueGroupAnalysis (class in dials.algorithms.symmetry.laue_group) LaueLeastSquaresResidualWithRmsdCutoff (class in dials.algorithms.refinement.target) LaueMixedWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) LaueReflectionManager (class in dials.algorithms.refinement.reflection_manager) LaueStatisticalWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) lbfgs_with_curvs (class in dials.algorithms.symmetry.cosym.engine) LBFGScurvs (class in dials.algorithms.refinement.engine) LeastSquaresPositionalResidualWithRmsdCutoff (class in dials.algorithms.refinement.target) LeastSquaresPositionalResidualWithRmsdCutoffSparse (class in dials.algorithms.refinement.target) LeastSquaresStillsResidualWithRmsdCutoff (class in dials.algorithms.refinement.target_stills)

LeastSquaresStillsResidualWithRmsdCutoffSparse (class in dials.algorithms.refinement.target_stills) LevenbergMarquardtIterations (class in dials.algorithms.refinement.engine) limit_image_range() (dials.algorithms.scaling.model.model.ArrayScalingModel method) (dials.algorithms.scaling.model.model.DoseDecay method) (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) load() (in module dials.util.nexus) load_error_model() (dials.algorithms.scaling.model.model.ScalingModelBase method) load_image() (dials.algorithms.spot_finding.factory.SpotFinderFactory static method) log_summary() (in module dials.util.export_mtz) LowResSpotMatch (class in dials.algorithms.indexing.lattice_search)

M

MADMergedMTZWriter (class in dials.util.export_mtz) make_apps (dials.util.installer.installer attribute) make_beam() (dxtbx.model.beam.BeamFactory static method) make_combined_plots() (in module dials.algorithms.scaling.model.model) make_detector() (dxtbx.model.detector.DetectorFactory static method) make_goniometer() (dxtbx.model.goniometer.GoniometerFactory static method) make_imageset() (dxtbx.imageset.ImageSetFactory static method) make_kappa_goniometer() (dxtbx.model.goniometer.GoniometerFactory static method) make_multi_axis_goniometer() (dxtbx.model.goniometer.GoniometerFactory static method) make_polarized_beam() (dxtbx.model.beam.BeamFactory static method) make_polychromatic_beam() (dxtbx.model.beam.BeamFactory static method) make_scan() (dxtbx.model.scan.ScanFactory static method) make_scan_from_properties() (dxtbx.model.scan.ScanFactory static method) make_sequence() (dxtbx.imageset.ImageSetFactory static method) mark_for_rejection() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) mask (dxtbx.imageset.ExternalLookup property) masker() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) master_path() (dxtbx.imageset.MemReader static method) match_wavelengths() (in module dials.util.export_mtz) max_length (dials.util.command_line.Command attribute) max_possible_wl (dials.util.export_mtz.WavelengthGroup attribute) max_shift_over_esd (dials.algorithms.refinement.engine.GaussNewtonIterations attribute) mean() (dials.algorithms.background.RadialAverage method) median_unit_cell() (in module dials.algorithms.symmetry) MemReader (class in dxtbx.imageset) merge_panel_scope_extracts_by_id() (in module dxtbx.model.detector) MergedMTZWriter (class in dials.util.export_mtz) message (dials.util.options.ArgumentHandlingErrorInfo attribute) metric_supergroup() (in module dials.algorithms.indexing.symmetry) min_wl (dials.util.export_mtz.WavelengthGroup attribute) minimize_scipy() (in module dials.algorithms.symmetry.cosym.engine) minimize_scitbx_lbfgs() (in module dials.algorithms.symmetry.cosym.engine) ml_aniso_normalisation() (dials.algorithms.symmetry.symmetry_base static method) ml_iso_normalisation() (dials.algorithms.symmetry.symmetry_base static method) model_likelihood (dials.algorithms.indexing.model_evaluation.Result attribute) ModelEvaluation (class in dials.algorithms.indexing.model_evaluation) ModelRank (class in dials.algorithms.indexing.model_evaluation) ModelRankFilter (class in dials.algorithms.indexing.model_evaluation) ModelRankWeighted (class in dials.algorithms.indexing.model_evaluation) module dials.algorithms.background dials.algorithms.indexing dials.algorithms.indexing.assign_indices dials.algorithms.indexing.basis_vector_search dials.algorithms.indexing.basis_vector_search.combinations dials.algorithms.indexing.basis_vector_search.optimise dials.algorithms.indexing.compare_orientation_matrices dials.algorithms.indexing.indexer dials.algorithms.indexing.lattice_search dials.algorithms.indexing.max_cell dials.algorithms.indexing.model_evaluation dials.algorithms.indexing.nearest_neighbor dials.algorithms.indexing.refinement dials.algorithms.indexing.stills_indexer dials.algorithms.indexing.symmetry dials.algorithms.integration.integrator dials.algorithms.profile_model dials.algorithms.refinement.engine dials.algorithms.refinement.refiner dials.algorithms.refinement.reflection_manager dials.algorithms.refinement.target dials.algorithms.refinement.target_stills dials.algorithms.refinement.weighting_strategies dials.algorithms.scaling dials.algorithms.scaling.model.model dials.algorithms.scaling.outlier_rejection dials.algorithms.spot_finding.factory dials.algorithms.spot_finding.finder dials.algorithms.spot_prediction.reflection_predictor dials.algorithms.symmetry dials.algorithms.symmetry.cosym dials.algorithms.symmetry.cosym.engine dials.algorithms.symmetry.cosym.target dials.algorithms.symmetry.laue_group dials.algorithms.symmetry.reindex_to_reference dials.array_family.flex dials.extensions.dispersion_spotfinder_threshold_ext dials.extensions.gaussian_rs_profile_model_ext dials.extensions.null_background_ext dials.extensions.simple_background_ext dials.extensions.simple_centroid_ext dials.util.command_line dials.util.export_mtz dials.util.export_text dials.util.image dials.util.installer dials.util.ioutil dials.util.nexus dials.util.options dxtbx.imageset dxtbx.model.beam dxtbx.model.crystal dxtbx.model.detector dxtbx.model.experiment_list dxtbx.model.goniometer dxtbx.model.profile dxtbx.model.scan dxtbx.serialize.imageset dxtbx.serialize.load dxtbx.serialize.xds

MosaicCrystalKabsch2010 (class in dxtbx.model) MosaicCrystalSauter2014 (class in dxtbx.model) MTZWriterBase (class in dials.util.export_mtz) mu (dials.algorithms.refinement.engine.LevenbergMarquardtIterations property) multi_axis() (dxtbx.model.goniometer.GoniometerFactory static method) multi_axis_goniometer_from_phil() (dxtbx.model.goniometer.GoniometerFactory static method) MultiAxisGoniometer (class in dxtbx.model.goniometer)

N

n() (dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator method) n_indexed (dials.algorithms.indexing.model_evaluation.Result attribute) n_params (dials.algorithms.scaling.model.model.ScalingModelBase property) name (dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt attribute) (dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt attribute) (dials.extensions.null_background_ext.NullBackgroundExt attribute) (dials.extensions.simple_background_ext.SimpleBackgroundExt attribute) (dials.extensions.simple_centroid_ext.SimpleCentroidExt attribute) (dials.util.options.ArgumentHandlingErrorInfo attribute)

NeighborAnalysis (class in dials.algorithms.indexing.nearest_neighbor) new() (dxtbx.imageset.ImageSetFactory static method) nframes_hist() (in module dials.algorithms.integration.integrator) NormDevOutlierRejection (class in dials.algorithms.scaling.outlier_rejection) NullBackgroundExt (class in dials.extensions.null_background_ext) nullify_all_single_file_reader_format_instances() (dxtbx.model.ExperimentList method) num_reflections() (dials.algorithms.integration.integrator.ReflectionManager method) num_scan_points (dxtbx.model.goniometer.Goniometer property) numerator() (dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator method)

O

optimise_basis_vectors() (in module dials.algorithms.indexing.basis_vector_search.optimise) OptionParser (class in dials.util.options)

OutlierRejectionBase (class in dials.algorithms.scaling.outlier_rejection) overwrite_from_phil() (dxtbx.model.detector.DetectorFactory static method)

P

p_cc_given_not_s (dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient property) p_cc_given_s (dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient property) p_s_given_cc (dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient property) parameter_vector_norm() (dials.algorithms.refinement.engine.AdaptLstbx method) Parameters (class in dials.algorithms.integration.integrator) Parameters.Filter (class in dials.algorithms.integration.integrator) Parameters.Profile (class in dials.algorithms.integration.integrator) Parameters.Profile.Validation (class in dials.algorithms.integration.integrator) params() (dxtbx.imageset.ImageSet method) parse_args() (dials.util.options.ArgumentParser method) (dials.util.options.PhilCommandParser method) parse_known_args() (dials.util.options.ArgumentParserBase method) partial_data() (dxtbx.imageset.ImageSetData method) partial_set() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) paths() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.MemReader method) PeakCentroidDistanceFilter (class in dials.algorithms.spot_finding.factory) pedestal (dxtbx.imageset.ExternalLookup property) per_image() (dials.algorithms.refinement.reflection_manager.BlockCalculator method) per_width() (dials.algorithms.refinement.reflection_manager.BlockCalculator method) phil (dials.util.options.ArgumentParser property) (dials.util.options.PhilCommandParser property) phil() (dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt static method) (dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt static method) (dials.extensions.simple_background_ext.SimpleBackgroundExt static method) phil_help (dials.algorithms.indexing.basis_vector_search.FFT1D attribute) (dials.algorithms.indexing.basis_vector_search.FFT3D attribute) (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch attribute) (dials.algorithms.indexing.basis_vector_search.Strategy attribute) (dials.algorithms.indexing.lattice_search.LowResSpotMatch attribute) (dials.algorithms.indexing.lattice_search.PinkIndexer attribute) (dials.algorithms.indexing.lattice_search.Strategy attribute) phil_scope (dials.algorithms.indexing.basis_vector_search.FFT1D attribute) (dials.algorithms.indexing.basis_vector_search.FFT3D attribute) (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch attribute) (dials.algorithms.indexing.basis_vector_search.Strategy attribute) (dials.algorithms.indexing.lattice_search.LowResSpotMatch attribute) (dials.algorithms.indexing.lattice_search.PinkIndexer attribute) (dials.algorithms.indexing.lattice_search.Strategy attribute) (dials.algorithms.scaling.model.model.ArrayScalingModel attribute) (dials.algorithms.scaling.model.model.DoseDecay attribute) (dials.algorithms.scaling.model.model.KBScalingModel attribute) (dials.algorithms.scaling.model.model.PhysicalScalingModel attribute) PhilCommandParser (class in dials.util.options) PhysicalScalingModel (class in dials.algorithms.scaling.model.model) PinkIndexer (class in dials.algorithms.indexing.lattice_search)

pixel_list_to_reflection_table() (in module dials.algorithms.spot_finding.finder) pixel_list_to_shoeboxes() (in module dials.algorithms.spot_finding.finder) plot_displacements() (in module dials.algorithms.indexing.stills_indexer) plot_histogram() (dials.algorithms.indexing.nearest_neighbor.NeighborAnalysis method) plot_model_components() (dials.algorithms.scaling.model.model.ArrayScalingModel method) (dials.algorithms.scaling.model.model.DoseDecay method) (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) plot_scaling_models() (in module dials.algorithms.scaling.model.model) predict() (dials.algorithms.refinement.target.Target method) predict_for_free_reflections() (dials.algorithms.refinement.target.Target method) predict_for_indexed() (dials.algorithms.refinement.refiner.Refiner method) predict_for_reflection_table() (dials.algorithms.refinement.refiner.Refiner method) (dials.algorithms.refinement.target.Target method) (dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff method) predictor() (dials.algorithms.spot_prediction.reflection_predictor.ReflectionPredictor method) prepare_for_step() (dials.algorithms.refinement.engine.Refinery method) print_exp_rmsd_table() (dials.algorithms.refinement.refiner.Refiner method) print_out_of_sample_rmsd_table() (dials.algorithms.refinement.refiner.Refiner method) print_panel_rmsd_table() (dials.algorithms.refinement.refiner.Refiner method) print_stats_on_matches() (dials.algorithms.refinement.reflection_manager.LaueReflectionManager method) (dials.algorithms.refinement.reflection_manager.ReflectionManager method) (dials.algorithms.refinement.reflection_manager.StillsReflectionManager method) print_step_table() (dials.algorithms.refinement.refiner.Refiner method) print_time (dials.util.command_line.Command attribute) process() (dials.algorithms.integration.integrator.Executor method) (dials.algorithms.integration.integrator.IntegratorExecutor method) (dials.algorithms.integration.integrator.ProfileModellerExecutor method) (dials.algorithms.integration.integrator.ProfileValidatorExecutor method) Processor2D (class in dials.algorithms.integration.integrator) Processor3D (class in dials.algorithms.integration.integrator) ProcessorClass (dials.algorithms.integration.integrator.Integrator2D attribute) (dials.algorithms.integration.integrator.Integrator3D attribute) (dials.algorithms.integration.integrator.IntegratorFlat3D attribute) (dials.algorithms.integration.integrator.IntegratorSingle2D attribute) (dials.algorithms.integration.integrator.IntegratorStills attribute) ProcessorFlat3D (class in dials.algorithms.integration.integrator) ProcessorSingle2D (class in dials.algorithms.integration.integrator) ProcessorStills (class in dials.algorithms.integration.integrator) product_name (dials.util.installer.installer attribute) product_specific_finalize_install() (dials.util.installer.installer method) ProfileModelFactory (class in dxtbx.model.profile) ProfileModellerExecutor (class in dials.algorithms.integration.integrator) profiles() (dxtbx.model.ExperimentList method) ProfileValidatorExecutor (class in dials.algorithms.integration.integrator) ProgressBar (class in dials.util.command_line) ProgressBarTimer (class in dials.util.command_line)

R

RadialAverage (class in dials.algorithms.background) read() (dxtbx.imageset.MemReader method) read_file() (dials.util.image.reader method) reader (class in dials.util.image) reader() (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) RealSpaceGridSearch (class in dials.algorithms.indexing.basis_vector_search) reason_for_termination (dials.algorithms.refinement.engine.Journal attribute) record_intensity_combination_Imid() (dials.algorithms.scaling.model.model.ScalingModelBase method) refine() (dials.algorithms.indexing.indexer.Indexer method) (dials.algorithms.indexing.stills_indexer.StillsIndexer method) (in module dials.algorithms.indexing.refinement) Refiner (class in dials.algorithms.refinement.refiner) RefinerFactory (class in dials.algorithms.refinement.refiner) Refinery (class in dials.algorithms.refinement.engine) ReflectionManager (class in dials.algorithms.integration.integrator) (class in dials.algorithms.refinement.reflection_manager) ReflectionManagerFactory (class in dials.algorithms.refinement.reflection_manager) ReflectionPredictor (class in dials.algorithms.spot_prediction.reflection_predictor) reflections_after_outlier_rejection() (dials.algorithms.refinement.refiner.RefinerFactory class method) reflections_and_experiments_from_files() (in module dials.util.options) reject_outliers() (in module dials.algorithms.scaling.outlier_rejection) remove_on_experiment_identifiers() (dxtbx.model.ExperimentList method) remove_sources_default (dials.util.installer.installer attribute) replace() (dxtbx.model.ExperimentList method) report() (dials.algorithms.integration.integrator.Integrator method) (dials.algorithms.integration.integrator.Integrator3DThreaded method) report_progress() (dials.algorithms.refinement.engine.LevenbergMarquardtIterations method) reset_accepted_reflections() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) reset_scan_points() (dxtbx.model.goniometer.Goniometer method) resolution_filter_from_array() (in module dials.algorithms.symmetry) resolution_filter_from_reflections_experiments() (in module dials.algorithms.symmetry) restart() (dials.algorithms.refinement.engine.AdaptLstbx method)

Result (class in dials.algorithms.indexing.model_evaluation) rmsd_names (dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff attribute) (dials.algorithms.refinement.target.Target attribute) (dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff attribute) (dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff attribute) rmsd_units (dials.algorithms.refinement.target.LaueLeastSquaresResidualWithRmsdCutoff attribute) (dials.algorithms.refinement.target.Target attribute) (dials.algorithms.refinement.target.TOFLeastSquaresResidualWithRmsdCutoff attribute) (dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff attribute) rmsds (dials.algorithms.indexing.model_evaluation.Result attribute) rmsds() (dials.algorithms.refinement.refiner.Refiner method) (dials.algorithms.refinement.target.Target method) rmsds_for_experiment() (dials.algorithms.refinement.target.Target method) rmsds_for_panel() (dials.algorithms.refinement.target.Target method) rmsds_for_reflection_table() (dials.algorithms.refinement.refiner.Refiner method) (dials.algorithms.refinement.target.Target method) rotate_around_origin() (dxtbx.model.Detector method) (dxtbx.model.goniometer.Goniometer method) rotate_crystal() (in module dials.util.export_mtz) rotation_matrix_differences() (in module dials.algorithms.indexing.compare_orientation_matrices) rotation_scan_manager() (dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory static method) run() (dials.algorithms.refinement.engine.GaussNewtonIterations method) (dials.algorithms.refinement.engine.LBFGScurvs method) (dials.algorithms.refinement.engine.LevenbergMarquardtIterations method) (dials.algorithms.refinement.engine.Refinery method) (dials.algorithms.refinement.engine.SimpleLBFGS method) (dials.algorithms.refinement.refiner.Refiner method) (dials.algorithms.scaling.outlier_rejection.OutlierRejectionBase method) (dials.algorithms.spot_finding.factory.BackgroundGradientFilter method) (dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter method) (dials.algorithms.spot_finding.factory.SpotDensityFilter method) (dials.algorithms.symmetry.cosym.CosymAnalysis method) run_lbfgs() (dials.algorithms.refinement.engine.AdaptLbfgs method)

S

scaling_models() (dxtbx.model.ExperimentList method) ScalingModelBase (class in dials.algorithms.scaling.model.model) ScanFactory (class in dxtbx.model.scan) scans() (dxtbx.model.ExperimentList method) ScanVaryingRefiner (class in dials.algorithms.refinement.refiner) score_by_fraction_indexed() (dials.algorithms.indexing.model_evaluation.ModelRankWeighted method) score_by_rmsd_xy() (dials.algorithms.indexing.model_evaluation.ModelRankWeighted method) score_by_volume() (dials.algorithms.indexing.model_evaluation.ModelRankWeighted method) score_vectors() (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch method) ScoreCorrelationCoefficient (class in dials.algorithms.symmetry.laue_group) ScoreSubGroup (class in dials.algorithms.symmetry.cosym) (class in dials.algorithms.symmetry.laue_group) ScoreSymmetryElement (class in dials.algorithms.symmetry.cosym) (class in dials.algorithms.symmetry.laue_group) search() (dxtbx.model.scan.ScanFactory static method) search_directions (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch property) search_vectors (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch property) select_on_experiment_identifiers() (dxtbx.model.ExperimentList method) selection_used_for_refinement() (dials.algorithms.refinement.refiner.Refiner method) sensor() (dxtbx.model.detector.DetectorFactory static method) set_angles() (dxtbx.model.goniometer.MultiAxisGoniometer method) set_axes() (dxtbx.model.goniometer.MultiAxisGoniometer method) set_beam() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) set_cholesky_factor() (dials.algorithms.refinement.engine.AdaptLstbx method) set_detector() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) set_dimensions() (dials.algorithms.symmetry.cosym.target.Target method) set_domain_size_ang() (dxtbx.model.MosaicCrystalSauter2014 method) set_error_model() (dials.algorithms.scaling.model.model.ScalingModelBase method) set_fixed_rotation() (dxtbx.model.goniometer.Goniometer method) set_format_class() (dxtbx.imageset.ImageSetData method) set_goniometer() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) set_half_mosaicity_deg() (dxtbx.model.MosaicCrystalSauter2014 method) set_last_cell() (dials.algorithms.refinement.engine.Journal method) set_mosaicity() (dxtbx.model.MosaicCrystalKabsch2010 method) set_nproc() (dials.algorithms.refinement.engine.DisableMPmixin method) (dials.algorithms.refinement.engine.Refinery method) set_params() (dxtbx.imageset.ImageSetData method) set_rotation_axis() (dxtbx.model.goniometer.Goniometer method) set_rotation_axis_datum() (dxtbx.model.goniometer.Goniometer method) set_scaling_model_as_scaled() (dials.algorithms.scaling.model.model.ScalingModelBase method) set_scaling_model_as_unscaled() (dials.algorithms.scaling.model.model.ScalingModelBase method) set_scan() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) (dxtbx.imageset.ImageSetData method) set_setting_rotation() (dxtbx.model.goniometer.Goniometer method) set_setting_rotation_at_scan_points() (dxtbx.model.goniometer.Goniometer method) set_shoebox_background_value() (in module dials.algorithms.background) set_template() (dxtbx.imageset.ImageSetData method) set_valid_image_range() (dials.algorithms.scaling.model.model.ScalingModelBase method)

set_vendor() (dxtbx.imageset.ImageSetData method) setup_indexing() (dials.algorithms.indexing.indexer.Indexer method) setup_mu() (dials.algorithms.refinement.engine.LevenbergMarquardtIterations method) shoebox_memory() (dials.algorithms.integration.integrator.JobList method) shoeboxes_to_reflection_table() (in module dials.algorithms.spot_finding.finder) show() (dxtbx.model.Crystal method) show_experiments() (dials.algorithms.indexing.indexer.Indexer method) simple() (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.detector.DetectorFactory static method) simple_directional() (dxtbx.model.beam.BeamFactory static method) SimpleBackgroundExt (class in dials.extensions.simple_background_ext) SimpleCentroidExt (class in dials.extensions.simple_centroid_ext) SimpleLBFGS (class in dials.algorithms.refinement.engine) SimpleNormDevOutlierRejection (class in dials.algorithms.scaling.outlier_rejection) single_axis() (dxtbx.model.goniometer.GoniometerFactory static method) single_axis_goniometer_from_phil() (dxtbx.model.goniometer.GoniometerFactory static method) single_axis_reverse() (dxtbx.model.goniometer.GoniometerFactory static method) single_file() (dxtbx.model.scan.ScanFactory static method) size() (dxtbx.imageset.ImageSet method) source_packages (dials.util.installer.installer attribute) SparseGradientsMixin (class in dials.algorithms.refinement.target) split() (dials.algorithms.integration.integrator.JobList method) (dials.algorithms.integration.integrator.ReflectionManager method) split_jacobian_into_blocks() (dials.algorithms.refinement.engine.Refinery method) split_matches_into_blocks() (dials.algorithms.refinement.target.Target method) SpotDensityFilter (class in dials.algorithms.spot_finding.factory) SpotFinder (class in dials.algorithms.spot_finding.finder) SpotFinderFactory (class in dials.algorithms.spot_finding.factory) stars (dials.algorithms.symmetry.cosym.ScoreSubGroup property) (dials.algorithms.symmetry.cosym.ScoreSymmetryElement property) start() (dials.util.command_line.Command class method) StatisticalWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) step_backward() (dials.algorithms.refinement.engine.AdaptLstbx method) step_forward() (dials.algorithms.refinement.engine.AdaptLstbx method) step_threshold (dials.algorithms.refinement.engine.GaussNewtonIterations attribute) stills_manager() (dials.algorithms.refinement.reflection_manager.ReflectionManagerFactory static method) StillsIndexer (class in dials.algorithms.indexing.stills_indexer) StillsIndexerBasisVectorSearch (class in dials.algorithms.indexing.stills_indexer) StillsIndexerKnownOrientation (class in dials.algorithms.indexing.stills_indexer) StillsIndexerLatticeSearch (class in dials.algorithms.indexing.stills_indexer) StillsReflectionManager (class in dials.algorithms.refinement.reflection_manager) StillsWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) Strategy (class in dials.algorithms.indexing.basis_vector_search) (class in dials.algorithms.indexing.lattice_search) (class in dials.algorithms.indexing.model_evaluation) subgroups_table() (dials.algorithms.symmetry.cosym.SymmetryAnalysis static method) summary() (dials.algorithms.integration.integrator.Integrator method) (dials.algorithms.integration.integrator.Integrator3DThreaded method) summary_table() (dials.algorithms.symmetry.cosym.SymmetryAnalysis static method) sym_ops_table() (dials.algorithms.symmetry.cosym.SymmetryAnalysis static method) symmetry_base (class in dials.algorithms.symmetry) SymmetryAnalysis (class in dials.algorithms.symmetry.cosym) SymmetryHandler (class in dials.algorithms.indexing.symmetry) system_phil (dials.util.options.ArgumentParser property) (dials.util.options.PhilCommandParser property)

T

Target (class in dials.algorithms.refinement.target) (class in dials.algorithms.symmetry.cosym.target) TargetedOutlierRejection (class in dials.algorithms.scaling.outlier_rejection) TargetFactory (class in dials.algorithms.refinement.target) tau (dials.algorithms.refinement.engine.LevenbergMarquardtIterations attribute) test_for_termination() (dials.algorithms.refinement.engine.Refinery method) test_objective_increasing_but_not_nref() (dials.algorithms.refinement.engine.Refinery method) test_rmsd_convergence() (dials.algorithms.refinement.engine.Refinery method) to_crystal() (in module dxtbx.serialize.xds) to_dict() (dials.algorithms.scaling.model.model.ScalingModelBase method) (dxtbx.model.Crystal method) (dxtbx.model.Detector method) (dxtbx.model.ExperimentList method) (dxtbx.model.goniometer.Goniometer method) (dxtbx.model.goniometer.MultiAxisGoniometer method) (dxtbx.model.MosaicCrystalKabsch2010 method) (dxtbx.model.MosaicCrystalSauter2014 method)

to_imageset() (in module dxtbx.serialize.xds) to_json_file() (dials.algorithms.refinement.engine.Journal method) to_xds (class in dxtbx.serialize.xds) TOFLeastSquaresResidualWithRmsdCutoff (class in dials.algorithms.refinement.target) TOFReflectionManager (class in dials.algorithms.refinement.reflection_manager) TOFSpotFinder (class in dials.algorithms.spot_finding.finder) traceback (dials.util.options.ArgumentHandlingErrorInfo attribute) trunccauchy_pdf() (in module dials.algorithms.symmetry.laue_group) try_read_experiments() (dials.util.options.Importer method) try_read_experiments_from_images() (dials.util.options.Importer method) try_read_reflections() (dials.util.options.Importer method) two_theta() (dxtbx.model.detector.DetectorFactory static method) type (dials.util.options.ArgumentHandlingErrorInfo attribute)

U

update() (dials.algorithms.scaling.model.model.ArrayScalingModel method) (dials.algorithms.scaling.model.model.DoseDecay method) (dials.algorithms.scaling.model.model.KBScalingModel method) (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) (dials.util.command_line.ProgressBar method) (dials.util.command_line.ProgressBarTimer method)

update_analysis() (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) update_detector_px_mm_data() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSet method) update_journal() (dials.algorithms.refinement.engine.Refinery method) update_matches() (dials.algorithms.refinement.target.Target method) update_residuals() (dials.algorithms.refinement.reflection_manager.LaueReflectionManager method) (dials.algorithms.refinement.reflection_manager.ReflectionManager method) (dials.algorithms.refinement.reflection_manager.TOFReflectionManager method)

V

validation (dials.util.options.ArgumentHandlingErrorInfo attribute)

W

warn_if_setting_unused_refinement_protocol_params() (dials.algorithms.indexing.stills_indexer.StillsIndexer method) WavelengthGroup (class in dials.util.export_mtz) wavelengths (dials.util.export_mtz.WavelengthGroup attribute)

weight() (dials.algorithms.background.RadialAverage method) weighted_mean (dials.util.export_mtz.WavelengthGroup attribute) where() (dxtbx.model.ExperimentList method) write_columns() (in module dials.util.export_mtz)

X

xds_detector_name() (in module dxtbx.serialize.xds)

XDS_INP() (dxtbx.serialize.xds.to_xds method) xparm_xds() (dxtbx.serialize.xds.to_xds method)