Index

A

accumulate() (dials.algorithms.integration.integrator.ReflectionManager method) (dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator method) achieved() (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() (dials.util.export_mtz.UnmergedMTZWriter method) 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_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 class method) all_sequences() (dxtbx.model.ExperimentList method) all_stills() (dxtbx.model.ExperimentList method) append() (dials.algorithms.indexing.model_evaluation.ModelRank method) (dials.algorithms.indexing.model_evaluation.ModelRankFilter method) (dxtbx.datablock.DataBlock 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) 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.datablock.DataBlockDumper method) (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.datablock.DataBlockDumper method) (dxtbx.model.ExperimentList method) as_pickle() (dxtbx.datablock.DataBlockDumper 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) AutoEncoder (class in dxtbx.datablock)

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.datablock) (class in dxtbx.model.experiment_list)

BeamDiff (class in dxtbx.datablock) 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_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_weights() (dials.algorithms.refinement.weighting_strategies.ConstantWeightingStrategy method) (dials.algorithms.refinement.weighting_strategies.ExternalDelPsiWeightingStrategy 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) 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) cluster_labels (dials.algorithms.symmetry.cosym.seed_clustering.seed_clustering attribute) 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) compact_simple_list() (in module dxtbx.serialize.dump) compact_simple_lists() (in module dxtbx.serialize.dump) 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 attribute) 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) (dials.algorithms.symmetry.cosym.target.Target 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_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 attribute) configure_components() (dials.algorithms.scaling.model.model.ArrayScalingModel 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) ConfigWriter (class in dials.util.options) consecutive_refinement_order (dials.algorithms.scaling.model.model.ArrayScalingModel attribute) (dials.algorithms.scaling.model.model.KBScalingModel attribute) (dials.algorithms.scaling.model.model.PhysicalScalingModel attribute) 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) CorrelationCoefficientAccumulator (class in dials.algorithms.symmetry.laue_group) CosymAnalysis (class in dials.algorithms.symmetry.cosym) create() (dials.algorithms.integration.integrator.IntegratorFactory static method) 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.engine.lbfgs_with_curvs method) (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 attribute) (dxtbx.imageset.ExternalLookupItemDouble attribute) 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) DataBlock (class in dxtbx.datablock) datablock() (in module dxtbx.serialize.dump) (in module dxtbx.serialize.load) DataBlockDictImporter (class in dxtbx.datablock) DataBlockDumper (class in dxtbx.datablock) DataBlockFactory (class in dxtbx.datablock) DataBlockFilenameImporter (class in dxtbx.datablock) DataBlockImageSetImporter (class in dxtbx.datablock) DataBlockTemplateImporter (class in dxtbx.datablock) default (dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt attribute) (dials.extensions.simple_centroid_ext.SimpleCentroidExt attribute) default() (dxtbx.datablock.AutoEncoder method) 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.datablock) (class in dxtbx.model.experiment_list) DetectorDiff (class in dxtbx.datablock) DetectorFactory (class in dxtbx.model.detector) detectors() (dxtbx.model.ExperimentList method) 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.seed_clustering (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.OptionParser attribute) (dials.util.options.PhilCommandParser attribute) difference_rotation_matrix_axis_angle() (in module dials.algorithms.indexing.compare_orientation_matrices) dim (dials.algorithms.refinement.target.Target attribute) (dials.algorithms.symmetry.cosym.target.Target attribute) DisableMPmixin (class in dials.algorithms.refinement.engine) DispersionSpotFinderThresholdExt (class in dials.extensions.dispersion_spotfinder_threshold_ext) dump() (in module dials.util.nexus) dx (dxtbx.imageset.ExternalLookup attribute) dxtbx.datablock (module) 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.dump (module) dxtbx.serialize.imageset (module) dxtbx.serialize.load (module) dxtbx.serialize.xds (module) dy (dxtbx.imageset.ExternalLookup attribute)

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 attribute) 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) experiment_list() (in module dxtbx.serialize.dump) (in module dxtbx.serialize.load) experiment_list_for_crystal() (dials.algorithms.indexing.stills_indexer.StillsIndexer method) experiment_type (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.datablock.DataBlock method) (dxtbx.model.ExperimentList method) external_lookup (dxtbx.imageset.ImageSet attribute) (dxtbx.imageset.ImageSetData attribute) ExternalDelPsiWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) ExternalLookup (class in dxtbx.imageset) ExternalLookupItemBool (class in dxtbx.imageset) ExternalLookupItemDouble (class in dxtbx.imageset) extract_imagesets() (dxtbx.datablock.DataBlock method) extract_sequences() (dxtbx.datablock.DataBlock method) extract_stills() (dxtbx.datablock.DataBlock method) 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 attribute) (dxtbx.imageset.ExternalLookupItemDouble attribute) 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.Strategy method) find_format() (dxtbx.datablock.FormatChecker 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) finished() (dials.algorithms.integration.integrator.ReflectionManager method) (dials.util.command_line.ProgressBar method) fix_initial_parameter() (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) flatten_experiments() (in module dials.util.options) flatten_reflections() (in module dials.util.options) format() (dxtbx.model.scan.ScanFactory static method) format_class() (dxtbx.datablock.DataBlock method) format_epilog() (dials.util.options.OptionParserBase method) format_help() (dials.util.options.OptionParser method) FormatChecker (class in dxtbx.datablock) fraction_indexed (dials.algorithms.indexing.model_evaluation.Result attribute) frame_hist() (in module dials.algorithms.integration.integrator) from_args() (dxtbx.datablock.DataBlockFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static method) from_data() (dials.algorithms.scaling.model.model.ArrayScalingModel 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_datablock_and_crystal() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_dict() (dials.algorithms.scaling.model.model.ArrayScalingModel 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.datablock.DataBlockFactory static method) (dxtbx.model.Crystal static method) (dxtbx.model.Detector static method) (dxtbx.model.MosaicCrystalKabsch2010 class method) (dxtbx.model.MosaicCrystalSauter2014 class method) (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.crystal.CrystalFactory 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.profile.ProfileModelFactory static method) (dxtbx.model.scan.ScanFactory static method) from_file() (dxtbx.model.ExperimentList static method) from_filenames() (dxtbx.datablock.DataBlockFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static method) from_format() (dxtbx.datablock.ImageMetadataRecord class method) from_imageset() (dxtbx.datablock.DataBlockFactory static method) (dxtbx.imageset.ImageGrid static method) from_imageset_and_crystal() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_imageset_json_file() (dxtbx.datablock.DataBlockFactory static method) from_in_memory() (dxtbx.datablock.DataBlockFactory static method) from_json() (dxtbx.datablock.DataBlockFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static method) from_json_file() (dials.algorithms.refinement.engine.Journal class method) (dxtbx.datablock.DataBlockFactory static 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.datablock.DataBlockFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static method) from_sequence_and_crystal() (dxtbx.model.experiment_list.ExperimentListFactory static method) from_serialized_format() (dxtbx.datablock.DataBlockFactory static method) (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_xds() (dxtbx.model.experiment_list.ExperimentListFactory static method)

G

gain (dxtbx.imageset.ExternalLookup attribute) 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)

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_space_group_type_from_xparm() (in module dials.util.ioutil) get_sym_ops() (dials.algorithms.symmetry.cosym.target.Target method) get_template() (dxtbx.imageset.ImageSequence method) (dxtbx.imageset.ImageSetData method) (dxtbx.serialize.xds.to_xds method) get_ub_matrix_from_xparm() (in module dials.util.ioutil) get_unit_cell_from_xparm() (in module dials.util.ioutil) get_vendor() (dxtbx.imageset.ImageSetData method) get_vendortype() (dxtbx.imageset.ImageSet method) Goniometer (class in dxtbx.model.goniometer) GoniometerComparison (class in dxtbx.datablock) (class in dxtbx.model.experiment_list) GoniometerDiff (class in dxtbx.datablock) GoniometerFactory (class in dxtbx.model.goniometer) goniometers() (dxtbx.model.ExperimentList method) gradient_threshold (dials.algorithms.refinement.engine.GaussNewtonIterations attribute)

H

has_dynamic_mask() (dxtbx.imageset.ImageSet 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 attribute) hkl_offset (dials.algorithms.indexing.model_evaluation.Result attribute)

I

id_ (dials.algorithms.scaling.model.model.ArrayScalingModel attribute) (dials.algorithms.scaling.model.model.KBScalingModel attribute) (dials.algorithms.scaling.model.model.PhysicalScalingModel attribute) (dials.algorithms.scaling.model.model.ScalingModelBase attribute) identifiers() (dxtbx.imageset.MemReader method) (dxtbx.model.ExperimentList method) identify_outliers() (dials.algorithms.indexing.stills_indexer.StillsIndexer method) ImageGrid (class in dxtbx.imageset) ImageMetadataRecord (class in dxtbx.datablock) 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.dump) (in module dxtbx.serialize.load) imageset_from_anyset() (dxtbx.imageset.ImageSetFactory static method) imageset_from_dict() (in module dxtbx.serialize.imageset) imageset_from_string() (in module dxtbx.serialize.load) imageset_to_dict() (in module dxtbx.serialize.imageset) imageset_to_string() (in module dxtbx.serialize.dump) 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 (dxtbx.datablock.OpeningPathIterator attribute), [1] 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) IntegratorFactory (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) InvalidDataBlockError 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 attribute) is_similar_to() (dxtbx.model.Detector method) (dxtbx.model.MosaicCrystalKabsch2010 method) (dxtbx.model.MosaicCrystalSauter2014 method) (dxtbx.model.goniometer.Goniometer method) is_single_file_reader() (dxtbx.imageset.MemReader static method) iter_groups() (dxtbx.datablock.FormatChecker method) iter_levelorder() (dxtbx.model.Detector method) iter_panels() (dxtbx.model.Detector method) iter_preorder() (dxtbx.model.Detector method) iter_sequences() (dxtbx.datablock.DataBlock method) iter_stills() (dxtbx.datablock.DataBlock 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

LaueGroupAnalysis (class in dials.algorithms.symmetry.laue_group) 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.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) load() (in module dials.util.nexus) load_image() (dials.algorithms.spot_finding.factory.SpotFinderFactory static method) 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_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_scan() (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 attribute) 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_shift_over_esd (dials.algorithms.refinement.engine.GaussNewtonIterations attribute)

mean() (dials.algorithms.background.RadialAverage method) MemReader (class in dxtbx.imageset) merge_metadata_from() (dxtbx.datablock.ImageMetadataRecord method) MergedMTZWriter (class in dials.util.export_mtz) message (dials.util.options.ArgumentHandlingErrorInfo attribute) metric_supergroup() (in module dials.algorithms.indexing.symmetry) 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) MosaicCrystalKabsch2010 (class in dxtbx.model) MosaicCrystalSauter2014 (class in dxtbx.model) MTZWriterBase (class in dials.util.export_mtz) mu (dials.algorithms.refinement.engine.LevenbergMarquardtIterations attribute) 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 attribute) 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) next() (dxtbx.datablock.OpeningPathIterator 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_images() (dxtbx.datablock.DataBlock method) num_reflections() (dials.algorithms.integration.integrator.ReflectionManager method) num_scan_points (dxtbx.model.goniometer.Goniometer attribute) numerator() (dials.algorithms.symmetry.laue_group.CorrelationCoefficientAccumulator method)

O

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

OptionParserBase (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 attribute) p_cc_given_s (dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient attribute) p_s_given_cc (dials.algorithms.symmetry.laue_group.ScoreCorrelationCoefficient attribute) 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.OptionParser method) (dials.util.options.OptionParserBase method) (dials.util.options.PhilCommandParser method) parse_range_list_string() (in module dials.util.command_line) 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 attribute) per_image() (dials.algorithms.refinement.reflection_manager.BlockCalculator method) per_width() (dials.algorithms.refinement.reflection_manager.BlockCalculator method) phil (dials.util.options.OptionParser attribute) (dials.util.options.PhilCommandParser attribute) phil() (dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt class method) (dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt class method) (dials.extensions.simple_background_ext.SimpleBackgroundExt class method) 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.Strategy attribute) (dials.algorithms.scaling.model.model.ArrayScalingModel 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) PixelListToReflectionTable (class in dials.algorithms.spot_finding.finder) PixelListToShoeboxes (class in 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.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.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)

Q

quasi_normalisation() (dials.algorithms.symmetry.symmetry_base static method)

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_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) (class in dials.algorithms.spot_finding.finder) rmsd_names (dials.algorithms.refinement.target.Target attribute) (dials.algorithms.refinement.target_stills.LeastSquaresStillsResidualWithRmsdCutoff attribute) rmsd_units (dials.algorithms.refinement.target.Target 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) rotation_matrix_differences() (in module dials.algorithms.indexing.compare_orientation_matrices) 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) ScanDiff (class in dxtbx.datablock) 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 attribute) search_vectors (dials.algorithms.indexing.basis_vector_search.RealSpaceGridSearch attribute) seed_clustering (class in dials.algorithms.symmetry.cosym.seed_clustering) 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) SequenceDiff (class in dxtbx.datablock) (class in dxtbx.model.experiment_list) 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) ShoeboxesToReflectionTable (class in 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() (dxtbx.model.scan.ScanFactory static method) 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) 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 attribute) (dials.algorithms.symmetry.cosym.ScoreSymmetryElement attribute) 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) 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.OptionParser attribute) (dials.util.options.PhilCommandParser attribute)

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_datablocks() (dxtbx.model.ExperimentList method) to_dict() (dials.algorithms.scaling.model.model.ScalingModelBase method) (dxtbx.datablock.DataBlock method) (dxtbx.model.Crystal method) (dxtbx.model.Detector method) (dxtbx.model.ExperimentList method) (dxtbx.model.MosaicCrystalKabsch2010 method) (dxtbx.model.MosaicCrystalSauter2014 method) (dxtbx.model.goniometer.Goniometer method) (dxtbx.model.goniometer.MultiAxisGoniometer method)

to_imageset() (in module dxtbx.serialize.xds) to_json_file() (dials.algorithms.refinement.engine.Journal method) to_xds (class in dxtbx.serialize.xds) 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

unhandled (dxtbx.datablock.OpeningPathIterator attribute) unique_beams() (dxtbx.datablock.DataBlock method) unique_detectors() (dxtbx.datablock.DataBlock method) unique_goniometers() (dxtbx.datablock.DataBlock method) unique_scans() (dxtbx.datablock.DataBlock method) UnmergedMTZWriter (class in dials.util.export_mtz)

update() (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)

V

validation (dials.util.options.ArgumentHandlingErrorInfo attribute)

W

weight() (dials.algorithms.background.RadialAverage method) where() (dxtbx.model.ExperimentList method)

write() (dials.util.options.ConfigWriter method) write_columns() (dials.util.export_mtz.UnmergedMTZWriter method)

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)