Index

A

accumulate() (dials.algorithms.symmetry.determine_space_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() (dxtbx.model.scan.ScanFactory static method) add_column() (dials.algorithms.refinement.engine.Journal method) add_constant_to_diagonal() (dials.algorithms.refinement.engine.LevenbergMarquardtIterations 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_approx_equal() (in module dxtbx.datablock) all_equal() (in module dxtbx.datablock) all_stills() (dxtbx.model.ExperimentList method) all_sweeps() (dxtbx.model.ExperimentList method) analyse_datasets (class in dials.algorithms.symmetry.cosym) append() (dials.algorithms.indexing.indexer.SolutionTrackerFilter method) (dials.algorithms.indexing.indexer.SolutionTrackerWeighted method) (dials.algorithms.indexing.indexer.vector_group method) (dials.array_family.flex.reflection_table_aux method) (dxtbx.datablock.DataBlock method) (dxtbx.model.ExperimentList method)

apply_hkl_offset() (in module dials.algorithms.indexing.indexer) apply_symmetry() (dials.algorithms.indexing.indexer.indexer_base method) are_experiment_identifiers_consistent() (dials.array_family.flex.reflection_table_aux method) ArgumentHandlingErrorInfo (class in dials.util.options) ArrayScalingModel (class in dials.algorithms.scaling.model.model) as_dict() (dials.algorithms.indexing.symmetry.refined_settings_list method) (dials.algorithms.symmetry.determine_space_group.ScoreSubGroup method) (dials.algorithms.symmetry.determine_space_group.ScoreSymmetryElement method) (dials.algorithms.symmetry.determine_space_group.determine_space_group method) as_file() (dxtbx.datablock.DataBlockDumper method) (dxtbx.model.experiment_list.ExperimentListDumper method) as_h5() (dials.array_family.flex.reflection_table_aux method) as_json() (dials.algorithms.symmetry.determine_space_group.determine_space_group method) (dxtbx.datablock.DataBlockDumper method) (dxtbx.model.experiment_list.ExperimentListDumper method) as_miller_array() (dials.array_family.flex.reflection_table_aux method) as_msgpack() (dials.array_family.flex.reflection_table_aux method) as_msgpack_file() (dials.array_family.flex.reflection_table_aux method) as_pickle() (dials.array_family.flex.reflection_table_aux method) (dxtbx.datablock.DataBlockDumper method) (dxtbx.model.experiment_list.ExperimentListDumper method) assert_experiment_identifiers_are_consistent() (dials.array_family.flex.reflection_table_aux method) AutoEncoder (class in dxtbx.datablock)

B

background_includes_bad_pixels (dials.array_family.flex.reflection_table_aux.flags attribute) BackgroundGradientFilter (class in dials.algorithms.spot_finding.factory) bad_for_refinement (dials.array_family.flex.reflection_table_aux.flags attribute) bad_for_scaling (dials.array_family.flex.reflection_table_aux.flags attribute) bad_reference (dials.array_family.flex.reflection_table_aux.flags attribute) bad_shoebox (dials.array_family.flex.reflection_table_aux.flags attribute) bad_spot (dials.array_family.flex.reflection_table_aux.flags attribute) 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) basis_vector_minimser (class in dials.algorithms.indexing.indexer)

basis_vector_target (class in dials.algorithms.indexing.indexer) BeamComparison (class in dxtbx.datablock) BeamDiff (class in dxtbx.datablock) BeamFactory (class in dxtbx.model.beam) beams() (dxtbx.model.ExperimentList method) best_solution() (dials.algorithms.indexing.indexer.SolutionTrackerFilter method) (dials.algorithms.indexing.indexer.SolutionTrackerWeighted method) bit_length() (dials.array_family.flex.reflection_table_aux.flags method) BlockCalculator (class in dials.algorithms.refinement.reflection_manager) bravais_setting (class in dials.algorithms.indexing.symmetry) build_up() (dials.algorithms.refinement.engine.AdaptLstbx method)

C

calculate_entering_flags() (dials.algorithms.indexing.indexer.indexer_base static method) (in module dials.algorithms.refinement.reflection_manager) 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.indexing.indexer.basis_vector_minimser method) (dials.algorithms.refinement.engine.AdaptLbfgs method) (dials.algorithms.symmetry.cosym.engine.lbfgs_with_curvs method) candidate_basis_vectors_fft1d() (dials.algorithms.indexing.fft1d.indexer_fft1d method) centroid_outlier (dials.array_family.flex.reflection_table_aux.flags attribute) check_child_formats() (dxtbx.datablock.FormatChecker method) check_flags() (dials.algorithms.spot_finding.factory.FilterRunner method) choose_best_orientation_matrix() (dials.algorithms.indexing.indexer.indexer_base method) clean_3d() (in module dials.algorithms.indexing.fft3d) clean_experiment_identifiers_map() (dials.array_family.flex.reflection_table_aux method) clear() (dials.array_family.flex.reflection_table_aux method) (dxtbx.model.ExperimentList method) cluster_analysis_dbscan() (dials.algorithms.indexing.fft3d.indexer_fft3d method) cluster_analysis_hcluster() (dials.algorithms.indexing.fft3d.indexer_fft3d method) cluster_labels (dials.algorithms.symmetry.cosym.seed_clustering.seed_clustering attribute) coefficient() (dials.algorithms.symmetry.determine_space_group.CorrelationCoefficientAccumulator method) coloured() (in module dials.util.command_line) cols() (dials.array_family.flex.reflection_table_aux method) Command (class in dials.util.command_line) compact_simple_list() (in module dxtbx.serialize.dump) compact_simple_lists() (in module dxtbx.serialize.dump) complex() (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.detector.DetectorFactory static method) components (dials.algorithms.scaling.model.model.ScalingModelBase attribute) compute_background() (dials.array_family.flex.reflection_table_aux method) (dials.extensions.null_background_ext.NullBackgroundExt method) (dials.extensions.simple_background_ext.SimpleBackgroundExt method) compute_bbox() (dials.array_family.flex.reflection_table_aux method) compute_centroid() (dials.array_family.flex.reflection_table_aux method) (dials.extensions.simple_centroid_ext.SimpleCentroidExt method) compute_corrections() (dials.array_family.flex.reflection_table_aux method) compute_d() (dials.array_family.flex.reflection_table_aux method) compute_d_single() (dials.array_family.flex.reflection_table_aux method) compute_fitted_intensity() (dials.array_family.flex.reflection_table_aux method) compute_functional() (dials.algorithms.symmetry.cosym.target.Target method) compute_functional_and_gradients() (dials.algorithms.indexing.indexer.basis_vector_minimser method) (dials.algorithms.indexing.indexer.basis_vector_target 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_mask() (dials.array_family.flex.reflection_table_aux method) compute_mean() (dials.algorithms.indexing.indexer.vector_group method) compute_miller_indices_in_asu() (dials.array_family.flex.reflection_table_aux method) compute_partiality() (dials.array_family.flex.reflection_table_aux method) compute_phi_range() (dials.array_family.flex.reflection_table_aux method) compute_ray_intersections() (dials.array_family.flex.reflection_table_aux 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_shoebox_overlap_fraction() (dials.array_family.flex.reflection_table_aux method) compute_summed_intensity() (dials.array_family.flex.reflection_table_aux method) compute_threshold() (dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt method) compute_zeta() (dials.array_family.flex.reflection_table_aux method) compute_zeta_multi() (dials.array_family.flex.reflection_table_aux method) config_parameterisation() (dials.algorithms.refinement.refiner.RefinerFactory static 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) conjugate() (dials.array_family.flex.reflection_table_aux.flags method) consecutive_refinement_order (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) ConstantWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) contains_invalid_pixels() (dials.array_family.flex.reflection_table_aux method) convergence_as_shift_over_esd (dials.algorithms.refinement.engine.GaussNewtonIterations attribute) copy() (dials.array_family.flex.reflection_table_aux method) correct_non_primitive_basis() (dials.algorithms.indexing.indexer.indexer_base method) CorrelationCoefficientAccumulator (class in dials.algorithms.symmetry.determine_space_group) create() (dials.algorithms.integration.integrator.IntegratorFactory static method) Crystal (class in dxtbx.model) crystal() (in module dxtbx.serialize.dump) (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() (dials.algorithms.integration.integrator.IntegratorExecutor method) (dials.algorithms.integration.integrator.ProfileModellerExecutor method) (dials.algorithms.integration.integrator.ProfileValidatorExecutor 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) debug_plot_candidate_basis_vectors() (dials.algorithms.indexing.indexer.indexer_base method) debug_plot_clusters() (dials.algorithms.indexing.fft3d.indexer_fft3d method) debug_plot_residuals() (in module dials.algorithms.indexing.refinement) debug_show_candidate_basis_vectors() (dials.algorithms.indexing.indexer.indexer_base method) debug_write_ccp4_map() (dials.algorithms.indexing.indexer.indexer_base method) debug_write_reciprocal_lattice_points_as_pdb() (dials.algorithms.indexing.indexer.indexer_base method) decode() (dxtbx.model.experiment_list.ExperimentListDict method) default (dials.extensions.dispersion_spotfinder_threshold_ext.DispersionSpotFinderThresholdExt attribute) (dials.extensions.gaussian_rs_profile_model_ext.GaussianRSProfileModelExt attribute) (dials.extensions.simple_centroid_ext.SimpleCentroidExt attribute) default() (dxtbx.datablock.AutoEncoder method) default_background_algorithm() (in module dials.array_family.flex) default_centroid_algorithm() (in module dials.array_family.flex) del_last_row() (dials.algorithms.refinement.engine.Journal method) del_selected() (dials.array_family.flex.reflection_table_aux method) denominator (dials.array_family.flex.reflection_table_aux.flags attribute) denominator() (dials.algorithms.symmetry.determine_space_group.CorrelationCoefficientAccumulator method) dest_dir_prefix (dials.util.installer.installer attribute) detect_non_primitive_basis() (in module dials.algorithms.indexing.indexer) Detector (class in dxtbx.model) DetectorComparison (class in dxtbx.datablock) 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) determine_space_group (class in dials.algorithms.symmetry.determine_space_group) dials.algorithms.background (module) dials.algorithms.indexing.compare_orientation_matrices (module) dials.algorithms.indexing.fft1d (module) dials.algorithms.indexing.fft3d (module) dials.algorithms.indexing.indexer (module) dials.algorithms.indexing.real_space_grid_search (module) dials.algorithms.indexing.refinement (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.determine_space_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) dials_crystal_from_orientation() (in module dials.algorithms.indexing.symmetry) dials_u_to_mosflm() (in module dials.util.export_mtz) 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.symmetry.cosym.target.Target attribute) DisableMPmixin (class in dials.algorithms.refinement.engine) DispersionSpotFinderThresholdExt (class in dials.extensions.dispersion_spotfinder_threshold_ext) dont_integrate (dials.array_family.flex.reflection_table_aux.flags attribute) dump() (in module dials.util.nexus) 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)

E

empty() (dials.array_family.flex.reflection_table_aux method) (dxtbx.model.ExperimentList method) empty_standard() (dials.array_family.flex.reflection_table_aux static 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) exception (dials.util.options.ArgumentHandlingErrorInfo attribute) excluded_for_refinement (dials.array_family.flex.reflection_table_aux.flags attribute) excluded_for_scaling (dials.array_family.flex.reflection_table_aux.flags attribute) experiment_identifiers() (dials.array_family.flex.reflection_table_aux method) experiment_list() (in module dxtbx.serialize.dump) (in module dxtbx.serialize.load) ExperimentList (class in dxtbx.model) ExperimentListDict (class in dxtbx.model.experiment_list) ExperimentListDumper (class in dxtbx.model.experiment_list) ExperimentListFactory (class in dxtbx.model.experiment_list)

ExperimentListTemplateImporter (class in dxtbx.model.experiment_list) export_as_json() (dials.algorithms.indexing.indexer.indexer_base method) export_mtz() (in module dials.util.export_mtz) export_reflections() (dials.algorithms.indexing.indexer.indexer_base method) export_text() (in module dials.util.export_text) extend() (dials.array_family.flex.reflection_table_aux method) (dxtbx.datablock.DataBlock method) (dxtbx.model.ExperimentList method) ExternalDelPsiWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) extract_imagesets() (dxtbx.datablock.DataBlock method) extract_shoeboxes() (dials.array_family.flex.reflection_table_aux method) extract_stills() (dxtbx.datablock.DataBlock method) extract_sweeps() (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

failed_during_background_modelling (dials.array_family.flex.reflection_table_aux.flags attribute) failed_during_profile_fitting (dials.array_family.flex.reflection_table_aux.flags attribute) failed_during_summation (dials.array_family.flex.reflection_table_aux.flags attribute) fft() (dials.algorithms.indexing.fft3d.indexer_fft3d method) filename_or_none() (in module dxtbx.serialize.imageset) filename_to_absolute() (in module dxtbx.serialize.imageset) FilenameAnalyser (class in dxtbx.imageset) filter_by_likelihood() (dials.algorithms.indexing.indexer.SolutionTrackerFilter method) filter_by_n_indexed() (dials.algorithms.indexing.indexer.SolutionTrackerFilter method) filter_by_volume() (dials.algorithms.indexing.indexer.SolutionTrackerFilter method) filter_doubled_cell() (in module dials.algorithms.indexing.indexer) filter_obs() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) filter_reflections_by_scan_range() (dials.algorithms.indexing.indexer.indexer_base method) (in module dials.algorithms.indexing.indexer) 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) FinalizerBase (class in dials.algorithms.integration.integrator) FinalizerClass (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) FinalizerRot (class in dials.algorithms.integration.integrator) FinalizerStills (class in dials.algorithms.integration.integrator) find() (dxtbx.model.ExperimentList method) find_basis_vector_combinations_cluster_analysis() (dials.algorithms.indexing.fft3d.indexer_fft3d method) find_candidate_basis_vectors() (dials.algorithms.indexing.fft1d.indexer_fft1d method) (dials.algorithms.indexing.fft3d.indexer_fft3d method) find_candidate_orientation_matrices() (dials.algorithms.indexing.indexer.indexer_base method) find_format() (dxtbx.datablock.FormatChecker method) find_lattices() (dials.algorithms.indexing.fft1d.indexer_fft1d method) (dials.algorithms.indexing.fft3d.indexer_fft3d method) (dials.algorithms.indexing.indexer.indexer_base method) (dials.algorithms.indexing.real_space_grid_search.indexer_real_space_grid_search method) find_matching_symmetry() (in module dials.algorithms.indexing.symmetry) find_max_cell() (dials.algorithms.indexing.indexer.indexer_base method) find_overlaps() (dials.array_family.flex.reflection_table_aux method) find_peaks() (dials.algorithms.indexing.fft3d.indexer_fft3d method) find_peaks_clean() (dials.algorithms.indexing.fft3d.indexer_fft3d method) finished() (dials.util.command_line.ProgressBar method) flatten_datablocks() (in module dials.util.options) flatten_experiments() (in module dials.util.options) flatten_reflections() (in module dials.util.options) foreground_includes_bad_pixels (dials.array_family.flex.reflection_table_aux.flags attribute) 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) frame_hist() (in module dials.algorithms.integration.integrator)

from_args() (dxtbx.datablock.DataBlockFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static 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 static method) (dxtbx.model.MosaicCrystalSauter2014 static 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.GoniometerFactory static method) (dxtbx.model.profile.ProfileModelFactory static method) (dxtbx.model.scan.ScanFactory static method) from_filenames() (dxtbx.datablock.DataBlockFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static method) from_h5() (dials.array_family.flex.reflection_table_aux static method) from_imageset() (dxtbx.datablock.DataBlockFactory 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() (dxtbx.datablock.DataBlockFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static method) from_mosflm_matrix() (dxtbx.model.crystal.CrystalFactory static method) from_msgpack() (dials.array_family.flex.reflection_table_aux static method) from_msgpack_file() (dials.array_family.flex.reflection_table_aux static method) from_observations() (dials.array_family.flex.reflection_table_aux static method) from_parameters() (dials.algorithms.indexing.indexer.indexer_base 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() (dials.array_family.flex.reflection_table_aux static method) from_pickle_file() (dxtbx.datablock.DataBlockFactory static method) (dxtbx.model.experiment_list.ExperimentListFactory static method) from_predictions() (dials.array_family.flex.reflection_table_aux static method) from_predictions_multi() (dials.array_family.flex.reflection_table_aux 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_sweep_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

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() (dxtbx.imageset.MemMasker method) 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_beam() (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.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) get_detector() (dxtbx.imageset.ImageSetLazy method) (dxtbx.serialize.xds.to_xds method) get_detectorbase() (dxtbx.imageset.ImageSetAux 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_flags() (dials.array_family.flex.reflection_table_aux method) get_format_class() (dxtbx.imageset.ImageSetAux method) get_free_reflections() (dials.algorithms.refinement.refiner.Refiner method) (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_gain() (dxtbx.imageset.ImageSetLazy method) get_goniometer() (dxtbx.imageset.ImageSetLazy method) (dxtbx.serialize.xds.to_xds method) get_half_mosaicity_deg() (dxtbx.model.MosaicCrystalSauter2014 method) get_indexed() (dials.algorithms.refinement.reflection_manager.ReflectionManager method)

get_inverse_ub_matrix_from_xparm() (in module dials.util.ioutil) 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) 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_steps() (dials.algorithms.refinement.engine.Refinery method) get_obs() (dials.algorithms.refinement.reflection_manager.ReflectionManager 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_ray_intersection() (dxtbx.model.Detector method) get_sample_size() (dials.algorithms.refinement.reflection_manager.ReflectionManager method) get_scan() (dxtbx.imageset.ImageSetLazy method) (dxtbx.serialize.xds.to_xds 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.ImageSweepAux 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_vendortype() (dxtbx.imageset.ImageSetAux method) GoniometerComparison (class in dxtbx.datablock) 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_key() (dials.array_family.flex.reflection_table_aux method) heading() (in module dials.util.command_line) help_keys() (dials.array_family.flex.reflection_table_aux method)

hierarchy() (dxtbx.model.Detector method) hist() (in module dials.algorithms.integration.integrator) hist_outline() (in module dials.algorithms.indexing.indexer)

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.MemMasker method) (dxtbx.imageset.MemReader method) (dxtbx.model.ExperimentList method) identify_likely_solutions() (in module dials.algorithms.indexing.symmetry) imag (dials.array_family.flex.reflection_table_aux.flags attribute) 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) ImageSetAux (class in dxtbx.imageset) ImageSetFactory (class in dxtbx.imageset) ImageSetLazy (class in dxtbx.imageset) imagesets() (dxtbx.model.ExperimentList method) imagesweep_from_dict() (in module dxtbx.serialize.imageset) imagesweep_to_dict() (in module dxtbx.serialize.imageset) ImageSweepAux (class in dxtbx.imageset) 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) in_powder_ring (dials.array_family.flex.reflection_table_aux.flags attribute) include_gui_packages (dials.util.installer.installer attribute) includes_bad_pixels (dials.array_family.flex.reflection_table_aux.flags attribute) indent (dials.util.command_line.Command attribute) index() (dials.algorithms.indexing.indexer.indexer_base method) index_reflections() (dials.algorithms.indexing.indexer.indexer_base method) indexed (dials.array_family.flex.reflection_table_aux.flags attribute) indexer_base (class in dials.algorithms.indexing.indexer) indexer_fft1d (class in dials.algorithms.indexing.fft1d) indexer_fft3d (class in dials.algorithms.indexing.fft3d) indexer_real_space_grid_search (class in dials.algorithms.indexing.real_space_grid_search) indices() (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)

InitializerClass (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) InitializerRot (class in dials.algorithms.integration.integrator) InitializerStills (class in dials.algorithms.integration.integrator) insert() (dials.array_family.flex.reflection_table_aux 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) (dials.array_family.flex.reflection_table_aux method) integrated (dials.array_family.flex.reflection_table_aux.flags attribute) integrated_prf (dials.array_family.flex.reflection_table_aux.flags attribute) integrated_sum (dials.array_family.flex.reflection_table_aux.flags attribute) 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) IntegratorVolume (class in dials.algorithms.integration.integrator) InvalidDataBlockError InvalidExperimentListError is_approximate_integer_multiple() (in module dials.algorithms.indexing.indexer) is_consistent() (dials.array_family.flex.reflection_table_aux method) (dxtbx.model.ExperimentList method) is_overloaded() (dials.array_family.flex.reflection_table_aux 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) is_single_file_reader() (dxtbx.imageset.MemReader method) isclose() (in module dials.util.export_mtz) 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_stills() (dxtbx.datablock.DataBlock method) iter_sweeps() (dxtbx.datablock.DataBlock method) iterate_experiments_and_indices() (dials.array_family.flex.reflection_table_aux method)

J

jacobian_condition_number() (dials.algorithms.refinement.engine.Refinery method)

Journal (class in dials.algorithms.refinement.engine)

K

kappa() (dxtbx.model.goniometer.GoniometerFactory static method) KBScalingModel (class in dials.algorithms.scaling.model.model)

kernel_normalisation() (dials.algorithms.symmetry.symmetry_base static method) keys() (dials.array_family.flex.reflection_table_aux method) known_axis() (dxtbx.model.goniometer.GoniometerFactory static method)

L

labelit_printout() (dials.algorithms.indexing.symmetry.refined_settings_list method) 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)

M

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_sweep() (dxtbx.imageset.ImageSetFactory static method) map_centroids_to_reciprocal_space() (dials.algorithms.indexing.indexer.indexer_base static method) map_centroids_to_reciprocal_space_grid() (dials.algorithms.indexing.fft3d.indexer_fft3d method) map_spots_pixel_to_mm_rad() (dials.algorithms.indexing.indexer.indexer_base static method) masker() (dxtbx.imageset.ImageSetAux method) master_path() (dxtbx.imageset.MemReader method) match() (dials.array_family.flex.reflection_table_aux method)

match_with_reference() (dials.array_family.flex.reflection_table_aux method) match_with_reference_without_copying_columns() (dials.array_family.flex.reflection_table_aux method) max_length (dials.util.command_line.Command attribute) max_shift_over_esd (dials.algorithms.refinement.engine.GaussNewtonIterations attribute) mean() (dials.algorithms.indexing.indexer.vector_group method) MemMasker (class in dxtbx.imageset) MemReader (class in dxtbx.imageset) 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_or_none() (dxtbx.model.experiment_list.ExperimentListDict static method) MosaicCrystalKabsch2010 (class in dxtbx.model) MosaicCrystalSauter2014 (class in dxtbx.model) 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)

N

n() (dials.algorithms.symmetry.determine_space_group.CorrelationCoefficientAccumulator method) n_params (dials.algorithms.scaling.model.model.ScalingModelBase attribute) name (dials.array_family.flex.reflection_table_aux.flags attribute) (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) names (dials.array_family.flex.reflection_table_aux.flags attribute) ncols() (dials.array_family.flex.reflection_table_aux method)

new() (dxtbx.imageset.ImageSetFactory static method) nframes_hist() (in module dials.algorithms.integration.integrator) normalise_components() (dials.algorithms.scaling.model.model.PhysicalScalingModel method) (dials.algorithms.scaling.model.model.ScalingModelBase method) NormDevOutlierRejection (class in dials.algorithms.scaling.outlier_rejection) nrows() (dials.array_family.flex.reflection_table_aux method) 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) numerator (dials.array_family.flex.reflection_table_aux.flags attribute) numerator() (dials.algorithms.symmetry.determine_space_group.CorrelationCoefficientAccumulator method)

O

observed (dials.array_family.flex.reflection_table_aux.flags attribute) op_string (dials.array_family.flex.reflection_table_selector attribute) optimise_basis_vectors() (in module dials.algorithms.indexing.indexer) optimise_peaks() (dials.algorithms.indexing.fft3d.indexer_fft3d method) OptionParser (class in dials.util.options) OptionParserBase (class in dials.util.options)

outlier_in_scaling (dials.array_family.flex.reflection_table_aux.flags attribute) OutlierRejectionBase (class in dials.algorithms.scaling.outlier_rejection) overlapped_bg (dials.array_family.flex.reflection_table_aux.flags attribute) overlapped_fg (dials.array_family.flex.reflection_table_aux.flags attribute) overloaded (dials.array_family.flex.reflection_table_aux.flags attribute) overwrite_from_phil() (dxtbx.model.detector.DetectorFactory static method)

P

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.ImageSetAux 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) paths() (dxtbx.imageset.ImageSetAux method) (dxtbx.imageset.MemMasker method) (dxtbx.imageset.MemReader method) PeakCentroidDistanceFilter (class in dials.algorithms.spot_finding.factory) 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) 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() (dials.array_family.flex.reflection_table_aux static method) plot_centroid_weights_histograms() (in module dials.algorithms.indexing.indexer) plot_dendrogram() (in module dials.algorithms.symmetry.cosym) plot_matrix() (in module dials.algorithms.symmetry.cosym) plot_rij_cumulative_frequency() (dials.algorithms.symmetry.cosym.target.Target method) plot_rij_histogram() (dials.algorithms.symmetry.cosym.target.Target method) plot_rij_matrix() (dials.algorithms.symmetry.cosym.target.Target method) plot_wij_cumulative_frequency() (dials.algorithms.symmetry.cosym.target.Target method)

plot_wij_histogram() (dials.algorithms.symmetry.cosym.target.Target method) plot_wij_matrix() (dials.algorithms.symmetry.cosym.target.Target method) 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) predicted (dials.array_family.flex.reflection_table_aux.flags attribute) 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.IntegratorExecutor method) (dials.algorithms.integration.integrator.ProfileModellerExecutor method) (dials.algorithms.integration.integrator.ProfileValidatorExecutor method) 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) 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

read() (dxtbx.imageset.MemReader method) read_file() (dials.util.image.reader method) reader (class in dials.util.image) reader() (dxtbx.imageset.ImageSetAux method) real (dials.array_family.flex.reflection_table_aux.flags attribute) real_space_grid_search() (dials.algorithms.indexing.real_space_grid_search.indexer_real_space_grid_search method) reason_for_termination (dials.algorithms.refinement.engine.Journal attribute) record_intensity_combination_Imid() (dials.algorithms.scaling.model.model.ScalingModelBase method) reference_spot (dials.array_family.flex.reflection_table_aux.flags attribute) refine() (dials.algorithms.indexing.indexer.indexer_base method) (in module dials.algorithms.indexing.refinement) refine_subgroup() (in module dials.algorithms.indexing.symmetry) refined_settings_factory_from_refined_triclinic() (in module dials.algorithms.indexing.symmetry) refined_settings_list (class in dials.algorithms.indexing.symmetry) Refiner (class in dials.algorithms.refinement.refiner) RefinerFactory (class in dials.algorithms.refinement.refiner) Refinery (class in dials.algorithms.refinement.engine) reflection_table_aux (class in dials.array_family.flex) reflection_table_aux.flags (class in dials.array_family.flex) reflection_table_selector (class in dials.array_family.flex) ReflectionManager (class in dials.algorithms.refinement.reflection_manager) ReflectionManagerFactory (class in dials.algorithms.refinement.reflection_manager) ReflectionPredictor (class in dials.algorithms.spot_prediction.reflection_predictor) reject_outliers() (in module dials.algorithms.scaling.outlier_rejection) reject_weight_outliers_selection() (in module dials.algorithms.indexing.indexer) remove_on_experiment_identifiers() (dials.array_family.flex.reflection_table_aux method) (dxtbx.model.ExperimentList method) remove_sources_default (dials.util.installer.installer attribute) reorder() (dials.array_family.flex.reflection_table_aux method) 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_ids() (dials.array_family.flex.reflection_table_aux method) resize() (dials.array_family.flex.reflection_table_aux method) restart() (dials.algorithms.refinement.engine.AdaptLstbx method) Result (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.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) rotation_matrix_differences() (in module dials.algorithms.indexing.compare_orientation_matrices) rows() (dials.array_family.flex.reflection_table_aux 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.spot_finding.factory.BackgroundGradientFilter method) (dials.algorithms.spot_finding.factory.PeakCentroidDistanceFilter method) (dials.algorithms.spot_finding.factory.SpotDensityFilter method) run_lbfgs() (dials.algorithms.refinement.engine.AdaptLbfgs method)

S

sampling_volume_map() (in module dials.algorithms.indexing.fft3d) 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.indexer.SolutionTrackerWeighted method) score_by_rmsd_xy() (dials.algorithms.indexing.indexer.SolutionTrackerWeighted method) score_by_rmsd_z() (dials.algorithms.indexing.indexer.SolutionTrackerWeighted method) score_by_volume() (dials.algorithms.indexing.indexer.SolutionTrackerWeighted method) ScoreSubGroup (class in dials.algorithms.symmetry.determine_space_group) ScoreSymmetryElement (class in dials.algorithms.symmetry.determine_space_group) search() (dxtbx.model.scan.ScanFactory static method) seed_clustering (class in dials.algorithms.symmetry.cosym.seed_clustering) select() (dials.array_family.flex.reflection_table_aux method) select_on_experiment_identifiers() (dials.array_family.flex.reflection_table_aux method) (dxtbx.model.ExperimentList method) selection_used_for_refinement() (dials.algorithms.refinement.refiner.Refiner method) sensor() (dxtbx.model.detector.DetectorFactory static method) set_cholesky_factor() (dials.algorithms.refinement.engine.AdaptLstbx 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_flags() (dials.array_family.flex.reflection_table_aux 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_scaling_model_as_scaled() (dials.algorithms.scaling.model.model.ScalingModelBase method) set_scaling_model_as_unscaled() (dials.algorithms.scaling.model.model.ScalingModelBase method) set_selected() (dials.array_family.flex.reflection_table_aux method) set_valid_image_range() (dials.algorithms.scaling.model.model.ScalingModelBase method) setup_indexing() (dials.algorithms.indexing.indexer.indexer_base method) setup_mu() (dials.algorithms.refinement.engine.LevenbergMarquardtIterations method) ShoeboxesToReflectionTable (class in dials.algorithms.spot_finding.finder) show() (dials.algorithms.scaling.model.model.ScalingModelBase method) (dxtbx.model.Crystal method) (dxtbx.model.MosaicCrystalKabsch2010 method) (dxtbx.model.MosaicCrystalSauter2014 method) show_experiments() (dials.algorithms.indexing.indexer.indexer_base method) show_rotation_matrix_differences() (in module dials.algorithms.indexing.compare_orientation_matrices) 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() (dials.array_family.flex.reflection_table_aux method) Solution (class in dials.algorithms.indexing.indexer) solution_scores() (dials.algorithms.indexing.indexer.SolutionTrackerWeighted method) SolutionTrackerFilter (class in dials.algorithms.indexing.indexer) SolutionTrackerWeighted (class in dials.algorithms.indexing.indexer) sort() (dials.array_family.flex.reflection_table_aux method) source_packages (dials.util.installer.installer attribute) SparseGradientsMixin (class in dials.algorithms.refinement.target) split_by_experiment_id() (dials.array_family.flex.reflection_table_aux method) split_indices_by_experiment_id() (dials.array_family.flex.reflection_table_aux method) split_jacobian_into_blocks() (dials.algorithms.refinement.engine.Refinery method) split_matches_into_blocks() (dials.algorithms.refinement.target.Target method) split_partial_indices() (dials.array_family.flex.reflection_table_aux method) split_partials() (dials.array_family.flex.reflection_table_aux method) split_partials_with_shoebox() (dials.array_family.flex.reflection_table_aux 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) 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) StillsReflectionManager (class in dials.algorithms.refinement.reflection_manager) StillsWeightingStrategy (class in dials.algorithms.refinement.weighting_strategies) strategy() (in module dials.array_family.flex) strong (dials.array_family.flex.reflection_table_aux.flags attribute) subsort() (dials.array_family.flex.reflection_table_aux method) summary() (dials.algorithms.integration.integrator.Integrator method) (dials.algorithms.integration.integrator.Integrator3DThreaded method) supergroup() (dials.algorithms.indexing.symmetry.refined_settings_list method) SweepDiff (class in dxtbx.datablock) symmetry_base (class in dials.algorithms.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)

to_imageset() (in module dxtbx.serialize.xds) to_xds (class in dxtbx.serialize.xds) traceback (dials.util.options.ArgumentHandlingErrorInfo attribute) triclinic() (dials.algorithms.indexing.symmetry.refined_settings_list method) trunccauchy_pdf() (in module dials.algorithms.symmetry.determine_space_group) try_read_datablocks() (dials.util.options.Importer method) try_read_datablocks_from_images() (dials.util.options.Importer method) try_read_experiments() (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) types() (dials.array_family.flex.reflection_table_aux method)

U

understand() (dxtbx.datablock.FormatChecker method) unique_beams() (dxtbx.datablock.DataBlock method) unique_detectors() (dxtbx.datablock.DataBlock method) unique_goniometers() (dxtbx.datablock.DataBlock method) unique_scans() (dxtbx.datablock.DataBlock method) unset_flags() (dials.array_family.flex.reflection_table_aux method) update() (dials.array_family.flex.reflection_table_aux method) (dials.util.command_line.ProgressBar method) (dials.util.command_line.ProgressBarTimer method)

update_analysis() (dials.algorithms.indexing.indexer.SolutionTrackerFilter method) update_journal() (dials.algorithms.refinement.engine.Refinery method) update_matches() (dials.algorithms.refinement.target.Target method) used_in_modelling (dials.array_family.flex.reflection_table_aux.flags attribute) used_in_refinement (dials.array_family.flex.reflection_table_aux.flags attribute) user_excluded_in_scaling (dials.array_family.flex.reflection_table_aux.flags attribute)

V

validation (dials.util.options.ArgumentHandlingErrorInfo attribute)

values (dials.array_family.flex.reflection_table_aux.flags attribute) vector_group (class in dials.algorithms.indexing.indexer)

W

where() (dxtbx.model.ExperimentList method)

write() (dials.util.options.ConfigWriter 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)