Index

_

__dict__ (xfel.clustering.cluster.Cluster attribute) __init__() (libtbx.program_template.ProgramTemplate method) (xfel.clustering.cluster.Cluster method) (xfel.clustering.singleframe.SingleFrame method)

__len__() (xfel.clustering.cluster.Cluster method) __module__ (xfel.clustering.cluster.Cluster attribute) (xfel.clustering.singleframe.SingleFrame attribute) __weakref__ (xfel.clustering.cluster.Cluster attribute)

A

a1_action() (cctbx.uctbx.krivy_gruber_1976.reduction method) a2_action() (cctbx.uctbx.krivy_gruber_1976.reduction method) a3_action() (cctbx.uctbx.krivy_gruber_1976.reduction method) a4_action() (cctbx.uctbx.krivy_gruber_1976.minimum_reduction method) (cctbx.uctbx.krivy_gruber_1976.reduction method) a5_action() (cctbx.uctbx.krivy_gruber_1976.reduction method) a6_action() (cctbx.uctbx.krivy_gruber_1976.reduction method) a7_action() (cctbx.uctbx.krivy_gruber_1976.reduction method) a8_action() (cctbx.uctbx.krivy_gruber_1976.reduction method) a_theorem_in_primitive_settings (class in cctbx.examples.location_part) aa_residue_axes_and_clusters (class in mmtbx.refinement.real_space) aaTables (mmtbx.rotamer.rotamer_eval.RotamerEval attribute) ab_cluster() (xfel.clustering.cluster.Cluster method) abs() (in module mmtbx.ncs.ncs) absence_type() (mmtbx.scaling.absences.conditions_for_operator method) absences (class in mmtbx.scaling.absences) absences_list (class in mmtbx.scaling.absences) absolute_center_cart() (iotbx.map_manager.map_manager method) absolute_rt_info() (iotbx.map_manager.shift_aware_rt method) accelerations() (mmtbx.dynamics.cartesian_dynamics.run method) (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) accept() (mmtbx.geometry.altloc.Description method) accepted (cctbx.symmetry_search.possible_symmetry attribute) AccessibleSurfaceAreas (class in mmtbx.geometry.asa) AccessibleSurfaceResult (class in mmtbx.geometry.asa) accessor() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.py_object method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) accute_angle() (scitbx.matrix.rec method) acentric_e_sq_minus_one_library (mmtbx.scaling.twin_analyses.wilson_moments attribute) acentric_f_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute) acentric_i_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute) action() (in module mmtbx.refinement.tardy) active_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) active_indices (mmtbx.density_modification.density_modification property) ad_hoc_single_atom_residue (class in mmtbx.monomer_library.pdb_interpretation) add() (cctbx.development.structure_factor_utils.collector method) (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method) (cctbx.web.asu_gallery.jv_index.point_group_table method) (cctbx.web.asu_gallery.jv_index.symbol_table method) (dxtbx.model.scan.ScanFactory static method) (mmtbx.geometry.altloc.Indexer method) (mmtbx.geometry.clash.ASUContent method) (mmtbx.geometry.topology.Molecule method) (mmtbx.refinement.real_space.fit_residue.monitor method) (mmtbx.refinement.refinement_flags.manager method) (mmtbx.refinement.rigid_body.rigid_body_shift_accumulator method) (mmtbx.utils.states method) add_angle_proxies (class in mmtbx.monomer_library.pdb_interpretation) add_angle_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) add_angles_in_place() (cctbx.geometry_restraints.manager.manager method) add_arg_like_h() (in module mmtbx.hydrogens.build_hydrogens) add_atom() (mmtbx.geometry.topology.Compound method) add_atoms_in() (mmtbx.geometry.indexing.structure_indexer method) add_bond() (mmtbx.geometry.topology.Compound method) add_bond_proxies (class in mmtbx.monomer_library.pdb_interpretation) add_bond_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) add_box() (mmtbx.maps.composite_omit_map.omit_regions method) add_buffer() (cctbx.crystal.direct_space_asu.direct_space_asu method) (cctbx.sgtbx.direct_space_asu.direct_space_asu method) add_ca_ha1_and_ha2() (in module mmtbx.hydrogens.build_hydrogens) add_ca_ha1_or_ha2() (in module mmtbx.hydrogens.build_hydrogens) add_cc() (mmtbx.ncs.ncs.ncs_group method) add_cc_list() (mmtbx.ncs.ncs.ncs method) add_cell() (xfel.command_line.cxi_merge.unit_cell_distribution method) add_cells() (xfel.command_line.cxi_merge.unit_cell_distribution method) add_chain_residue_id() (mmtbx.ncs.ncs.ncs_group method) add_chi_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) add_chirality_proxies (class in mmtbx.monomer_library.pdb_interpretation) add_chirality_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) add_column() (iotbx.cif.model.loop method) add_columns() (iotbx.cif.model.loop method) add_coordinate_restraints() (in module mmtbx.geometry_restraints.reference) add_crystal_symmetry_to_model_if_necessary() (iotbx.map_model_manager.map_model_manager method) add_cycle() (mmtbx.density_modification.dm_stats method) add_default_options() (mmtbx.validation.molprobity.MolProbityParser method) add_dihedral_proxies (class in mmtbx.monomer_library.pdb_interpretation) add_dihedral_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) add_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method) add_empty() (mmtbx.validation.graphics.residue_bin method) add_fan() (in module mmtbx.kinemage.validation) add_frame() (xfel.command_line.cxi_merge.scaling_manager method) add_gradients() (in module cctbx.xray.minimization) add_hhh() (in module mmtbx.hydrogens.build_hydrogens) add_identity_op() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) add_if_missing() (libtbx.group_args method) add_if_not_duplicated() (cctbx.geometry_restraints.angle_proxy_registry method) (cctbx.geometry_restraints.chirality_proxy_registry method) (cctbx.geometry_restraints.dihedral_proxy_registry method) (cctbx.geometry_restraints.parallelity_proxy_registry method) (cctbx.geometry_restraints.planarity_proxy_registry method) add_label() (iotbx.map_manager.map_manager method) add_limitation() (iotbx.map_manager.map_manager method) add_lone_pairs_for_peptyde_o() (in module mmtbx.ias) add_map_from_fourier_coefficients() (iotbx.map_model_manager.map_model_manager method) add_map_manager() (iotbx.map_model_manager.match_map_model_ncs method) add_map_manager_by_id() (iotbx.map_model_manager.map_model_manager method) add_miller_array() (iotbx.cif.miller_arrays_as_cif_block method) add_model() (iotbx.map_model_manager.match_map_model_ncs method) add_model_by_id() (iotbx.map_model_manager.map_model_manager method) add_ncs_object() (iotbx.map_model_manager.match_map_model_ncs method) add_new_bond_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) add_new_hbond_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) add_new_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method) add_nodes_to_query_if_needed_in_place() (in module mmtbx.wwpdb.rcsb_web_services) add_note() (mmtbx.ncs.ncs.ncs_group method) add_occupancy_selection() (in module mmtbx.refinement.occupancies) add_operator() (mmtbx.ncs.ligands.group_operators method) add_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method) add_pairs() (cctbx.euclidean_model_matching.match_refine method) add_parallelities_in_place() (cctbx.geometry_restraints.manager.manager method) add_parallelity_proxies (class in mmtbx.monomer_library.pdb_interpretation) add_parallelity_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) add_planarities_in_place() (cctbx.geometry_restraints.manager.manager method) add_planarity_proxies (class in mmtbx.monomer_library.pdb_interpretation) add_planarity_proxies() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) add_plane() (cctbx.sgtbx.direct_space_asu.direct_space_asu method) add_planes() (cctbx.sgtbx.direct_space_asu.direct_space_asu method) add_point_group_type() (cctbx.web.asu_gallery.jv_index.point_group_table method) add_position() (cctbx.euclidean_model_matching.model method) add_positions() (cctbx.euclidean_model_matching.model method) add_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) add_residue() (mmtbx.validation.graphics.residue_bin method) add_residues_in_common_list() (mmtbx.ncs.ncs.ncs_group method) add_ring_h() (in module mmtbx.hydrogens.build_hydrogens) add_rmsd_list() (mmtbx.ncs.ncs.ncs_group method) add_rotamer_restraints() (in module mmtbx.refinement.geometry_minimization) add_row() (iotbx.cif.model.loop method) add_scatterer() (cctbx.neutron.structure method) (cctbx.xray.structure.structure method) add_scatterers() (cctbx.neutron.structure method) (cctbx.xray.structure.structure method) add_selected() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) add_source_info() (mmtbx.ncs.ncs.ncs method) add_spring() (in module mmtbx.kinemage.validation) add_tiles_to_cbf() (in module xfel.cftbx.detector.cspad_cbf_tbx) add_to_info() (iotbx.map_model_manager.map_model_manager method) add_to_validation_counts() (mmtbx.validation.ramalyze.ramalyze method) add_tuples_int() (in module iotbx.map_manager) add_water() (mmtbx.validation.experimental.real_space method) add_wavelength_info() (mmtbx.scaling.make_param.phil_lego method) adjust_class() (in module mmtbx.monomer_library.linking_setup) adjust_cosine() (in module cctbx.macro_mol.rotation_parameters) adjust_fraction() (in module cctbx.r_free_utils) adjust_magnification() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) adjust_occupancy() (cctbx.xray.structure.structure method) adjust_u_iso() (cctbx.xray.structure.structure method) adjust_weight_sample_rate() (mmtbx.refinement.real_space.individual_sites.refinery method) adopt_den_manager() (cctbx.geometry_restraints.manager.manager method) adopt_init_args() (in module libtbx) adopt_optional_init_args() (in module libtbx) adopt_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) adopt_reference_dihedral_manager() (cctbx.geometry_restraints.manager.manager method) adopt_set() (cctbx.miller.array method) adopt_xray_structure() (iotbx.pdb.hierarchy.root method) adp_aniso_restraints (class in cctbx.adp_restraints) adp_refinement() (mmtbx.den.refinement.manager method) adp_similarity_deviation() (cctbx.adp_restraints.energies.energies method) adp_stats (mmtbx.validation.molprobity.molprobity attribute) af_shared_atom (class in iotbx.pdb.hierarchy) afix_parser (class in iotbx.shelx.parsers) Aggregator (class in mmtbx.geometry.altloc) algebraic() (cctbx.sgtbx.harker.plane_fractional method) algorithm() (cctbx.xray.structure_factors.manager.managed_calculation_base method) algorithm2 (class in cctbx.merging.brehm_diederichs) align_chain() (mmtbx.validation.sequence.validation method) align_model() (mmtbx.building.make_library.ensembler method) all (mmtbx.validation.model_properties.model_statistics attribute) all() (cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter method) (cctbx.maptbx.peak_cluster_analysis method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) all_approx_equal() (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) all_approx_equal_relatively() (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) all_associated_i_seqs() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary method) all_atoms_are_in_main_conf() (in module mmtbx.monomer_library.pdb_interpretation) all_bonds() (mmtbx.ias.manager method) all_cells() (cctbx.crystal.find_best_cell.find_best_cell method) all_cut_points() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) all_eq() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) all_frames_intensity_stats() (xfel.clustering.cluster.Cluster method) all_ge() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) all_gt() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) all_le() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) all_lt() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) all_master_params() (in module mmtbx.hydrogens.find) all_ne() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) all_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method) all_selection() (cctbx.miller.set method) (cctbx.xray.structure.structure method) all_site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method) all_size (scitbx.array_family.flex.smart_selection property) all_with_effective_resolution() (cctbx.maptbx.peak_cluster_analysis method) alpha_beta (class in mmtbx.max_lik.maxlik) alpha_beta() (in module mmtbx.max_lik.max_like_non_uniform) (mmtbx.max_lik.maxlik.alpha_beta method) (mmtbx.max_lik.maxlik.alpha_beta_calc method) (mmtbx.max_lik.maxlik.alpha_beta_est_manager method) (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method) (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method) (mmtbx.twinning.twin_f_model.twin_model_manager method) alpha_beta_calc (class in mmtbx.max_lik.maxlik) alpha_beta_est_manager (class in mmtbx.max_lik.maxlik) alpha_beta_f() (mmtbx.twinning.twin_f_model.twin_model_manager method) alpha_beta_for_each_reflection() (mmtbx.max_lik.maxlik.alpha_beta_est_manager method) alpha_beta_w() (mmtbx.twinning.twin_f_model.twin_model_manager method) alphas() (iotbx.shelx.hklf.reader method) alt_atom_id (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) Alternate (class in mmtbx.geometry.altloc) alternate_conformations_as_multiple_models() (in module mmtbx.disorder.backbone) alternative_find_best_cell (class in cctbx.crystal.find_best_cell) altid_for() (in module mmtbx.geometry.altloc) altloc (iotbx.pdb.hierarchy.atom_group property) (iotbx.pdb.hierarchy.atom_with_labels property) (iotbx.pdb.hierarchy.conformer property) (mmtbx.disorder.analyze_model.atom_group_proxy attribute) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) altloc() (mmtbx.ions.environment.atom_contact method) altloc_averaged_calculation() (in module mmtbx.geometry.asa) altloc_indices() (iotbx.pdb.hierarchy.root method) altloc_strategy_from_atom() (in module mmtbx.geometry.clash) altlocs_present() (iotbx.pdb.hierarchy.root method) amore_alpha_beta_gamma (class in cctbx.macro_mol.rotation_parameters) amore_alpha_beta_gamma_as_matrix() (in module cctbx.macro_mol.rotation_parameters) amore_alpha_beta_gamma_from_matrix() (in module cctbx.macro_mol.rotation_parameters) amore_alpha_beta_gamma_normalize() (in module cctbx.macro_mol.rotation_parameters) amore_kappa_l_m_n (class in cctbx.macro_mol.rotation_parameters) amore_kappa_l_m_n_as_matrix() (in module cctbx.macro_mol.rotation_parameters) amore_kappa_l_m_n_from_matrix() (in module cctbx.macro_mol.rotation_parameters) amore_kappa_l_m_n_normalize() (in module cctbx.macro_mol.rotation_parameters) amplitude (class in cctbx.xray.observation_types) amplitude_normalisations() (cctbx.miller.array method) (cctbx.miller.set method) amplitude_quasi_normalisations() (cctbx.miller.array method) amplitude_unit_weighting (class in cctbx.xray.weighting_schemes) amplitudes() (cctbx.miller.array method) (mmtbx.maps.map_coeffs_mtz_label_manager method) analyse() (mmtbx.scaling.pair_analyses.reindexing method) analyze() (in module mmtbx.validation.analyze_peptides) analyze_absences (class in mmtbx.scaling.absences) analyze_aniso_correction() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method) analyze_intensity_statistics() (cctbx.miller.array method) (in module mmtbx.scaling.twin_analyses) analyze_measurability (class in mmtbx.scaling.data_statistics) analyze_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) analyze_resolution_limits (class in mmtbx.scaling.data_statistics) analyze_substructure() (mmtbx.ions.identify.manager method) analyze_water() (mmtbx.ions.identify.manager method) (mmtbx.ions.svm.manager method) analyze_waters() (mmtbx.ions.identify.manager method) (mmtbx.ions.svm.manager method) angle (class in mmtbx.validation.restraints) angle() (iotbx.pdb.hierarchy.atom method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) angle_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) angle_delta_deg() (in module cctbx.geometry_restraints) angle_deviations() (cctbx.geometry_restraints.energies.energies method) angle_deviations_weighted() (cctbx.geometry_restraints.energies.energies method) angle_deviations_z() (cctbx.geometry_restraints.energies.energies method) angle_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute) angle_outlier_as_kinemage() (in module mmtbx.kinemage.validation) angle_proxy_registry (class in cctbx.geometry_restraints) angle_rmsd (mmtbx.validation.molprobity.summary attribute) angles (class in mmtbx.validation.restraints) (mmtbx.validation.restraints.combined attribute) (mmtbx.validation.rna_validate.rna_validation attribute) anglesForAA (mmtbx.rotamer.sidechain_angles.SidechainAngles attribute) anglesForRot (mmtbx.rotamer.sidechain_angles.SidechainAngles attribute) ANGSTROMS_TO_EV (xfel.clustering.singleframe.SingleFrame attribute) aniso_b_min (mmtbx.scaling.xtriage.xtriage_analyses property) aniso_b_ratio (mmtbx.scaling.xtriage.xtriage_analyses property) aniso_range_of_b (mmtbx.scaling.xtriage.xtriage_analyses property) aniso_ratio_p_value() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method) anisotropic_correction() (in module mmtbx.scaling.absolute_scaling) (mmtbx.density_modification.density_modification method) anisotropic_scaling() (mmtbx.bulk_solvent.scaler.run method) anneal() (mmtbx.building.box_build_refine_base method) annealing_callback (class in mmtbx.refinement.print_statistics) ano_scaling (class in mmtbx.scaling.fa_estimation) anom (mmtbx.validation.waters.water attribute) anom_density (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] ANOM_PEAK (mmtbx.ions.identify.AtomProperties attribute) anomalous (class in mmtbx.scaling.data_statistics) (mmtbx.map_names attribute) anomalous_completeness() (cctbx.miller.array method) anomalous_differences() (cctbx.miller.array method) anomalous_flag (mmtbx.validation.experimental.data_statistics attribute) anomalous_flag() (cctbx.miller.set method) anomalous_map() (mmtbx.twinning.twin_f_model.twin_model_manager method) anomalous_probability_plot() (cctbx.miller.array method) anomalous_reflection_intensity_primitive_cell() (in module cctbx.sgtbx.subgroups) anomalous_residual (mmtbx.map_names attribute) anomalous_scatterer_group (class in cctbx.xray.scatterer) anomalous_signal() (cctbx.miller.array method) anonymize_ions() (in module mmtbx.ions.utils) any (class in cctbx.xray.observation_types) any_compatible_crystal_symmetry() (cctbx.sgtbx.space_group_info method) any_compatible_unit_cell() (cctbx.sgtbx.space_group_info method) any_file() (in module iotbx.file_reader) any_file_fast() (in module iotbx.file_reader) any_file_fast_input (class in iotbx.file_reader) any_file_input (class in iotbx.file_reader) any_generator_set (class in cctbx.sgtbx) any_generator_set() (cctbx.sgtbx.space_group_info method) any_reflection_file (class in iotbx.reflection_file_reader) append() (cctbx.web.asu_gallery.jvx.faceSet method) (cctbx.web.asu_gallery.jvx.lineSet method) (cctbx.web.asu_gallery.jvx.pointSet method) (iotbx.pdb.hierarchy.af_shared_atom method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) append_atom() (iotbx.pdb.hierarchy.atom_group method) append_atom_group() (iotbx.pdb.hierarchy.residue_group method) append_atom_with_other_parent() (iotbx.pdb.hierarchy.atom_group method) append_chain() (iotbx.pdb.hierarchy.model method) append_custom_proxy() (cctbx.geometry_restraints.proxy_registry_base method) append_emsley8k_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) append_emsley_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) append_fixed_site() (cctbx.maptbx.peak_cluster_analysis method) append_model() (iotbx.pdb.hierarchy.root method) append_neighbours() (mmtbx.geometry.asa.SeparateCheckerBuilder static method) append_oldfield_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) append_phi_psi_2_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) append_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) append_residue_group() (iotbx.pdb.hierarchy.chain method) (mmtbx.disorder.analyze_model.disordered_segment method) apply_aniso_b_cart_to_f_array_info() (in module iotbx.map_model_manager) apply_atom_selection() (iotbx.pdb.hierarchy.root method) apply_back_b_iso() (mmtbx.twinning.twin_f_model.twin_model_manager method) apply_back_trace_of_overall_exp_scale_matrix() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.bulk_solvent.scaler.run method) apply_change_in_place() (mmtbx.monomer_library.cif_types.chem_mod_angle method) (mmtbx.monomer_library.cif_types.chem_mod_bond method) (mmtbx.monomer_library.cif_types.chem_mod_chir method) (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method) (mmtbx.monomer_library.cif_types.chem_mod_tor method) (mmtbx.monomer_library.cif_types.chem_mod_tree method) apply_change_of_basis() (cctbx.miller.array method) (in module cctbx.sgtbx.direct_space_asu.reference_table) apply_chem_mod_list() (in module mmtbx.monomer_library.cif_types) apply_cob_to_vector() (mmtbx.ncs.ncs.ncs_group method) apply_debye_waller_factors() (cctbx.miller.array method) apply_default_filter() (in module mmtbx.polygon) apply_eucl_ops() (cctbx.euclidean_model_matching.match_refine method) apply_final() (mmtbx.building.extend_sidechains.conformation_scorer method) apply_gaussian_noise() (in module xfel.cxi.display_powder_arcs) apply_glyco_link_using_proxies_and_atoms() (in module mmtbx.monomer_library.glyco_utils) apply_ligand_ncs (class in mmtbx.ncs.ligands) apply_mask() (iotbx.map_manager.map_manager method) apply_mask_inplace() (mmtbx.utils.extract_box_around_model_and_map method) apply_mask_to_map() (iotbx.map_model_manager.map_model_manager method) apply_mask_to_maps() (iotbx.map_model_manager.map_model_manager method) apply_mod() (mmtbx.monomer_library.cif_types.comp_comp_id method) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) apply_ncs_to_dv_results() (in module iotbx.map_model_manager) apply_ncs_to_sites() (mmtbx.ncs.ncs.ncs method) apply_new_sites_to_hierarchies() (mmtbx.maps.superpose.common_frame_of_reference method) apply_new_sites_to_xray_structure() (mmtbx.maps.superpose.common_frame_of_reference method) apply_overall_scale() (mmtbx.bulk_solvent.scaler.run method) apply_phil_str() (mmtbx.secondary_structure.manager method) apply_rigid_body_shift() (cctbx.xray.structure.structure method) apply_rigid_body_shift_obj() (cctbx.xray.structure.structure method) apply_rotation_translation() (iotbx.pdb.hierarchy.root method) apply_rt() (iotbx.map_manager.shift_aware_rt method) apply_scale_to_original_data() (mmtbx.scaling.outlier_rejection.outlier_manager method) apply_scaling() (cctbx.miller.array method) apply_shelxl_extinction_correction() (cctbx.miller.array method) apply_shift() (cctbx.xray.structure.structure method) apply_shifts() (cctbx.geometry_restraints.lbfgs.lbfgs method) (cctbx.xray.minimization.lbfgs method) (mmtbx.refinement.group.group_minimizer method) (mmtbx.refinement.minimization.lbfgs method) apply_sign_correction() (cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria method) apply_special_position_ops_d_target_d_site() (cctbx.xray.structure.structure method) apply_spectral_scaling() (iotbx.map_manager.map_manager method) apply_sub_pixel_metrology() (in module xfel.command_line.radial_average) apply_symmetry() (cctbx.neutron.scatterer method) (cctbx.neutron.structure method) apply_symmetry_sites() (cctbx.xray.structure.structure method) apply_symmetry_u_stars() (cctbx.xray.structure.structure method) apply_transformation() (in module mmtbx.refinement.group) (in module mmtbx.refinement.rigid_body) apply_transformation_() (in module mmtbx.refinement.rigid_body) apply_transforms() (in module mmtbx.ncs.ncs_utils) approx_curvs() (cctbx.omz.dev.refinement method) approx_quads (cctbx.omz.dev.xfgc_info attribute) areas (mmtbx.geometry.asa.AccessibleSurfaceAreas property) arg() (cctbx.miller.array method) args (mmtbx.command_line.load_model_and_data attribute) around_atom (class in mmtbx.real_space) array (class in cctbx.miller) array() (cctbx.miller.merge_equivalents method) (cctbx.miller.set method) array_info (class in cctbx.miller) as_1d() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) as_amplitude_array() (cctbx.miller.array method) as_anomalous_array() (cctbx.miller.array method) as_anomalous_set() (cctbx.miller.set method) as_ave (mmtbx.refinement.print_statistics.stats_table attribute) as_bool() (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) as_boost_rational() (scitbx.matrix.rec method) as_bullseye_kinemage() (mmtbx.validation.cbetadev.cbetadev method) as_bullseye_label() (mmtbx.validation.cbetadev.cbeta method) as_bullseye_point() (mmtbx.validation.cbetadev.cbeta method) as_chem_comp() (mmtbx.monomer_library.cif_types.chem_mod_angle method) (mmtbx.monomer_library.cif_types.chem_mod_atom method) (mmtbx.monomer_library.cif_types.chem_mod_bond method) (mmtbx.monomer_library.cif_types.chem_mod_chir method) (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method) (mmtbx.monomer_library.cif_types.chem_mod_tor method) (mmtbx.monomer_library.cif_types.chem_mod_tree method) as_cif() (mmtbx.monomer_library.glyco_utils.glyco_link_class method) as_cif_block() (cctbx.crystal.symmetry method) (cctbx.miller.array method) (cctbx.xray.structure.structure method) (iotbx.pdb.hierarchy.root method) (mmtbx.monomer_library.cif_types.link_link_id method) (mmtbx.tls.tools.tls_groups method) as_cif_loop() (mmtbx.monomer_library.cif_types.looped_data method) as_cif_simple() (cctbx.miller.array method) (cctbx.xray.structure.structure method) as_clash_obj() (mmtbx.validation.clashscore.probe_line_info method) as_CObjectZYX() (in module cctbx.maptbx) as_coot_data() (mmtbx.validation.cbetadev.cbetadev method) (mmtbx.validation.clashscore.clashscore method) (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.rotalyze.rotalyze method) (mmtbx.validation.validation method) as_csv() (mmtbx.validation.ramalyze.ramachandran method) as_dict_of_chain_id_resseq_as_int_residue_names() (iotbx.pdb.hierarchy.root method) as_dict_of_resseq_as_int_residue_names() (iotbx.pdb.hierarchy.chain method) as_dict_of_resseq_residue_names() (iotbx.pdb.hierarchy.chain method) as_double() (cctbx.miller.array method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) as_emma_model() (cctbx.xray.structure.structure method) as_exp_i_sum() (cctbx.examples.structure_factor_derivatives.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factor method) as_flex_double_matrix() (scitbx.matrix.rec method) as_flex_int_matrix() (scitbx.matrix.rec method) as_float() (scitbx.array_family.flex.double method) (scitbx.matrix.rec method) as_float_asu() (cctbx.crystal.direct_space_asu.direct_space_asu method) as_float_cut_plane() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) as_forward_compatible_hierarchy() (iotbx.pdb.hierarchy.root method) as_forward_compatible_string() (iotbx.pdb.hierarchy.root method) as_full_size_map() (iotbx.map_manager.map_manager method) as_g_alpha() (cctbx.examples.structure_factor_derivatives.parameters method) as_geometry_restraints_motif() (mmtbx.monomer_library.cif_types.comp_comp_id method) as_geometry_restraints_motif_manipulation() (mmtbx.monomer_library.cif_types.link_link_id method) (mmtbx.monomer_library.cif_types.mod_mod_id method) as_gruber_matrix() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.gruber_parameterization method) as_gui_table_data() (mmtbx.validation.model_properties.xray_structure_statistics method) (mmtbx.validation.validation method) as_hierarchical_JSON() (mmtbx.validation.cbetadev.cbeta method) (mmtbx.validation.clashscore.clash method) (mmtbx.validation.ramalyze.ramachandran method) (mmtbx.validation.restraints.restraint method) (mmtbx.validation.rna_validate.rna_angle method) (mmtbx.validation.rna_validate.rna_bond method) (mmtbx.validation.rna_validate.rna_pucker method) (mmtbx.validation.rotalyze.rotamer method) as_hkl() (in module cctbx.sgtbx.rational_matrices_point_groups) (in module cctbx.sgtbx.reticular_pg_tools) as_int() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.vec3_int method) (scitbx.matrix.rec method) as_intensity_array() (cctbx.miller.array method) as_JSON() (mmtbx.validation.cbetadev.cbeta method) (mmtbx.validation.cbetadev.cbetadev method) (mmtbx.validation.clashscore.clash method) (mmtbx.validation.clashscore.clashscore method) (mmtbx.validation.entity method) (mmtbx.validation.ramalyze.ramachandran method) (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.restraints.chiralities method) (mmtbx.validation.restraints.restraint method) (mmtbx.validation.restraints.restraint_validation method) (mmtbx.validation.rna_validate.rna_angle method) (mmtbx.validation.rna_validate.rna_angles method) (mmtbx.validation.rna_validate.rna_bond method) (mmtbx.validation.rna_validate.rna_bonds method) (mmtbx.validation.rna_validate.rna_pucker method) (mmtbx.validation.rna_validate.rna_puckers method) (mmtbx.validation.rna_validate.rna_validation method) (mmtbx.validation.rotalyze.rotalyze method) (mmtbx.validation.rotalyze.rotamer method)

as_kinemage() (mmtbx.validation.cbetadev.cbeta method) (mmtbx.validation.cbetadev.cbetadev method) (mmtbx.validation.entity method) (mmtbx.validation.ramalyze.ramachandran method) (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.restraints.angle method) (mmtbx.validation.restraints.bond method) (mmtbx.validation.restraints.chirality method) (mmtbx.validation.restraints.combined method) (mmtbx.validation.restraints.dihedral method) (mmtbx.validation.restraints.planarity method) (mmtbx.validation.restraints.restraint_validation method) (mmtbx.validation.validation method) as_list() (cctbx.examples.g_exp_i_alpha_derivatives.parameters method) (cctbx.examples.structure_factor_derivatives.parameters method) (mmtbx.validation.entity method) as_list_of_lists() (scitbx.matrix.rec method) as_list_of_residue_names() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.root method) as_long() (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) as_map_manager() (cctbx.miller.array method) as_map_model_manager() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) as_map_model_manager_with_resampled_maps() (iotbx.map_model_manager.map_model_manager method) as_markup_for_kinemage() (mmtbx.validation.ramalyze.ramalyze method) as_mat3() (scitbx.matrix.rec method) as_match_map_model_ncs() (iotbx.map_model_manager.map_model_manager method) as_miller_array() (iotbx.xds.read_ascii.reader method) as_miller_arrays() (iotbx.cif.reader method) (iotbx.reflection_file_reader.any_reflection_file method) (iotbx.shelx.hklf.reader method) (iotbx.xds.integrate_hkl.reader method) (iotbx.xds.read_ascii.reader method) as_mmcif_records() (mmtbx.validation.molprobity.molprobity method) as_mmcif_string() (iotbx.pdb.hierarchy.root method) as_model_manager() (iotbx.pdb.hierarchy.root method) as_mtz_dataset() (cctbx.miller.array method) as_multi_criterion_view() (mmtbx.validation.molprobity.molprobity method) as_multi_model_hierarchy() (mmtbx.building.make_library.ensembler method) as_ncs_spec_string() (mmtbx.ncs.ncs.ncs method) as_new_hierarchy() (iotbx.pdb.hierarchy.chain method) as_niggli_matrix() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.gruber_parameterization method) as_non_anomalous_array() (cctbx.miller.array method) as_non_anomalous_set() (cctbx.miller.set method) as_numpy_array() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) as_original_arrays() (iotbx.cif.reader method) as_p1_map() (mmtbx.maps.composite_omit_map.run method) as_padded_sequence() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) as_pdb_file() (cctbx.xray.structure.structure method) as_pdb_hierarchy() (mmtbx.utils.run_reduce_with_timeout method) as_pdb_input() (iotbx.pdb.hierarchy.root method) as_pdb_or_mmcif_string() (iotbx.pdb.hierarchy.root method) as_pdb_records() (mmtbx.secondary_structure.proteins.find_helices_simple method) as_pdb_remark_290() (cctbx.crystal.symmetry method) as_pdb_string() (iotbx.pdb.ext.input method) (iotbx.pdb.hierarchy.root method) as_phases_phs() (cctbx.miller.array method) as_phil_str() (mmtbx.secondary_structure.manager method) as_py_code() (cctbx.crystal.symmetry method) (cctbx.xray.structure.structure method) as_reference_setting() (cctbx.crystal.symmetry method) (cctbx.sgtbx.space_group_info method) as_restraint_group_phil() (mmtbx.secondary_structure.proteins.find_helices_simple method) as_restraint_groups() (mmtbx.secondary_structure.proteins.find_helices_simple method) as_rgb_scale_string() (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) as_scitbx_matrix() (in module scitbx.array_family.flex) (scitbx.array_family.flex.double method) as_sec_str_sequence() (iotbx.pdb.hierarchy.conformer method) as_selection_string() (mmtbx.validation.entity method) as_sequence() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) (iotbx.pdb.hierarchy.root method) as_size_t() (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) as_str() (cctbx.crystal.symmetry method) (iotbx.pdb.hierarchy.overall_counts method) (iotbx.pdb.hierarchy.root method) as_string() (mmtbx.validation.cbetadev.cbeta method) (mmtbx.validation.clashscore.clash method) (mmtbx.validation.clashscore.nqh_flip method) (mmtbx.validation.entity method) (mmtbx.validation.experimental.residue_real_space method) (mmtbx.validation.model_properties.atom_occupancy method) (mmtbx.validation.model_properties.residue_bfactor method) (mmtbx.validation.model_properties.residue_occupancy method) (mmtbx.validation.ramalyze.ramachandran method) (mmtbx.validation.restraints.restraint method) (mmtbx.validation.rna_validate.rna_angle method) (mmtbx.validation.rna_validate.rna_bond method) (mmtbx.validation.rna_validate.rna_pucker method) (mmtbx.validation.rotalyze.rotamer method) (mmtbx.validation.rotalyze.rotamer_ensemble method) (mmtbx.validation.waters.water method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) as_sym_mat3() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.gruber_parameterization method) (scitbx.matrix.rec method) as_table_row_molprobity() (mmtbx.validation.entity method) as_table_row_phenix() (mmtbx.validation.cbetadev.cbeta method) (mmtbx.validation.clashscore.clash method) (mmtbx.validation.clashscore.nqh_flip method) (mmtbx.validation.entity method) (mmtbx.validation.experimental.residue_real_space method) (mmtbx.validation.model_properties.atom_occupancy method) (mmtbx.validation.model_properties.residue_occupancy method) (mmtbx.validation.ramalyze.ramachandran method) (mmtbx.validation.restraints.bond method) (mmtbx.validation.restraints.chirality method) (mmtbx.validation.restraints.planarity method) (mmtbx.validation.restraints.restraint method) (mmtbx.validation.rna_validate.rna_angle method) (mmtbx.validation.rna_validate.rna_bond method) (mmtbx.validation.rna_validate.rna_pucker method) (mmtbx.validation.rotalyze.rotamer method) (mmtbx.validation.waters.water method) as_trace() (xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis method) as_unit_cell() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.gruber_parameterization method) as_vec3_double() (scitbx.array_family.flex.vec3_int method) as_xray_observations() (cctbx.miller.array method) as_xray_structure() (cctbx.euclidean_model_matching.model method) as_xyz() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method) as_z_scores() (scitbx.array_family.flex.double method) assemble_constraint_groups_3d() (in module mmtbx.refinement.occupancies) assemble_symops() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method) assert_all_attributes_defined() (mmtbx.validation.residue method) assert_equal() (cctbx.maptbx.positivity_constrained_density_modification method) assert_file_type() (iotbx.file_reader.any_file_input method) assert_min_distance_sym_equiv() (cctbx.crystal.special_position_settings method) assert_model_is_consistent() (in module mmtbx.utils) assert_pdb_hierarchy_xray_structure_sync() (mmtbx.refinement.real_space.structure_monitor method) assert_same_gridding() (in module cctbx.maptbx) assert_water_is_consistent() (in module mmtbx.hydrogens.find) (in module mmtbx.utils) assert_xray_structures_equal() (in module mmtbx.utils) assign() (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) assign_charge() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) assign_directly() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) assign_from_monomer_mapping() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) assign_r_free_flags_by_shells() (in module cctbx.r_free_utils) assign_random_r_free_flags() (in module cctbx.r_free_utils) assistant (class in cctbx.miller.reindexing) asu (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points attribute) asu_001() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_002() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_003() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_004() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_005() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_006() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_007() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_008() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_009() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_01() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_010() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_011() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_012() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_013() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_014() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_015() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_016() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_017() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_018() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_019() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_02() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_020() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_021() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_022() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_023() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_024() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_025() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_026() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_027() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_028() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_029() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_03() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_030() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_031() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_032() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_033() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_034() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_035() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_036() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_037() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_038() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_039() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_04() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_040() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_041() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_042() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_043() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_044() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_045() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_046() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_047() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_048() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_049() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_05() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_050() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_051() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_052() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_053() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_054() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_055() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_056() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_057() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_058() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_059() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_06() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_060() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_061() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_062() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_063() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_064() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_065() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_066() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_067() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_068() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_069() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_07() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_070() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_071() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_072() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_073() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_074() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_075() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_076() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_077() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_078() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_079() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_08() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_080() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_081() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_082() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_083() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_084() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_085() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_086() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_087() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_088() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_089() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_09() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_090() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_091() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_092() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_093() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_094() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_095() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_096() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_097() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_098() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_099() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_10() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_100() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_101() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_102() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_103() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_104() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_105() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_106() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_107() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_108() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_109() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_11() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_110() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_111() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_112() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_113() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_114() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_115() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_116() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_117() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_118() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_119() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_12() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_120() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_121() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_122() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_123() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_124() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_125() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_126() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_127() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_128() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_129() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_13() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_130() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_131() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_132() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_133() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_134() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_135() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_136() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_137() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_138() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_139() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_14() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_140() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_141() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_142() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_143() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_144() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_145() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_146() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_147() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_148() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_149() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_15() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_150() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_151() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_152() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_153() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_154() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_155() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_156() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_157() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_158() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_159() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_16() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_160() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_161() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_162() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_163() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_164() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_165() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_166() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_167() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_168() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_169() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_17() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) asu_170() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_171() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_172() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_173() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_174() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_175() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_176() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_177() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_178() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_179() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_180() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_181() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_182() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_183() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_184() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_185() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_186() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_187() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_188() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_189() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_190() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_191() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_192() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_193() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_194() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_195() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_196() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_197() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_198() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_199() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_200() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_201() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_202() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_203() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_204() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_205() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_206() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_207() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_208() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_209() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_210() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_211() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_212() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_213() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_214() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_215() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_216() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_217() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_218() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_219() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_220() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_221() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_222() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_223() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_224() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_225() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_226() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_227() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_228() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_229() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_230() (in module cctbx.sgtbx.direct_space_asu.reference_table) asu_as_jvx() (in module cctbx.web.asu_gallery.jv_asu) asu_map_from_fmodel() (mmtbx.maps.composite_omit_map.run method) asu_mapping_for() (mmtbx.geometry.clash.Case method) asu_mappings() (cctbx.crystal.special_position_settings method) (cctbx.crystal.symmetry method) (cctbx.xray.structure.structure method) asu_mask (class in mmtbx.masks) asu_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) asu_show_() (in module cctbx.sgtbx.direct_space_asu.proto) ASUContent (class in mmtbx.geometry.clash) asymmetric_unit_in_p1() (cctbx.xray.structure.structure method) at_first_index() (cctbx.miller.set method) atom (class in iotbx.pdb.hierarchy) Atom (class in mmtbx.geometry.topology) atom (class in mmtbx.ias) (class in mmtbx.validation) (mmtbx.geometry.clash.AtomDescriptor property) (mmtbx.ions.environment.atom_contact attribute), [1] (mmtbx.ions.environment.ChemicalEnvironment attribute), [1] atom_as_str() (in module mmtbx.hydrogens.find) atom_base (class in mmtbx.validation) atom_bfactor (class in mmtbx.validation.model_properties) atom_by_id() (mmtbx.monomer_library.cif_types.comp_comp_id method) atom_contact (class in mmtbx.ions.environment) atom_curves (class in cctbx.maptbx) atom_dict() (mmtbx.monomer_library.cif_types.comp_comp_id method) atom_for (mmtbx.geometry.topology.Compound property) atom_group (class in iotbx.pdb.hierarchy) (mmtbx.geometry.clash.SymmetryEquivalent property) atom_group_as_hierarchy() (in module mmtbx.building) atom_group_id_str() (mmtbx.validation.atom_base method) (mmtbx.validation.residue method) atom_group_proxy (class in mmtbx.disorder.analyze_model) atom_groups() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue_group method) (iotbx.pdb.hierarchy.root method) (mmtbx.disorder.analyze_model.residue_group_proxy method) atom_groups_size() (iotbx.pdb.hierarchy.residue_group method) atom_i_seq() (mmtbx.ions.environment.atom_contact method) atom_id (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) atom_id_no_altloc() (mmtbx.ions.environment.atom_contact method) atom_ids() (mmtbx.monomer_library.cif_types.chem_comp_bond method) (mmtbx.monomer_library.cif_types.chem_comp_tor method) (mmtbx.monomer_library.cif_types.comp_comp_id method) atom_info (class in mmtbx.validation) atom_info_str (mmtbx.ions.svm.svm_prediction attribute), [1] atom_iselection() (mmtbx.maps.write_xplor_map_file method) atom_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute) atom_name() (mmtbx.ions.environment.atom_contact method) atom_name_interpretation (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) atom_names_given (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) atom_names_mappings (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) atom_occupancy (class in mmtbx.validation.model_properties) atom_pair() (mmtbx.geometry.clash.ClashingPair method) atom_parser (class in iotbx.shelx.parsers) atom_radius_as_central_peak_width() (in module cctbx.maptbx) atom_scat() (in module mmtbx.hydrogens.find) atom_selection (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atoms attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.clash attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.entity attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.ligands.ligand_validation attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.planarity attribute) (mmtbx.validation.restraints.restraint attribute) (mmtbx.validation.rna_validate.rna_angle attribute) (mmtbx.validation.rna_validate.rna_bond attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) atom_selection() (in module mmtbx.utils) (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) atom_selection_cache() (iotbx.pdb.hierarchy.root method) atom_selection_string() (mmtbx.validation.clashscore.nqh_flip method) (mmtbx.validation.residue method) atom_type_flags (class in mmtbx.ions) atom_types (mmtbx.ions.svm.svm_prediction attribute), [1] atom_weight() (mmtbx.ions.identify.AtomProperties method) atom_with_labels (class in iotbx.pdb.hierarchy) AtomDescriptor (class in mmtbx.geometry.clash) atomic_number() (cctbx.eltbx.attenuation_coefficient.nist_elements method) atomic_number_list() (cctbx.eltbx.attenuation_coefficient.nist_elements method) atomic_weights() (cctbx.xray.structure.structure method) atomname_token (class in iotbx.shelx.tokens) AtomProperties (class in mmtbx.ions.identify) atoms (class in mmtbx.validation) (mmtbx.geometry.topology.Compound property) (mmtbx.geometry.topology.Molecule property) (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer attribute) atoms() (in module cctbx.development.run_shelx) (in module cctbx.development.run_shelx76) (iotbx.pdb.ext.input method) (iotbx.pdb.hierarchy.atom_group method) (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue method) (iotbx.pdb.hierarchy.residue_group method) (iotbx.pdb.hierarchy.root method) (iotbx.pdb.mmcif.cif_input method) (mmtbx.disorder.analyze_model.atom_group_proxy method) (mmtbx.geometry.clash.Model method) atoms_below_fofc_map_level() (mmtbx.building.local_density_quality method) atoms_below_two_fofc_map_level() (mmtbx.building.local_density_quality method) atoms_info (mmtbx.validation.atoms attribute) (mmtbx.validation.clashscore.clash attribute) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.planarity attribute) (mmtbx.validation.restraints.restraint attribute) (mmtbx.validation.rna_validate.rna_angle attribute) (mmtbx.validation.rna_validate.rna_bond attribute) atoms_outside_density() (mmtbx.building.local_density_quality method) atoms_proxy (class in mmtbx.disorder.analyze_model) atoms_reset_serial() (iotbx.pdb.hierarchy.root method) atoms_size() (iotbx.pdb.hierarchy.atom_group method) (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue method) (iotbx.pdb.hierarchy.residue_group method) (iotbx.pdb.hierarchy.root method) atoms_to_observations_ratio() (mmtbx.validation.molprobity.molprobity method) atoms_with_i_seq_mismatch() (iotbx.pdb.hierarchy.root method) atoms_with_labels() (iotbx.pdb.ext.input method) (iotbx.pdb.hierarchy.root method) (iotbx.pdb.mmcif.cif_input method) atomsForAngle (mmtbx.rotamer.sidechain_angles.SidechainAngles attribute) atomsMoveWithAngle (mmtbx.rotamer.sidechain_angles.SidechainAngles attribute) auto_anomalous() (cctbx.miller.set method) AutoType (class in libtbx) average_all() (mmtbx.scaling.fa_estimation.cns_fa_driver method) average_b_cart() (cctbx.crystal.symmetry method) average_bijvoet_mates() (cctbx.miller.array method) average_mixin (class in xfel.cxi.cspad_ana.average_tbx) average_neighbors() (cctbx.miller.array method) average_sites_cart() (in module mmtbx.refinement.orca) average_u_cart() (cctbx.crystal.symmetry method) axes_and_atoms_aa_specific() (in module mmtbx.utils.rotatable_bonds) axis_and_angle_as_r3_derivative_wrt_angle() (scitbx.matrix.rec method) axis_and_angle_as_r3_rotation_matrix() (scitbx.matrix.rec method) axis_and_angle_as_unit_quaternion() (scitbx.matrix.rec method) axis_type (mmtbx.scaling.twin_analyses.twin_law attribute)

B

b (iotbx.pdb.hierarchy.atom property) b2_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.gruber_1973.reduction method) b3_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.gruber_1973.reduction method) b4_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.gruber_1973.reduction method) b5_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.gruber_1973.reduction method) b_cart() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.twinning.twin_f_model.twin_model_manager method) b_factor_cutoff (mmtbx.validation.clashscore.clashscore attribute) b_factor_sharpening_by_map_kurtosis_maximization() (in module mmtbx.maps) b_histogram (mmtbx.validation.model_properties.xray_structure_statistics attribute) b_iso (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.waters.water attribute) b_iso() (mmtbx.twinning.twin_f_model.twin_model_manager method) b_iso_mean (mmtbx.validation.ligands.ligand_validation attribute) b_iso_mean() (mmtbx.validation.molprobity.molprobity method) b_iso_min_max_mean() (cctbx.xray.structure.structure method) b_iso_or_b_equiv() (cctbx.xray.structure.structure method) b_max (mmtbx.validation.model_properties.xray_structure_statistics attribute) b_mean (mmtbx.validation.model_properties.xray_structure_statistics attribute) b_mean_hoh (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] b_min (mmtbx.validation.model_properties.xray_structure_statistics attribute) b_part() (mmtbx.twinning.twin_f_model.twin_model_manager method) b_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method) b_sols() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) b_update() (in module cctbx.omz.bfgs) back() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) backrub_angle (mmtbx.disorder.backbone.backrub_residue attribute) backrub_move() (in module mmtbx.refinement.real_space.fit_residue) backrub_residue (class in mmtbx.disorder.backbone) bad_adps (mmtbx.validation.model_properties.xray_structure_statistics attribute) bad_coord_atom (mmtbx.ions.atom_type_flags attribute) BAD_COORD_ATOM (mmtbx.ions.identify.AtomProperties attribute) bad_coord_residue (mmtbx.ions.atom_type_flags attribute) BAD_COORD_RESIDUE (mmtbx.ions.identify.AtomProperties attribute) BAD_FPP (mmtbx.ions.identify.AtomProperties attribute) bad_geom (mmtbx.ions.atom_type_flags attribute) BAD_GEOMETRY (mmtbx.ions.identify.AtomProperties attribute) bad_halide (mmtbx.ions.atom_type_flags attribute) BAD_HALIDE (mmtbx.ions.identify.AtomProperties attribute) bad_hydrogens (mmtbx.utils.detect_hydrogen_nomenclature_problem attribute) bad_valence (mmtbx.ions.atom_type_flags attribute) BAD_VALENCES (mmtbx.ions.identify.AtomProperties attribute) bad_vectors (mmtbx.ions.atom_type_flags attribute) BAD_VECTORS (mmtbx.ions.identify.AtomProperties attribute) base() (cctbx.web.cgi_utils.server_info method) base_pair_selection() (mmtbx.secondary_structure.manager method) base_pair_selections() (mmtbx.secondary_structure.manager method) base_symbol() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) base_symbol_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table) basic_analyses (class in mmtbx.scaling.basic_analyses) basic_wilson_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method) basis_of_mirror_plane_with_normal() (in module cctbx.math_module) basis_type (class in cctbx.crystal_orientation) basis_vector_geometry() (in module cctbx.web.asu_gallery.jv_asu) batch_as_miller_array() (iotbx.xds.read_ascii.reader method) batch_numbers() (iotbx.shelx.hklf.reader method) bcr_approx() (cctbx.maptbx.atom_curves method) BeamFactory (class in dxtbx.model.beam) beamstop_shadow_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method) begincalibcycle() (xfel.cxi.cspad_ana.mod_mar.mod_mar method) beginjob() (xfel.cxi.cspad_ana.average_tbx.average_mixin method) (xfel.cxi.cspad_ana.common_mode.common_mode_correction method) (xfel.cxi.cspad_ana.mod_average.mod_average method) (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method) (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method) (xfel.cxi.cspad_ana.mod_filter.mod_filter method) (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method) (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method) (xfel.cxi.cspad_ana.mod_mar.mod_mar method) (xfel.cxi.cspad_ana.mod_param.mod_param method) (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method) (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method) (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method) best() (cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter method) best_approximation() (in module cctbx.eltbx.xray_scattering)

best_bravais__() (cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter method) best_by_CC() (xfel.clustering.cluster.Cluster method) best_cell() (cctbx.crystal.symmetry method) best_partition_representatives() (cctbx.sgtbx.cosets.left_decomposition_point_groups_only method) best_superpositions_on_other() (cctbx.euclidean_model_matching.model method) beta_ideal (mmtbx.validation.cbetadev.cbetadev attribute) beta_selection() (mmtbx.secondary_structure.manager method) beta_selections() (mmtbx.secondary_structure.manager method) bijvoet_ratios() (cctbx.miller.array method) bin2index() (mmtbx.rotamer.n_dim_table.NDimTable method) bin2index_limit() (mmtbx.rotamer.n_dim_table.NDimTable method) bin_generator_equal_range() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) bin_generator_equal_size() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) binary_filter() (iotbx.map_manager.map_manager method) binned_correlation() (in module xfel.cxi.cxi_cc) binned_data() (mmtbx.validation.molprobity.multi_criterion_view method) binner (class in cctbx.miller) binner() (cctbx.miller.set method) bivariate_histogram() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) block (class in iotbx.cif.model) blue_color_model (class in mmtbx.polygon.output) bond (class in mmtbx.validation.restraints) bond_angle_registry (class in mmtbx.conformation_dependent_library.bond_angle_registry) bond_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) bond_density (class in mmtbx.ias) bond_deviations() (cctbx.geometry_restraints.energies.energies method) bond_deviations_weighted() (cctbx.geometry_restraints.energies.energies method) bond_deviations_z() (cctbx.geometry_restraints.energies.energies method) bond_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute) bond_outlier_as_kinemage() (in module mmtbx.kinemage.validation) bond_rmsd (mmtbx.validation.molprobity.summary attribute) bond_simple_proxy_registry (class in cctbx.geometry_restraints) bonds (class in mmtbx.validation.restraints) (mmtbx.geometry.topology.Compound property) (mmtbx.validation.restraints.combined attribute) (mmtbx.validation.rna_validate.rna_validation attribute) bookkeeping_section() (iotbx.pdb.ext.input method) bool (class in scitbx.array_family.flex) bool_element_size (scitbx.array_family.flex.smart_selection attribute) bool_md5() (in module scitbx.array_family.flex) box_all_maps_around_density_and_shift_origin() (iotbx.map_model_manager.map_model_manager method) box_all_maps_around_mask_and_shift_origin() (iotbx.map_model_manager.map_model_manager method) box_all_maps_around_model_and_shift_origin() (iotbx.map_model_manager.map_model_manager method) box_all_maps_around_unique_and_shift_origin() (iotbx.map_model_manager.map_model_manager method) box_all_maps_with_bounds_and_shift_origin() (iotbx.map_model_manager.map_model_manager method) box_around_selection() (mmtbx.maps.write_xplor_map_file method) box_build_refine_base (class in mmtbx.building) box_iterator() (mmtbx.maps.composite_omit_map.run method) box_map_coefficients() (mmtbx.utils.extract_box_around_model_and_map method) box_map_coefficients_as_fft_map() (mmtbx.utils.extract_box_around_model_and_map method) box_max() (cctbx.sgtbx.direct_space_asu.direct_space_asu method) box_min() (cctbx.sgtbx.direct_space_asu.direct_space_asu method) box_refinement_manager (class in mmtbx.refinement.real_space.individual_sites) boxes (class in cctbx.maptbx) (mmtbx.maps.composite_omit_map.omit_regions attribute) boxes_by_dimension (class in cctbx.maptbx) bracketed_link() (in module cctbx.web.asu_gallery.jvx) bravais_lattice (class in cctbx.sgtbx.bravais_types) break_indices() (iotbx.pdb.ext.input method) brick() (cctbx.sgtbx.space_group_info method) britton_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property) britton_test (class in mmtbx.scaling.twin_analyses) browse() (cctbx.examples.location_part.symmetries_with_nonzero_location_parts method) bs_ave (mmtbx.refinement.print_statistics.stats_table attribute) build_all_chain_proxies (class in mmtbx.monomer_library.pdb_interpretation) build_angle_start_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils) build_bfgs_memory() (cctbx.omz.dev.refinement method) build_chain_proxies (class in mmtbx.monomer_library.pdb_interpretation) build_conformation_dependent_angle_proxies() (in module mmtbx.monomer_library.conformation_dependent_restraints) build_crystal_structures() (iotbx.cif.reader method) build_den_proxies() (mmtbx.den.den_restraints method) build_den_restraints() (mmtbx.den.den_restraints method) build_dict() (iotbx.pdb.hierarchy.af_shared_atom method) build_dod_and_od() (in module mmtbx.hydrogens.find) build_edge_list() (in module cctbx.eltbx.distance_based_connectivity) build_i_q_packed_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils) build_it() (cctbx.sgtbx.pointgroup_tools.point_group_graph method) build_miller_arrays() (iotbx.cif.reader method) build_miller_set() (cctbx.crystal.symmetry method) build_name_hash() (in module mmtbx.kinemage.validation) (in module mmtbx.validation.utils) build_reticular_twin_laws() (in module cctbx.sgtbx.reticular_pg_tools) build_rotamer_tor_atom_ids_by_tor_id() (in module mmtbx.monomer_library.rotamer_utils) build_scatterers() (cctbx.development.random_structure.xray_structure method) build_selections() (mmtbx.secondary_structure.proteins.find_helices_simple method) build_set() (in module cctbx.miller) build_simple_two_way_bond_sets() (in module cctbx.crystal.distance_based_connectivity) build_up() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) (scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls method) build_water_hydrogens_from_map() (in module mmtbx.hydrogens.find) build_water_hydrogens_from_map2() (in module mmtbx.hydrogens.find) build_xray_structure_with_carbon_along_x() (in module cctbx.examples.fft_map_electron_density_around_atom) bulk_solvent (class in mmtbx.masks) bulk_solvent_and_scale() (mmtbx.den.refinement.manager method) bulk_solvent_and_scales (class in mmtbx.bulk_solvent.bulk_solvent_and_scaling) bulk_solvent_mask() (mmtbx.masks.manager method) (mmtbx.twinning.twin_f_model.twin_model_manager method) bulk_solvent_scaling() (mmtbx.bulk_solvent.scaler.run method) by_index_selection() (cctbx.xray.structure.structure method)

C

c (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute) c_alpha (class in mmtbx.validation.ramalyze) c_beta_deviations (mmtbx.validation.molprobity.summary attribute) c_obs (cctbx.omz.cif_refine.extract_from_cif_files attribute) (cctbx.omz.cod_select_and_pickle.cod_data attribute) ca() (mmtbx.refinement.refinement_flags.manager method) cache_restraint() (iotbx.shelx.parsers.restraint_parser method) calc_correlation() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method) calc_k() (in module cctbx.xray.targets.r1) calc_shelxl_wght_ls() (cctbx.omz.dev.refinement method) calc_t() (in module cctbx.xray.targets.r1) calc_weights_if_needed() (cctbx.omz.dev.refinement method) calculate() (in module mmtbx.geometry.asa) (in module mmtbx.geometry.clash) (xfel.cxi.cspad_ana.xes_finalise.first_moment_analysis method) calculate_angles (class in cctbx.crystal) calculate_base_for_coordinates() (in module mmtbx.geometry.shared_types) calculate_cell_content() (in module cctbx.development.run_shelx) calculate_contents() (in module mmtbx.geometry.clash) calculate_dihedrals (class in cctbx.crystal) calculate_distances (class in cctbx.crystal) calculate_exp_i_two_phi_peaks() (in module cctbx.examples.phase_o_phrenia) calculate_ideal_and_deviation (class in mmtbx.validation.cbetadev) calculate_mean_intensities() (in module cctbx.french_wilson) calculate_rms() (cctbx.euclidean_model_matching.match_refine method) calculate_shortest_diff() (cctbx.euclidean_model_matching.match_refine method) calculate_shortest_diffs() (cctbx.euclidean_model_matching.match_refine method) calculate_shortest_dist() (cctbx.euclidean_model_matching.match_refine method) calculate_solvent_mask() (mmtbx.density_modification.density_modification method) calculate_structure_content() (mmtbx.secondary_structure.manager method) calculate_valence() (mmtbx.ions.parameter_server method) calculate_valences() (mmtbx.ions.parameter_server method) calculated (cctbx.xray.weighting_schemes.shelx_weighting property) calib2sections() (in module xfel.cxi.cspad_ana.parse_calib) calib2tensor3() (in module xfel.cxi.cspad_ana.parse_calib) call_back() (mmtbx.refinement.print_statistics.refinement_monitor method) callback_after_step() (cctbx.examples.unit_cell_refinement.refinery method) (cctbx.omz.dev.refinement method) (cctbx.xray.minimization.lbfgs method) (mmtbx.refinement.geometry_minimization.lbfgs method) (mmtbx.refinement.minimization.lbfgs method) calls_and_accumulated_time (class in cctbx.xray.structure_factors.global_counters) capacity() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) carbonyl_oxygen_angle() (in module mmtbx.disorder.analyze_model) cart_to_grid_units() (iotbx.map_manager.map_manager method) cartesian_dynamics (class in mmtbx.dynamics.ensemble_cd) cartesian_polygon() (in module cctbx.web.asu_gallery.jv_asu) Case (class in mmtbx.geometry.clash) cast_map_coeff_params() (in module mmtbx.maps) cb_op() (cctbx.crystal.find_best_cell.find_best_cell method) (cctbx.euclidean_model_matching.model method) cb_op_as_rational() (in module cctbx.sgtbx.rational_matrices_point_groups) (in module cctbx.sgtbx.reticular_pg_tools) cb_ops (cctbx.miller.reindexing.assistant attribute) cb_ops_in_niggli_setting() (cctbx.crystal.reindex.reindexing_operators method) cb_update() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.reduction_base method) cbcaa() (in module xfel.cxi.cspad_ana.cspad_tbx) cbeta (class in mmtbx.validation.cbetadev) cbeta_dev() (in module mmtbx.kinemage.validation) cbeta_outliers() (mmtbx.validation.molprobity.molprobity method) cbetadev (class in mmtbx.validation.cbetadev) (mmtbx.validation.molprobity.molprobity attribute) cbf_file_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx) cc (mmtbx.validation.experimental.residue_real_space property) (mmtbx.validation.ligands.ligand_validation attribute) (mmtbx.validation.waters.water property) cc() (mmtbx.ncs.ncs.ncs_group method) CC() (xfel.metrology.quadrant.one_panel method) (xfel.metrology.quadrant.one_sensor method) cc_anom() (cctbx.miller.array method) cc_model_map() (mmtbx.building.box_build_refine_base method) cc_one_half() (cctbx.miller.array method) cc_one_half_outer (mmtbx.scaling.xtriage.merging_statistics property) cc_one_half_sigma_tau() (cctbx.miller.array method) cc_peak() (in module cctbx.maptbx) cc_to_other_map_manager() (iotbx.map_manager.map_manager method) ccp4_alpha_beta_gamma_fcalc_fobs (class in cctbx.macro_mol.rotation_parameters) ccp4_alpha_beta_gamma_fobs_fcalc (class in cctbx.macro_mol.rotation_parameters) ccp4_map() (in module mmtbx.maps.fem) ccp4_partial_charge (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) ccp4_phi_omega_kappa_fcalc_fobs (class in cctbx.macro_mol.rotation_parameters) ccp4_phi_omega_kappa_fcalc_fobs_params_to_matrix() (in module cctbx.macro_mol.rotation_parameters) ccp4_phi_omega_kappa_fobs_fcalc (class in cctbx.macro_mol.rotation_parameters) ccp4_phi_omega_kappa_fobs_fcalc_matrix_to_params() (in module cctbx.macro_mol.rotation_parameters) ccp4_type_energy (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) cctbx module cctbx.adp_restraints module cctbx.adp_restraints.energies module cctbx.adp_restraints.flags module cctbx.adptbx module cctbx.array_family module cctbx.array_family.flex module cctbx.command_line module cctbx.command_line.brehm_diederichs module cctbx.command_line.cod_select_and_pickle module cctbx.command_line.euclidean_model_matching module cctbx.command_line.find_reticular_twin_laws module cctbx.command_line.form_factor_query module cctbx.command_line.precession_view module cctbx.command_line.space_group_info module cctbx.command_line.structure_factor_timings module cctbx.command_line.subgroups module cctbx.command_line.version module cctbx.command_line.wavelength_units module cctbx.covariance module cctbx.crystal module cctbx.crystal.burzlaff_zimmermann_dewolff module cctbx.crystal.close_packing module cctbx.crystal.coordination_sequences module cctbx.crystal.direct_space_asu module cctbx.crystal.distance_based_connectivity module cctbx.crystal.find_best_cell module cctbx.crystal.reindex module cctbx.crystal_orientation module cctbx.development module cctbx.development.cns_density_modification module cctbx.development.debug_utils module cctbx.development.direct_or_fft module cctbx.development.electron_density_sampling module cctbx.development.fmt_utils module cctbx.development.make_cns_input module cctbx.development.make_settings module cctbx.development.random_structure module cctbx.development.run_shelx module cctbx.development.run_shelx76 module cctbx.development.space_group_option_parser module cctbx.development.structure_factor_utils module cctbx.dmtbx module cctbx.eltbx module cctbx.eltbx.attenuation_coefficient module cctbx.eltbx.chemical_elements module cctbx.eltbx.covalent_radii module cctbx.eltbx.development module cctbx.eltbx.development.combine_fits module cctbx.eltbx.development.create_n_gaussian_raw_cpp module cctbx.eltbx.development.e_scattering_plots module cctbx.eltbx.development.format_gaussian_fits module cctbx.eltbx.development.hydrogen_plots module cctbx.eltbx.development.itvc_approx module cctbx.eltbx.development.itvc_cross_validation module cctbx.eltbx.development.itvc_fits module cctbx.eltbx.development.itvc_section61_io module cctbx.eltbx.development.kissel_fits module cctbx.eltbx.development.kissel_io module cctbx.eltbx.development.rez_rez_grant module cctbx.eltbx.distance_based_connectivity module cctbx.eltbx.e_scattering module cctbx.eltbx.formula module cctbx.eltbx.fp_fdp module cctbx.eltbx.gaussian_fit module cctbx.eltbx.henke module cctbx.eltbx.icsd_radii module cctbx.eltbx.neutron module cctbx.eltbx.sasaki module cctbx.eltbx.tiny_pse module cctbx.eltbx.van_der_waals_radii module cctbx.eltbx.wavelengths module cctbx.eltbx.xray_scattering module cctbx.euclidean_model_matching module cctbx.examples module cctbx.examples.adp_symmetry_constraints module cctbx.examples.all_axes module cctbx.examples.analyze_adp module cctbx.examples.change_hand_p31 module cctbx.examples.convert_ccp4_symop_lib module cctbx.examples.cr2o3_consistency_checks module cctbx.examples.cr2o3_primitive_cell module cctbx.examples.exp_i_alpha_derivatives module cctbx.examples.f_model_example module cctbx.examples.fft_map_electron_density_around_atom module cctbx.examples.find_distances_using_cpp_objects module cctbx.examples.find_sys_abs_equiv_space_groups module cctbx.examples.g_exp_i_alpha_derivatives module cctbx.examples.g_exp_i_partial_derivatives module cctbx.examples.getting_started module cctbx.examples.hirshfeld_test module cctbx.examples.le_page_1982_vs_lebedev_2005 module cctbx.examples.lebedev_2005_perturbation module cctbx.examples.list_non_principal_continuous_shifts module cctbx.examples.location_part module cctbx.examples.map_skewness module cctbx.examples.maximum_subgroups module cctbx.examples.miller_common_sets module cctbx.examples.miller_transform module cctbx.examples.neutron_structure_factors module cctbx.examples.phase_o_phrenia module cctbx.examples.quartz_structure module cctbx.examples.random_f_calc module cctbx.examples.random_puckers module cctbx.examples.reduced_cell_two_folds module cctbx.examples.site_symmetry_constraints module cctbx.examples.site_symmetry_table module cctbx.examples.space_group_matrices module cctbx.examples.space_subgroups module cctbx.examples.steve_collins module cctbx.examples.structure_factor_calculus module cctbx.examples.structure_factor_calculus.site_derivatives module cctbx.examples.structure_factor_calculus.sites_derivatives module cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives module cctbx.examples.structure_factor_calculus.u_star_derivatives module cctbx.examples.structure_factor_derivatives module cctbx.examples.structure_factor_derivatives_2 module cctbx.examples.structure_factor_derivatives_3 module cctbx.examples.structure_factor_derivatives_4 module cctbx.examples.sub_group_graph module cctbx.examples.symops_530 module cctbx.examples.trigonal_r_vs_tetragonal_i module cctbx.examples.unit_cell_minimizers module cctbx.examples.unit_cell_refinement module cctbx.french_wilson module cctbx.geometry module cctbx.geometry_restraints module cctbx.geometry_restraints.energies module cctbx.geometry_restraints.flags module cctbx.geometry_restraints.lbfgs module cctbx.geometry_restraints.manager module cctbx.macro_mol module cctbx.macro_mol.rotation_parameters module cctbx.maptbx module cctbx.maptbx.mem module cctbx.maptbx.real_space_refinement_simple module cctbx.masks module cctbx.math_module module cctbx.merging module cctbx.merging.brehm_diederichs module cctbx.miller module cctbx.miller.display module cctbx.miller.reindexing module cctbx.multipolar module cctbx.neutron module cctbx.omz module cctbx.omz.bfgs module cctbx.omz.cif_refine module cctbx.omz.cod_refine module cctbx.omz.cod_select_and_pickle module cctbx.omz.dev module cctbx.omz.eval_iso_vs_refined module cctbx.omz.pdb_dev module cctbx.omz.tardy_adaptor module cctbx.r_free_utils module cctbx.run_examples module cctbx.run_tests module cctbx.sgtbx module cctbx.sgtbx.bravais_types module cctbx.sgtbx.cosets module cctbx.sgtbx.direct_space_asu module cctbx.sgtbx.direct_space_asu.check_redundancies module cctbx.sgtbx.direct_space_asu.cut_plane module cctbx.sgtbx.direct_space_asu.facet_analysis module cctbx.sgtbx.direct_space_asu.plane_group_reference_table module cctbx.sgtbx.direct_space_asu.proto module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table module cctbx.sgtbx.direct_space_asu.reference_table module cctbx.sgtbx.direct_space_asu.short_cuts module cctbx.sgtbx.harker module cctbx.sgtbx.lattice_symmetry module cctbx.sgtbx.literal_description module cctbx.sgtbx.plane_groups module cctbx.sgtbx.pointgroup_tools module cctbx.sgtbx.rational_matrices_point_groups module cctbx.sgtbx.reticular_pg_tools module cctbx.sgtbx.reticular_twin_laws module cctbx.sgtbx.show_cosets module cctbx.sgtbx.sub_lattice_tools module cctbx.sgtbx.subgroups module cctbx.sgtbx.symbol_confidence module cctbx.sgtbx.sys_abs_equiv module cctbx.source_generators module cctbx.source_generators.eltbx module cctbx.source_generators.eltbx.generate_henke_cpp module cctbx.source_generators.eltbx.generate_sasaki_cpp module cctbx.source_generators.flex_fwd_h module cctbx.statistics module cctbx.symmetry_search module cctbx.translation_search module cctbx.uctbx.determine_unit_cell module cctbx.uctbx.gruber_1973 module cctbx.uctbx.gruber_1973_table_1 module cctbx.uctbx.krivy_gruber_1976 module cctbx.uctbx.reduction_base module cctbx.web module cctbx.web.all_axes module cctbx.web.asu_gallery module cctbx.web.asu_gallery.guide_to_notation module cctbx.web.asu_gallery.jv_asu module cctbx.web.asu_gallery.jv_index module cctbx.web.asu_gallery.jvx module cctbx.web.asu_gallery.web_links module cctbx.web.browse_settings module cctbx.web.cgi_utils module cctbx.web.change_basis module cctbx.web.change_hand module cctbx.web.change_setting module cctbx.web.dispatcher module cctbx.web.emma module cctbx.web.explore_symmetry module cctbx.web.frac_cart module cctbx.web.io_utils module cctbx.web.iotbx_cif_validate module cctbx.web.lattice_symmetry module cctbx.web.libtbx_help module cctbx.web.multiple_cell module cctbx.web.phase_o_phrenia module cctbx.web.replay module cctbx.web.shelx module cctbx.web.structure_factors module cctbx.web.structure_factors_pdb module cctbx.web.wyckoff module cctbx.xray module cctbx.xray.ext module cctbx.xray.minimization module cctbx.xray.observation_types module cctbx.xray.observations module cctbx.xray.scatterer module cctbx.xray.structure module cctbx.xray.structure_factors module cctbx.xray.structure_factors.from_scatterers module cctbx.xray.structure_factors.from_scatterers_direct module cctbx.xray.structure_factors.from_scatterers_direct_parallel module cctbx.xray.structure_factors.from_scatterers_fft module cctbx.xray.structure_factors.global_counters module cctbx.xray.structure_factors.gradient_flags module cctbx.xray.structure_factors.gradients module cctbx.xray.structure_factors.gradients_base module cctbx.xray.structure_factors.gradients_direct module cctbx.xray.structure_factors.gradients_fft module cctbx.xray.structure_factors.manager module cctbx.xray.structure_factors.misc module cctbx.xray.target_functors module cctbx.xray.targets module cctbx.xray.targets.r1 module cctbx.xray.weighting_schemes module ccv() (in module cctbx.maptbx) cell_equivalent_p1() (cctbx.crystal.symmetry method) center() (scitbx.array_family.flex.histogram_slot_info method) (scitbx.array_family.flex.weighted_histogram_slot_info method) center_of_mass() (cctbx.xray.structure.structure method) center_of_mass_info() (mmtbx.dynamics.cartesian_dynamics.run method) (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) centerOf() (mmtbx.rotamer.n_dim_table.NDimTable method) centers() (mmtbx.ncs.ncs.ncs_group method) centric_e_sq_minus_one_library (mmtbx.scaling.twin_analyses.wilson_moments attribute) centric_f_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute) centric_flags() (cctbx.miller.set method) centric_i_ratio_library (mmtbx.scaling.twin_analyses.wilson_moments attribute) centring_translation_peak_sites() (cctbx.symmetry_search.structure_factor_symmetry method) cfft() (cctbx.xray.structure_factors.manager.manager method) chain (class in iotbx.pdb.hierarchy) (class in mmtbx.validation.sequence) (mmtbx.geometry.clash.SymmetryEquivalent property) chain() (iotbx.pdb.hierarchy.atom method) chain_id (iotbx.pdb.hierarchy.atom_with_labels property) (mmtbx.building.make_library.related_chain attribute) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) chain_ids() (iotbx.pdb.hierarchy.root method) chain_indices() (iotbx.pdb.ext.input method) chain_residue_id() (mmtbx.ncs.ncs.ncs_group method) chain_type (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) chain_type() (iotbx.pdb.hierarchy.root method) chain_types() (iotbx.pdb.hierarchy.root method) chainid (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) chains() (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.root method) Chains_info (class in mmtbx.ncs.ncs_search) chains_size() (iotbx.pdb.hierarchy.model method) change_atom_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method) change_basis() (cctbx.crystal.special_position_settings method) (cctbx.crystal.symmetry method) (cctbx.euclidean_model_matching.model method) (cctbx.miller.array method) (cctbx.miller.set method) (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method) (cctbx.sgtbx.direct_space_asu.direct_space_asu method) (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method) (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method) (cctbx.sgtbx.space_group_info method) (cctbx.xray.structure.structure method)

change_hand() (cctbx.euclidean_model_matching.model method) (cctbx.sgtbx.space_group_info method) (cctbx.xray.structure.structure method) change_input_to_minimum_cell() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method) change_of_basis() (mmtbx.ncs.ncs.ncs method) change_of_basis_op() (cctbx.uctbx.reduction_base.reduction_base method) change_of_basis_op_to() (cctbx.sgtbx.space_group_info method) change_of_basis_op_to_best_cell() (cctbx.crystal.symmetry method) (cctbx.sgtbx.lattice_symmetry.metric_subgroups method) change_of_basis_op_to_inverse_hand() (cctbx.crystal.symmetry method) change_of_basis_op_to_minimum_cell() (cctbx.crystal.symmetry method) change_of_basis_op_to_niggli_cell() (cctbx.crystal.symmetry method) change_of_basis_op_to_other_hand() (cctbx.sgtbx.space_group_info method) change_of_basis_op_to_primitive_setting() (cctbx.crystal.symmetry method) (cctbx.sgtbx.space_group_info method) change_of_basis_op_to_reference_setting() (cctbx.crystal.symmetry method) (cctbx.sgtbx.space_group_info method) change_origin() (cctbx.symmetry_search.possible_symmetry method) change_space_group() (cctbx.maptbx.crystal_gridding method) change_symmetry() (cctbx.miller.array method) (in module mmtbx.scaling.xtriage) character_tests() (cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria method) charge (iotbx.pdb.hierarchy.atom property) (mmtbx.ions.environment.atom_contact attribute), [1] (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) charge_as_int() (iotbx.pdb.hierarchy.atom method) (mmtbx.ions.metal_parameters method) charge_tidy() (iotbx.pdb.hierarchy.atom method) chebyshev_common_mode() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method) chebyshev_fit() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method) check() (mmtbx.scaling.absences.absences method) check_all() (mmtbx.refinement.refinement_flags.manager method) check_all_classes() (in module mmtbx.monomer_library.linking_mixins) check_and_add_hydrogen() (in module mmtbx.validation.clashscore) check_and_report_reduce_failure() (in module mmtbx.validation.clashscore) check_and_set_crystal_symmetry() (in module mmtbx.utils) check_anisou() (in module cctbx.development.run_shelx) check_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) check_at_bond_vector() (in module mmtbx.ias) check_comp() (in module mmtbx.monomer_library.cif_triage) check_compatibility_with_sampling_grid() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) check_condition() (mmtbx.scaling.absences.absences method) check_conditions() (mmtbx.scaling.absences.analyze_absences method) check_correlation() (in module cctbx.development.structure_factor_utils) check_den_pair_consistency() (mmtbx.den.den_restraints method) check_file_type() (iotbx.file_reader.any_file_input method) check_files() (in module mmtbx.command_line) check_first_last() (cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table method) check_for_acid() (in module mmtbx.monomer_library.linking_utils) check_for_pathological_input_data() (in module mmtbx.scaling.xtriage) check_for_peptide_links() (in module mmtbx.monomer_library.linking_mixins) check_fpp_ratio() (mmtbx.ions.identify.AtomProperties method) check_image() (in module xfel.command_line.cxi_stream_to_pickle) check_ion_environment() (mmtbx.ions.identify.AtomProperties method) check_key_is_unique() (iotbx.cif.model.loop method) check_mask() (mmtbx.scaling.absences.absences method) check_model_and_set_to_match_map_if_necessary() (iotbx.map_model_manager.match_map_model_ncs method) check_multiplicities() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) check_phase_restrictions() (in module cctbx.development.structure_factor_utils) check_pixel_histogram_fit() (in module xfel.command_line.view_pixel_histograms) check_r1() (in module cctbx.development.run_shelx) check_regression() (in module cctbx.development.structure_factor_utils) check_sites_match() (in module mmtbx.refinement.real_space) check_size() (cctbx.xray.structure_factors.gradients_base.gradients_base method) check_stop_file() (iotbx.map_model_manager.map_model_manager method) check_strong_wolfe() (cctbx.omz.dev.xfgc_info method) check_supported() (in module mmtbx.ions) check_table_name() (mmtbx.rotamer.ramachandran_eval.RamachandranEval method) check_u_cart() (in module mmtbx.tls.ladp) check_valence() (in module mmtbx.monomer_library.linking_utils) check_valence_and_acid() (in module mmtbx.monomer_library.linking_utils) chem_comp (class in mmtbx.monomer_library.cif_types) (mmtbx.monomer_library.cif_types.comp_comp_id attribute) chem_comp_angle (class in mmtbx.monomer_library.cif_types) chem_comp_atom (class in mmtbx.monomer_library.cif_types) (class in mmtbx.wwpdb.standard_geometry_cif) chem_comp_bond (class in mmtbx.monomer_library.cif_types) chem_comp_chir (class in mmtbx.monomer_library.cif_types) chem_comp_deriv (class in mmtbx.monomer_library.cif_types) chem_comp_plane_atom (class in mmtbx.monomer_library.cif_types) chem_comp_rotamer_info (class in mmtbx.monomer_library.cif_types) chem_comp_synonym (class in mmtbx.monomer_library.cif_types) chem_comp_synonym_atom (class in mmtbx.monomer_library.cif_types) chem_comp_tor (class in mmtbx.monomer_library.cif_types) chem_comp_tree (class in mmtbx.monomer_library.cif_types) chem_env (mmtbx.ions.identify.ion_result attribute) chem_link (class in mmtbx.monomer_library.cif_types) chem_link_angle (class in mmtbx.monomer_library.cif_types) chem_link_bond (class in mmtbx.monomer_library.cif_types) chem_link_chir (class in mmtbx.monomer_library.cif_types) chem_link_plane (class in mmtbx.monomer_library.cif_types) chem_link_tor (class in mmtbx.monomer_library.cif_types) chem_mod (class in mmtbx.monomer_library.cif_types) chem_mod_angle (class in mmtbx.monomer_library.cif_types) chem_mod_atom (class in mmtbx.monomer_library.cif_types) chem_mod_bond (class in mmtbx.monomer_library.cif_types) chem_mod_chir (class in mmtbx.monomer_library.cif_types) chem_mod_ids (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) chem_mod_plane_atom (class in mmtbx.monomer_library.cif_types) chem_mod_tor (class in mmtbx.monomer_library.cif_types) chem_mod_tree (class in mmtbx.monomer_library.cif_types) chem_plane (class in mmtbx.monomer_library.cif_types) chemical_id_search() (in module mmtbx.wwpdb.rcsb_web_services) ChemicalEnvironment (class in mmtbx.ions.environment) chemistry (mmtbx.ions.environment.ChemicalEnvironment attribute), [1] chemlex() (in module cctbx.eltbx.attenuation_coefficient) chi_angles (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) chi_angles() (mmtbx.rotamer.rotamer_eval.RotamerEval method) chir_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute) chiral_outlier_as_kinemage() (in module mmtbx.kinemage.validation) chiralities (class in mmtbx.validation.restraints) (mmtbx.validation.restraints.combined attribute) chirality (class in mmtbx.validation.restraints) chirality_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) chirality_deviations() (cctbx.geometry_restraints.energies.energies method) chirality_proxy_registry (class in cctbx.geometry_restraints) chisPerAA (mmtbx.rotamer.sidechain_angles.SidechainAngles attribute) choose_best_set() (iotbx.map_model_manager.map_model_manager method) choose_h_for_water() (in module mmtbx.hydrogens.find) chunk_selections() (iotbx.pdb.hierarchy.root method) cif (class in iotbx.cif.model) cif_file_names (mmtbx.command_line.load_model_and_data attribute) cif_input (class in iotbx.pdb.mmcif) cif_keywords() (mmtbx.monomer_library.cif_types.looped_data method) cif_object (mmtbx.monomer_library.cif_types.comp_comp_id attribute) cif_objects (mmtbx.command_line.load_model_and_data attribute) cif_output_holder (class in mmtbx.monomer_library.pdb_interpretation) cif_symmetry_code() (cctbx.sgtbx.space_group_info method) circ_len() (in module mmtbx.disorder.backbone) circ_mean() (in module mmtbx.disorder.backbone) circ_stddev() (in module mmtbx.disorder.backbone) clampInclusive() (mmtbx.rotamer.n_dim_table.NDimTable method) clash (class in mmtbx.validation.clashscore) clash_dict (mmtbx.validation.clashscore.clashscore attribute) clash_dict_b_cutoff (mmtbx.validation.clashscore.clashscore attribute) clash_guard() (mmtbx.monomer_library.pdb_interpretation.process method) ClashCalculation (class in mmtbx.geometry.clash) ClashCollection (class in mmtbx.geometry.clash) ClashCountCalculation (class in mmtbx.geometry.clash) clashes (mmtbx.validation.molprobity.molprobity attribute) clashing_with() (mmtbx.geometry.clash.ASUContent method) ClashingPair (class in mmtbx.geometry.clash) ClashPoint (class in mmtbx.geometry.clash) clashscore (class in mmtbx.validation.clashscore) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.molprobity.summary attribute) clashscore() (mmtbx.validation.molprobity.molprobity method) clashscore_b_cutoff (mmtbx.validation.clashscore.clashscore attribute) class_ (iotbx.shelx.tokens.residue_token attribute) classic_lbfgs() (cctbx.omz.dev.refinement method) classification (mmtbx.monomer_library.cif_types.comp_comp_id attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) clean_up() (libtbx.program_template.ProgramTemplate method) clean_up_ions() (in module mmtbx.ions.build) clear() (iotbx.pdb.hierarchy.af_shared_atom method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) clear_binner() (cctbx.miller.set method) clear_label_asym_id_lookups() (iotbx.pdb.hierarchy.root method) clear_labels() (cctbx.miller.display.scene method) clear_up_cosets() (cctbx.sgtbx.cosets.double_cosets method) close_contact (mmtbx.ions.atom_type_flags attribute) CLOSE_CONTACT (mmtbx.ions.identify.AtomProperties attribute) closest_distances() (cctbx.xray.structure.structure method) closest_rational() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method) closest_to_mean() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils) cluster (class in mmtbx.refinement.real_space) Cluster (class in xfel.clustering.cluster) cluster_erosion() (in module cctbx.crystal) cluster_height_fraction() (cctbx.maptbx.peak_cluster_analysis method) (cctbx.maptbx.peak_search_parameters method) cluster_site_info (class in cctbx.maptbx) cns_axis_x_axis_y_axis_z_axis_kappa (class in cctbx.macro_mol.rotation_parameters) cns_fa_driver (class in mmtbx.scaling.fa_estimation) cns_psi_phi_kappa (class in cctbx.macro_mol.rotation_parameters) cns_theta1_theta2_theta3 (class in cctbx.macro_mol.rotation_parameters) cns_theta_123_as_p2m() (in module cctbx.macro_mol.rotation_parameters) cns_theta_123_from_p2m() (in module cctbx.macro_mol.rotation_parameters) cns_theta_plus_theta2_theta_minus (class in cctbx.macro_mol.rotation_parameters) co_factor_matrix_transposed() (scitbx.matrix.rec method) cod_data (class in cctbx.omz.cod_select_and_pickle) cod_id (cctbx.omz.cod_select_and_pickle.cod_data attribute) col (class in scitbx.matrix) collect() (mmtbx.refinement.minimization.monitor method) (mmtbx.refinement.monitors method) (mmtbx.refinement.print_statistics.refinement_monitor method) collect_arrays() (in module iotbx.reflection_file_reader) collect_cuts() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) collect_ions() (in module mmtbx.ions.utils) collect_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp) collect_residue_torsion_angles() (in module mmtbx.rotamer.sidechain_angles) collect_sidechain_chi_angles() (in module mmtbx.rotamer.sidechain_angles) collect_tab_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp) collect_tables() (in module cctbx.source_generators.eltbx.generate_henke_cpp) (in module cctbx.source_generators.eltbx.generate_sasaki_cpp) collector (class in cctbx.development.structure_factor_utils) color_model (class in mmtbx.polygon.output) color_server (class in cctbx.sgtbx.direct_space_asu.check_redundancies) colored_grid_point (class in cctbx.sgtbx.direct_space_asu.check_redundancies) column_index() (iotbx.xds.read_ascii.reader method) combine() (cctbx.miller.array method) combine_ligands_and_hierarchy() (in module mmtbx.ncs.ligands) combine_maps() (in module mmtbx.maps.composite_omit_map) combine_split_structure() (in module mmtbx.wwpdb.utils) combine_tables() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp) combine_tls_and_u_local() (in module mmtbx.tls.tools) combine_with() (mmtbx.maps.composite_omit_map.omit_regions method) combine_with_other() (cctbx.euclidean_model_matching.model method) combined (class in mmtbx.validation.restraints) combined_cb_ops() (cctbx.crystal.reindex.reindexing_operators method) combined_scaling (class in mmtbx.scaling.fa_estimation) command_stream (class in iotbx.shelx.lexer) commands_allowing_atom_names (iotbx.shelx.lexer.command_stream attribute) commit_entries() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method) commit_progress_entries() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method) common_frame_of_reference (class in mmtbx.maps.superpose) common_map_values() (in module mmtbx.refinement.real_space) common_mode() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method) common_mode_correction (class in xfel.cxi.cspad_ana.common_mode) common_set() (cctbx.miller.set method) common_sets() (cctbx.miller.set method) comp_comp_id (class in mmtbx.monomer_library.cif_types) comp_id (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer attribute) comparator() (mmtbx.scaling.absences.sgi_iterator method) compare_abs_lists() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method) compare_cb_op_as_hkl() (in module cctbx.sgtbx) compare_derivatives() (in module cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives) (in module cctbx.examples.structure_factor_calculus.u_star_derivatives) (in module scitbx.array_family.flex) compare_groups() (in module cctbx.sgtbx.rational_matrices_point_groups) (in module cctbx.sgtbx.reticular_pg_tools) compare_hierarchy() (in module mmtbx.utils) compare_ions() (in module mmtbx.ions.utils) compare_lattice (class in cctbx.sgtbx.sub_lattice_tools) compare_ligands() (in module mmtbx.validation.ligands) compare_ligands_impl() (in module mmtbx.validation.ligands) compare_peaks_with_positions() (mmtbx.solvent.ensemble_ordered_solvent.manager method) compare_points() (in module cctbx.source_generators.eltbx.generate_henke_cpp) compare_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) compatible_symmetries() (in module cctbx.sgtbx.pointgroup_tools) complete_array() (cctbx.miller.array method) complete_set() (cctbx.miller.set method) complete_with() (cctbx.miller.array method) complete_with_bin_average() (cctbx.miller.array method) completeness (mmtbx.validation.experimental.data_statistics attribute) completeness() (cctbx.miller.set method) completeness_enforcement (class in mmtbx.scaling.data_statistics) completeness_outer (mmtbx.validation.experimental.data_statistics attribute) complex() (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.detector.DetectorFactory static method) complex_double (class in scitbx.array_family.flex) component (class in mmtbx.scaling.matthews) composite_distance_predicate() (mmtbx.geometry.indexing.structure_indexer method) composite_predicate (class in mmtbx.geometry.indexing) CompositeCheckerBuilder (class in mmtbx.geometry.asa) composition() (iotbx.pdb.hierarchy.root method) Compound (class in mmtbx.geometry.topology) compute() (cctbx.xray.weighting_schemes.amplitude_unit_weighting method) (cctbx.xray.weighting_schemes.intensity_quasi_unit_weighting method) (cctbx.xray.weighting_schemes.pure_statistical_weighting method) (cctbx.xray.weighting_schemes.shelx_weighting method) (cctbx.xray.weighting_schemes.simple_shelx_weighting method) compute_coefs() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method) (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method) compute_determinant() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method) (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method) compute_f_atoms() (mmtbx.twinning.twin_f_model.twin_model_manager method) compute_f_calc() (in module mmtbx.maps) compute_f_mask() (mmtbx.masks.manager method) compute_fa_values() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method) (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method) compute_finite_difference_gradients_if_requested() (xfel.metrology.mark10.fit_translation4 method) compute_fo_minus_fo_map (class in mmtbx.maps.fobs_minus_fobs_map) compute_functional() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method) compute_functional_and_gradients() (cctbx.examples.unit_cell_refinement.refinery method) (cctbx.geometry_restraints.lbfgs.lbfgs method) (cctbx.maptbx.real_space_refinement_simple.lbfgs method) (cctbx.maptbx.real_space_refinement_simple.magnification_anisotropic_minimization method) (cctbx.merging.brehm_diederichs.minimize method) (cctbx.merging.brehm_diederichs.minimize_divide method) (cctbx.omz.dev.refinement method) (cctbx.symmetry_search.shift_refinement method) (cctbx.xray.minimization.lbfgs method) (mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization method) (mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization method) (mmtbx.refinement.anomalous_scatterer_groups.minimizer method) (mmtbx.refinement.group.group_minimizer method) (mmtbx.refinement.minimization.lbfgs method) (mmtbx.refinement.minimization_ncs_constraints.lbfgs method) (mmtbx.refinement.occupancies.minimizer method) (mmtbx.refinement.real_space.rigid_body.refine method) (mmtbx.refinement.rigid_body.rigid_body_minimizer method) (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method) (mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling method) (mmtbx.scaling.pair_analyses.f_double_prime_ratio method) (mmtbx.scaling.sigmaa_estimation.sigmaa_point_estimator method) (mmtbx.scaling.ta_alpha_beta_calc.sigmaa_point_estimator method) (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method) (mmtbx.tls.tools.tls_from_uaniso_minimizer method) (mmtbx.tls.tools.tls_from_uiso_minimizer method) (mmtbx.tls.tools.tls_xray_target_minimizer method) (mmtbx.twinning.probabalistic_detwinning.detwin method) (xfel.metrology.flatfile.optimise_rectangle method) (xfel.metrology.flatfile.optimise_rectangle_2 method) (xfel.metrology.flatfile.optimise_rectangle_3 method) (xfel.metrology.mark1.fit_translation method) (xfel.metrology.mark10.fit_translation4 method) (xfel.metrology.mark3.fit_translation2 method) compute_gradient() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method) compute_gradient_fd() (mmtbx.scaling.pair_analyses.f_double_prime_ratio method) compute_maha_l() (mmtbx.scaling.twin_analyses.twin_results_interpretation method) compute_map() (mmtbx.density_modification.density_modification method) (mmtbx.refinement.real_space.structure_monitor method) compute_map_and_combine() (in module mmtbx.maps.kick) compute_map_coefficients (class in mmtbx.maps) compute_map_coefficients() (mmtbx.density_modification.density_modification method) (mmtbx.twinning.twin_f_model.twin_model_manager method) compute_original_map() (mmtbx.maps.fem.run method) compute_phase_source() (mmtbx.density_modification.density_modification method) compute_ratios() (mmtbx.scaling.twin_analyses.wilson_moments method) compute_refined_matches() (in module cctbx.euclidean_model_matching) compute_step() (cctbx.omz.dev.refinement method) compute_step_just_grads() (cctbx.omz.dev.refinement method) compute_step_using_curvs() (cctbx.omz.dev.refinement method) compute_target() (cctbx.geometry_restraints.lbfgs.lbfgs method) (cctbx.xray.minimization.lbfgs method) (mmtbx.refinement.minimization.lbfgs method) (mmtbx.refinement.real_space.score method) (mmtbx.refinement.real_space.score3 method) (mmtbx.refinement.real_space.score4 method) compute_transform_grad() (in module mmtbx.ncs.ncs_utils) compute_xplor_maps() (in module mmtbx.maps) concatenate() (cctbx.miller.array method) (cctbx.miller.set method) (cctbx.xray.structure.structure method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) concatenate_inplace() (cctbx.xray.structure.structure method) condense_as_ranges() (in module scitbx.array_family.flex) condensed_probe (mmtbx.validation.clashscore.clashscore attribute) condensed_probe_line_info (class in mmtbx.validation.clashscore) condition() (mmtbx.scaling.absences.conditions_for_operator method) condition_ (mmtbx.ligands.xtal_screens.solution attribute) condition_name() (mmtbx.ligands.xtal_screens.solution method) condition_number_ (mmtbx.ligands.xtal_screens.solution attribute) conditions_for_operator (class in mmtbx.scaling.absences) conf_altloc (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) confid() (iotbx.pdb.hierarchy.atom_group method) conformation_dependent_restraints (class in mmtbx.monomer_library.conformation_dependent_restraints) conformation_scorer (class in mmtbx.building.extend_sidechains) conformer (class in iotbx.pdb.hierarchy) conformer_i_seq (class in mmtbx.monomer_library.pdb_interpretation) conformers() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.residue_group method) conjugate() (cctbx.miller.array method) connected_segment_from() (mmtbx.geometry.topology.Compound method) connected_segments() (mmtbx.geometry.topology.Compound method) connectivity_annotation_section() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) connectivity_section() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) consensus_model() (cctbx.euclidean_model_matching.delegating_model_matches method) conservative_pair_proxies (class in cctbx.xray.structure) conservative_pair_proxies() (cctbx.xray.structure.structure method) consistency_controls() (in module xfel.metrology.mark0) consistent_set_and_model() (in module xfel.command_line.cxi_merge) consolidated_edges_with_cut_points (class in cctbx.sgtbx.direct_space_asu.facet_analysis) constant (cctbx.sgtbx.special_op_simplified_term attribute) constraints (iotbx.shelx.parsers.afix_parser attribute) construct_complete_residues() (in module mmtbx.validation.ramalyze) construct_complete_sidechain() (in module mmtbx.validation.rotalyze) construct_fourth() (in module mmtbx.validation.cbetadev) construct_geometry_restraints_manager() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) construct_hierarchy() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) construct_hierarchy_BIOMT_expanded() (iotbx.pdb.ext.input method) construct_hierarchy_MTRIX_expanded() (iotbx.pdb.ext.input method) construct_miller_set() (mmtbx.twinning.twin_f_model.twin_model_manager method) construct_nice_cb_op() (in module cctbx.sgtbx.cosets) construct_non_crystallographic_conserving_bonds_and_angles() (in module cctbx.geometry_restraints.manager) construct_rational_point_group() (in module cctbx.sgtbx.rational_matrices_point_groups) (in module cctbx.sgtbx.reticular_pg_tools) construct_tardy_tree() (cctbx.geometry_restraints.manager.manager method) construct_twin_laws() (cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws method) contacts (mmtbx.ions.environment.ChemicalEnvironment attribute), [1] contacts_no_alts (mmtbx.ions.environment.ChemicalEnvironment attribute), [1] container_type (scitbx.matrix.rec attribute) containment_predicate (class in mmtbx.geometry.indexing) contains() (mmtbx.rotamer.rotamer_eval.NamedRot method) contains_break_records() (iotbx.pdb.hierarchy.root method) contains_dna() (iotbx.pdb.hierarchy.root method) contains_hetero() (iotbx.pdb.hierarchy.root method) contains_nucleic_acid() (iotbx.pdb.hierarchy.root method) contains_protein() (iotbx.pdb.hierarchy.root method) contains_rna() (iotbx.pdb.hierarchy.root method) contiguous_ss_selections() (in module mmtbx.secondary_structure) contour_plot_DEPRECATED_DOES_NOT_APPLY_SUBPIXEL_METROLOGY() (xfel.mono_simulation.mono_treatment.refinement method) convergence_as_shift_over_esd (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit attribute) conversion_info() (iotbx.pdb.hierarchy.root method) convert() (mmtbx.monomer_library.pdb_interpretation.conformer_i_seq method) convert_2x2() (in module xfel.command_line.convert_gain_map) convert_all() (mmtbx.monomer_library.server.ener_lib method) (mmtbx.monomer_library.server.server method) convert_ccp4_tor_list() (mmtbx.monomer_library.server.server method) convert_comp_list() (in module mmtbx.monomer_library.server) (mmtbx.monomer_library.server.server method) convert_comp_synonym_atom_list() (mmtbx.monomer_library.server.server method) convert_comp_synonym_list() (mmtbx.monomer_library.server.server method) convert_deriv_list_dict() (mmtbx.monomer_library.server.server method) convert_detector() (in module xfel.command_line.convert_gain_map) (in module xfel.command_line.convert_gain_map_cbf) convert_dict_to_excel() (in module mmtbx.conformation_dependent_library.tst_cdl) convert_dict_to_gnuplot() (in module mmtbx.conformation_dependent_library.tst_cdl) convert_dict_to_kin2Dcont() (in module mmtbx.conformation_dependent_library.tst_cdl) convert_dict_to_scilab() (in module mmtbx.conformation_dependent_library.tst_cdl) convert_histogram_data() (in module mmtbx.polygon.output) convert_lib_atom() (mmtbx.monomer_library.server.ener_lib method) convert_lib_synonym() (mmtbx.monomer_library.server.ener_lib method) convert_lib_vdw() (mmtbx.monomer_library.server.ener_lib method) convert_link_list() (in module mmtbx.monomer_library.server) (mmtbx.monomer_library.server.server method) convert_list_block() (in module mmtbx.monomer_library.server) convert_met_to_semet() (iotbx.pdb.hierarchy.root method) convert_mod_list() (in module mmtbx.monomer_library.server) (mmtbx.monomer_library.server.server method) convert_multi_word_text_to_forward_compatible() (iotbx.pdb.hierarchy.root method) convert_semet_to_met() (iotbx.pdb.hierarchy.root method) convert_tlso_group_info_to_lists() (in module iotbx.map_model_manager) convert_to_anisotropic() (cctbx.xray.structure.structure method) convert_to_histogram() (in module mmtbx.polygon) convert_to_isotropic() (cctbx.xray.structure.structure method) convert_to_non_anomalous() (mmtbx.maps.kick.run method) convert_to_non_anomalous_if_ratio_pairs_lone_less_than() (cctbx.miller.array method) converter_base (class in cctbx.macro_mol.rotation_parameters) coord_geom (mmtbx.ions.atom_type_flags attribute) coordinate_adaptor() (in module mmtbx.geometry.asa) coordinate_degrees_of_freedom_counts() (cctbx.xray.structure.structure method) coordinate_of() (mmtbx.geometry.indexing.structure_indexer static method) coordinate_offset() (mmtbx.ncs.ncs.ncs method) coordinate_shifts (class in mmtbx.refinement.print_statistics) coordinates() (in module cctbx.development.make_cns_input) coordinates_from_form() (in module cctbx.web.cgi_utils) COORDING_GEOMETRY (mmtbx.ions.identify.AtomProperties attribute) coot_todo() (mmtbx.validation.rotalyze.rotalyze method) (mmtbx.validation.validation method) copy() (cctbx.miller.array method) (cctbx.miller.set method) (iotbx.cif.model.cif method) (iotbx.cif.model.loop method) (libtbx.group_args method) copy_cbf_header() (in module xfel.cftbx.detector.cspad_cbf_tbx) copy_rot_trans() (mmtbx.ncs.ncs.ncs_group method) copy_selected() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) copy_to_byte_str() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) copy_to_scatterers_in_place() (cctbx.xray.scatterer.anomalous_scatterer_group method) copy_vector_list() (mmtbx.ncs.ncs.ncs_group method) core_parameters (class in scitbx.lbfgs) corners() (xfel.cxi.cspad_ana.parse_calib.Section method) corners_asic() (xfel.cxi.cspad_ana.parse_calib.Section method) correct_hydrogen_geometries() (in module mmtbx.monomer_library.correct_hydrogen_geometries) correct_sequence() (in module mmtbx.building.extend_sidechains) correct_special_position() (in module cctbx.crystal) correction_vectors (class in xfel.metrology.mark0) correlation() (cctbx.miller.array method) (in module xfel.cxi.cxi_cc) correlation_analyses (class in mmtbx.scaling.twin_analyses) cos_alpha (class in cctbx.examples.structure_factor_calculus.site_derivatives) (class in cctbx.examples.structure_factor_calculus.sites_derivatives) cos_angle() (scitbx.array_family.flex.double method) (scitbx.matrix.rec method) cos_sin_table() (cctbx.xray.structure_factors.manager.manager method) coset_lookup() (in module cctbx.sgtbx.pointgroup_tools) cosets() (in module cctbx.sgtbx.reticular_pg_tools) cosets_form() (cctbx.sgtbx.literal_description.literal_description method) count() (cctbx.sgtbx.harker.planes_cartesian method) (mmtbx.geometry.clash.ClashPoint method) (mmtbx.geometry.topology.GreedyMatch method) (mmtbx.geometry.topology.RascalMatch method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) count_and_fraction_in_bins() (cctbx.miller.array method) count_atoms_per_chain() (mmtbx.den.den_restraints method) count_coordinating_residues() (in module mmtbx.ions.utils) count_dict_values() (mmtbx.validation.test_utils method) count_non_hydrogen_atoms() (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer method) count_occupancies() (mmtbx.refinement.refinement_flags.manager method) count_rotatable() (in module mmtbx.hydrogens) counter (class in mmtbx.maps.fem) counterexamples() (in module cctbx.crystal.burzlaff_zimmermann_dewolff) counters (class in mmtbx.monomer_library.pdb_interpretation) counts() (iotbx.map_model_manager.map_model_manager method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) create() (mmtbx.geometry.clash.Case class method) (mmtbx.geometry.topology.Compound class method) create_all_new_restraints() (mmtbx.secondary_structure.manager method) create_all_subgroups() (in module cctbx.examples.maximum_subgroups) create_and_populate_indexer() (in module mmtbx.geometry.asa) create_den_manager() (cctbx.geometry_restraints.manager.manager method) create_description() (in module mmtbx.geometry.asa) create_disulfides() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) create_fine_spacing_array() (in module iotbx.map_model_manager) create_fmodel() (mmtbx.maps.fem.run method) create_helix_hydrogen_bond_proxies() (in module mmtbx.secondary_structure.proteins) create_link() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) create_manager() (in module mmtbx.ions.identify) create_map_from_pdb_and_mtz() (in module mmtbx.maps.utils) create_map_manager_with_value_list() (in module iotbx.map_model_manager) create_mask_around_atoms() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) create_mask_around_density() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) create_mask_around_edges() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) create_mask_with_map_data() (iotbx.map_manager.map_manager method) create_masked_copies_of_maps() (iotbx.map_model_manager.map_model_manager method) create_model_manager() (mmtbx.command_line.load_model_and_data method) create_omit_regions() (in module mmtbx.maps.composite_omit_map) create_plot_panel() (xfel.cxi.gfx.status_plot.StatusFrame method) (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame method) create_protein_hbond_proxies() (mmtbx.secondary_structure.manager method) create_sheet_hydrogen_bond_proxies() (in module mmtbx.secondary_structure.proteins) create_spherical_mask() (iotbx.map_model_manager.map_model_manager method) create_target_functors() (mmtbx.fmodels method) createFromText() (mmtbx.rotamer.n_dim_table.NDimTable static method) cross() (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) cross_check() (in module cctbx.eltbx.development.format_gaussian_fits) cross_correlation_cutoff_for_centring (cctbx.symmetry_search.structure_factor_symmetry attribute) cross_correlation_peaks() (cctbx.symmetry_search.structure_factor_symmetry method) cross_product_as_unit_axis() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method) cross_product_matrix() (in module scitbx.matrix) crystal() (in module dxtbx.serialize.load) crystal_density() (cctbx.xray.structure.structure method) crystal_family_symbols (cctbx.sgtbx.bravais_types.bravais_lattice attribute) crystal_gridding (class in cctbx.maptbx) crystal_gridding() (cctbx.miller.set method) (cctbx.xray.structure_factors.manager.manager method) crystal_gridding_tags (class in cctbx.maptbx) crystal_symmetry (mmtbx.command_line.load_model_and_data attribute) (mmtbx.validation.molprobity.molprobity attribute) crystal_symmetry() (cctbx.maptbx.crystal_gridding method) (cctbx.miller.set method) (cctbx.web.emma.web_to_models method) (cctbx.xray.structure.structure method) (iotbx.file_reader.any_file_input method) (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) (iotbx.xds.read_ascii.reader method) (mmtbx.refinement.tardy.potential_object method) crystal_symmetry_from_cryst1() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) crystal_symmetry_is_compatible_with_symmetry_from_file (class in cctbx.miller) crystal_symmetry_is_compatible_with_symmetry_from_file() (cctbx.miller.array method) crystal_symmetry_parser (class in iotbx.shelx.parsers) crystal_symmetry_to_ncs() (in module mmtbx.ncs.ncs) crystal_system_table (class in cctbx.web.asu_gallery.jv_index) CrystalFactory (class in dxtbx.model.crystal) crystallographic_section() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) crystfel_to_cctbx_coord_system() (in module xfel.command_line.cxi_stream_to_pickle) cspad2x2_bad_pixel_mask_cxi_run7() (in module xfel.cxi.cspad_ana.xes_finalise) CsPad2x2Image() (in module xfel.cxi.cspad_ana.cspad_tbx) cspad_unbound_pixel_mask() (in module xfel.cxi.cspad_ana.xes_finalise) CsPadDetector() (in module xfel.cxi.cspad_ana.cspad_tbx) CsPadElement() (in module xfel.cxi.cspad_ana.cspad_tbx) cubic_unit_cell_around_centered_scatterers() (cctbx.xray.structure.structure method) cull_braggs() (xfel.cxi.gfx.trials_plot.Run method) (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) cumulative_intensity_distribution (class in cctbx.statistics) curv_est_factor (cctbx.omz.dev.shift_limit_pair attribute) curv_est_shift() (cctbx.omz.dev.shift_limit_pair method) curvatures (class in cctbx.examples.g_exp_i_alpha_derivatives) (class in cctbx.examples.structure_factor_derivatives) (class in cctbx.examples.structure_factor_derivatives_2) curvatures() (cctbx.merging.brehm_diederichs.minimize method) (xfel.metrology.mark1.fit_translation method) (xfel.metrology.mark3.fit_translation2 method) curve() (mmtbx.scaling.relative_wilson.relative_wilson method) curvs (cctbx.omz.dev.xfgc_info attribute) custom_cdl_dict (class in mmtbx.conformation_dependent_library.cdl_database) custom_init() (libtbx.program_template.ProgramTemplate method) customized_copy() (cctbx.crystal.symmetry method) (cctbx.miller.array method) (cctbx.miller.set method) (cctbx.xray.structure.structure method) (in module cctbx.xray.observations) (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) cut (class in cctbx.sgtbx.direct_space_asu.cut_plane) cut_and_copy_map() (mmtbx.utils.extract_box_around_model_and_map method) cut_expr (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute) cut_expr_ops (class in cctbx.sgtbx.direct_space_asu.cut_plane) cut_expression (class in cctbx.sgtbx.direct_space_asu.cut_plane) cut_point_positions() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method) cut_points (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points attribute) cutoff_values() (in module iotbx.map_model_manager)

D

d2_alphas() (cctbx.examples.exp_i_alpha_derivatives.exp_i_alpha_sum method) d2_cos_alpha_d_site_finite() (in module cctbx.examples.structure_factor_calculus.site_derivatives) d2_cos_alpha_d_sites_finite() (in module cctbx.examples.structure_factor_calculus.sites_derivatives) d2_debye_waller_d_u_finite() (in module cctbx.examples.structure_factor_calculus.u_star_derivatives) d2_exp_i_hx_d_sites_finite() (in module cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives) d2_g_alpha_d_params() (cctbx.examples.structure_factor_derivatives.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factor method) d2_params() (cctbx.examples.g_exp_i_alpha_derivatives.g_exp_i_alpha_sum method) d2_site() (cctbx.examples.structure_factor_calculus.site_derivatives.cos_alpha method) d2_sites() (cctbx.examples.structure_factor_calculus.sites_derivatives.cos_alpha method) (cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives.exp_i_hx method) d2_target_d_alphas() (cctbx.examples.exp_i_alpha_derivatives.exp_i_alpha_sum method) d2_target_d_params() (cctbx.examples.g_exp_i_alpha_derivatives.g_exp_i_alpha_sum method) (cctbx.examples.structure_factor_derivatives.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factors method) (cctbx.examples.structure_factor_derivatives_3.structure_factor method) (cctbx.examples.structure_factor_derivatives_3.structure_factors method) (cctbx.examples.structure_factor_derivatives_4.structure_factor method) (cctbx.examples.structure_factor_derivatives_4.structure_factors method) d2_target_d_params_diag() (cctbx.examples.structure_factor_derivatives_4.structure_factor method) (cctbx.examples.structure_factor_derivatives_4.structure_factors method) d2_target_d_params_diag_cpp() (cctbx.examples.structure_factor_derivatives_4.structure_factors method) d2_target_d_sites() (cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives.exp_i_hx method) d2_u() (cctbx.examples.structure_factor_calculus.u_star_derivatives.debye_waller method) d2f_d_params() (cctbx.examples.structure_factor_derivatives_3.structure_factor method) (cctbx.examples.structure_factor_derivatives_4.structure_factor method) d2f_d_params_diag() (cctbx.examples.structure_factor_derivatives_4.structure_factor method) d99 (class in cctbx.maptbx) d_alphas() (cctbx.examples.exp_i_alpha_derivatives.exp_i_alpha_sum method) d_cos_alpha_d_site_finite() (in module cctbx.examples.structure_factor_calculus.site_derivatives) d_cos_alpha_d_sites_finite() (in module cctbx.examples.structure_factor_calculus.sites_derivatives) d_debye_waller_d_u_finite() (in module cctbx.examples.structure_factor_calculus.u_star_derivatives) d_e_pot_d_sites() (mmtbx.refinement.real_space.rigid_body.refine method) (mmtbx.refinement.tardy.potential_object method) d_exp_i_hx_d_sites_finite() (in module cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives) d_g_alpha_d_params() (cctbx.examples.structure_factor_derivatives.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factor method) d_log_p() (mmtbx.twinning.probabalistic_detwinning.detwin method) d_max (mmtbx.validation.experimental.data_statistics attribute) (mmtbx.validation.molprobity.pdb_header_info attribute) d_max_min() (cctbx.miller.set method) (mmtbx.validation.molprobity.molprobity method) d_max_outer (mmtbx.validation.experimental.data_statistics attribute) d_min (cctbx.omz.dev.dynamic_shift_limit_u_iso attribute) (mmtbx.density_modification.density_modification property) (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] (mmtbx.validation.experimental.data_statistics attribute) (mmtbx.validation.molprobity.pdb_header_info attribute) (mmtbx.validation.molprobity.summary attribute) d_min() (cctbx.maptbx.crystal_gridding method) (cctbx.miller.set method) (cctbx.xray.structure_factors.manager.manager method) (mmtbx.validation.molprobity.molprobity method) d_min_along_a_b_c_star() (cctbx.miller.set method) d_min_corner() (in module cctbx.maptbx) d_min_from_fsc() (cctbx.miller.array method) d_min_from_map() (in module cctbx.maptbx) d_min_outer (mmtbx.validation.experimental.data_statistics attribute) d_params() (cctbx.examples.g_exp_i_alpha_derivatives.g_exp_i_alpha_sum method) d_site() (cctbx.examples.structure_factor_calculus.site_derivatives.cos_alpha method) d_sites() (cctbx.examples.structure_factor_calculus.sites_derivatives.cos_alpha method) (cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives.exp_i_hx method) d_spacings() (cctbx.miller.set method) d_star_cubed() (cctbx.miller.set method) d_star_sq() (cctbx.miller.set method) d_t_d_k_overall_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) d_t_d_k_part_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) d_t_d_k_sol_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) d_t_d_twin_fraction_ref() (mmtbx.twinning.twin_f_model.twin_fraction_object method) d_t_d_u_part_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) d_t_d_u_sol_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) d_t_d_u_star_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) d_target_d_alphas() (cctbx.examples.exp_i_alpha_derivatives.exp_i_alpha_sum method) d_target_d_f_calc() (cctbx.xray.structure_factors.gradients_base.gradients_base method) d_target_d_f_calc_work() (mmtbx.refinement.targets.target_result method) (mmtbx.twinning.twin_f_model.target_result method) d_target_d_f_model_work() (mmtbx.refinement.targets.target_result method) (mmtbx.twinning.twin_f_model.target_result method) d_target_d_fdp() (cctbx.xray.structure_factors.gradients_base.gradients_base method) d_target_d_fp() (cctbx.xray.structure_factors.gradients_base.gradients_base method) d_target_d_occupancy() (cctbx.xray.structure_factors.gradients_base.gradients_base method) d_target_d_params() (cctbx.examples.g_exp_i_alpha_derivatives.g_exp_i_alpha_sum method) (cctbx.examples.structure_factor_derivatives.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factors method) (cctbx.examples.structure_factor_derivatives_3.structure_factor method) (cctbx.examples.structure_factor_derivatives_3.structure_factors method) (cctbx.examples.structure_factor_derivatives_4.structure_factor method) (cctbx.examples.structure_factor_derivatives_4.structure_factors method) d_target_d_site_cart() (cctbx.xray.structure_factors.gradients_direct.gradients_direct method) (cctbx.xray.structure_factors.gradients_fft.gradients_fft method) (mmtbx.refinement.targets.target_result_mixin method) d_target_d_site_frac() (cctbx.xray.structure_factors.gradients_direct.gradients_direct method) (cctbx.xray.structure_factors.gradients_fft.gradients_fft method) d_target_d_sites() (cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives.exp_i_hx method) d_target_d_u_cart() (cctbx.xray.structure_factors.gradients_direct.gradients_direct method) (cctbx.xray.structure_factors.gradients_fft.gradients_fft method) d_target_d_u_iso() (cctbx.xray.structure_factors.gradients_base.gradients_base method) d_target_d_u_star() (cctbx.xray.structure_factors.gradients_direct.gradients_direct method) (cctbx.xray.structure_factors.gradients_fft.gradients_fft method) d_u() (cctbx.examples.structure_factor_calculus.u_star_derivatives.debye_waller method) da() (cctbx.examples.exp_i_alpha_derivatives.least_squares method) daa() (cctbx.examples.exp_i_alpha_derivatives.least_squares method) dab() (cctbx.examples.exp_i_alpha_derivatives.least_squares method) damping_value (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping attribute) data() (cctbx.miller.array method) (mmtbx.real_space.around_atom method) (mmtbx.real_space.sampled_model_density method) (mmtbx.validation.molprobity.multi_criterion_view method) (scitbx.array_family.flex.py_object method) (xfel.command_line.convert_gain_map.fake_cspad_ElementV2 method) data_analysis (class in mmtbx.scaling) data_as_flex_arrays() (mmtbx.scaling.relative_wilson.summary method) data_at_first_index() (cctbx.miller.array method) data_of() (mmtbx.geometry.indexing.structure_indexer static method) data_offsets() (iotbx.pdb.hierarchy.atom static method) data_size (mmtbx.utils.guess_observation_type attribute) data_statistics (class in mmtbx.validation.experimental) data_stats (mmtbx.validation.molprobity.molprobity attribute) data_strength_and_completeness (class in mmtbx.scaling.data_statistics) data_summary (class in mmtbx.scaling.xtriage) data_target_and_grads() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space method) (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method) data_type() (mmtbx.twinning.twin_f_model.twin_model_manager method) data_version (mmtbx.validation.rotalyze.rotalyze attribute) db() (cctbx.examples.exp_i_alpha_derivatives.least_squares method) dbb() (cctbx.examples.exp_i_alpha_derivatives.least_squares method) de_deuterate() (iotbx.pdb.hierarchy.root method) debug_info (scitbx.lstbx.normal_eqns.non_linear_ls_with_separable_scale_factor_BLAS_2 property) debye_waller (class in cctbx.examples.structure_factor_calculus.u_star_derivatives) debye_waller_factor_u_star_curvatures() (in module cctbx.adptbx) debye_waller_factor_u_star_gradients() (in module cctbx.adptbx) debye_waller_factors() (cctbx.miller.set method) decode_atom_str() (in module mmtbx.validation.utils) decode_atom_string() (in module mmtbx.validation.clashscore) decode_one_variable() (iotbx.shelx.parsers.variable_decoder method) decode_resolve_map_coeffs() (in module mmtbx.maps.utils) decode_variables() (in module iotbx.shelx.parsers) (iotbx.shelx.parsers.variable_decoder method) decremental_fits() (in module cctbx.eltbx.gaussian_fit) deep_copy() (cctbx.miller.array method) (cctbx.miller.set method) (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.root method) (mmtbx.ias.ias method) (mmtbx.masks.manager method) (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) (mmtbx.refinement.refinement_flags.manager method) (mmtbx.twinning.twin_f_model.scaling_parameters_object method) (mmtbx.twinning.twin_f_model.twin_model_manager method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) deep_copy_ops_to_keep() (mmtbx.ncs.ncs.ncs_group method) deep_copy_order() (mmtbx.ncs.ncs.ncs_group method) deep_copy_scatterers() (cctbx.xray.structure.structure method) deepcopy() (iotbx.cif.model.cif method) (iotbx.cif.model.loop method) def_gt_0() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.gruber_parameterization method) def_test() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.gruber_parameterization method) default_2wmad() (mmtbx.scaling.make_param.phil_lego method) default_3wmad() (mmtbx.scaling.make_param.phil_lego method) default_rip() (mmtbx.scaling.make_param.phil_lego method) default_sad() (mmtbx.scaling.make_param.phil_lego method) default_sir() (mmtbx.scaling.make_param.phil_lego method) default_siras() (mmtbx.scaling.make_param.phil_lego method) define_metric() (cctbx.sgtbx.direct_space_asu.direct_space_asu method) degree_as_radians() (in module cctbx.macro_mol.rotation_parameters) degree_from_radians() (in module cctbx.macro_mol.rotation_parameters) delegating_model_matches (class in cctbx.euclidean_model_matching) delete_atom_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method) delete_index() (cctbx.miller.set method) delete_indices() (cctbx.miller.set method) delete_inv() (mmtbx.ncs.ncs.ncs_group method) delete_mask() (iotbx.map_manager.map_manager method) delete_row() (iotbx.cif.model.loop method) delrsq_functional() (xfel.metrology.mark0.correction_vectors method) delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) (mmtbx.scaling.twin_analyses.obliquity attribute) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.restraint attribute) (mmtbx.validation.rna_validate.rna_angle attribute) (mmtbx.validation.rna_validate.rna_bond attribute) delta_angle (mmtbx.validation.rna_validate.rna_pucker attribute) delta_estimation_minus_cos() (in module cctbx.omz.dev) delta_f_prime_f_double_prime_ratio (class in mmtbx.scaling.pair_analyses) delta_generator (class in mmtbx.scaling.pair_analyses) delta_le_page (mmtbx.scaling.twin_analyses.twin_law attribute) delta_le_page() (mmtbx.scaling.twin_analyses.twin_law_quality method) delta_lebedev (mmtbx.scaling.twin_analyses.twin_law attribute) delta_lebedev() (mmtbx.scaling.twin_analyses.twin_law_quality method) delta_max (mmtbx.validation.restraints.planarity attribute)

delta_santoro (mmtbx.scaling.twin_analyses.twin_law attribute) delta_santoro() (mmtbx.scaling.twin_analyses.twin_law_quality method) demo() (in module cctbx.examples.cr2o3_consistency_checks) (in module cctbx.examples.cr2o3_primitive_cell) (in module cctbx.examples.miller_common_sets) (in module cctbx.examples.site_symmetry_table) den_restraints (class in mmtbx.den) density_at_atom() (mmtbx.building.local_density_quality method) density_at_model_sites() (iotbx.map_model_manager.map_model_manager method) density_at_sites_cart() (iotbx.map_manager.map_manager method) density_calculator (class in mmtbx.scaling.matthews) density_modification (class in mmtbx.density_modification) density_truncation() (mmtbx.density_modification.density_modification method) deposition_date() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) depth1_cuts() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) derive_result_group_list() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method) Description (class in mmtbx.geometry.altloc) description (scitbx.lstbx.normal_eqns.non_linear_ls_with_separable_scale_factor_BLAS_2 property) descriptor (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) descriptor_for (mmtbx.geometry.topology.Molecule property) descriptor_for() (mmtbx.geometry.clash.ASUContent method) descriptors (mmtbx.geometry.topology.Compound property) descriptors() (mmtbx.geometry.clash.SphereModel method) det() (cctbx.macro_mol.rotation_parameters.matrix33 method) detached_copy() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_group method) (iotbx.pdb.hierarchy.atom_with_labels method) (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue_group method) detect_hydrogen_nomenclature_problem (class in mmtbx.utils) detect_outliers() (mmtbx.scaling.pair_analyses.outlier_rejection method) detect_outliers_rms() (mmtbx.scaling.pair_analyses.outlier_rejection method) detect_outliers_sigma() (mmtbx.scaling.pair_analyses.outlier_rejection method) detect_outliers_solve() (mmtbx.scaling.pair_analyses.outlier_rejection method) detect_problem() (in module libtbx.easy_mp) detect_pseudo_translations (class in mmtbx.scaling.twin_analyses) detect_sequence_disorder() (mmtbx.disorder.analyze_model.disordered_segment method) DETECTOR_NORMAL (xfel.metrology.mark0.correction_vectors attribute) detector_origin_analysis() (xfel.metrology.mark10.fit_translation4 method) DetectorFactory (class in dxtbx.model.detector) DetectorPlot (class in xfel.cxi.gfx.wx_detectors) DetectorPlotFrame (class in xfel.cxi.gfx.wx_detectors) determinant() (scitbx.matrix.rec method) determine_chemical_element_simple() (iotbx.pdb.hierarchy.atom method) determine_mean_I_mproc() (in module xfel.command_line.postrefine) determine_n_bins() (mmtbx.twinning.twin_f_model.twin_model_manager method) detwin (class in mmtbx.twinning.probabalistic_detwinning) detwin_data() (cctbx.miller.array method) (mmtbx.twinning.twin_f_model.twin_model_manager method) detwin_miller_array() (in module mmtbx.twinning.probabalistic_detwinning) developmental_algorithms() (cctbx.omz.dev.refinement method) deviation (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute) (mmtbx.validation.cbetadev.cbeta attribute) df_d_params() (cctbx.examples.structure_factor_derivatives_3.structure_factor method) (cctbx.examples.structure_factor_derivatives_4.structure_factor method) DFC (mmtbx.map_names attribute) diag (class in scitbx.matrix) dict_with_default_0 (class in libtbx) diff_map (class in mmtbx.refinement.real_space.individual_sites) difference_vectors_cart() (cctbx.xray.structure.structure method) different_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute) dihedral (class in mmtbx.validation.restraints) (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute) dihedral_angle() (in module scitbx.matrix) dihedral_angle_def (class in cctbx.crystal) dihedral_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) dihedral_deviations() (cctbx.geometry_restraints.energies.energies method) dihedral_NABB (mmtbx.validation.cbetadev.cbeta attribute) dihedral_proxy_registry (class in cctbx.geometry_restraints) dihedrals (class in mmtbx.validation.restraints) (mmtbx.validation.restraints.combined attribute) direct (cctbx.crystal_orientation.basis_type attribute) direct() (in module mmtbx.geometry.indexing) direct_space_asu (class in cctbx.crystal.direct_space_asu) (class in cctbx.sgtbx.direct_space_asu) direct_space_asu() (cctbx.crystal.symmetry method) (cctbx.sgtbx.space_group_info method) direct_summation_at_point() (cctbx.miller.array method) direct_summation_cuda_platform (class in cctbx.xray.structure_factors.from_scatterers_direct_parallel) direct_summation_simple (class in cctbx.xray.structure_factors.from_scatterers_direct_parallel) directory_input (class in iotbx.file_reader) disagreeable_reflections() (cctbx.miller.array method) discard_conflicting_pdb_element_column() (in module mmtbx.monomer_library.pdb_interpretation) discard_last() (cctbx.maptbx.peak_cluster_analysis method) discard_scattering_type_registry() (cctbx.xray.structure.structure method) discard_sigmas() (cctbx.miller.array method) discard_symmetry() (cctbx.geometry_restraints.manager.manager method) discard_table() (cctbx.geometry_restraints.proxy_registry_base method) discard_tables() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method) (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) disordered_segment (class in mmtbx.disorder.analyze_model) display() (xfel.cxi.display_spots.wrapper_of_callback method) display_all() (mmtbx.ncs.ncs.ncs method) display_calib() (in module xfel.cxi.cspad_ana.display_calib) display_r() (in module cctbx.web.change_basis) display_rt() (in module cctbx.web.change_basis) display_summary() (mmtbx.ncs.ncs.ncs_group method) display_with_callback() (xfel.cxi.display_spots.wrapper_of_callback method) display_wx_plots() (mmtbx.validation.molprobity.molprobity method) (mmtbx.validation.molprobity.multi_criterion_view method) (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.rotalyze.rotalyze method) dist2() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils) distance() (cctbx.sgtbx.harker.plane_cartesian method) (in module xfel.command_line.radial_average) (iotbx.pdb.hierarchy.atom method) (mmtbx.ions.environment.atom_contact method) distance_based_clustering (class in cctbx.crystal) distance_based_simple_two_way_bond_sets() (iotbx.pdb.hierarchy.root method) distance_from() (mmtbx.ions.environment.atom_contact method) (xfel.clustering.singleframe.SingleFrame method) distance_from_center() (mmtbx.ncs.ligands.group_operators method) distance_from_plane() (in module scitbx.matrix) distance_matrix() (scitbx.array_family.flex.vec2_double method) distance_squared() (in module mmtbx.den) DistanceCalculation (class in mmtbx.geometry.clash) distances() (cctbx.xray.structure.structure method) (mmtbx.real_space.around_atom method) distances_from() (mmtbx.geometry.topology.Compound method) distances_info (cctbx.crystal.show_distances attribute) distances_to_peaks() (in module mmtbx.hydrogens.find) distl_filter() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method) distl_hitfinder (class in xfel.cxi.cspad_ana.hitfinder_tbx) distribution_as_array() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method) distribution_as_xplor_file() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method) divisor() (in module cctbx.sgtbx.sub_lattice_tools) dm_stats (class in mmtbx.density_modification) do() (scitbx.lstbx.normal_eqns_solving.iterations method) (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations method) (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations_encapsulated_eqns method) (scitbx.lstbx.normal_eqns_solving.naive_iterations method) (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping method) (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit method) do_damping() (scitbx.lstbx.normal_eqns_solving.iterations method) do_dirty_work() (in module cctbx.development.cns_density_modification) do_photon_counting() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method) do_scale_shifts() (scitbx.lstbx.normal_eqns_solving.iterations method) do_sigma_scaling() (xfel.cxi.cspad_ana.common_mode.common_mode_correction method) dot() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) dot3() (in module cctbx.sgtbx.harker) dot6fdot() (in module cctbx.development.fmt_utils) dot6fdot_list() (in module cctbx.development.fmt_utils) dot6g_list() (in module cctbx.development.fmt_utils) dot6gdot() (in module cctbx.development.fmt_utils) dot6gdot_list() (in module cctbx.development.fmt_utils) double (class in scitbx.array_family.flex) double_cosets (class in cctbx.sgtbx.cosets) double_step_filtration() (cctbx.miller.array method) double_unique() (in module cctbx.sgtbx.cosets) dpack() (in module xfel.cxi.cspad_ana.cspad_tbx) draw() (mmtbx.polygon.output.renderer method) draw_box() (mmtbx.polygon.output.renderer method) draw_dashed_line() (mmtbx.polygon.output.renderer method) draw_filled_circle() (cctbx.command_line.precession_view.render_pil method) (cctbx.command_line.precession_view.render_postscript method) (cctbx.miller.display.render_2d method) draw_labels() (mmtbx.polygon.output.renderer method) draw_line() (cctbx.command_line.precession_view.render_pil method) (cctbx.command_line.precession_view.render_postscript method) (cctbx.miller.display.render_2d method) draw_open_circle() (cctbx.command_line.precession_view.render_pil method) (cctbx.command_line.precession_view.render_postscript method) (cctbx.miller.display.render_2d method) draw_plot() (in module xfel.cxi.gfx.status_plot) (mmtbx.rotamer.graphics.rotarama_plot_mixin method) (mmtbx.validation.graphics.rotarama_plot_mixin method) draw_plot_to_file() (in module xfel.cxi.gfx.status_plot) draw_ramachandran_plot() (in module mmtbx.rotamer.graphics) (in module mmtbx.validation.ramalyze) draw_rotamer_plot() (in module mmtbx.rotamer.graphics) (in module mmtbx.validation.rotalyze) draw_solid_line() (mmtbx.polygon.output.renderer method) draw_text() (cctbx.command_line.precession_view.render_pil method) (cctbx.command_line.precession_view.render_postscript method) (cctbx.miller.display.render_2d method) dummy_map_manager() (in module iotbx.map_manager) dummy_miller_set() (in module cctbx.development.direct_or_fft) dummy_structure() (in module cctbx.development.direct_or_fft) dummy_validation (class in mmtbx.validation) dump_as_mtz() (xfel.clustering.cluster.Cluster method) dump_den_network() (mmtbx.den.den_restraints method) dump_file_list() (xfel.clustering.cluster.Cluster method) dump_sites() (in module mmtbx.ions.svm.dump_sites) dump_statistics() (mmtbx.refinement.print_statistics.refinement_monitor method) duplicate_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) duplicate_id() (iotbx.map_model_manager.map_model_manager method) duplicate_map_manager() (iotbx.map_model_manager.map_model_manager method) dwritef() (in module xfel.cxi.cspad_ana.cspad_tbx) dwritef2() (in module xfel.cxi.cspad_ana.cspad_tbx) dxtbx.model.beam module dxtbx.model.crystal module dxtbx.model.detector module dxtbx.model.goniometer module dxtbx.model.scan module dxtbx.serialize.load module dxtbx.serialize.xds module dynamic_shift_limit_site (class in cctbx.omz.dev) dynamic_shift_limit_u_iso (class in cctbx.omz.dev)

E

e_pot() (cctbx.omz.tardy_adaptor.potential_object method) (mmtbx.refinement.tardy.potential_object method) each_abs() (scitbx.matrix.rec method) each_mod_short() (scitbx.matrix.rec method) each_normalize() (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) easy (class in mmtbx.refinement.real_space.individual_sites) edge_geometry() (in module cctbx.web.asu_gallery.jv_asu) edge_inclusive_flag (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute) edge_list (cctbx.omz.cif_refine.extract_from_cif_files attribute) (cctbx.omz.cod_select_and_pickle.cod_data attribute) edge_object (class in cctbx.sgtbx.pointgroup_tools) edge_position() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) edge_segment (class in cctbx.sgtbx.direct_space_asu.facet_analysis) edge_with_cut_points (class in cctbx.sgtbx.direct_space_asu.facet_analysis) edit_blank_altloc() (iotbx.pdb.hierarchy.residue_group method) effective_resolution() (cctbx.maptbx.peak_cluster_analysis method) (cctbx.maptbx.peak_search_parameters method) eight_point_interpolation() (scitbx.array_family.flex.double method) eight_point_interpolation_with_gradients() (scitbx.array_family.flex.double method) electron_density_map() (mmtbx.twinning.twin_f_model.twin_model_manager method) element (iotbx.pdb.hierarchy.atom property) (iotbx.shelx.tokens.element_token attribute) (mmtbx.ions.environment.atom_contact attribute), [1] (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.waters.water attribute) element_is_hydrogen() (iotbx.pdb.hierarchy.atom method) element_is_ion() (iotbx.pdb.hierarchy.atom method) element_is_negative_ion() (iotbx.pdb.hierarchy.atom method) element_is_positive_ion() (iotbx.pdb.hierarchy.atom method) element_of() (in module mmtbx.geometry.clash) element_selection() (cctbx.xray.structure.structure method) element_size() (scitbx.array_family.flex.bool static method) (scitbx.array_family.flex.complex_double static method) (scitbx.array_family.flex.double static method) (scitbx.array_family.flex.float static method) (scitbx.array_family.flex.int static method) (scitbx.array_family.flex.long static method) (scitbx.array_family.flex.size_t static method) (scitbx.array_family.flex.std_string static method) (scitbx.array_family.flex.sym_mat3_double static method) (scitbx.array_family.flex.vec2_double static method) (scitbx.array_family.flex.vec3_double static method) (scitbx.array_family.flex.vec3_int static method) element_token (class in iotbx.shelx.tokens) ElementAccumulator (class in mmtbx.geometry.clash) elements() (mmtbx.geometry.clash.Model method) eliminate_outside_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) eliminate_sys_absent() (cctbx.miller.array method) eliminate_weak_pairs() (cctbx.euclidean_model_matching.match_refine method) ellipsoidal_resolutions_and_indices_by_sigma() (cctbx.miller.array method) ellipsoidal_truncation_by_sigma() (cctbx.miller.array method) empirical_proof() (in module cctbx.examples.g_exp_i_partial_derivatives) empty (class in cctbx.geometry_restraints.lbfgs) (class in cctbx.sgtbx) (class in cctbx.statistics) (class in cctbx.web.cgi_utils) (class in cctbx.web.replay) (class in mmtbx.chemical_components.cif_parser) (class in mmtbx.monomer_library.linking_utils) (class in xfel.cxi.display_spots) Empty() (in module mmtbx.geometry.altloc) enable_multiprocessing_if_possible() (in module libtbx.easy_mp) end_points (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points attribute) endjob() (xfel.cxi.cspad_ana.average_tbx.average_mixin method) (xfel.cxi.cspad_ana.common_mode.common_mode_correction method) (xfel.cxi.cspad_ana.mod_average.mod_average method) (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method) (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method) (xfel.cxi.cspad_ana.mod_filter.mod_filter method) (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method) (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method) (xfel.cxi.cspad_ana.mod_mar.mod_mar method) (xfel.cxi.cspad_ana.mod_param.mod_param method) (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method) (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method) (xfel.cxi.cspad_ana.mod_xes.mod_xes method) (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method) ener_lib (class in mmtbx.monomer_library.server) ener_lib_as_nonbonded_params() (in module mmtbx.monomer_library.pdb_interpretation) energies (class in cctbx.adp_restraints.energies) (class in cctbx.geometry_restraints.energies) energies_iso (class in cctbx.adp_restraints) energies_sites() (cctbx.geometry_restraints.manager.manager method) energy_lib_atom (class in mmtbx.monomer_library.cif_types) energy_lib_synonym (class in mmtbx.monomer_library.cif_types) energy_lib_vdw (class in mmtbx.monomer_library.cif_types) enforce_positive_amplitudes() (cctbx.miller.array method) enforce_positive_sigmas() (cctbx.miller.array method) ensemble_generator (class in mmtbx.tls.tls_as_xyz) ensemble_mean_geometry_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) ensemble_mean_hierarchy() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils) ensemble_reduction() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) ensemble_rmsf_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) ensembler (class in mmtbx.building.make_library) enter_block() (cctbx.eltbx.development.itvc_section61_io.table6111 method) enter_entry() (cctbx.eltbx.development.itvc_section61_io.table6111 method) entier() (in module cctbx.uctbx.gruber_1973) entities (mmtbx.geometry.altloc.Aggregator property) entity (class in mmtbx.validation) enumerate_reduced_cell_two_folds() (in module cctbx.examples.le_page_1982_vs_lebedev_2005) env_distance() (in module xfel.cxi.cspad_ana.cspad_tbx) env_dxtbx_from_slac_metrology() (in module xfel.cftbx.detector.cspad_cbf_tbx) env_injector_xyz() (in module xfel.cxi.cspad_ana.cspad_tbx) env_laser_status() (in module xfel.cxi.cspad_ana.cspad_tbx) env_sifoil() (in module xfel.cxi.cspad_ana.cspad_tbx) env_wavelength_sxr() (in module xfel.cxi.cspad_ana.cspad_tbx) eobs_and_ecalc_miller_array_normalizers() (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method) eps_eq() (cctbx.uctbx.reduction_base.gruber_parameterization method) (cctbx.uctbx.reduction_base.minimum_reduction_mixin method) eps_gt() (cctbx.uctbx.reduction_base.gruber_parameterization method) eps_lt() (cctbx.uctbx.reduction_base.gruber_parameterization method) epsilon (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) epsilon_angle (mmtbx.validation.rna_validate.rna_pucker attribute) epsilons() (cctbx.miller.set method) equal() (cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria method) equal_penalty() (cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria method) equivalent_sigma_from_cumulative_histogram_match() (in module mmtbx.utils) erase_scatterers() (cctbx.xray.structure.structure method) error() (mmtbx.map_names method) error_count() (iotbx.cif.reader method) error_strs (mmtbx.ions.identify.AtomProperties attribute) errors() (iotbx.pdb.hierarchy.overall_counts method) errors_and_warnings() (iotbx.pdb.hierarchy.overall_counts method) escape() (in module cctbx.web.multiple_cell) esd_as_weight() (in module mmtbx.monomer_library.cif_types) estimate_d_min() (mmtbx.scaling.xtriage.xtriage_analyses method) estimate_scale_k1() (mmtbx.bulk_solvent.scaler.run method) estimate_signal_to_noise() (in module xfel.command_line.overlay_spectra) (in module xfel.command_line.smooth_spectrum) euclidean_match_symmetry (class in cctbx.euclidean_model_matching) euler_frac_to_rot_trans() (in module mmtbx.ncs.ncs) eval_logs() (in module cctbx.omz.eval_iso_vs_refined) eval_residue_completeness() (in module mmtbx.rotamer.rotamer_eval) eval_sidechain_completeness() (in module mmtbx.rotamer.rotamer_eval) evalScore() (mmtbx.validation.ramalyze.ramalyze static method) evaluate (class in mmtbx.monomer_library.rna_sugar_pucker_analysis) evaluate() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) (mmtbx.rotamer.ramachandran_eval.RamachandranEval method) (mmtbx.rotamer.rotamer_eval.RotamerEval method) evaluate_after_end() (mmtbx.refinement.rigid_body.manager method) evaluate_backrub_pair_impl() (in module mmtbx.disorder.backbone) evaluate_model (class in mmtbx.refinement.select_best_starting_model) evaluate_model() (mmtbx.refinement.select_best_starting_model.select_model method) evaluate_registry_process_result() (in module mmtbx.monomer_library.pdb_interpretation) evaluate_residue() (in module mmtbx.validation.rotalyze) (mmtbx.rotamer.rotamer_eval.RotamerEval method) (mmtbx.validation.rotalyze.residue_evaluator method) evaluate_residue_2() (mmtbx.rotamer.rotamer_eval.RotamerEval method) evaluate_rotamer() (in module mmtbx.validation.rotalyze) evaluate_sites() (mmtbx.rotamer.ramachandran_eval.RamachandranEval method) evaluateScore() (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.rotalyze.rotalyze method) evaluation (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) event() (xfel.cxi.cspad_ana.average_tbx.average_mixin method) (xfel.cxi.cspad_ana.common_mode.common_mode_correction method) (xfel.cxi.cspad_ana.mod_average.mod_average method) (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method) (xfel.cxi.cspad_ana.mod_dump.mod_dump method) (xfel.cxi.cspad_ana.mod_dump_bitmap.mod_dump_bitmap method) (xfel.cxi.cspad_ana.mod_event_info.mod_event_info method) (xfel.cxi.cspad_ana.mod_filter.mod_filter method) (xfel.cxi.cspad_ana.mod_hdf5.mod_hdf5 method) (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method) (xfel.cxi.cspad_ana.mod_illumination_filter.mod_illumination_filter method) (xfel.cxi.cspad_ana.mod_mar.mod_mar method) (xfel.cxi.cspad_ana.mod_param.mod_param method) (xfel.cxi.cspad_ana.mod_pulnix_dump.mod_pulnix_dump method) (xfel.cxi.cspad_ana.mod_radial_average.mod_radial_average method) (xfel.cxi.cspad_ana.mod_xes.mod_xes method) (xfel.cxi.cspad_ana.pixel_histograms.pixel_histograms method) everything (mmtbx.validation.experimental.real_space attribute) evt_beam_charge() (in module xfel.cxi.cspad_ana.cspad_tbx) evt_get_quads() (in module xfel.cxi.cspad_ana.cspad_tbx) evt_pulse_energy() (in module xfel.cxi.cspad_ana.cspad_tbx) evt_pulse_length() (in module xfel.cxi.cspad_ana.cspad_tbx) evt_repetition_rate() (in module xfel.cxi.cspad_ana.cspad_tbx) evt_seqno() (in module xfel.cxi.cspad_ana.cspad_tbx) evt_time() (in module xfel.cxi.cspad_ana.cspad_tbx) evt_timestamp() (in module xfel.cxi.cspad_ana.cspad_tbx) evt_wavelength() (in module xfel.cxi.cspad_ana.cspad_tbx) exact_density() (cctbx.maptbx.atom_curves method) exact_density_at_r() (cctbx.maptbx.atom_curves method)

exact_gradient_at_r() (cctbx.maptbx.atom_curves method) examine_model() (mmtbx.building.make_library.extract_related_models method) examples() (in module cctbx.examples.steve_collins) exception_handling_parameters (class in scitbx.lbfgs) exchangeable_hd_selections() (iotbx.pdb.hierarchy.root method) exclude() (mmtbx.geometry.indexing.containment_predicate static method) exclude_outliers_from_reference_restraints_selection() (in module mmtbx.geometry_restraints.reference) exclude_pairs() (cctbx.euclidean_model_matching.match_refine method) exclude_predicate() (mmtbx.geometry.indexing.structure_indexer class method) exclusion() (mmtbx.geometry.indexing.containment_predicate class method) exclusive_or() (scitbx.array_family.flex.bool method) exercise() (in module cctbx.crystal.find_best_cell) (in module cctbx.development.make_cns_input) (in module cctbx.development.run_shelx) (in module cctbx.development.run_shelx76) (in module cctbx.examples.g_exp_i_partial_derivatives) (in module cctbx.examples.miller_transform) (in module cctbx.examples.structure_factor_calculus.site_derivatives) (in module cctbx.examples.structure_factor_calculus.sites_derivatives) (in module cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives) (in module cctbx.examples.structure_factor_calculus.u_star_derivatives) (in module cctbx.sgtbx.bravais_types) (in module cctbx.sgtbx.reticular_twin_laws) (in module cctbx.sgtbx.sub_lattice_tools) (in module mmtbx.den.plot_weights) (in module mmtbx.maps.superpose) (in module mmtbx.rotamer.rotamer_eval) (in module mmtbx.scaling.matthews) (in module mmtbx.scaling.thorough_outlier_test) (in module mmtbx.validation.utils) exercise_alternative() (in module cctbx.crystal.find_best_cell) exercise_triple() (in module scitbx.array_family.flex) exp_i_alpha_sum (class in cctbx.examples.exp_i_alpha_derivatives) exp_i_hx (class in cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives) exp_table_one_over_step_size() (cctbx.xray.structure_factors.manager.manager method) expand (class in mmtbx.refinement.orca) expand() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method) (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method) expand_angle_proxies() (in module mmtbx.refinement.orca) expand_bond_params_table() (in module mmtbx.refinement.orca) expand_dihedral_or_chirality_proxies() (in module mmtbx.refinement.orca) expand_mask() (iotbx.map_model_manager.map_model_manager method) expand_model_or_conformer_indices() (in module mmtbx.refinement.orca) expand_nonbonded_types() (in module mmtbx.refinement.orca) expand_pair_sym_table() (in module mmtbx.refinement.orca) expand_planarity_proxies() (in module mmtbx.refinement.orca) expand_shelx_latt() (in module cctbx.web.explore_symmetry) expand_site_symmetry_table() (in module mmtbx.refinement.orca) expand_to_p1() (cctbx.crystal.symmetry method) (cctbx.euclidean_model_matching.model method) (cctbx.miller.array method) (cctbx.miller.set method) (cctbx.xray.structure.structure method) (iotbx.pdb.hierarchy.root method) expand_to_p1_iselection() (cctbx.miller.set method) expand_with_ncs() (cctbx.geometry_restraints.angle_proxy_registry method) (cctbx.geometry_restraints.bond_simple_proxy_registry method) (cctbx.geometry_restraints.chirality_proxy_registry method) (cctbx.geometry_restraints.dihedral_proxy_registry method) (cctbx.geometry_restraints.parallelity_proxy_registry method) (cctbx.geometry_restraints.planarity_proxy_registry method) (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method) (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) expected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) expected_intensity (class in mmtbx.scaling.absolute_scaling) expected_labels() (in module cctbx.eltbx.development.format_gaussian_fits) experiment_list() (in module dxtbx.serialize.load) experiment_type() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) experimental_data_target_and_gradients (class in mmtbx.utils) explain_members() (mmtbx.twinning.twin_f_model.twin_model_manager method) export() (mmtbx.twinning.twin_f_model.twin_model_manager method) export_as_cns_hkl() (cctbx.miller.array method) export_as_scalepack_unmerged() (cctbx.miller.array method) export_as_shelx_hklf() (cctbx.miller.array method) export_f_obs_flags_as_mtz() (mmtbx.twinning.twin_f_model.twin_model_manager method) export_molprobity_result_as_kinemage() (in module mmtbx.kinemage.validation) export_r_free_flags_for_ccp4() (in module cctbx.r_free_utils) export_r_free_flags_for_shelx() (in module cctbx.r_free_utils) export_ramachandran_distribution() (in module mmtbx.validation.utils) export_rotamer_distribution() (in module mmtbx.validation.utils) export_to() (in module scitbx.array_family.flex) extend() (cctbx.web.asu_gallery.jvx.pointSet method) (iotbx.pdb.hierarchy.af_shared_atom method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) extend_and_refine (class in mmtbx.building.extend_sidechains) extend_flags() (in module cctbx.r_free_utils) extend_helix_operators() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) extend_protein_model() (in module mmtbx.building.extend_sidechains) extend_residue() (in module mmtbx.building.extend_sidechains) extent (mmtbx.rotamer.graphics.ramachandran_plot_mixin attribute) (mmtbx.rotamer.graphics.rotarama_plot_mixin attribute) (mmtbx.validation.graphics.rotarama_plot_mixin attribute) (mmtbx.validation.ramalyze.ramachandran_plot_mixin attribute) external_origin_as_grid_units() (iotbx.map_manager.map_manager method) external_origin_is_compatible_with_gridding() (iotbx.map_manager.map_manager method) external_sharpen() (iotbx.map_model_manager.map_model_manager method) extra_operators() (in module cctbx.sgtbx.reticular_pg_tools) extract_all_cuts() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method) (cctbx.sgtbx.direct_space_asu.direct_space_asu method) extract_all_maps_around_density() (iotbx.map_model_manager.map_model_manager method) extract_all_maps_around_mask() (iotbx.map_model_manager.map_model_manager method) extract_all_maps_around_model() (iotbx.map_model_manager.map_model_manager method) extract_all_maps_around_unique() (iotbx.map_model_manager.map_model_manager method) extract_all_maps_with_bounds() (iotbx.map_model_manager.map_model_manager method) extract_and_superpose() (in module mmtbx.building.make_library) extract_atoms_from_residue_group() (in module mmtbx.validation.cbetadev) extract_authors() (iotbx.pdb.ext.input method) extract_b() (iotbx.pdb.hierarchy.af_shared_atom method) (mmtbx.disorder.analyze_model.atoms_proxy method) extract_backrub_residue_groups() (in module mmtbx.disorder.backbone) extract_block() (scitbx.matrix.rec method) extract_bonds_to_omit() (in module mmtbx.monomer_library.rotamer_utils) extract_box_around_model_and_map (class in mmtbx.utils) extract_chi_atoms() (mmtbx.rotamer.sidechain_angles.SidechainAngles method) extract_connectivity() (iotbx.pdb.ext.input method) extract_coordinates() (mmtbx.validation.sequence.chain method) extract_cryst1_z_columns() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) extract_element() (iotbx.pdb.hierarchy.af_shared_atom method) extract_f_model_core_constants() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) extract_fdp() (iotbx.pdb.hierarchy.af_shared_atom method) extract_fp() (iotbx.pdb.hierarchy.af_shared_atom method) extract_from() (in module iotbx.shelx.crystal_symmetry_from_ins) extract_from_cif_files (class in cctbx.omz.cif_refine) extract_from_scatterers_in_place() (cctbx.xray.scatterer.anomalous_scatterer_group method) extract_header_year() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) extract_hetero() (iotbx.pdb.hierarchy.af_shared_atom method) extract_hoh_peaks() (in module mmtbx.hydrogens.find) extract_i_seq() (iotbx.pdb.hierarchy.af_shared_atom method) extract_ias (class in mmtbx.ias) extract_iselection() (in module mmtbx.building) extract_ligand_atom_group() (in module mmtbx.validation.ligands) extract_ligand_residue() (in module mmtbx.validation.ligands) extract_ligand_residues() (in module mmtbx.ncs.ligands) extract_LINK_records() (iotbx.pdb.ext.input method) extract_loggraph() (mmtbx.density_modification.dm_stats method) extract_map_coeffs() (in module mmtbx.maps.utils) extract_name() (iotbx.pdb.hierarchy.af_shared_atom method) extract_occ() (iotbx.pdb.hierarchy.af_shared_atom method) (mmtbx.disorder.analyze_model.atoms_proxy method) extract_partial_occupancy_selections() (in module mmtbx.refinement.occupancies) extract_peptide_fragments_by_sequence() (in module mmtbx.building.make_library) extract_phenix_refine_map_coeffs() (in module mmtbx.maps.utils) extract_point_group_symmetry() (mmtbx.ncs.ncs.ncs_group method) extract_polygon_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) extract_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) extract_related_models (class in mmtbx.building.make_library) extract_remark_iii_records() (iotbx.pdb.ext.input method) extract_residue_groups() (mmtbx.validation.sequence.chain method) extract_secondary_structure() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) extract_segid() (iotbx.pdb.hierarchy.af_shared_atom method) extract_serial() (iotbx.pdb.hierarchy.af_shared_atom method) extract_sigb() (iotbx.pdb.hierarchy.af_shared_atom method) extract_sigocc() (iotbx.pdb.hierarchy.af_shared_atom method) extract_sigxyz() (iotbx.pdb.hierarchy.af_shared_atom method) extract_tls_and_u_total_from_pdb() (in module mmtbx.utils) extract_tls_from_pdb() (in module mmtbx.tls.tools) extract_tls_params() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) extract_tmp_as_size_t() (iotbx.pdb.hierarchy.af_shared_atom method) extract_u_cart_plus_u_iso() (cctbx.xray.structure.structure method) extract_u_iso_or_u_equiv() (cctbx.xray.structure.structure method) extract_uij() (iotbx.pdb.hierarchy.af_shared_atom method) extract_validation_results() (mmtbx.disorder.analyze_model.disordered_segment method) extract_wavelength() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) extract_xray_structure() (iotbx.pdb.hierarchy.root method) (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) extract_xyz() (iotbx.pdb.hierarchy.af_shared_atom method) extreme_wilson_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)

F

f() (cctbx.examples.exp_i_alpha_derivatives.exp_i_alpha_sum method) (cctbx.examples.exp_i_alpha_derivatives.least_squares method) (cctbx.examples.g_exp_i_alpha_derivatives.g_exp_i_alpha_sum method) (cctbx.examples.structure_factor_calculus.site_derivatives.cos_alpha method) (cctbx.examples.structure_factor_calculus.sites_derivatives.cos_alpha method) (cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives.exp_i_hx method) (cctbx.examples.structure_factor_calculus.u_star_derivatives.debye_waller method) (cctbx.examples.structure_factor_derivatives.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factor method) (cctbx.examples.structure_factor_derivatives_2.structure_factors method) (cctbx.examples.structure_factor_derivatives_3.structure_factor method) (cctbx.examples.structure_factor_derivatives_3.structure_factors method) (cctbx.examples.structure_factor_derivatives_4.structure_factor method) (cctbx.examples.structure_factor_derivatives_4.structure_factors method) f_000 (class in mmtbx.utils) f_000() (cctbx.xray.structure.structure method) f_as_f_sq() (cctbx.miller.array method) f_bulk() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_bulk_t() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_bulk_w() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_calc() (cctbx.xray.structure_factors.from_scatterers_direct.from_scatterers_direct method) (cctbx.xray.structure_factors.from_scatterers_direct_parallel.fcalc_container method) (cctbx.xray.structure_factors.from_scatterers_fft.from_scatterers_fft method) (mmtbx.twinning.twin_f_model.twin_model_manager method) f_calc_t() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_calc_w() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_double_prime_ratio (class in mmtbx.scaling.pair_analyses) f_mask() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_mask_t() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_mask_w() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_model() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_model_example() (in module cctbx.examples.f_model_example) f_model_scaled_with_k1_composite_work_free() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_model_t() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_model_w() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_obs (mmtbx.command_line.load_model_and_data attribute) f_obs() (cctbx.xray.target_functors.intensity_correlation method) (cctbx.xray.target_functors.unified_least_squares_residual method) (mmtbx.twinning.twin_f_model.twin_model_manager method) f_obs_active (mmtbx.density_modification.density_modification property) f_obs_and_f_calc_agree_well() (cctbx.omz.cod_select_and_pickle.cod_data method) f_obs_f_calc_fan_outlier_selection() (cctbx.miller.array method) f_obs_filled (mmtbx.map_names attribute) f_obs_minus_f_calc() (cctbx.miller.array method) f_obs_minus_xray_structure_f_calc() (cctbx.miller.set method) f_obs_work() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_ordered_solvent() (in module mmtbx.max_lik.max_like_non_uniform) f_part1() (mmtbx.twinning.twin_f_model.twin_model_manager method) f_sq_as_f() (cctbx.miller.array method) f_w_binning() (in module cctbx.french_wilson) fab_elbow_angle (class in mmtbx.utils.fab_elbow_angle) face (class in cctbx.web.asu_gallery.jvx) face_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) face_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) faceSet (class in cctbx.web.asu_gallery.jvx) fake_config (class in xfel.command_line.convert_gain_map) fake_cspad_ElementV2 (class in xfel.command_line.convert_gain_map) fake_env (class in xfel.command_line.convert_gain_map) fake_evt (class in xfel.command_line.convert_gain_map) fake_get_config() (in module xfel.command_line.convert_gain_map) fast (mmtbx.validation.clashscore.clashscore attribute) fast_maps_from_hkl_file (class in mmtbx.maps.utils) fast_minimum_reduction (class in cctbx.uctbx.gruber_1973) fatal_problems_message() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) fatal_problems_report() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) fav_percent (mmtbx.validation.ramalyze.ramalyze attribute) fb_bulk() (mmtbx.twinning.twin_f_model.twin_model_manager method) fb_bulk_t() (mmtbx.twinning.twin_f_model.twin_model_manager method) fb_bulk_w() (mmtbx.twinning.twin_f_model.twin_model_manager method) FC (mmtbx.map_names attribute) fcalc_container (class in cctbx.xray.structure_factors.from_scatterers_direct_parallel) fcalc_from_distribution() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method) fdp (iotbx.pdb.hierarchy.atom property) fetch_labels() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_with_labels method) fetch_pdb_data() (in module mmtbx.wwpdb.utils) fetch_similar_pdb_ids() (in module mmtbx.building.make_library) fft_map (class in cctbx.miller) fft_map() (cctbx.miller.array method) fft_vs_direct() (mmtbx.twinning.twin_f_model.twin_model_manager method) figures_of_merit() (mmtbx.twinning.twin_f_model.twin_model_manager method) figures_of_merit_() (in module mmtbx.max_lik.maxlik) figures_of_merit_t() (mmtbx.twinning.twin_f_model.twin_model_manager method) figures_of_merit_work() (mmtbx.twinning.twin_f_model.twin_model_manager method) file() (cctbx.web.cgi_utils.server_info method) file_content (iotbx.file_reader.any_file_input property) file_content() (iotbx.reflection_file_reader.any_reflection_file method) file_info() (iotbx.file_reader.any_file_input method) (iotbx.file_reader.directory_input method) file_name (iotbx.file_reader.any_file_input property) (mmtbx.validation.molprobity.molprobity attribute) file_name() (iotbx.reflection_file_reader.any_reflection_file method) file_object (iotbx.file_reader.any_file_input property) file_server (iotbx.file_reader.any_file_input property) file_type (iotbx.file_reader.any_file_input property) file_type() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) (iotbx.reflection_file_reader.any_reflection_file method) fill() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) FILLED (mmtbx.map_names attribute) filter() (in module mmtbx.geometry.indexing) (scitbx.lbfgs.exception_handling_parameters method) filter_and_convert() (in module mmtbx.polygon) filter_by_distance() (in module mmtbx.solvent.ordered_solvent) filter_dicts() (mmtbx.validation.clashscore.probe_clashscore_manager method) filter_indices() (scitbx.array_family.flex.bool method) filter_negative_intensities() (xfel.clustering.singleframe.SingleFrame method) filter_outlying_pixels() (in module xfel.cxi.cspad_ana.xes_finalise) filter_pdb_file (class in mmtbx.wwpdb.utils) filter_shift() (cctbx.euclidean_model_matching.euclidean_match_symmetry method) (in module cctbx.euclidean_model_matching) filter_svm_outputs() (in module mmtbx.ions.svm.utils) filtered_commands() (iotbx.shelx.parsers.afix_parser method) (iotbx.shelx.parsers.atom_parser method) (iotbx.shelx.parsers.crystal_symmetry_parser method) (iotbx.shelx.parsers.instruction_parser method) (iotbx.shelx.parsers.restraint_parser method) (iotbx.shelx.parsers.wavelength_parser method) final_choice (mmtbx.ions.svm.svm_prediction attribute), [1] finalise_one_run (class in xfel.cxi.cspad_ana.histogram_finalise) (class in xfel.cxi.cspad_ana.xes_finalise) finalize() (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method) (mmtbx.refinement.real_space.fit_residue.monitor method) finalize_and_save_data() (xfel.command_line.cxi_merge.scaling_manager method) finalize_target_and_gradients() (cctbx.adp_restraints.energies.energies method) find_absent_indices() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method) find_all_conformers (class in mmtbx.refinement.real_space.fit_residue) find_and_build_ions() (in module mmtbx.ions.build) find_anomalous_scatterer_groups() (in module mmtbx.refinement.anomalous_scatterer_groups) find_anomalous_scatterers() (in module mmtbx.ions.identify) find_approximate_helices() (mmtbx.secondary_structure.manager method) find_atom_by() (iotbx.pdb.hierarchy.residue method) find_atom_group() (mmtbx.validation.validation method) find_atom_group_index() (iotbx.pdb.hierarchy.residue_group method) find_atom_index() (iotbx.pdb.hierarchy.atom_group method) find_atom_pairs() (mmtbx.den.den_restraints method) find_automatically() (mmtbx.secondary_structure.manager method) find_backrubs() (in module mmtbx.disorder.backbone) find_base_pairs() (mmtbx.secondary_structure.manager method) find_best() (mmtbx.utils.guess_observation_type method) find_best_cell (class in cctbx.crystal.find_best_cell) find_centring_translations() (cctbx.symmetry_search.structure_factor_symmetry method) find_chain_index() (iotbx.pdb.hierarchy.model method) find_closest_base_name() (in module iotbx.file_reader) find_compatible_space_groups (class in cctbx.sgtbx.pointgroup_tools) find_coordination_geometry() (in module mmtbx.ions.geometry) find_data_arrays() (in module mmtbx.wwpdb.utils) find_data_dir() (in module mmtbx.chemical_components) find_distances() (in module cctbx.examples.find_distances_using_cpp_objects) find_ensemble_backrubs() (in module mmtbx.disorder.backbone) find_helices_simple (class in mmtbx.secondary_structure.proteins) find_hydrogen_peaks() (in module mmtbx.hydrogens.find) find_it() (cctbx.crystal.find_best_cell.alternative_find_best_cell method) find_k_sol_b_sol() (iotbx.map_model_manager.map_model_manager method) find_left_over_symops() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method) find_logs() (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame method) find_map_symmetry() (iotbx.map_manager.map_manager method) find_maximum() (mmtbx.scaling.twin_analyses.correlation_analyses method) find_missing_atoms() (mmtbx.validation.molprobity.molprobity method) find_model_index() (iotbx.pdb.hierarchy.root method) find_mon_lib_file() (in module mmtbx.monomer_library.server) find_n_highest_grid_points_as_sites_cart() (iotbx.map_manager.map_manager method) find_ncs_in_hierarchy() (in module mmtbx.ncs.ncs_search) find_nearby_atoms() (in module mmtbx.ions.environment) (mmtbx.ions.identify.manager method) find_node() (in module cctbx.crystal.coordination_sequences) find_overlapping_selections() (in module mmtbx.utils) find_peak() (in module mmtbx.refinement.real_space.fit_residue) (mmtbx.ias.find_peak_at_bond method) find_peak_at_bond (class in mmtbx.ias) find_peaks() (mmtbx.solvent.ensemble_ordered_solvent.manager method) find_peptide_flips() (mmtbx.disorder.analyze_model.disordered_segment method) find_pure_altloc_ranges() (iotbx.pdb.hierarchy.chain method) find_region_max_value() (in module mmtbx.validation.ramalyze) find_residue() (mmtbx.validation.validation method) find_residue_group_index() (iotbx.pdb.hierarchy.chain method) find_rotarama_data_dir() (in module mmtbx.rotamer.rotamer_eval) find_row() (iotbx.cif.model.loop method) find_sec_str() (mmtbx.secondary_structure.manager method) find_sequence_mismatches() (in module mmtbx.validation.utils) find_similar_chains() (in module mmtbx.building.make_library) find_source_dir() (in module mmtbx.rotamer.sidechain_angles) (mmtbx.rotamer.rotamer_eval.RotamerID method) find_space_group() (cctbx.symmetry_search.structure_factor_symmetry method) find_triples() (in module cctbx.sgtbx.sub_lattice_tools) find_triples_slowly() (in module cctbx.sgtbx.sub_lattice_tools) find_version() (iotbx.xds.xparm.reader static method) finish_job() (in module mmtbx.maps.fobs_minus_fobs_map) (in module mmtbx.scaling.xtriage) finite_difference_test() (mmtbx.refinement.group.group_minimizer method) (mmtbx.refinement.minimization_ncs_constraints.lbfgs method) finite_differences_grads_of_xray_target_wrt_tls() (in module mmtbx.tls.tools) first_chain_id() (iotbx.pdb.hierarchy.root method) first_index() (cctbx.miller.set method) first_moment_analysis (class in xfel.cxi.cspad_ana.xes_finalise) first_resseq_as_int() (iotbx.pdb.hierarchy.root method) fit_backbone() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method) fit_c_beta() (mmtbx.refinement.real_space.fit_residue.run method) fit_gaussian() (in module mmtbx.ions.utils) fit_input (class in cctbx.eltbx.development.hydrogen_plots) fit_one_histogram() (xfel.command_line.view_pixel_histograms.pixel_histograms method) fit_parameters (class in cctbx.eltbx.gaussian_fit) fit_proline() (mmtbx.refinement.real_space.fit_residue.run method) fit_residue_in_box() (mmtbx.building.box_build_refine_base method) fit_rotamers() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method) fit_rotatable() (in module mmtbx.hydrogens) fit_rotatable2() (in module mmtbx.hydrogens) fit_side_chain() (mmtbx.refinement.real_space.fit_residue.run method)

fit_translation (class in xfel.metrology.mark1) fit_translation2 (class in xfel.metrology.mark3) fit_translation4 (class in xfel.metrology.mark10) fit_water() (in module mmtbx.hydrogens.find) fits_in_pdb_format() (iotbx.pdb.hierarchy.root method) fitted_gaussian (class in cctbx.eltbx.xray_scattering) FIX() (in module cctbx.development.run_shelx) fix_altlocs_and_filter() (in module mmtbx.solvent.ordered_solvent) fixed_site_indices() (cctbx.maptbx.peak_cluster_analysis method) flag_names_and_labels (mmtbx.ions.atom_type_flags attribute) flags (class in cctbx.adp_restraints.flags) (class in cctbx.geometry_restraints.flags) (scitbx.array_family.flex.smart_selection property) flatten() (in module mmtbx.refinement.real_space) (in module mmtbx.refinement.real_space.fit_residue) flip_atoms_in_ncs_groups() (in module mmtbx.ncs.ncs_utils) flip_symmetric_amino_acids() (iotbx.pdb.hierarchy.root method) float (class in scitbx.array_family.flex) flush() (mmtbx.scaling.xtriage_output method) flush_log() (in module mmtbx.monomer_library.pdb_interpretation) fmod_positive() (in module cctbx.macro_mol.rotation_parameters) fmodel (mmtbx.command_line.load_model_and_data attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.waters.water attribute) fmodel_from_xray_structure (class in mmtbx.utils) fmodel_manager() (in module mmtbx.utils) fmodel_manager2() (in module mmtbx.utils) fmodel_neutron (mmtbx.fmodels attribute) fmodel_neutron() (mmtbx.fmodels method) fmodel_simple() (in module mmtbx.utils) fmodel_statistics_by_resolution() (mmtbx.validation.molprobity.molprobity method) fmodel_statistics_graph_data() (mmtbx.validation.molprobity.molprobity method) fmodel_xray (mmtbx.fmodels attribute) fmodel_xray() (mmtbx.fmodels method) fmodels (class in mmtbx) fmt3vec (cctbx.symmetry_search.possible_symmetry attribute) fmt_nums() (in module cctbx.web.change_basis) FO (mmtbx.map_names attribute) fo_density (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] fo_fc_alpha_over_eps_beta() (in module mmtbx.max_lik.maxlik) fo_minus_fo_master_params() (in module mmtbx.maps.fobs_minus_fobs_map) focus() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) focus_size_1d() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) fofc (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.waters.water attribute) fofc_density (mmtbx.ions.environment.ScatteringEnvironment attribute) FOFC_HOLE (mmtbx.ions.identify.AtomProperties attribute) fofc_map() (mmtbx.twinning.twin_f_model.twin_model_manager method) fofc_max (mmtbx.validation.ligands.ligand_validation attribute) fofc_mean (mmtbx.validation.ligands.ligand_validation attribute) fofc_min (mmtbx.validation.ligands.ligand_validation attribute) FOFC_PEAK (mmtbx.ions.identify.AtomProperties attribute) fofo_density (mmtbx.ions.environment.ScatteringEnvironment attribute) fom() (in module mmtbx.max_lik.maxlik) (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method) (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method) force_complex() (cctbx.xray.structure_factors.manager.manager method) form_factor() (cctbx.maptbx.atom_curves method) (in module mmtbx.max_lik.max_like_non_uniform) (mmtbx.max_lik.maxlik.alpha_beta_calc method) format() (mmtbx.map_names method) format_all_for_biomt() (mmtbx.ncs.ncs.ncs method) format_all_for_group_specification() (mmtbx.ncs.ncs.ncs method) format_all_for_phenix_refine() (mmtbx.ncs.ncs.ncs method) format_all_for_resolve() (mmtbx.ncs.ncs.ncs method) format_anisou_record() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_with_labels method) format_atom_record() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_with_labels method) format_atom_record_group() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_with_labels method) format_chi_angles() (mmtbx.validation.rotalyze.rotamer method) format_correction_for_H() (iotbx.pdb.hierarchy.root method) format_distances_for_error_message() (in module cctbx.geometry_restraints.manager) format_exception_message() (in module mmtbx.monomer_library.pdb_interpretation) format_fasta() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) (iotbx.pdb.hierarchy.root method) format_for_biomt() (mmtbx.ncs.ncs.ncs_group method) format_for_phenix_refine() (mmtbx.ncs.ncs.ncs_group method) format_for_resolve() (mmtbx.ncs.ncs.ncs_group method) format_group_specification() (mmtbx.ncs.ncs.ncs_group method) format_html() (cctbx.web.asu_gallery.jv_index.crystal_system_table method) (cctbx.web.asu_gallery.jv_index.plane_group_table method) (cctbx.web.asu_gallery.jv_index.point_group_table method) (cctbx.web.asu_gallery.jv_index.symbol_table method) format_info_string() (mmtbx.refinement.real_space.residue_monitor method) format_it() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method) format_map_coeffs_for_resolve() (in module mmtbx.maps.utils) format_max() (scitbx.array_family.flex.double method) format_mean() (scitbx.array_family.flex.double method) format_min() (scitbx.array_family.flex.double method) format_object_from_data() (in module xfel.cftbx.detector.cspad_cbf_tbx) format_old() (mmtbx.validation.cbetadev.cbeta method) (mmtbx.validation.clashscore.clash method) (mmtbx.validation.entity method) (mmtbx.validation.ramalyze.ramachandran method) (mmtbx.validation.rotalyze.rotamer method) format_phil_for_ncs() (mmtbx.ncs.ncs.ncs method) format_phil_for_phenix_refine() (mmtbx.ncs.ncs.ncs method) format_ramachandran_plot_title() (in module mmtbx.rotamer.graphics) (in module mmtbx.validation.ramalyze) format_rms_info() (cctbx.omz.dev.refinement method) format_scale_matrix() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.bulk_solvent.scaler.run method) format_score() (mmtbx.validation.entity method) format_sigatm_record() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_with_labels method) format_siguij_record() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_with_labels method) format_stats_for_phenix_gui() (mmtbx.refinement.print_statistics.refinement_monitor method) format_summary() (mmtbx.density_modification.dm_stats method) (scitbx.array_family.flex.smart_selection method) format_time() (in module xfel.cxi.gfx.status_plot) format_value() (mmtbx.polygon.output.renderer method) format_values() (mmtbx.validation.restraints.planarity method) (mmtbx.validation.restraints.restraint method) (mmtbx.validation.rna_validate.rna_angle method) (mmtbx.validation.rna_validate.rna_bond method) (mmtbx.validation.rna_validate.rna_pucker method) formate_values() (mmtbx.validation.restraints.bond method) FormatError, [1] formats (mmtbx.validation.molprobity.summary attribute) formula (class in cctbx.eltbx.formula) formula_49() (in module mmtbx.tls.tls_as_xyz) forward_compatible_hierarchy_as_standard() (iotbx.pdb.hierarchy.root method) fourier_coefficients_as_map_manager() (iotbx.map_manager.map_manager method) fourier_filter() (in module xfel.command_line.smooth_spectrum) fp (iotbx.pdb.hierarchy.atom property) (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] fpp (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] frac2int() (in module cctbx.command_line.precession_view) frac_max (mmtbx.maps.composite_omit_map.omit_box attribute) frac_min (mmtbx.maps.composite_omit_map.omit_box attribute) fraction_of_nearby_grid_points_above_cutoff() (mmtbx.building.local_density_quality method) fraction_outliers() (mmtbx.scaling.data_statistics.possible_outliers method) fread_matrix() (in module xfel.cxi.cspad_ana.parse_calib) fread_tensor3() (in module xfel.cxi.cspad_ana.parse_calib) fread_vector() (in module xfel.cxi.cspad_ana.parse_calib) french_wilson() (cctbx.miller.array method) french_wilson_scale() (in module cctbx.french_wilson) frequencies_from_rotamer (mmtbx.rotamer.sidechain_angles.SidechainAngles attribute) from_cif() (cctbx.miller.array class method) (cctbx.xray.structure.structure class method) from_crystal_symmetries() (xfel.clustering.cluster.Cluster class method) from_dict() (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.crystal.CrystalFactory static method) (dxtbx.model.detector.DetectorFactory static method) (dxtbx.model.goniometer.Goniometer static method) (dxtbx.model.goniometer.GoniometerFactory static method) (dxtbx.model.goniometer.MultiAxisGoniometer static method) (dxtbx.model.scan.ScanFactory static method) from_directories() (xfel.clustering.cluster.Cluster class method) from_expts() (xfel.clustering.cluster.Cluster class method) from_files() (xfel.clustering.cluster.Cluster class method) from_iterable() (xfel.clustering.cluster.Cluster class method) from_list() (xfel.clustering.cluster.Cluster class method) from_mosflm_matrix() (dxtbx.model.crystal.CrystalFactory static method) from_phil() (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_scatterers (class in cctbx.xray.structure_factors.from_scatterers) from_scatterers_direct (class in cctbx.xray.structure_factors.from_scatterers_direct) from_scatterers_fft (class in cctbx.xray.structure_factors.from_scatterers_fft) from_shelx() (cctbx.xray.structure.structure class method) from_structure() (mmtbx.geometry.topology.Compound class method) front() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) frozenset() (mmtbx.geometry.clash.ClashingPair method) fs() (cctbx.examples.structure_factor_derivatives_2.structure_factors method) (cctbx.examples.structure_factor_derivatives_3.structure_factors method) (cctbx.examples.structure_factor_derivatives_4.structure_factors method) fsc (mmtbx.validation.experimental.real_space attribute) fsc() (cctbx.miller.array method) full_sys_abs_mask() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method) full_width_half_max() (in module xfel.command_line.overlay_spectra) func() (mmtbx.refinement.real_space.fit_residue.find_all_conformers method) funcl (cctbx.omz.dev.xfgc_info attribute) functional() (cctbx.examples.unit_cell_minimizers.refinery method) (cctbx.xray.minimization.occupancy_penalty_exp method) (mmtbx.scaling.relative_scaling.refinery method) functional_only() (cctbx.merging.brehm_diederichs.minimize_divide method) fw_acentric() (in module cctbx.french_wilson) fw_centric() (in module cctbx.french_wilson)

G

g_exp_i_alpha_sum (class in cctbx.examples.g_exp_i_alpha_derivatives) g_function() (cctbx.miller.array method) gamma (mmtbx.scaling.absolute_scaling.gamma_protein attribute) gamma_nucleic (class in mmtbx.scaling.absolute_scaling) gamma_protein (class in mmtbx.scaling.absolute_scaling) gaussian_filter() (iotbx.map_manager.map_manager method) general_positions_only() (cctbx.maptbx.peak_cluster_analysis method) (cctbx.maptbx.peak_search_parameters method) generate_angles_nested() (in module mmtbx.refinement.real_space) generate_atoms_from_atom_groups() (in module mmtbx.monomer_library.glyco_utils) (in module mmtbx.monomer_library.linking_utils) generate_bijvoet_mates() (cctbx.miller.array method) generate_bivoet_mates() (cctbx.miller.set method) generate_cb_op_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools) generate_chemical_components_codes() (in module mmtbx.chemical_components) generate_comparison_selections() (cctbx.merging.brehm_diederichs.algorithm2 method) generate_data_from_streams() (in module xfel.command_line.print_pickle) generate_dna_rna_fragments() (in module mmtbx.conformation_dependent_library) generate_from_phil() (dxtbx.model.detector.DetectorFactory static method) generate_inverse_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools) generate_loop_data() (mmtbx.monomer_library.cif_types.looped_data method) generate_map() (iotbx.map_model_manager.map_model_manager method) generate_master_phil_with_inputs() (in module mmtbx.command_line) generate_matrix() (in module cctbx.sgtbx.sub_lattice_tools) generate_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools) generate_missing_reflections() (cctbx.miller.display.scene method) generate_ncs_ops() (in module mmtbx.ncs.ncs) generate_p1_box() (in module mmtbx.maps.superpose) generate_protein_fragments() (in module mmtbx.conformation_dependent_library) generate_protein_threes() (in module mmtbx.conformation_dependent_library) generate_protein_tuples() (in module mmtbx.conformation_dependent_library) generate_r_free_flags() (cctbx.miller.set method) generate_r_free_flags_basic() (cctbx.miller.set method) generate_r_free_flags_on_lattice_symmetry() (cctbx.miller.set method) generate_random_f_calc() (in module cctbx.examples.random_f_calc) generate_reindex_sets() (cctbx.merging.brehm_diederichs.algorithm2 method) generate_residue_tuples() (in module mmtbx.conformation_dependent_library) generate_sidechain_clusters() (in module mmtbx.building) generate_singles() (in module cctbx.euclidean_model_matching) generate_streams_from_path() (in module xfel.command_line.print_pickle) generate_systematic_absences() (cctbx.miller.display.scene method) (in module cctbx.miller.display) generate_tlsos() (in module mmtbx.tls.tools) generate_torsion_restraints() (in module mmtbx.geometry_restraints.reference) generate_twin_operators() (cctbx.merging.brehm_diederichs.algorithm2 method) generate_view_data() (cctbx.miller.display.scene method) generate_water_omit_map (class in mmtbx.maps.utils) generator() (in module iotbx.shelx.writer) generic_metal_run() (in module mmtbx.monomer_library.bondlength_defaults) generic_polar_normalize() (in module cctbx.macro_mol.rotation_parameters) generic_simple_input_phil() (in module mmtbx.command_line) geometry (class in cctbx.web.asu_gallery.jvx) (mmtbx.command_line.load_model_and_data attribute) (mmtbx.ions.environment.ChemicalEnvironment attribute), [1] geometry_minimization() (mmtbx.building.box_build_refine_base method) geometry_restraints_manager() (mmtbx.monomer_library.pdb_interpretation.process method) geometry_restraints_proxy_registries (class in mmtbx.monomer_library.pdb_interpretation) geostd_list_cif() (in module mmtbx.monomer_library.server) get() (cctbx.omz.bfgs.memory_element method) (cctbx.omz.dev.shift_limit_pair method) (cctbx.sgtbx.symmetry_equivalent_pair_interactions method) (iotbx.cif.model.cif method) get_1_char_after_key() (mmtbx.ncs.ncs.ncs method) get_1_value_after_key() (mmtbx.ncs.ncs.ncs method) get_3_values_after_key() (mmtbx.ncs.ncs.ncs method) get_absolute_label_position() (mmtbx.polygon.output.histogram_layout method) get_absolute_rt_info() (iotbx.map_manager.shift_aware_rt method) get_active_data() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method) get_active_infos() (cctbx.omz.dev.refinement method) get_alignment() (mmtbx.validation.sequence.chain method) get_all_angle_proxies() (cctbx.geometry_restraints.manager.manager method) get_all_bond_proxies() (cctbx.geometry_restraints.manager.manager method) get_all_conformer_distances() (mmtbx.disorder.analyze_model.disordered_segment method) get_all_edge_segments() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) get_all_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method) get_all_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) get_allowed_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method) get_allowed_goal() (mmtbx.validation.ramalyze.ramalyze method) get_alpha() (mmtbx.scaling.twin_analyses.britton_test method) get_alpha_angle() (dxtbx.model.goniometer.KappaGoniometer method) get_alpha_beta() (in module mmtbx.monomer_library.glyco_utils) get_alternative_name() (in module mmtbx.chemical_components) get_altid_controls() (in module mmtbx.kinemage.validation) get_altloc() (in module mmtbx.validation.molprobity.mp_geo) (mmtbx.validation.atoms method) get_altloc_from_id_str() (in module mmtbx.validation.ramalyze) get_altloc_from_three() (in module mmtbx.validation.ramalyze) get_angle() (mmtbx.monomer_library.cif_types.comp_comp_id method) (mmtbx.monomer_library.cif_types.link_link_id method) (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method) get_angle_outliers() (cctbx.geometry_restraints.energies.energies method) (in module mmtbx.kinemage.validation) get_angle_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method) get_angles() (dxtbx.model.goniometer.MultiAxisGoniometer method) get_angles_from_included_bonds() (in module mmtbx.monomer_library.linking_utils) get_anomalous_map() (in module mmtbx.maps.utils) get_anomeric_carbon() (in module mmtbx.monomer_library.glyco_utils) get_anomeric_hydrogen() (in module mmtbx.monomer_library.glyco_utils) get_any_linking_carbon() (in module mmtbx.monomer_library.glyco_utils) get_any_map_manager() (iotbx.map_model_manager.map_model_manager method) get_as_atom_group() (in module mmtbx.chemical_components) get_as_hierarchy() (in module mmtbx.chemical_components) get_asu() (in module cctbx.sgtbx.direct_space_asu.plane_group_reference_table) (in module cctbx.sgtbx.direct_space_asu.reference_table) get_atom() (iotbx.pdb.hierarchy.atom_group method) get_atom_dict() (mmtbx.rotamer.rotamer_eval.RotamerEval method) get_atom_names() (in module mmtbx.chemical_components) get_atom_selection() (in module mmtbx.utils) get_atom_selection_cache() (iotbx.pdb.hierarchy.root method) get_atom_selections() (in module mmtbx.utils) get_atom_type() (mmtbx.ions.identify.AtomProperties method) get_atom_type_symbol() (in module mmtbx.chemical_components) get_atoms_info() (in module mmtbx.validation) get_atoms_str() (in module mmtbx.validation.molprobity.mp_geo) get_auth_asym_id() (iotbx.pdb.hierarchy.root method) get_auth_asym_id_iseq() (iotbx.pdb.hierarchy.root method) get_auth_seq_id() (iotbx.pdb.hierarchy.root method) get_auth_seq_id_iseq() (iotbx.pdb.hierarchy.root method) get_average_cell_dimensions() (xfel.command_line.cxi_merge.unit_cell_distribution method) get_average_scale_factors() (in module iotbx.map_model_manager) get_axes() (dxtbx.model.goniometer.MultiAxisGoniometer method) get_axes_and_atoms_i_seqs() (in module mmtbx.tls.ladp) get_b_iso() (mmtbx.ions.identify.manager method) get_bad_hydrogen_i_seqs() (in module mmtbx.monomer_library.correct_hydrogen_geometries) get_basepair_target_distance() (in module mmtbx.monomer_library.bondlength_defaults) get_basic_histogram_data() (in module mmtbx.polygon.output) get_beam() (dxtbx.serialize.xds.to_xds method) get_best_model() (mmtbx.refinement.select_best_starting_model.select_model method) get_beta_ideal() (mmtbx.validation.cbetadev.cbetadev method) get_bin() (mmtbx.validation.graphics.residue_binner method) get_bin_centers() (in module cctbx.french_wilson) get_bin_color() (mmtbx.polygon.output.blue_color_model method) (mmtbx.polygon.output.color_model method) (mmtbx.polygon.output.grayscale_color_model method) (mmtbx.polygon.output.rainbow_color_model method) (mmtbx.polygon.output.red_color_model method) (mmtbx.polygon.output.rmb_color_model method) get_bond() (in module mmtbx.monomer_library.cif_types) (mmtbx.monomer_library.cif_types.comp_comp_id method) (mmtbx.monomer_library.cif_types.link_link_id method) get_bond_and_angle_outliers() (in module mmtbx.validation.molprobity.mp_geo) get_bond_outliers() (cctbx.geometry_restraints.energies.energies method) (in module mmtbx.kinemage.validation) get_bond_pairs() (in module mmtbx.chemical_components) get_bond_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method) get_bonded() (in module mmtbx.monomer_library.linking_utils) get_bonded_from_atom_groups() (in module mmtbx.monomer_library.linking_utils) get_bonds_angles_rmsds() (mmtbx.validation.restraints.combined method) get_bool_selection_to_keep() (in module mmtbx.ncs.ncs_search) get_boundaries_from_sensor_ID() (in module xfel.command_line.cxi_merge) get_boxes_to_tile_map() (iotbx.map_manager.map_manager method) get_C1_carbon() (in module mmtbx.monomer_library.glyco_utils) get_c_beta_torsion_proxies() (cctbx.geometry_restraints.manager.manager method) (in module mmtbx.geometry_restraints.c_beta) get_c_symmetry() (in module mmtbx.ncs.ncs) get_calib_file_path() (in module xfel.cftbx.detector.cspad_cbf_tbx) get_calphas() (in module mmtbx.disorder.backbone) get_cas_from_three() (in module mmtbx.validation.ramalyze) get_cb_resseq_to_skip() (iotbx.map_model_manager.map_model_manager method) get_cb_target_angle_pair() (in module mmtbx.geometry_restraints.c_beta) get_cbetas() (in module mmtbx.disorder.backbone) get_center() (in module mmtbx.validation.rotalyze) get_center_and_radius() (cctbx.miller.display.render_2d method) get_center_of_box_frac() (in module iotbx.map_model_manager) get_centroid_hierarchy() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils) get_chain_color() (in module mmtbx.kinemage.validation) get_chain_xyz() (in module mmtbx.ncs.ncs_search) get_chains_info() (in module mmtbx.ncs.ncs_search) get_charge() (mmtbx.ions.parameter_server method) get_charges() (mmtbx.ions.parameter_server method) get_chi1_chi2() (mmtbx.validation.rotalyze.rotamer method) get_chi_torsion_proxies() (cctbx.geometry_restraints.manager.manager method) get_chir_bonds_and_angles() (mmtbx.monomer_library.cif_types.comp_comp_id method) (mmtbx.monomer_library.cif_types.link_link_id method) get_chir_volume_ideal() (in module mmtbx.monomer_library.cif_types) (mmtbx.monomer_library.cif_types.comp_comp_id method) (mmtbx.monomer_library.cif_types.link_link_id method) get_chiral_i_seqs() (mmtbx.monomer_library.glyco_utils.glyco_link_class method) get_chiral_sign() (in module mmtbx.monomer_library.glyco_utils) get_chiral_volume() (in module mmtbx.monomer_library.linking_utils) get_chirality_outliers() (cctbx.geometry_restraints.energies.energies method) get_cif_dictionary() (in module mmtbx.chemical_components) get_cif_filename() (in module mmtbx.chemical_components) get_cif_float() (in module mmtbx.wwpdb.standard_geometry_cif) get_cif_int() (in module mmtbx.wwpdb.standard_geometry_cif) get_cif_link_entries() (cctbx.geometry_restraints.manager.manager method) get_cif_number() (in module mmtbx.wwpdb.standard_geometry_cif) get_cis_pro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method) get_clashscore() (mmtbx.validation.clashscore.clashscore method) get_clashscore_b_cutoff() (mmtbx.validation.clashscore.clashscore method) get_classes() (in module mmtbx.monomer_library.linking_utils) get_classification() (mmtbx.monomer_library.cif_types.comp_comp_id method) get_code() (mmtbx.monomer_library.glyco_utils.glyco_link_class method) get_color_key() (mmtbx.polygon.output.renderer method) get_comp_comp_id_and_atom_name_interpretation() (mmtbx.monomer_library.server.server method) get_comp_comp_id_direct() (mmtbx.monomer_library.server.server method) get_comp_comp_id_mod() (mmtbx.monomer_library.server.server method) get_completeness() (mmtbx.scaling.xtriage.xtriage_summary method) get_condensed_clashes() (mmtbx.validation.clashscore.probe_clashscore_manager method) get_condition() (mmtbx.ligands.xtal_screens.server method) get_conformer_distances() (mmtbx.disorder.analyze_model.disordered_segment method) get_conformer_indices() (iotbx.pdb.hierarchy.root method) get_contours() (in module mmtbx.validation.ramalyze) get_converter_by_docstring() (in module cctbx.macro_mol.rotation_parameters) get_converters() (in module cctbx.macro_mol.rotation_parameters) get_coordinate_shift() (iotbx.map_model_manager.match_map_model_ncs method) get_coordinates_for_alignment_range() (mmtbx.validation.sequence.chain method) get_coordinates_for_alignment_ranges() (mmtbx.validation.sequence.chain method) get_copy_master_selections_from_match_dict() (in module mmtbx.ncs.ncs_search) get_counts_and_histograms() (iotbx.map_model_manager.map_model_manager method) get_covalent_angle_proxies() (cctbx.geometry_restraints.manager.manager method) get_covalent_bond_proxies() (cctbx.geometry_restraints.manager.manager method) get_cspad_cbf_handle() (in module xfel.cftbx.detector.cspad_cbf_tbx) get_current_eq_distances() (mmtbx.den.den_restraints method) get_cursor() (xfel.cxi.correction_vector_plot.manage_sql method) get_cycle_stats() (mmtbx.density_modification.dm_stats method) get_d_symmetry() (in module mmtbx.ncs.ncs) get_data_file() (mmtbx.scaling.xtriage.xtriage_summary method) get_db_result() (in module mmtbx.conformation_dependent_library.utils) get_default_bondlength() (in module mmtbx.monomer_library.bondlength_defaults) get_default_header() (in module mmtbx.kinemage.validation) get_default_map_coefficients_phil() (in module mmtbx.maps.utils) get_default_ss_params() (mmtbx.secondary_structure.manager static method) get_den_atom_pairs() (mmtbx.den.den_restraints method) get_density_along_line() (iotbx.map_manager.map_manager method) get_detector() (dxtbx.serialize.xds.to_xds method) get_diagonal_extend() (in module cctbx.web.asu_gallery.jv_asu) get_diff_score_towards_periodic() (in module cctbx.maptbx) get_difference_maps() (in module mmtbx.building) get_diffs_for_matching_target_and_model() (iotbx.map_model_manager.map_model_manager method) get_dihedral() (in module mmtbx.validation.ramalyze) get_dihedral_outliers() (cctbx.geometry_restraints.energies.energies method) get_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method) get_dihedral_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method) get_direction() (dxtbx.model.goniometer.KappaGoniometer method) get_distance2() (in module mmtbx.monomer_library.glyco_utils) (in module mmtbx.monomer_library.linking_utils) get_edge_score_towards_periodic() (in module cctbx.maptbx) get_edge_vectors() (in module cctbx.web.asu_gallery.jv_asu) get_edge_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) get_eigenvector() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method) get_element() (mmtbx.ions.parameter_server method) get_element_and_charge_symbols() (in module cctbx.eltbx.xray_scattering) get_errors() (iotbx.cif.model.cif method) get_expected_count() (mmtbx.validation.cbetadev.cbetadev method) get_experiment_type() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) get_f_calc() (cctbx.omz.dev.refinement method) get_f_cbs() (cctbx.omz.dev.refinement method) get_favored_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method) get_favored_goal() (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.rotalyze.rotalyze method) get_favored_peaks() (in module mmtbx.validation.ramalyze) get_favored_regions() (in module mmtbx.validation.ramalyze) get_field_simple() (in module mmtbx.chemical_components) get_filtered_n_angle_proxies() (cctbx.geometry_restraints.energies.energies method) get_filtered_n_bond_proxies() (cctbx.geometry_restraints.energies.energies method) get_filtered_n_dihedral_proxies() (cctbx.geometry_restraints.energies.energies method) get_filtered_n_planarity_proxies() (cctbx.geometry_restraints.energies.energies method) get_final_maps_and_cc (class in mmtbx.ncs.ligands) get_fixed_rotation() (dxtbx.model.goniometer.Goniometer method) get_flag_captions() (mmtbx.ions.atom_type_flags method) get_fom_for_plot() (mmtbx.density_modification.dm_stats method) get_footer() (in module mmtbx.kinemage.validation) get_forwards_reverse_helix() (mmtbx.ncs.ncs.ncs_group method) get_fp() (mmtbx.ions.identify.manager method) get_fpp() (mmtbx.ions.identify.manager method) get_frame_dictionary() (xfel.cxi.correction_vector_plot.manage_sql method) get_frames_from_mysql() (xfel.metrology.mark0.correction_vectors method) get_func() (in module mmtbx.chemical_components.cif_parser) get_general_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method) get_gly_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method) get_glyco_link_atoms() (in module mmtbx.monomer_library.glyco_utils) get_goniometer() (dxtbx.serialize.xds.to_xds method) get_grid_values() (in module mmtbx.conformation_dependent_library.utils) get_group() (in module mmtbx.chemical_components) get_hand() (in module mmtbx.monomer_library.linking_utils) get_hash_indexer_for() (in module mmtbx.geometry.asa) get_hbond_proxies_iseqs() (cctbx.geometry_restraints.manager.manager method) get_header() (in module mmtbx.chemical_components) get_helical_symmetry() (in module mmtbx.ncs.ncs) get_helix_parameters() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) get_helix_theta() (mmtbx.ncs.ncs.ncs_group method) get_helix_types() (mmtbx.secondary_structure.manager method) get_helix_z_translation() (mmtbx.ncs.ncs.ncs_group method) get_high_resolution_and_residue_count_for_structures() (in module mmtbx.wwpdb.rcsb_web_services) get_high_resolution_for_structures() (in module mmtbx.wwpdb.rcsb_web_services) get_highlighted_residues() (mmtbx.validation.sequence.chain method) get_histogram_colors() (mmtbx.polygon.output.color_model method) get_hydrogen_names() (in module mmtbx.chemical_components) get_ias_selection() (mmtbx.ias.manager method) get_ileval_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method) get_index() (in module mmtbx.conformation_dependent_library.utils) get_indices_from_index() (in module iotbx.map_manager) get_info() (iotbx.map_model_manager.map_model_manager method) get_info_from_match_dict() (in module mmtbx.ncs.ncs_search) get_initial_b_iso() (mmtbx.ions.identify.manager method) get_initial_scale() (in module mmtbx.twinning.twin_f_model) get_inverse_matrix() (mmtbx.maps.superpose.common_frame_of_reference method) get_inverses() (mmtbx.ncs.ncs.ncs_group method) get_inverted_atoms() (in module mmtbx.validation.utils) get_ions() (in module mmtbx.kinemage.validation) get_isomer() (mmtbx.monomer_library.glyco_utils.glyco_link_class method) get_k_total() (mmtbx.bulk_solvent.scaler.run method) get_kappa_angle() (dxtbx.model.goniometer.KappaGoniometer method) get_kappa_axis() (dxtbx.model.goniometer.KappaGoniometer method) get_kin_lots() (in module mmtbx.kinemage.validation) get_kriber_coseq_file() (in module cctbx.crystal.coordination_sequences) get_ksdssp_exe_path() (in module mmtbx.secondary_structure) get_label_alt_id_atom() (iotbx.pdb.hierarchy.root method) get_label_alt_id_iseq() (iotbx.pdb.hierarchy.root method) get_label_asym_id() (iotbx.pdb.hierarchy.root method) get_label_asym_id_iseq() (iotbx.pdb.hierarchy.root method) get_label_seq_id() (iotbx.pdb.hierarchy.root method) get_label_seq_id_iseq() (iotbx.pdb.hierarchy.root method) get_lib_link() (in module mmtbx.monomer_library.pdb_interpretation) get_lib_link_peptide() (in module mmtbx.monomer_library.pdb_interpretation) get_ligand_info_for_structures() (in module mmtbx.wwpdb.rcsb_web_services) get_line_segments() (mmtbx.polygon.output.polygon_layout method) get_linear_indexer_for() (in module mmtbx.geometry.asa) get_link_carbon() (in module mmtbx.monomer_library.glyco_utils) get_link_carbon_on_distance() (in module mmtbx.monomer_library.glyco_utils) get_link_oxygen() (in module mmtbx.monomer_library.glyco_utils) get_link_oxygen_on_distance() (in module mmtbx.monomer_library.glyco_utils) get_link_phi_carbon() (in module mmtbx.monomer_library.glyco_utils) get_link_records() (iotbx.pdb.ext.input method) get_list_of_best_ncs_copy_map_correlation() (in module mmtbx.ncs.ncs_utils) get_log_p_solc() (in module mmtbx.scaling.matthews) get_managers() (in module mmtbx.conformation_dependent_library.tst_cdl) get_map() (in module mmtbx.maps.fem) (in module mmtbx.maps.kick) (mmtbx.ions.identify.manager method) get_map_coeff_labels() (in module mmtbx.maps.utils) get_map_coeffs_as_fp_phi() (in module iotbx.map_model_manager) get_map_coeffs_for_build() (in module mmtbx.maps.utils) get_map_counts() (in module iotbx.map_model_manager) get_map_data_by_id() (iotbx.map_model_manager.map_model_manager method) get_map_gaussian_fit() (mmtbx.ions.identify.manager method) get_map_histograms() (in module iotbx.map_model_manager) get_map_manager_by_id() (iotbx.map_model_manager.map_model_manager method) get_map_model_manager_with_selected() (iotbx.map_model_manager.map_model_manager method) get_map_rmse() (iotbx.map_model_manager.map_model_manager method) get_map_sphere_variance() (mmtbx.ions.identify.manager method) get_maps_from_fmodel() (in module mmtbx.maps.utils) (mmtbx.maps.utils.fast_maps_from_hkl_file method) get_mask_as_map_manager() (iotbx.map_manager.map_manager method) get_master_phil() (in module cctbx.omz.cod_refine) (in module cctbx.omz.dev) (in module mmtbx.kinemage.validation) (in module mmtbx.validation.analyze_peptides) (in module mmtbx.validation.molprobity.mp_geo) get_match_rmsd() (in module mmtbx.ncs.ncs_search) get_matching_atom_group() (in module mmtbx.validation.ramalyze) get_matching_atoms() (in module mmtbx.ncs.ncs_search) get_matthews_coeff() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) get_maximal_subgroup() (cctbx.sgtbx.pointgroup_tools.point_group_graph method) (in module cctbx.examples.maximum_subgroups) get_mean_coordinate() (in module mmtbx.validation.sequence) get_mean_coordinate_for_alignment_range() (mmtbx.validation.sequence.chain method) get_mean_coordinate_for_alignment_ranges() (mmtbx.validation.sequence.chain method) get_mean_intensity() (in module cctbx.french_wilson) get_mean_xyz() (in module mmtbx.validation.restraints) get_merging_statistics() (mmtbx.scaling.xtriage.xtriage_summary method) get_metal_parameters() (mmtbx.ions.parameter_server method) get_min_fractional() (in module cctbx.web.asu_gallery.jv_asu) get_min_max_table() (in module mmtbx.conformation_dependent_library.tst_cdl) get_missing_chains() (mmtbx.validation.sequence.validation method) get_mk2_sets() (in module cctbx.uctbx.gruber_1973_table_1) get_mmtbx_icalc() (in module xfel.cxi.display_powder_arcs) get_mmtype_from_resname() (in module mmtbx.validation.utils) get_model_by_id() (iotbx.map_model_manager.map_model_manager method) get_model_from_other() (iotbx.map_model_manager.map_model_manager method) get_model_map_stats() (in module mmtbx.building) get_n_angle_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_bond_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_c_beta_torsion_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_chi_torsion_proixes() (cctbx.geometry_restraints.manager.manager method) get_n_den_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_emsley8k_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) get_n_emsley_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) get_n_hangle_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_hbond_proxies() (cctbx.geometry_restraints.manager.manager method)

get_n_oldfield_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) get_n_parallelity_bp_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_phi_psi_2_proxies() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) get_n_planarity_bp_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_planarity_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_proxies() (mmtbx.den.den_restraints method) (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) get_n_ramachandran_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_real_for_grid_spacing() (iotbx.map_manager.map_manager method) get_n_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_reference_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_residues_of_classes() (iotbx.pdb.hierarchy.overall_counts method) get_n_stacking_proxies() (cctbx.geometry_restraints.manager.manager method) get_n_total_by_model() (mmtbx.validation.restraints.bonds method) (mmtbx.validation.restraints.planarities method) (mmtbx.validation.restraints.restraint_validation method) get_name() (in module mmtbx.chemical_components) get_names() (dxtbx.model.goniometer.MultiAxisGoniometer method) get_nconfs() (in module mmtbx.disorder.analyze_model) get_ncs_from_map() (iotbx.map_model_manager.map_model_manager method) get_ncs_from_model() (iotbx.map_model_manager.map_model_manager method) get_ncs_from_text() (in module mmtbx.ncs.ncs) get_ncs_name() (mmtbx.ncs.ncs.ncs method) get_nearby_water_selection() (in module mmtbx.building) get_new_fcalc_map() (mmtbx.ncs.ligands.sample_operators method) get_new_group() (mmtbx.ncs.ncs.ncs_group method) get_next() (cctbx.web.emma.web_to_models method) get_non_hydrogen_atom_indices() (in module mmtbx.building) get_normalization_data_for_unit_binning() (in module iotbx.map_model_manager) get_num_scan_points() (dxtbx.model.goniometer.Goniometer method) get_obs_from_mysql() (xfel.metrology.mark0.correction_vectors method) get_observations() (in module xfel.command_line.cxi_merge) get_occupancy() (in module mmtbx.validation.rotalyze) get_omega() (in module mmtbx.validation.analyze_peptides) get_omega_angle() (dxtbx.model.goniometer.KappaGoniometer method) get_omega_atoms() (in module mmtbx.rotamer) (in module mmtbx.validation.ramalyze) get_omega_axis() (dxtbx.model.goniometer.KappaGoniometer method) get_optimal_indexer_for() (in module mmtbx.geometry.asa) get_optimization_grid() (mmtbx.den.den_restraints method) get_order_dict() (mmtbx.ncs.ncs.ncs_group method) get_original_cs() (mmtbx.utils.extract_box_around_model_and_map method) (mmtbx.utils.shift_origin method) get_outlier_count() (mmtbx.validation.cbetadev.cbetadev method) get_outlier_percent() (mmtbx.validation.cbetadev.cbetadev method) get_outlier_plot_values() (mmtbx.validation.graphics.residue_bin method) (mmtbx.validation.molprobity.residue_multi_criterion method) get_outliers() (mmtbx.validation.restraints.angles method) (mmtbx.validation.restraints.bonds method) (mmtbx.validation.restraints.chiralities method) (mmtbx.validation.restraints.dihedrals method) (mmtbx.validation.restraints.planarities method) (mmtbx.validation.restraints.restraint_validation method) get_outliers_count_and_fraction() (mmtbx.validation.validation method) get_outliers_fraction_for_model() (mmtbx.validation.validation method) get_outliers_goal() (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.rotalyze.rotalyze method) (mmtbx.validation.validation method) get_outliers_table() (mmtbx.validation.sequence.chain method) get_overall_correlation() (xfel.command_line.cxi_merge.scaling_manager method) get_overall_counts() (iotbx.pdb.hierarchy.root method) get_p1_map_unscaled() (mmtbx.maps.composite_omit_map.run method) get_parallelity_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method) get_pdb_chains() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method) get_pdb_oxygen() (in module mmtbx.hydrogens.find) get_peptide_c_alpha_selection() (iotbx.pdb.hierarchy.root method) get_phi() (in module mmtbx.validation.ramalyze) get_phi_angle() (dxtbx.model.goniometer.KappaGoniometer method) get_phi_axis() (dxtbx.model.goniometer.KappaGoniometer method) get_phi_psi_atoms() (in module mmtbx.rotamer) get_phi_psi_dict() (in module mmtbx.validation.cbetadev) get_phi_psi_indices() (in module mmtbx.rotamer) get_phi_psi_residues_count() (mmtbx.validation.ramalyze.ramalyze method) get_phil() (in module xfel.command_line.metrology) (in module xfel.metrology.mark0) get_planarity_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method) get_planes() (mmtbx.monomer_library.cif_types.comp_comp_id method) (mmtbx.monomer_library.cif_types.link_link_id method) (mmtbx.monomer_library.cif_types.mod_mod_id method) get_plot_data() (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.rotalyze.rotalyze method) get_plot_statistics() (xfel.command_line.cxi_merge.scaling_manager method) get_plots() (mmtbx.validation.ramalyze.ramalyze method) get_point_in_plane() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) get_pointer_to_old_dv_id_dict() (in module iotbx.map_model_manager) get_polygon_intersection() (mmtbx.polygon.output.histogram_layout method) get_polygon_statistics() (mmtbx.validation.molprobity.molprobity method) get_preliminary_ncs_groups() (in module mmtbx.ncs.ncs_search) get_prepro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method) get_previous_conformer() (mmtbx.disorder.analyze_model.disordered_segment method) get_processes() (in module libtbx.easy_mp) get_program() (in module mmtbx.wwpdb.utils) get_program_name() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) get_psi() (in module mmtbx.validation.ramalyze) get_r_factor() (mmtbx.utils.guess_observation_type method) get_r_free_as_bool() (in module cctbx.r_free_utils) get_r_free_stats() (in module cctbx.r_free_utils) get_r_rfree_sigma() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) get_r_value_total() (mmtbx.scaling.twin_analyses.symmetry_issues method) get_r_work_rfree_for_structures() (in module mmtbx.wwpdb.rcsb_web_services) get_radii() (in module mmtbx.refinement.real_space) get_radius() (in module mmtbx.refinement.real_space) get_ranges() (mmtbx.validation.graphics.residue_binner method) get_rdl_database() (in module mmtbx.conformation_dependent_library.rdl_database) get_real_space_plot_values() (mmtbx.validation.graphics.residue_bin method) (mmtbx.validation.molprobity.residue_multi_criterion method) get_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method) get_refine_selection() (in module mmtbx.ncs.ncs_utils) get_reflection_file_server() (mmtbx.utils.process_command_line_args method) get_reflection_info() (cctbx.miller.display.scene method) get_relative_cc() (in module cctbx.maptbx) get_relative_sequence_copy_number() (mmtbx.validation.sequence.validation method) get_relative_wilson() (mmtbx.scaling.xtriage.xtriage_summary method) get_res_range_after_key() (mmtbx.ncs.ncs.ncs method) get_residue_bonds() (in module mmtbx.kinemage.validation) get_residue_group_data() (mmtbx.validation.molprobity.multi_criterion_view method) get_residue_ids() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) get_residue_key() (in module mmtbx.validation.rotalyze) get_residue_name_from_selection() (in module mmtbx.secondary_structure.utils) get_residue_names_and_classes() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) get_residue_names_padded() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) get_residue_ramachandran_data() (in module mmtbx.rotamer.graphics) get_residue_range() (mmtbx.validation.graphics.residue_bin method) get_residue_rotamer_data() (in module mmtbx.rotamer.graphics) get_resolution_at_point() (cctbx.miller.display.scene method) get_resolution_where_significant_data_present() (in module cctbx.maptbx) get_restraint_values() (in module mmtbx.conformation_dependent_library) get_restraints_group() (in module mmtbx.chemical_components) get_restraints_loading_flags() (in module mmtbx.monomer_library.pdb_interpretation) get_restraints_tg() (mmtbx.refinement.group.group_minimizer method) get_restraints_used() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) get_result_class() (mmtbx.validation.cbetadev.cbetadev method) (mmtbx.validation.clashscore.clashscore method) (mmtbx.validation.experimental.real_space method) (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.restraints.angles method) (mmtbx.validation.restraints.bonds method) (mmtbx.validation.restraints.chiralities method) (mmtbx.validation.restraints.dihedrals method) (mmtbx.validation.restraints.planarities method) (mmtbx.validation.rna_validate.rna_angles method) (mmtbx.validation.rna_validate.rna_bonds method) (mmtbx.validation.rna_validate.rna_puckers method) (mmtbx.validation.rotalyze.rotalyze method) (mmtbx.validation.validation method) (mmtbx.validation.waters.waters method) get_result_count() (mmtbx.validation.cbetadev.cbetadev method) get_results() (libtbx.program_template.ProgramTemplate method) (mmtbx.pdbtools.modify method) get_results_as_PDB_JSON() (mmtbx.validation.molprobity.MolProbityTemplate method) get_rhs() (in module iotbx.xds.read_ascii) get_ring_carbon() (in module mmtbx.monomer_library.glyco_utils) get_ring_oxygen() (in module mmtbx.monomer_library.glyco_utils) get_ring_oxygen_substitute() (in module mmtbx.monomer_library.glyco_utils) get_rms_f_list() (iotbx.map_model_manager.map_model_manager method) get_rms_info() (cctbx.omz.dev.refinement method) get_rmsf_B_factor_per_residue_per_atom() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils) get_rna_backbone_dihedrals() (in module mmtbx.validation.utils) get_rna_pucker_ref() (mmtbx.validation.rna_validate.rna_pucker_ref method) get_rot_y() (in module mmtbx.ncs.ncs) get_rot_z() (in module mmtbx.ncs.ncs) get_rotamer_angles() (mmtbx.rotamer.sidechain_angles.SidechainAngles method) get_rotamer_expectation_frequencies() (mmtbx.rotamer.sidechain_angles.SidechainAngles method) get_rotamer_iterator() (in module mmtbx.refinement.real_space.fit_residue) (mmtbx.refinement.real_space.fit_residue.run method) get_rotamers() (mmtbx.rotamer.sidechain_angles.SidechainAngles method) get_rotarama_data() (in module mmtbx.validation.utils) get_rotation_axis() (dxtbx.model.goniometer.Goniometer method) get_rotation_axis_datum() (dxtbx.model.goniometer.Goniometer method) get_rows() (in module mmtbx.monomer_library.server) get_scale_factor() (cctbx.command_line.precession_view.render_pil method) (cctbx.command_line.precession_view.render_postscript method) (cctbx.miller.display.render_2d method) get_scan() (dxtbx.serialize.xds.to_xds method) get_scan_axis() (dxtbx.model.goniometer.KappaGoniometer method) (dxtbx.model.goniometer.MultiAxisGoniometer method) get_segid_as_chainid() (in module mmtbx.validation.utils) get_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method) get_selected() (mmtbx.validation.graphics.residue_bin method) get_selected_hierarchys() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils) get_selected_sites() (mmtbx.building.box_build_refine_base method) get_selection_inside_box() (in module iotbx.map_model_manager) get_selection_string_from_chain_dict() (iotbx.map_model_manager.map_model_manager method) get_selection_strings() (mmtbx.den.den_restraints method) get_selection_to_sites_map() (in module mmtbx.geometry_restraints.reference) get_selections_and_boxes_to_split_model() (in module iotbx.map_model_manager) get_selections_for_segments() (in module iotbx.map_model_manager) get_selections_from_boxes() (in module iotbx.map_model_manager) get_sequence_n_copies() (in module mmtbx.validation.sequence) get_sequence_n_copies_from_files() (in module mmtbx.validation.sequence) 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_shifted_cs() (mmtbx.utils.extract_box_around_model_and_map method) get_shifts() (mmtbx.refinement.print_statistics.coordinate_shifts method) get_simple_bonds() (mmtbx.secondary_structure.manager method) get_single_atom_selection_string() (in module mmtbx.refinement.anomalous_scatterer_groups) get_sites_cart_from_index() (in module iotbx.map_manager) get_sites_carts() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils) get_sites_cc() (mmtbx.ncs.ligands.sample_operators method) get_skip_waters_and_hetero_lines() (in module iotbx.map_model_manager) get_smiles() (in module mmtbx.chemical_components) get_solvent_content() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) (mmtbx.utils.extract_box_around_model_and_map method) get_space_group_info() (cctbx.web.emma.web_to_models method) get_space_groups_compatible_with_likely_point_group() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method) get_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise) get_sphere_selection() (in module mmtbx.solvent.ordered_solvent) get_split_maps_and_models() (in module iotbx.map_model_manager) get_statistics_for_phenix_gui() (mmtbx.validation.molprobity.molprobity method) get_statistics_percentiles() (in module mmtbx.polygon) get_stats() (mmtbx.density_modification.density_modification method) get_stats_and_histogram_data() (in module mmtbx.polygon.output) get_strict_valence_flag() (mmtbx.ions.identify.manager method) get_struct_conn_mmcif() (cctbx.geometry_restraints.manager.manager method) get_sugar_xyz_mean() (mmtbx.validation.rna_validate.rna_puckers method) get_symops_from_supergroup_that_are_not_in_subgroup() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method) get_table() (in module cctbx.eltbx.attenuation_coefficient) get_table_data() (mmtbx.validation.sequence.validation method) get_target_value() (mmtbx.refinement.real_space.fit_residue.run method) get_template() (dxtbx.serialize.xds.to_xds method) get_test_space_group_symbols() (in module cctbx.development.debug_utils) get_tg() (mmtbx.refinement.group.group_minimizer method) get_theta_along_z() (mmtbx.ncs.ncs.ncs_group method) get_tile_center() (in module xfel.command_line.radial_average) get_tile_coords() (in module xfel.command_line.radial_average) get_tile_id() (in module xfel.command_line.radial_average) get_times() (in module cctbx.development.direct_or_fft) get_tlso_group_info_from_model() (in module iotbx.map_model_manager) get_tlso_resid() (in module iotbx.map_model_manager) get_trans_along_z() (mmtbx.ncs.ncs.ncs_group method) get_trans_pro_count_and_fraction() (mmtbx.validation.ramalyze.ramalyze method) get_transformation() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method) get_transformed_model2() (cctbx.euclidean_model_matching.match_refine method) get_twin_laws() (in module mmtbx.scaling.twin_analyses) get_type() (in module mmtbx.chemical_components) get_type_conditions() (in module cctbx.uctbx.gruber_1973_table_1) get_typed_field() (in module mmtbx.chemical_components.cif_parser) get_u_cart() (in module mmtbx.tls.tools) get_unique_altloc() (in module mmtbx.solvent.ordered_solvent) get_unique_altloc2() (in module mmtbx.solvent.ordered_solvent) get_unit_cell() (cctbx.web.emma.web_to_models method) get_unknown_atoms() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) get_user_supplied_restraints() (cctbx.geometry_restraints.manager.manager method) get_valence() (mmtbx.ions.environment.ChemicalEnvironment method) get_valence_params() (mmtbx.ions.parameter_server method) get_vector_flat() (mmtbx.refinement.real_space.cluster method) get_volume() (in module mmtbx.monomer_library.linking_utils) get_voxelizer_for() (in module mmtbx.geometry.asa) get_weight() (in module mmtbx.ncs.ncs_utils) get_weighted_outlier_count() (mmtbx.validation.cbetadev.cbetadev method) get_weighted_outlier_percent() (mmtbx.validation.cbetadev.cbetadev method) get_weighted_result_count() (mmtbx.validation.cbetadev.cbetadev method) get_weights_for_unit_binning() (in module iotbx.map_model_manager) get_wildcard_string() (in module iotbx.file_reader) get_wildcard_strings() (in module iotbx.file_reader) get_window_around_residue() (in module mmtbx.building) get_xray_structure() (cctbx.maptbx.atom_curves method) get_y_limits() (mmtbx.validation.molprobity.multi_criterion_view method) get_z_scores() (mmtbx.scaling.relative_wilson.relative_wilson method) getConfig() (xfel.command_line.convert_gain_map.fake_env method) getCsPadQuads() (xfel.command_line.convert_gain_map.fake_evt method) getOptBool() (in module xfel.cxi.cspad_ana.cspad_tbx) getOptEvalOrString() (in module xfel.cxi.cspad_ana.cspad_tbx) getOptFloat() (in module xfel.cxi.cspad_ana.cspad_tbx) getOptInteger() (in module xfel.cxi.cspad_ana.cspad_tbx) getOptROI() (in module xfel.cxi.cspad_ana.cspad_tbx) getOptString() (in module xfel.cxi.cspad_ana.cspad_tbx) getOptStrings() (in module xfel.cxi.cspad_ana.cspad_tbx) GetSize() (cctbx.command_line.precession_view.render_pil method) (cctbx.command_line.precession_view.render_postscript method) (cctbx.miller.display.render_2d method) getTime() (xfel.command_line.convert_gain_map.fake_evt method) glyco_link_class (class in mmtbx.monomer_library.glyco_utils) Goniometer (class in dxtbx.model.goniometer) GoniometerFactory (class in dxtbx.model.goniometer) good_atoms_selection() (in module mmtbx.maps.fem) grad_occ() (mmtbx.utils.experimental_data_target_and_gradients method) grad_sites_cart() (mmtbx.utils.experimental_data_target_and_gradients method) gradient() (cctbx.xray.minimization.occupancy_penalty_exp method) gradient_flags (class in cctbx.xray.structure_factors.gradient_flags) gradient_threshold (scitbx.lstbx.normal_eqns_solving.iterations attribute) gradients (class in cctbx.examples.g_exp_i_alpha_derivatives) (class in cctbx.examples.structure_factor_derivatives) (class in cctbx.examples.structure_factor_derivatives_2) (class in cctbx.examples.structure_factor_derivatives_3) (class in cctbx.xray.structure_factors.gradients) gradients() (cctbx.examples.unit_cell_minimizers.refinery method) (in module cctbx.examples.unit_cell_minimizers) (in module cctbx.examples.unit_cell_refinement) (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints method) (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple method) (mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space method) (mmtbx.scaling.relative_scaling.refinery method) gradients_base (class in cctbx.xray.structure_factors.gradients_base) gradients_calculator() (mmtbx.dynamics.simulated_annealing.run method) gradients_calculator_geometry_restraints (class in mmtbx.dynamics.cartesian_dynamics) gradients_calculator_real_space_simple (class in mmtbx.dynamics.cartesian_dynamics) gradients_calculator_reciprocal_space (class in mmtbx.dynamics.cartesian_dynamics) gradients_direct (class in cctbx.xray.structure_factors.gradients_direct) gradients_fft (class in cctbx.xray.structure_factors.gradients_fft) gradients_work() (cctbx.xray.targets.r1.target method) (cctbx.xray.targets.shelxl_wght_ls method) gradients_wrt_atomic_parameters() (mmtbx.refinement.targets.target_result_mixin method) gradients_wrt_par() (mmtbx.refinement.group.target_and_grads method) gradients_wrt_r() (mmtbx.refinement.rigid_body.target_and_grads method) gradients_wrt_t() (mmtbx.refinement.rigid_body.target_and_grads method) grads (cctbx.omz.dev.xfgc_info attribute) grads_and_curvs_target_simple() (cctbx.xray.structure.structure method) grads_asu_to_one_ncs() (in module mmtbx.refinement.minimization_ncs_constraints) grads_one_ncs_to_asu() (in module mmtbx.refinement.minimization_ncs_constraints) graphviz_pg_graph() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method) grayscale_color_model (class in mmtbx.polygon.output) GreedyMatch (class in mmtbx.geometry.topology) grid (class in scitbx.array_family.flex) (xfel.mono_simulation.mono_treatment.refinement attribute) (xfel.mono_simulation.mono_treatment.refinement2 attribute) grid_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) grid_max() (in module mmtbx.maps.composite_omit_map) grid_resolution_factor (cctbx.symmetry_search.structure_factor_symmetry attribute) grid_resolution_factor() (cctbx.xray.structure_factors.manager.manager method) grid_sample_around_c_n_axis() (mmtbx.refinement.real_space.fit_residue.run_with_minimization method) grid_units_to_cart() (iotbx.map_manager.map_manager method) gridding() (cctbx.crystal.symmetry method) group() (cctbx.sgtbx.space_group_info method) (mmtbx.geometry.clash.SphereModelGroup method) group_args (class in libtbx) group_chains_and_sequences() (in module mmtbx.validation.sequence) group_files (class in iotbx.file_reader) group_minimizer (class in mmtbx.refinement.group) group_occupancy_grads() (mmtbx.utils.experimental_data_target_and_gradients method) group_operators (class in mmtbx.ncs.ligands) group_planes() (in module mmtbx.monomer_library.cif_types) groups_parent_setting() (cctbx.sgtbx.subgroups.subgroups method) groups_primitive_setting() (cctbx.sgtbx.subgroups.subgroups method) gruber_parameterization (class in cctbx.uctbx.reduction_base) guess_b_iso_real() (mmtbx.ions.identify.manager method) guess_chemical_elements() (iotbx.pdb.hierarchy.root method) guess_file_type() (in module iotbx.file_reader) guess_molecular_weight() (mmtbx.ions.identify.manager method) guess_observation_type (class in mmtbx.utils) guess_scattering_type_is_a_mixture_of_xray_and_neutron() (cctbx.xray.structure.structure method) guess_scattering_type_neutron() (cctbx.xray.structure.structure method) guesstimate() (mmtbx.scaling.matthews.p_vm_calculator method) guesstimate_mod_hkl() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method) gui_formats (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.clashscore.nqh_flips attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) gui_list_headers (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.clashscore.nqh_flips attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) gui_output (mmtbx.scaling.loggraph_output attribute) (mmtbx.scaling.xtriage_output attribute)

H

h (mmtbx.scaling.twin_analyses.obliquity attribute) h0_scaling() (in module cctbx.omz.bfgs) h_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property) h_peak (class in mmtbx.hydrogens.find) h_test (class in mmtbx.scaling.twin_analyses) h_update() (in module cctbx.omz.bfgs) had_too_small_a_step() (scitbx.lstbx.normal_eqns_solving.iterations method) (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations_encapsulated_eqns method) half_dataset_anomalous_correlation() (cctbx.miller.array method) half_map_sharpen() (iotbx.map_model_manager.map_model_manager method) halton_x() (in module mmtbx.scaling.absence_likelihood) harmonic_restraints() (cctbx.geometry_restraints.manager.manager method) has_abnormal_intensity_statistics() (mmtbx.scaling.twin_analyses.twin_results_interpretation method) has_compatible_ligands() (mmtbx.ions.identify.AtomProperties method) has_cuts() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) has_gradient_converged_to_zero() (scitbx.lstbx.normal_eqns_solving.iterations method) has_heavy_atoms() (in module mmtbx.validation.rotalyze) has_higher_symmetry() (mmtbx.scaling.twin_analyses.twin_results_interpretation method) has_icodes() (iotbx.pdb.hierarchy.root method) has_pseudo_translational_symmetry() (mmtbx.scaling.twin_analyses.twin_results_interpretation method) has_siguij() (iotbx.pdb.hierarchy.atom static method) has_twinning() (cctbx.miller.array method) (mmtbx.scaling.twin_analyses.twin_results_interpretation method) hash() (mmtbx.geometry.indexing.structure_indexer class method) hash_indexer_for() (in module mmtbx.geometry.clash) have_bad_sigmas() (cctbx.omz.cod_select_and_pickle.cod_data method) have_close_contacts() (cctbx.omz.cod_select_and_pickle.cod_data method) have_conformers() (iotbx.pdb.hierarchy.residue_group method) have_duplicates() (cctbx.sgtbx.cosets.double_cosets method) have_good_timing_estimates() (cctbx.xray.structure_factors.manager.manager method) have_redundant_data() (cctbx.omz.cod_select_and_pickle.cod_data method) have_shelxl_compatible_scattering_types() (cctbx.omz.cod_select_and_pickle.cod_data method) have_suitable_hetero_distance() (in module cctbx.development.random_structure) have_sym (cctbx.crystal.show_distances attribute) have_sys_absent() (cctbx.omz.cod_select_and_pickle.cod_data method) have_zero_occupancies() (cctbx.omz.cod_select_and_pickle.cod_data method) hd_selection() (cctbx.xray.structure.structure method) hdf5pack() (in module xfel.cxi.cspad_ana.cspad_tbx) head() (in module cctbx.web.asu_gallery.jvx) header() (mmtbx.validation.cbetadev.cbeta static method) (mmtbx.validation.clashscore.clash static method) (mmtbx.validation.entity static method) (mmtbx.validation.experimental.residue_real_space static method) (mmtbx.validation.ramalyze.ramachandran static method) (mmtbx.validation.restraints.bond static method) (mmtbx.validation.restraints.planarity static method) (mmtbx.validation.restraints.restraint static method) (mmtbx.validation.rna_validate.rna_angle static method) (mmtbx.validation.rna_validate.rna_bond static method) (mmtbx.validation.rna_validate.rna_pucker static method) (mmtbx.validation.rotalyze.rotamer static method) (mmtbx.validation.waters.water static method)

header_info (mmtbx.validation.molprobity.molprobity attribute) heights() (cctbx.maptbx.peak_cluster_analysis method) helix_rt_forwards() (mmtbx.ncs.ncs.ncs_group method) helix_rt_reverse() (mmtbx.ncs.ncs.ncs_group method) helix_selection() (mmtbx.secondary_structure.manager method) helix_selections() (mmtbx.secondary_structure.manager method) hemisphere_acentrics() (cctbx.miller.array method) hemispheres_acentrics() (cctbx.miller.array method) hendrickson_lattman() (in module cctbx) hermann_mauguin() (cctbx.web.asu_gallery.jv_index.point_group_symbols method) hessian() (cctbx.examples.unit_cell_minimizers.refinery method) (in module cctbx.examples.unit_cell_minimizers) (mmtbx.scaling.relative_scaling.refinery method) hessian_transform() (mmtbx.scaling.relative_scaling.refinery method) hessians_work() (cctbx.xray.targets.r1.target method) (cctbx.xray.targets.shelxl_wght_ls method) hetero (iotbx.pdb.hierarchy.atom property) heterogen_section() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) hexagonal_sampling() (in module cctbx.crystal.close_packing) hg_two_loop_recursion() (in module cctbx.omz.bfgs) hide_points() (cctbx.web.asu_gallery.jvx.pointSet method) hierarchy() (iotbx.map_model_manager.map_model_manager method) HIGH_2FOFC (mmtbx.ions.identify.AtomProperties attribute) high_anom (mmtbx.ions.atom_type_flags attribute) HIGH_B (mmtbx.ions.identify.AtomProperties attribute) high_b_iso (mmtbx.ions.atom_type_flags attribute) high_fdp (mmtbx.ions.atom_type_flags attribute) high_fofc (mmtbx.ions.atom_type_flags attribute) high_occ (mmtbx.ions.atom_type_flags attribute) HIGH_OCC (mmtbx.ions.identify.AtomProperties attribute) high_resolution_for_twin_tests() (mmtbx.scaling.data_statistics.data_strength_and_completeness method) high_two_fofc (mmtbx.ions.atom_type_flags attribute) hist_outline() (in module xfel.command_line.view_pixel_histograms) histogram() (mmtbx.density_modification.local_standard_deviation_map method) histogram_finalise (class in xfel.cxi.cspad_ana.histogram_finalise) histogram_layout (class in mmtbx.polygon.output) histogram_slot_info (class in scitbx.array_family.flex) histograms() (iotbx.map_model_manager.map_model_manager method) HKLF() (in module cctbx.development.run_shelx) hl_coeffs (mmtbx.command_line.load_model_and_data attribute) hl_coeffs() (mmtbx.twinning.twin_f_model.twin_model_manager method) hl_coeffs_in_original_setting (mmtbx.density_modification.density_modification property) Hn() (in module cctbx.maptbx.mem) hoppe_gassmann_modification() (cctbx.miller.array method) hsv2rgb() (in module mmtbx.polygon.output) html_head_title() (in module cctbx.web.asu_gallery) html_loader() (in module cctbx.web.asu_gallery.jvx) Hw() (in module cctbx.maptbx.mem) hydrogen_bond_from_selection_pair() (in module mmtbx.secondary_structure.utils) hydrogen_deuterium_aliases() (mmtbx.monomer_library.cif_types.comp_comp_id method) hydrogens (mmtbx.validation.molprobity.molprobity attribute)

I

i_atom_by_id() (mmtbx.monomer_library.cif_types.comp_comp_id method) i_conformer (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) i_inv_j_multiplication_table (cctbx.miller.reindexing.assistant attribute) i_j_inv_multiplication_table (cctbx.miller.reindexing.assistant attribute) i_j_multiplication_table (cctbx.miller.reindexing.assistant attribute) i_mod (mmtbx.disorder.backbone.backrub_residue attribute) i_over_sig_i() (cctbx.miller.array method) i_over_sigma_outer_shell (mmtbx.scaling.xtriage.xtriage_analyses property) i_over_sigma_outer_shell() (mmtbx.scaling.data_statistics.data_strength_and_completeness method) i_seq (cctbx.crystal.sym_pair attribute) (iotbx.pdb.hierarchy.atom property) (mmtbx.ions.svm.svm_prediction attribute), [1] (mmtbx.validation.molprobity.residue_multi_criterion attribute) i_seqs() (cctbx.crystal.sym_pair method) i_seqs_by_value() (scitbx.array_family.flex.std_string method) i_seqs_from_atoms() (iotbx.shelx.parsers.restraint_parser method) i_sigi_completeness_stats (class in mmtbx.scaling.data_statistics) i_vars (cctbx.sgtbx.special_op_simplified_term attribute) ias (class in mmtbx.ias) ias_counters (class in mmtbx.ias) ias_position_at_lone_pairs() (in module mmtbx.ias) ias_site_position() (in module mmtbx.ias) iass_as_xray_structure() (mmtbx.ias.manager method) ice_ring_checker (class in mmtbx.scaling.data_statistics) icode (iotbx.pdb.hierarchy.atom_with_labels property) (iotbx.pdb.hierarchy.residue property) (iotbx.pdb.hierarchy.residue_group property) (mmtbx.disorder.analyze_model.residue_group_proxy attribute) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) id (iotbx.pdb.hierarchy.chain property) (iotbx.pdb.hierarchy.model property) id() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) id_dict (class in mmtbx.monomer_library.server) id_str (mmtbx.disorder.backbone.backrub_residue attribute) (mmtbx.validation.ligands.ligand_validation attribute) (mmtbx.validation.ramalyze.c_alpha attribute) id_str() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_group method) (iotbx.pdb.hierarchy.atom_with_labels method) (iotbx.pdb.hierarchy.residue method) (iotbx.pdb.hierarchy.residue_group method) (mmtbx.disorder.analyze_model.residue_group_proxy method) (mmtbx.ions.environment.atom_contact method) (mmtbx.validation.atom_base method) (mmtbx.validation.clashscore.clash method) (mmtbx.validation.clashscore.nqh_flip method) (mmtbx.validation.entity method) (mmtbx.validation.model_properties.atom_occupancy method) (mmtbx.validation.residue method) (mmtbx.validation.restraints.restraint method) (mmtbx.validation.rna_validate.rna_angle method) (mmtbx.validation.rna_validate.rna_bond method) (mmtbx.validation.waters.water method) id_str_no_atom_name() (mmtbx.validation.clashscore.clash method) id_str_old() (mmtbx.validation.ramalyze.ramachandran method) (mmtbx.validation.rotalyze.rotamer method) id_str_src_atom_no_atom_name() (mmtbx.validation.clashscore.clash method) ideal (mmtbx.validation.cbetadev.calculate_ideal_and_deviation attribute) ideal_xyz (mmtbx.validation.cbetadev.cbeta attribute) idealized_calpha_angles() (in module mmtbx.validation.cbetadev) identifier() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp) identify() (mmtbx.rotamer.rotamer_eval.RotamerID method) identity (class in scitbx.matrix) (mmtbx.building.make_library.related_chain attribute) identity() (in module mmtbx.geometry.asa) (mmtbx.ions.identify.AtomProperties method) identity_op_id() (mmtbx.ncs.ncs.ncs_group method) identity_op_id_in_first_group() (mmtbx.ncs.ncs.ncs method) identity_predicate (class in mmtbx.geometry.indexing) identity_predicate() (mmtbx.geometry.indexing.structure_indexer class method) ignore_hd (mmtbx.validation.model_properties.model_statistics attribute) ignored_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) image() (cctbx.maptbx.atom_curves method) (in module xfel.cxi.cspad_ana.cspad_tbx) image_from_3d() (cctbx.maptbx.atom_curves method) image_from_miller_indices() (cctbx.maptbx.atom_curves method) image_template() (in module xfel.command_line.cxi_stream_to_pickle) image_xpp() (in module xfel.cxi.cspad_ana.cspad_tbx) ImageFactory() (in module xfel.cxi.average_spots) (in module xfel.cxi.display_spots) imageset() (in module dxtbx.serialize.load) img_add() (in module xfel.cxi.average_spots) 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) import_eq_distances() (mmtbx.den.den_restraints method) import_ncs_group() (mmtbx.ncs.ncs.ncs method) improper_cnab_from_atoms() (in module mmtbx.rotamer) improper_ncab_from_atoms() (in module mmtbx.rotamer) in_which_cuts() (cctbx.sgtbx.direct_space_asu.direct_space_asu method) INCIDENT_BEAM (xfel.metrology.mark0.correction_vectors attribute) include() (mmtbx.geometry.indexing.containment_predicate static method) include_predicate() (mmtbx.geometry.indexing.structure_indexer class method) inclusion() (mmtbx.geometry.indexing.containment_predicate class method) inclusive (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute) incomplete (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) incomplete_info (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) increment_and_track_up_from_zero() (scitbx.array_family.flex.size_t method) increment_category_counts() (mmtbx.validation.restraints.chiralities method) incremental_clustering (class in cctbx.crystal) incremental_fits() (in module cctbx.eltbx.gaussian_fit) incremental_pairs() (cctbx.crystal.special_position_settings method) index() (cctbx.web.asu_gallery.jvx.pointSet method) index1d() (cctbx.macro_mol.rotation_parameters.matrix33 method) index_span() (cctbx.miller.set method) Indexer (class in mmtbx.geometry.altloc) indices (scitbx.array_family.flex.smart_selection property) indices() (cctbx.miller.set method) inflate() (mmtbx.refinement.refinement_flags.manager method) info (iotbx.pdb.hierarchy.root property) (mmtbx.validation.experimental.data_statistics attribute) info() (cctbx.miller.array method) (iotbx.map_model_manager.map_model_manager method) (mmtbx.twinning.twin_f_model.twin_model_manager method) init_calc_wilson() (xfel.clustering.singleframe.SingleFrame method) init_ncs_group() (mmtbx.ncs.ncs.ncs method) init_oper() (mmtbx.ncs.ncs.ncs method) init_slots_with_none() (cctbx.omz.cif_refine.extract_from_cif_files method) initialize() (mmtbx.refinement.real_space.rsr_model method) (mmtbx.refinement.real_space.structure_monitor method) (mmtbx.secondary_structure.manager method) (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method) initialize_map_data() (iotbx.map_manager.map_manager method) initialize_maps() (iotbx.map_model_manager.map_model_manager method) initialize_table() (cctbx.geometry_restraints.bond_simple_proxy_registry method) (cctbx.geometry_restraints.proxy_registry_base method) initialize_tables() (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method) initialize_tables_and_insert_command() (xfel.cxi.correction_vector_plot.manage_sql method) inner_loop() (in module mmtbx.maps.fem) inp_as_xray_structures() (in module cctbx.web.phase_o_phrenia) inp_from_form() (in module cctbx.web.cgi_utils) input (class in iotbx.pdb.ext) input() (in module iotbx.pdb) insert() (iotbx.pdb.hierarchy.af_shared_atom method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) (xfel.cxi.correction_vector_plot.manage_sql method) insert_atom() (iotbx.pdb.hierarchy.atom_group method) insert_atom_group() (iotbx.pdb.hierarchy.residue_group method) insert_atom_into_model() (in module mmtbx.hydrogens.find) insert_chain() (iotbx.pdb.hierarchy.model method) insert_model() (iotbx.pdb.hierarchy.root method) insert_residue_group() (iotbx.pdb.hierarchy.chain method) Inserter (class in mmtbx.geometry.altloc) inside_zero_one() (in module cctbx.euclidean_model_matching) instruction_parser (class in iotbx.shelx.parsers) int (class in scitbx.array_family.flex) integrand() (cctbx.maptbx.atom_curves method) integrate_one_image() (in module xfel.cxi.integrate_image_api) (in module xfel.cxi.strong_zulu) intensities() (cctbx.miller.array method) intensity (class in cctbx.xray.observation_types) intensity_correlation (class in cctbx.xray.target_functors) intensity_flag (mmtbx.command_line.load_model_and_data attribute) intensity_group (cctbx.miller.reindexing.assistant attribute) intensity_quasi_normalisations() (cctbx.miller.array method) intensity_quasi_unit_weighting (class in cctbx.xray.weighting_schemes) intensity_statistics() (xfel.clustering.cluster.Cluster method) interaction_counts_with() (mmtbx.geometry.indexing.structure_indexer method) interaction_ranges_with() (mmtbx.geometry.indexing.structure_indexer method) interactions_with() (mmtbx.geometry.indexing.structure_indexer method) interleaved_lbfgs_minimization (class in mmtbx.dynamics.cartesian_dynamics) (class in mmtbx.dynamics.ensemble_cd) interleaved_minimization() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) interpolate() (cctbx.maptbx.peak_search_parameters method) (in module cctbx.french_wilson) (in module xfel.command_line.smooth_spectrum) interpolate_2d() (in module mmtbx.conformation_dependent_library.utils) interpolate_at_point() (in module mmtbx.conformation_dependent_library.utils) interpret_coordinate_line() (in module cctbx.web.io_utils) interpret_form_data() (in module cctbx.web.all_axes) (in module cctbx.web.browse_settings) (in module cctbx.web.change_basis) (in module cctbx.web.change_hand) (in module cctbx.web.change_setting) (in module cctbx.web.emma) (in module cctbx.web.explore_symmetry) (in module cctbx.web.frac_cart) (in module cctbx.web.iotbx_cif_validate) (in module cctbx.web.lattice_symmetry) (in module cctbx.web.libtbx_help) (in module cctbx.web.phase_o_phrenia) (in module cctbx.web.shelx) (in module cctbx.web.structure_factors) (in module cctbx.web.structure_factors_pdb) (in module cctbx.web.wyckoff) interpret_generic_coordinate_line() (in module cctbx.web.emma) interpret_skip_columns() (in module cctbx.web.io_utils) intersection() (in module cctbx.adptbx) (in module cctbx.sgtbx.direct_space_asu.facet_analysis) (scitbx.array_family.flex.size_t method) intersection_i_seqs() (scitbx.array_family.flex.size_t method) intersection_of_scatterers() (cctbx.xray.structure.structure method) inv_perms (cctbx.miller.reindexing.assistant attribute) inverse() (iotbx.map_manager.shift_aware_rt method) (scitbx.matrix.rec method) inverse_hand() (cctbx.crystal.symmetry method) inverse_permutation() (scitbx.array_family.flex.size_t method) inverse_transform_hierarchy() (mmtbx.maps.superpose.common_frame_of_reference method) inversion (class in scitbx.matrix) invert_hand() (iotbx.map_manager.map_manager method) invert_matrices() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) involves_broken_bonds() (in module mmtbx.monomer_library.pdb_interpretation) involves_special_positions() (mmtbx.monomer_library.pdb_interpretation.special_position_dict method) ion_anomalous_vector() (in module mmtbx.ions.svm) ion_class() (in module mmtbx.ions.svm) ion_electron_density_vector() (in module mmtbx.ions.svm) ion_geometry_vector() (in module mmtbx.ions.svm) ion_master_phil() (in module mmtbx.ions.identify) ion_model_vector() (in module mmtbx.ions.svm) ion_nearby_atoms_vector() (in module mmtbx.ions.svm) ion_result (class in mmtbx.ions.identify) ion_valence_vector() (in module mmtbx.ions.svm) ion_vector() (in module mmtbx.ions.svm) iotbx.file_reader module iotbx.map_manager module iotbx.map_model_manager module iotbx.reflection_file_reader module iotbx.shelx module iotbx.shelx.crystal_symmetry_from_ins module iotbx.shelx.hklf module iotbx.shelx.lexer module iotbx.shelx.parsers module

iotbx.shelx.tokens module iotbx.shelx.write_ins module iotbx.shelx.writer module iotbx.xds.integrate_hkl module iotbx.xds.read_ascii module iotbx.xds.spot_xds module iotbx.xds.xds_inp module iotbx.xds.xparm module iplace() (in module xfel.cxi.cspad_ana.cspad_tbx) iround() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.vec3_double method) is_0_based() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) is_2p (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) is_2p_delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) is_2p_o3p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) is_2p_p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) is_3p_delta (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) is_allowed_origin_shift() (cctbx.sgtbx.space_group_info method) is_any_proxy_set() (cctbx.geometry_restraints.bond_simple_proxy_registry method) is_approx_zero() (scitbx.matrix.rec method) is_approximately_helical() (in module mmtbx.secondary_structure.proteins) is_atom_group_pair_linked() (in module mmtbx.monomer_library.linking_utils) is_atom_metal_coordinated() (in module mmtbx.monomer_library.linking_utils) is_atom_pair_linked() (in module mmtbx.monomer_library.linking_utils) is_atom_pair_linked_tuple() (in module mmtbx.monomer_library.linking_utils) is_bad_water() (mmtbx.validation.waters.water method) is_bonded_atoms() (cctbx.geometry_restraints.manager.manager method) is_bool() (mmtbx.refinement.refinement_flags.manager method) is_bool_array() (cctbx.miller.array method) is_bounded_by_constant() (in module cctbx.maptbx) is_buerger_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method) is_ca_only() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.root method) is_carboxy_terminus (mmtbx.ions.environment.atom_contact attribute) is_cbeta_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method) is_centric() (mmtbx.scaling.xtriage.xtriage_summary method) is_chemical_components_file() (in module mmtbx.chemical_components) is_cis_peptide() (in module mmtbx.rotamer) (in module mmtbx.validation.analyze_peptides) (in module mmtbx.validation.ramalyze) is_clash_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method) is_code() (in module mmtbx.chemical_components) is_col_zero() (scitbx.matrix.rec method) is_compatible_anomalous_scattering() (mmtbx.ions.identify.AtomProperties method) is_compatible_model() (iotbx.map_manager.map_manager method) is_compatible_ncs_object() (iotbx.map_manager.map_manager method) is_compatible_site() (mmtbx.ions.identify.AtomProperties method) is_compatible_unit_cell() (cctbx.crystal.symmetry method) is_complex_array() (cctbx.miller.array method) is_consistent_with_wrapping() (iotbx.map_manager.map_manager method) is_converged() (cctbx.maptbx.mem.run method) (mmtbx.bulk_solvent.scaler.run method) is_correct() (mmtbx.monomer_library.glyco_utils.glyco_link_class method) is_correctly_identified() (mmtbx.ions.identify.AtomProperties method) is_delta_outlier (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) is_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method) is_dummy_map_manager() (iotbx.map_manager.map_manager method) is_elliptically_truncated() (mmtbx.scaling.data_statistics.analyze_resolution_limits method) is_empty() (cctbx.crystal.symmetry method) is_epsilon_outlier (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) is_equivalent() (cctbx.sgtbx.symmetry_equivalent_pair_interactions method) is_favorable_halide_environment() (in module mmtbx.ions.halides) is_first_after_break (iotbx.pdb.hierarchy.atom_with_labels property) is_first_conformer_in_chain (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) is_first_in_chain (iotbx.pdb.hierarchy.atom_with_labels property) is_flags_good() (mmtbx.bulk_solvent.scaler.run method) is_forward_compatible_hierarchy() (iotbx.pdb.hierarchy.root method) is_full_size() (iotbx.map_manager.map_manager method) is_geometry_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method) is_glyco_amino_bond() (in module mmtbx.monomer_library.linking_utils) is_glyco_bond() (in module mmtbx.monomer_library.linking_utils) is_handedness_swap() (mmtbx.validation.restraints.chirality method) is_heavy_atom() (mmtbx.validation.waters.water method) is_helical_along_z() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) is_hendrickson_lattman_array() (cctbx.miller.array method) is_hierarchy_altloc_consistent() (iotbx.pdb.hierarchy.root method) is_identical_hierarchy() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue_group method) is_identical_symmetry() (cctbx.crystal.symmetry method) is_identity() (cctbx.sgtbx.special_op_simplified_term method) (in module mmtbx.ncs.ncs) is_in_asu() (cctbx.miller.set method) is_in_chain() (mmtbx.validation.atoms method) is_in_coset() (cctbx.sgtbx.cosets.double_cosets method) is_in_group() (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method) (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method) is_in_list_of_cosets() (cctbx.sgtbx.cosets.double_cosets method) is_in_range() (in module mmtbx.ncs.ncs) is_in_same_conformer_as() (iotbx.pdb.hierarchy.atom method) is_incomplete() (cctbx.crystal.symmetry method) is_inside() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression method) (cctbx.sgtbx.direct_space_asu.direct_space_asu method) is_inside_mask() (in module iotbx.map_model_manager) is_integer_array() (cctbx.miller.array method) is_integrate_hkl_file() (iotbx.xds.integrate_hkl.reader static method) is_iterate (cctbx.omz.dev.xfgc_info attribute) is_joined_at_calpha() (in module mmtbx.disorder.analyze_model) is_map_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method) is_mask() (iotbx.map_manager.map_manager method) is_match() (mmtbx.monomer_library.pdb_interpretation.link_match_one method) is_matching_mod_for() (mmtbx.monomer_library.cif_types.chem_mod_angle method) (mmtbx.monomer_library.cif_types.chem_mod_bond method) (mmtbx.monomer_library.cif_types.chem_mod_chir method) (mmtbx.monomer_library.cif_types.chem_mod_plane_atom method) (mmtbx.monomer_library.cif_types.chem_mod_tor method) (mmtbx.monomer_library.cif_types.chem_mod_tree method) is_monomer_library_file() (in module mmtbx.monomer_library) is_n_glyco_bond() (in module mmtbx.monomer_library.linking_utils) is_na() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) is_negatively_charged_oxygen() (in module mmtbx.ions.halides) is_niggli_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method) is_nonsense() (cctbx.crystal.symmetry method) is_o_glyco_bond() (in module mmtbx.monomer_library.linking_utils) is_odd_numbered() (in module xfel.cxi.util) is_one_of() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) is_outlier() (mmtbx.validation.entity method) is_padded() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) is_part_of_segment() (mmtbx.disorder.analyze_model.disordered_segment method) is_patterson_symmetry() (cctbx.crystal.symmetry method) is_peptide() (mmtbx.monomer_library.cif_types.comp_comp_id method) is_periodic() (in module cctbx.maptbx) is_phenix_refinement() (mmtbx.validation.molprobity.pdb_header_info method) is_pinwheel_region() (in module xfel.cxi.display_powder_arcs) is_point_group_symmetry() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) is_populated (mmtbx.validation.molprobity.multi_criterion_view attribute) is_positive_definite_u() (cctbx.xray.structure.structure method) is_proper_match() (mmtbx.monomer_library.pdb_interpretation.link_match method) is_protein() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) is_proxy_present() (in module mmtbx.geometry_restraints.ramachandran) is_proxy_set() (cctbx.geometry_restraints.bond_simple_proxy_registry method) is_pseudochiral() (mmtbx.validation.restraints.chirality method) is_pure_main_conf (iotbx.pdb.hierarchy.residue property) is_r3_identity_matrix() (scitbx.matrix.rec method) is_r3_rotation_matrix() (scitbx.matrix.rec method) is_r3_rotation_matrix_rms() (scitbx.matrix.rec method) is_ramachandran_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method) is_real_array() (cctbx.miller.array method) is_reference_setting() (cctbx.sgtbx.space_group_info method) is_residue_specified() (in module mmtbx.chemical_components) is_reticular_polyholohedral() (in module cctbx.sgtbx.reticular_pg_tools) is_rna() (mmtbx.monomer_library.cif_types.comp_comp_id method) is_rna2p (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) is_rna_dna (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) is_rna_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method) is_rotamer_outlier() (mmtbx.validation.molprobity.residue_multi_criterion method) is_same_model_as_before() (in module mmtbx.monomer_library.pdb_interpretation) is_same_residue() (mmtbx.validation.residue method) is_same_residue_group() (mmtbx.validation.residue method) is_same_transform() (in module mmtbx.ncs.ncs) is_schrodinger_installed() (in module mmtbx.geometry_restraints.external) is_self_clash() (mmtbx.geometry.clash.ClashingPair method) is_similar() (cctbx.xray.structure.structure method) (iotbx.map_manager.map_manager method) (iotbx.map_manager.shift_aware_rt method) (mmtbx.validation.clashscore.probe_line_info method) is_similar_hierarchy() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue_group method) (iotbx.pdb.hierarchy.root method) is_similar_ncs_group() (mmtbx.ncs.ncs.ncs_group method) is_similar_ncs_object() (mmtbx.ncs.ncs.ncs method) is_similar_symmetry() (cctbx.crystal.symmetry method) is_similar_to() (dxtbx.model.goniometer.Goniometer method) is_single_residue_object() (mmtbx.validation.atom method) (mmtbx.validation.atoms method) (mmtbx.validation.entity method) (mmtbx.validation.residue method) is_size_t() (mmtbx.refinement.refinement_flags.manager method) is_square() (scitbx.matrix.rec method) is_square_matrix() (scitbx.array_family.flex.double method) is_standard_glyco_link() (in module mmtbx.monomer_library.glyco_utils) is_string_array() (cctbx.miller.array method) is_stub_residue() (in module mmtbx.building) is_subgroup() (cctbx.sgtbx.cosets.left_decomposition method) (in module cctbx.sgtbx.reticular_pg_tools) is_super_set() (scitbx.array_family.flex.bool method) is_supported_donor() (mmtbx.ions.parameter_server method) is_supported_element() (mmtbx.ions.parameter_server method) is_terminus (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) is_trans_peptide() (in module mmtbx.validation.analyze_peptides) is_trivial_1d() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) is_twin_fmodel_manager() (mmtbx.twinning.twin_f_model.twin_model_manager method) is_twinned() (mmtbx.scaling.xtriage.xtriage_analyses method) is_unique_set_under_symmetry() (cctbx.miller.set method) is_unmerged_intensity_array() (cctbx.miller.array method) is_unusual (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) is_useful() (cctbx.omz.cod_select_and_pickle.cod_data method) is_valid_index() (scitbx.array_family.flex.grid method) is_water() (mmtbx.monomer_library.cif_types.comp_comp_id method) is_water_last() (mmtbx.solvent.ensemble_ordered_solvent.manager method) is_xds_inp_file() (iotbx.xds.xds_inp.reader static method) is_xparm_file() (iotbx.xds.xparm.reader static method) is_xray_amplitude_array() (cctbx.miller.array method) is_xray_data_array() (cctbx.miller.array method) is_xray_intensity_array() (cctbx.miller.array method) is_xray_reconstructed_amplitude_array() (cctbx.miller.array method) is_zero() (scitbx.matrix.rec method) iselection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) (scitbx.array_family.flex.bool method) iso_b_wilson (mmtbx.scaling.xtriage.xtriage_analyses property) isotropic_adp_deviation() (cctbx.adp_restraints.energies.energies method) isPrePro() (in module mmtbx.validation.ramalyze) issue_merohedral_twinning() (iotbx.shelx.parsers.instruction_parser method) iter_molprobity_gui_fields() (mmtbx.validation.molprobity.summary method) iter_residue_groups() (in module mmtbx.building) (mmtbx.validation.sequence.chain method) iter_results() (mmtbx.validation.model_properties.xray_structure_statistics method) (mmtbx.validation.validation method) iter_until_loop() (in module mmtbx.monomer_library.conv_v2_v3) iterate_sites() (in module mmtbx.ions.svm.utils) iteration_limit() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.reduction_base method) iteration_limit_exceeded iterations (class in scitbx.lstbx.normal_eqns_solving) iterations() (cctbx.maptbx.mem.run method) iterator() (in module mmtbx.rotamer) iterrows() (iotbx.cif.model.loop method) ito_vol_c_2011_table_4_3_2_2_elements() (in module cctbx.eltbx.e_scattering) ito_vol_c_2011_table_4_3_2_2_entry_as_gaussian() (in module cctbx.eltbx.e_scattering) itvc_sampling_selection() (cctbx.eltbx.development.kissel_io.table method)

J

j_mod (mmtbx.disorder.backbone.backrub_residue attribute) j_seq (cctbx.crystal.sym_pair attribute) jacobian_frame_rotx (xfel.metrology.mark10.fit_translation4 attribute) join_edge() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method) join_hierarchies() (in module mmtbx.building.make_library) join_point() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method) join_selections() (in module mmtbx.maps.composite_omit_map)

join_symmetry() (cctbx.crystal.symmetry method) journaled_non_linear_ls (class in scitbx.lstbx.normal_eqns_solving) jvx() (cctbx.web.asu_gallery.jvx.faceSet method) (cctbx.web.asu_gallery.jvx.geometry method) (cctbx.web.asu_gallery.jvx.lineSet method) (cctbx.web.asu_gallery.jvx.pointSet method) jvx_item_colors() (in module cctbx.web.asu_gallery.jvx)

K

k (mmtbx.map_names attribute) k_anisotropic() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.bulk_solvent.scaler.run method) k_isotropic() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.bulk_solvent.scaler.run method) k_mask_grid_search() (mmtbx.bulk_solvent.scaler.run method) k_masks() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.bulk_solvent.scaler.run method) k_overall_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) k_part() (mmtbx.twinning.twin_f_model.twin_model_manager method) k_part_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) k_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method) k_sol_b_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method) k_sol_b_sol_b_cart_minimizer() (in module mmtbx.bulk_solvent.bulk_solvent_and_scaling) k_sol_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) k_sol_u_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method) k_sols() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.twinning.twin_f_model.twin_model_manager method) kappa() (dxtbx.model.goniometer.GoniometerFactory static method) KappaGoniometer (class in dxtbx.model.goniometer)

kb_range() (in module mmtbx.bulk_solvent.bulk_solvent_and_scaling) (in module mmtbx.twinning.twin_f_model) kernel_normalisation (class in mmtbx.scaling.absolute_scaling) keys() (iotbx.cif.model.block method) (iotbx.cif.model.cif method) (iotbx.cif.model.loop method) keywise_printout() (in module xfel.command_line.print_pickle) kick_fmodel() (in module mmtbx.maps.kick) kick_map_coeffs() (in module mmtbx.maps.kick) kin_vec() (in module mmtbx.kinemage) kinemage_file (mmtbx.validation.molprobity.molprobity attribute) kinemage_header (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.restraint_validation attribute) kinemage_key() (mmtbx.validation.restraints.restraint method) kinetic_energy_and_temperature (class in mmtbx.dynamics) kinetic_energy_as_temperature() (in module mmtbx.dynamics) kinetic_energy_stats() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) known_axis() (dxtbx.model.goniometer.GoniometerFactory static method) ksol_bsol_result (class in mmtbx.bulk_solvent.bulk_solvent_and_scaling)

L

l_test (class in mmtbx.scaling.twin_analyses) l_test_mean_l (mmtbx.scaling.xtriage.xtriage_analyses property) l_test_mean_l_squared (mmtbx.scaling.xtriage.xtriage_analyses property) label (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) labeled_fit (class in cctbx.eltbx.development.format_gaussian_fits) labelit_check_pdb_symmetry_form() (cctbx.sgtbx.literal_description.literal_description method) labelit_check_pdb_symmetry_short() (cctbx.sgtbx.literal_description.literal_description method) labels (mmtbx.validation.graphics.residue_bin attribute) (mmtbx.validation.molprobity.summary attribute) labels() (mmtbx.monomer_library.pdb_interpretation.source_info_server method) labels_refine() (cctbx.xray.scatterer.anomalous_scatterer_group method) laser_status (class in xfel.cxi.cspad_ana.mod_event_info) last() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) last_resseq_as_int() (iotbx.pdb.hierarchy.root method) LATT_SYMM() (in module iotbx.shelx.write_ins) lattice_group (cctbx.miller.reindexing.assistant attribute) lattice_group_info() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method) LatticeCharacter (class in cctbx.crystal.burzlaff_zimmermann_dewolff) launcher (class in mmtbx.maps.fobs_minus_fobs_map) (class in mmtbx.scaling.xtriage) lbfgs (class in cctbx.geometry_restraints.lbfgs) (class in cctbx.maptbx.real_space_refinement_simple) (class in cctbx.xray.minimization) (class in mmtbx.refinement.geometry_minimization) (class in mmtbx.refinement.minimization) (class in mmtbx.refinement.minimization_ncs_constraints) lbfgs_emulation() (cctbx.omz.dev.refinement method) lcm_of_denominators() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) le_page_1982_delta_details (class in cctbx.sgtbx) least_squares (class in cctbx.examples.exp_i_alpha_derivatives) (class in cctbx.xray.target_functors) least_squares_residual (in module cctbx.xray.target_functors) least_squares_residual_for_amplitude (class in cctbx.xray.target_functors) left_decomposition (class in cctbx.sgtbx.cosets) left_decomposition_point_groups_only (class in cctbx.sgtbx.cosets) len_peaks() (in module mmtbx.hydrogens.find) length() (mmtbx.geometry.topology.GreedyMatch method) (mmtbx.geometry.topology.McGregorMatch method) (mmtbx.geometry.topology.RascalMatch method) (scitbx.matrix.rec method) length_sq() (scitbx.matrix.rec method) level() (in module cctbx.sgtbx.symbol_confidence) levenberg_marquardt_iterations (class in scitbx.lstbx.normal_eqns_solving) levenberg_marquardt_iterations_encapsulated_eqns (class in scitbx.lstbx.normal_eqns_solving) lex_scatterer() (iotbx.shelx.parsers.atom_parser method) lhs (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute) lib_link (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) libtbx module ligand_validation (class in mmtbx.validation.ligands) ligands (mmtbx.validation.model_properties.model_statistics property) ligands() (mmtbx.ligands.xtal_screens.solution method) ligands_ (mmtbx.ligands.xtal_screens.solution attribute) like_coord (mmtbx.ions.atom_type_flags attribute) LIKE_COORD (mmtbx.ions.identify.AtomProperties attribute) likelihood() (in module mmtbx.scaling.absences) limit_frac_min_frac_max() (in module mmtbx.utils) line (class in cctbx.web.asu_gallery.jvx) line_sample_point() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) line_search() (cctbx.omz.dev.refinement method) linear_indexer_for() (in module mmtbx.geometry.clash) lines (class in xfel.cxi.correction_vector_plot) lineSet (class in cctbx.web.asu_gallery.jvx) link_link_id (class in mmtbx.monomer_library.cif_types) link_match (class in mmtbx.monomer_library.pdb_interpretation) link_match_one (class in mmtbx.monomer_library.pdb_interpretation) link_to_previous (iotbx.pdb.hierarchy.residue property) (iotbx.pdb.hierarchy.residue_group property)

LinkExploreSymmetry() (in module cctbx.web.multiple_cell) linking_mixins (class in mmtbx.monomer_library.linking_mixins) list (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points attribute) list() (mmtbx.scaling.absences.sgi_iterator method) list_3d_as_bool_selection() (in module mmtbx.refinement.occupancies) list_all_axes() (in module cctbx.examples.all_axes) list_dict (mmtbx.validation.clashscore.clashscore attribute) literal_description (class in cctbx.sgtbx.literal_description) literals() (xfel.cxi.correction_vector_plot.lines method) load_all_models_in_directory() (in module mmtbx.building.make_library) load_and_validate_unmerged_data() (in module mmtbx.command_line) load_cc_data() (in module xfel.cxi.cxi_cc) load_cxi_phil() (in module xfel.phil_preferences) load_data() (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) load_db() (in module mmtbx.polygon) load_den_network() (mmtbx.den.den_restraints method) load_emsley8k_tables() (in module mmtbx.geometry_restraints.ramachandran) load_model_and_data (class in mmtbx.command_line) load_mon_lib_file() (in module mmtbx.monomer_library.server) load_pdb_models() (in module mmtbx.building.make_library) load_phi_psi_2_tables() (in module mmtbx.geometry_restraints.ramachandran) load_related_models_from_pdb() (in module mmtbx.building.make_library) load_related_models_in_directory() (in module mmtbx.building.make_library) load_result() (in module xfel.command_line.cxi_merge) load_tables() (in module mmtbx.geometry_restraints.ramachandran) loc_res() (in module cctbx.maptbx) local_altloc_from_atoms() (mmtbx.validation.rna_validate.rna_puckers method) local_density_quality (class in mmtbx.building) local_fsc() (iotbx.map_model_manager.map_model_manager method) local_lsq_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method) local_moment_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method) local_nikonov_scaling() (mmtbx.scaling.relative_scaling.local_scaling_driver method) local_overlap_map() (cctbx.miller.array method) local_resolution_map() (iotbx.map_model_manager.map_model_manager method) local_scale (class in cctbx.maptbx) local_scaling_driver (class in mmtbx.scaling.relative_scaling) local_standard_deviation_map (class in mmtbx.density_modification) local_standard_deviation_map() (cctbx.miller.array method) local_standard_deviations_gradients() (in module cctbx.maptbx.real_space_refinement_simple) local_standard_deviations_target() (in module cctbx.maptbx.real_space_refinement_simple) local_standard_deviations_target_per_site() (in module cctbx.maptbx.real_space_refinement_simple) log (mmtbx.command_line.load_model_and_data attribute) log_binned_completeness (class in mmtbx.scaling.data_statistics) log_binning() (cctbx.miller.set method) log_p() (in module mmtbx.scaling.absence_likelihood) (mmtbx.twinning.probabalistic_detwinning.detwin method) loggraph_output (class in mmtbx.scaling) lone_set() (cctbx.miller.set method) lone_sets() (cctbx.miller.set method) long (class in scitbx.array_family.flex) long_form() (cctbx.sgtbx.literal_description.literal_description method) looks_like_ccp4_flags() (in module cctbx.r_free_utils) looks_like_halide_ion() (mmtbx.ions.identify.manager method) looks_like_nucleotide_phosphate_site() (mmtbx.ions.identify.AtomProperties method) lookup() (mmtbx.monomer_library.conformation_dependent_restraints.pgd_server method) lookup_i_proxy() (cctbx.geometry_restraints.angle_proxy_registry method) (cctbx.geometry_restraints.dihedral_proxy_registry method) loop (class in iotbx.cif.model) loop() (cctbx.development.random_structure.wyckoff_pair_generator method) loop_over_space_groups() (cctbx.development.space_group_option_parser.space_group_processed_options method) loop_over_super_cells() (in module cctbx.examples.space_subgroups) loop_res_fac() (in module cctbx.examples.fft_map_electron_density_around_atom) loop_space_groups() (in module cctbx.development.debug_utils) looped_data (class in mmtbx.monomer_library.cif_types) looped_ids() (mmtbx.monomer_library.cif_types.looped_data method) low_anom (mmtbx.ions.atom_type_flags attribute) LOW_B (mmtbx.ions.identify.AtomProperties attribute) low_b_iso (mmtbx.ions.atom_type_flags attribute) low_d_cut (mmtbx.scaling.xtriage.xtriage_analyses property) low_fdp (mmtbx.ions.atom_type_flags attribute) low_fofc (mmtbx.ions.atom_type_flags attribute) low_occ (mmtbx.ions.atom_type_flags attribute) LOW_OCC (mmtbx.ions.identify.AtomProperties attribute) low_two_fofc (mmtbx.ions.atom_type_flags attribute) low_volume_density_elimination() (in module mmtbx.maps.fem) lower() (scitbx.array_family.flex.std_string method) lower_bidiagonal() (in module scitbx.array_family.flex) ls_ff_weights() (in module mmtbx.refinement.targets) (in module mmtbx.twinning.twin_f_model) ls_rel_scale_driver (class in mmtbx.scaling.relative_scaling) ls_sigma_weights() (in module mmtbx.refinement.targets) (in module mmtbx.twinning.twin_f_model)

M

macro_cycle_header() (in module mmtbx.refinement.print_statistics) macromolecule_fraction() (mmtbx.scaling.matthews.density_calculator method) macromolecules (mmtbx.validation.model_properties.model_statistics property) magnification() (mmtbx.ncs.ncs.ncs method) magnification_anisotropic_minimization (class in cctbx.maptbx.real_space_refinement_simple) main() (in module cctbx.eltbx.development.combine_fits) (in module cctbx.eltbx.development.format_gaussian_fits) (in module cctbx.eltbx.development.itvc_approx) (in module cctbx.eltbx.development.itvc_cross_validation) (in module cctbx.eltbx.development.itvc_fits) (in module cctbx.eltbx.development.kissel_fits) (in module cctbx.eltbx.development.kissel_io) (in module xfel.cxi.average_spots) make_and_place_nodes_and_connections() (cctbx.sgtbx.pointgroup_tools.point_group_graph method) make_beam() (dxtbx.model.beam.BeamFactory static method) make_big_header() (in module mmtbx.scaling.xtriage) make_detector() (dxtbx.model.detector.DetectorFactory static method) make_flips_if_necessary_torsion() (in module mmtbx.ncs.ncs_search) make_g6() (xfel.clustering.singleframe.SingleFrame static method) make_goniometer() (dxtbx.model.goniometer.GoniometerFactory static method) make_header() (in module mmtbx.refinement.print_statistics) make_int_pickle() (in module xfel.command_line.cxi_stream_to_pickle) make_kappa_goniometer() (dxtbx.model.goniometer.GoniometerFactory static method) make_list_of_target_xs_up_to_order (class in cctbx.sgtbx.sub_lattice_tools) make_log_beam_stop() (mmtbx.scaling.outlier_rejection.outlier_manager method) make_log_model() (mmtbx.scaling.outlier_rejection.outlier_manager method) make_log_wilson() (mmtbx.scaling.outlier_rejection.outlier_manager method) make_md5() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table) make_multi_axis_goniometer() (dxtbx.model.goniometer.GoniometerFactory static method) make_multikin() (in module mmtbx.kinemage.validation) make_new_cell_and_symmetry() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method) make_new_xs() (cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs method) (cctbx.sgtbx.sub_lattice_tools.make_list_of_target_xs_up_to_order method) make_peak_dict() (in module mmtbx.hydrogens.find) make_permutations() (in module cctbx.sgtbx.sub_lattice_tools) make_pg_r_table() (mmtbx.scaling.twin_analyses.symmetry_issues method) make_point() (in module cctbx.web.asu_gallery.jvx) make_polarized_beam() (dxtbx.model.beam.BeamFactory static method) make_polychromatic_beam() (dxtbx.model.beam.BeamFactory static method) make_probe_dots() (in module mmtbx.kinemage.validation) make_r_table() (mmtbx.scaling.twin_analyses.symmetry_issues method) make_scan() (dxtbx.model.scan.ScanFactory static method) make_scan_from_properties() (dxtbx.model.scan.ScanFactory static method) make_scatterer_labels_shelx_compatible_in_place() (cctbx.xray.structure.structure method) make_sub_cluster() (xfel.clustering.cluster.Cluster method) make_sub_header() (in module mmtbx.refinement.print_statistics) make_sym_op_table() (mmtbx.scaling.twin_analyses.twin_results_interpretation method) make_sys_abs_list() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method) make_tlso_compatible_with_u_positive_definite() (in module mmtbx.tls.tools) make_triples() (in module cctbx.sgtbx.sub_lattice_tools) make_up_hl_coeffs() (cctbx.miller.array method) makeAtomDict() (in module mmtbx.rotamer.sidechain_angles) manage_sql (class in xfel.cxi.correction_vector_plot) managed_calculation_base (class in cctbx.xray.structure_factors.manager) manager (class in cctbx.geometry_restraints.manager) (class in cctbx.xray.structure_factors.manager) (class in mmtbx.den.refinement) (class in mmtbx.ias) (class in mmtbx.ions.identify) (class in mmtbx.ions.svm) (class in mmtbx.masks) (class in mmtbx.refinement.adp_refinement) (class in mmtbx.refinement.ensemble_refinement.ensemble_utils) (class in mmtbx.refinement.group) (class in mmtbx.refinement.occupancies) (class in mmtbx.refinement.refinement_flags) (class in mmtbx.refinement.rigid_body) (class in mmtbx.secondary_structure) (class in mmtbx.solvent.ensemble_ordered_solvent) (class in mmtbx.solvent.ordered_solvent) manager() (cctbx.xray.structure_factors.manager.managed_calculation_base method) (in module mmtbx.dynamics.simulated_annealing) mandatory_factors() (cctbx.maptbx.crystal_gridding method) mandatory_grid_factors() (cctbx.xray.structure_factors.manager.manager method) map_accumulator() (in module cctbx.maptbx) map_and_map_coeff_master_params() (in module mmtbx.maps) map_as_fourier_coefficients() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) map_cc() (mmtbx.refinement.real_space.structure_monitor method) map_cc_histogram_per_atom() (mmtbx.refinement.real_space.structure_monitor method) map_coefficients() (cctbx.maptbx.mem.run method) (mmtbx.maps.composite_omit_map.run method) (mmtbx.twinning.twin_f_model.twin_model_manager method) (mmtbx.utils.extract_box_around_model_and_map method) map_coefficients_from_fmodel() (in module mmtbx.maps) map_coefficients_to_map() (in module cctbx.maptbx) map_coeffs_from_map() (mmtbx.maps.kick.run method) map_coeffs_from_mtz_file() (in module mmtbx.maps.utils) map_coeffs_in_original_setting (mmtbx.density_modification.density_modification property) map_coeffs_list (mmtbx.maps.composite_omit_map.omit_region_results attribute) map_coeffs_mtz_label_manager (class in mmtbx.maps) map_correlation() (cctbx.miller.array method) map_data() (iotbx.map_model_manager.map_model_manager method) map_data_1() (iotbx.map_model_manager.map_model_manager method) map_data_2() (iotbx.map_model_manager.map_model_manager method) map_data_list() (iotbx.map_model_manager.map_model_manager method) map_detector_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx) map_dict() (iotbx.map_model_manager.map_model_manager method) map_id_list() (iotbx.map_model_manager.map_model_manager method) map_info() (iotbx.map_model_manager.map_model_manager method) map_inside_unit_cell() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) map_manager (class in iotbx.map_manager) (class in mmtbx.hydrogens) map_manager() (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) map_manager_1() (iotbx.map_model_manager.map_model_manager method) map_manager_2() (iotbx.map_model_manager.map_model_manager method) map_manager_mask() (iotbx.map_model_manager.map_model_manager method) map_managers() (iotbx.map_model_manager.map_model_manager method) map_map_cc() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) map_map_fsc() (iotbx.map_model_manager.map_model_manager method) map_model_cc() (iotbx.map_model_manager.map_model_manager method) map_model_manager (class in iotbx.map_model_manager) map_names (class in mmtbx) map_of_coeff_scaled() (in module mmtbx.max_lik.max_like_non_uniform) map_peak_3d_as_2d() (in module cctbx.maptbx) map_peak_filter() (in module mmtbx.hydrogens.find) map_stats (mmtbx.ions.svm.svm_prediction attribute), [1] map_stats() (mmtbx.ions.identify.manager method) map_to_asu() (cctbx.miller.array method) (cctbx.miller.set method) map_to_map_coefficients() (in module cctbx.maptbx) map_values_along_line_connecting_two_points() (in module cctbx.maptbx) maps (class in mmtbx.solvent.ordered_solvent) maps_including_IO_master_params() (in module mmtbx.maps) marks (mmtbx.validation.graphics.residue_bin attribute) markup (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) mask() (in module cctbx.maptbx) (mmtbx.density_modification.local_standard_deviation_map method) mask_all_maps_around_atoms() (iotbx.map_model_manager.map_model_manager method) mask_all_maps_around_density() (iotbx.map_model_manager.map_model_manager method) mask_all_maps_around_edges() (iotbx.map_model_manager.map_model_manager method) mask_as_xplor_map() (mmtbx.masks.bulk_solvent method) mask_data_whole_uc() (mmtbx.masks.asu_mask method) mask_from_xray_structure (class in mmtbx.masks) mask_grid() (in module mmtbx.maps.superpose) mask_info() (iotbx.map_model_manager.map_model_manager method) massage_data (class in mmtbx.scaling.massage_twin_detwin_data) master_params() (in module mmtbx.dynamics.simulated_annealing) (in module mmtbx.pdbtools) (in module mmtbx.solvent.ensemble_ordered_solvent) (in module mmtbx.solvent.ordered_solvent) master_phil (mmtbx.command_line.load_model_and_data attribute) master_phil() (in module mmtbx.ions.svm.dump_sites) match_bijvoet_mates() (cctbx.miller.set method) match_cb_to_ca() (iotbx.map_model_manager.map_model_manager method) match_dihedral_to_name() (in module mmtbx.validation.utils) match_dod() (in module mmtbx.hydrogens.find) match_indices() (cctbx.miller.set method) match_map_model_ncs (class in iotbx.map_model_manager) match_model_b_to_map() (iotbx.map_model_manager.map_model_manager method) match_od() (in module mmtbx.hydrogens.find) match_record (class in cctbx.command_line.euclidean_model_matching) match_refine (class in cctbx.euclidean_model_matching) match_refine_times() (in module cctbx.euclidean_model_matching) match_rt_from_ref_eucl_rt() (in module cctbx.euclidean_model_matching) match_runs() (in module xfel.command_line.auto_submit) match_sort_function() (in module cctbx.euclidean_model_matching) matching_set() (cctbx.miller.array method) mathematica_form() (scitbx.array_family.flex.double method) (scitbx.matrix.rec method) MathForm_adp() (in module cctbx.development.fmt_utils) MathFormMx33() (in module cctbx.development.fmt_utils) MathFormVec3() (in module cctbx.development.fmt_utils) matlab_form() (scitbx.matrix.rec method) matrix33 (class in cctbx.macro_mol.rotation_parameters) matrix_back_substitution() (scitbx.array_family.flex.double method) matrix_back_substitution_given_transpose() (scitbx.array_family.flex.double method) matrix_copy_block() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) matrix_copy_column() (scitbx.array_family.flex.double method) matrix_copy_lower_to_upper_triangle_in_place() (scitbx.array_family.flex.double method) matrix_copy_lower_triangle() (scitbx.array_family.flex.double method) matrix_copy_upper_to_lower_triangle_in_place() (scitbx.array_family.flex.double method) matrix_copy_upper_triangle() (scitbx.array_family.flex.double method) matrix_determinant_via_lu() (scitbx.array_family.flex.double method) matrix_diagonal() (scitbx.array_family.flex.double method) matrix_diagonal_add_in_place() (scitbx.array_family.flex.double method) matrix_diagonal_product() (scitbx.array_family.flex.double method) matrix_diagonal_set_in_place() (scitbx.array_family.flex.double method) matrix_diagonal_sum() (scitbx.array_family.flex.double method) matrix_forward_substitution() (scitbx.array_family.flex.double method) matrix_forward_substitution_given_transpose() (scitbx.array_family.flex.double method) matrix_inversion() (scitbx.array_family.flex.double method) matrix_inversion_in_place() (scitbx.array_family.flex.double method) matrix_is_symmetric() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) matrix_lower_bidiagonal() (scitbx.array_family.flex.double method) matrix_lower_triangle_as_packed_l() (scitbx.array_family.flex.double method) matrix_lu_back_substitution() (scitbx.array_family.flex.double method) matrix_lu_decomposition_in_place() (scitbx.array_family.flex.double method) matrix_multiply() (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) matrix_multiply_packed_u() (scitbx.array_family.flex.double method) matrix_multiply_packed_u_multiply_lhs_transpose() (scitbx.array_family.flex.double method) matrix_multiply_transpose() (scitbx.array_family.flex.double method) matrix_norm_1() (scitbx.array_family.flex.double method) matrix_norm_frobenius() (scitbx.array_family.flex.double method) matrix_norm_inf() (scitbx.array_family.flex.double method) matrix_outer_product() (scitbx.array_family.flex.double method) matrix_packed_l_as_lower_triangle() (scitbx.array_family.flex.double method) matrix_packed_l_as_symmetric() (scitbx.array_family.flex.double method) matrix_packed_u_as_symmetric() (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) matrix_packed_u_as_upper_triangle() (scitbx.array_family.flex.double method) matrix_packed_u_diagonal() (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) matrix_packed_u_diagonal_add_in_place() (scitbx.array_family.flex.double method) matrix_packed_u_swap_rows_and_columns_in_place() (scitbx.array_family.flex.double method) matrix_paste_block_in_place() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) matrix_paste_column_in_place() (scitbx.array_family.flex.double method) matrix_rot90() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) matrix_swap_columns_in_place() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) matrix_swap_rows_in_place() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) matrix_symmetric_as_packed_l() (scitbx.array_family.flex.double method) matrix_symmetric_as_packed_u() (scitbx.array_family.flex.double method) matrix_symmetric_upper_triangle_quadratic_form() (scitbx.array_family.flex.double method) matrix_symmetric_upper_triangle_swap_rows_and_columns_in_place() (scitbx.array_family.flex.double method) matrix_to_params() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method) (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method) (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method) (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method) (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method) (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method) (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method) (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method) (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method) (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method) matrix_trace() (scitbx.array_family.flex.double method) matrix_transpose() (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) matrix_transpose_in_place() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) matrix_transpose_multiply() (scitbx.array_family.flex.double method) matrix_transpose_multiply_as_packed_u() (scitbx.array_family.flex.double method) matrix_transpose_multiply_diagonal_multiply_as_packed_u() (scitbx.array_family.flex.double method) matrix_upper_bidiagonal() (scitbx.array_family.flex.double method) matrix_upper_triangle_as_packed_u() (scitbx.array_family.flex.double method) matthews_analysis() (mmtbx.density_modification.density_modification method) matthews_n_copies() (mmtbx.scaling.xtriage.xtriage_analyses method) matthews_rupp (class in mmtbx.scaling.matthews) max (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) max() (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) (xfel.cxi.gfx.trials_plot.Run method) max_absolute() (cctbx.xray.structure.meaningful_site_cart_differences method) max_b_factor (mmtbx.validation.clashscore.clash attribute) max_clusters() (cctbx.maptbx.peak_cluster_analysis method) (cctbx.maptbx.peak_search_parameters method) max_d_min_delta() (mmtbx.scaling.data_statistics.analyze_resolution_limits method) max_default() (in module scitbx.array_family.flex) max_distance() (cctbx.xray.structure.structure method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) max_distance_between_any_pair_with_id() (scitbx.array_family.flex.vec3_double method) max_distance_between_conformers() (mmtbx.disorder.analyze_model.disordered_segment method) (mmtbx.disorder.analyze_model.process_pdb_hierarchy method) max_element_length() (scitbx.array_family.flex.std_string method) max_estimated_twin_fraction (mmtbx.scaling.xtriage.xtriage_analyses property) max_fofc_value() (mmtbx.building.local_density_quality method) max_grid_height() (cctbx.maptbx.peak_cluster_analysis method) max_index() (scitbx.matrix.rec method) max_like (class in cctbx.xray.target_functors) max_number_of_shells() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method) max_operators() (mmtbx.ncs.ncs.ncs method) max_peaks() (cctbx.maptbx.peak_search_parameters method) max_prime() (cctbx.maptbx.crystal_gridding method) (cctbx.xray.structure_factors.manager.manager method) max_rmsd_between_conformers() (mmtbx.disorder.analyze_model.disordered_segment method) (mmtbx.disorder.analyze_model.process_pdb_hierarchy method) max_shift_over_esd (scitbx.lstbx.normal_eqns_solving.naive_iterations_with_damping_and_shift_limit attribute) max_twin_fraction() (mmtbx.scaling.twin_analyses.twin_results_interpretation method) McGregorMatch (class in mmtbx.geometry.topology) md5() (scitbx.array_family.flex.bool method) mean (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) mean() (cctbx.miller.array method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) mean_default() (in module scitbx.array_family.flex) mean_density_at_sites() (mmtbx.building.box_build_refine_base method) mean_distance() (cctbx.xray.structure.structure method) mean_of_intensity_divided_by_epsilon() (cctbx.miller.array method) mean_of_squared_sigma_divided_by_epsilon() (cctbx.miller.array method) mean_phase_error() (cctbx.miller.array method) mean_scattering_density() (cctbx.xray.structure.structure method) mean_sq() (cctbx.miller.array method) mean_weighted() (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) mean_weighted_phase_error() (cctbx.miller.array method) meaningful_site_cart_differences (class in cctbx.xray.structure) measurability() (cctbx.miller.array method) measureAngle() (mmtbx.rotamer.sidechain_angles.SidechainAngles method) measureChiAngles() (mmtbx.rotamer.sidechain_angles.SidechainAngles method) meets_main_conditions() (cctbx.uctbx.reduction_base.gruber_parameterization method) meets_primary_conditions() (cctbx.uctbx.reduction_base.gruber_parameterization method) memory_element (class in cctbx.omz.bfgs) memory_id() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_group method) (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue method) (iotbx.pdb.hierarchy.residue_group method) (iotbx.pdb.hierarchy.root method) merge() (libtbx.group_args method) merge_and_overwrite_cifs() (in module mmtbx.monomer_library.server) merge_atom_groups() (iotbx.pdb.hierarchy.residue_group method) merge_atoms_at_end_to_residues() (iotbx.pdb.hierarchy.root method) merge_data_and_guess_space_groups() (in module mmtbx.scaling.twin_analyses) merge_dict() (mmtbx.validation.validation method) (xfel.clustering.cluster.Cluster method) merge_disconnected_residue_groups_with_pure_altloc() (iotbx.pdb.hierarchy.chain method) merge_equivalents (class in cctbx.miller) merge_equivalents() (cctbx.miller.array method) merge_panel_scope_extracts_by_id() (in module dxtbx.model.detector) merge_residue_groups() (iotbx.pdb.hierarchy.chain method) merge_split_maps_and_models() (iotbx.map_model_manager.map_model_manager method) merge_two_dicts() (mmtbx.validation.atoms method) merging (mmtbx.validation.molprobity.molprobity attribute) merging_and_model_statistics() (in module mmtbx.validation.experimental) merging_statistics (class in mmtbx.scaling.xtriage) metal_parameters (class in mmtbx.ions) metric_r() (cctbx.sgtbx.reticular_twin_laws.symmetry_safe_sublattice_xs method) metric_subgroups (class in cctbx.sgtbx.lattice_symmetry) metric_supergroup() (in module cctbx.sgtbx.lattice_symmetry) MetricCriteria (class in cctbx.crystal.burzlaff_zimmermann_dewolff) metro_phil_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx) metrology2phil() (in module xfel.cftbx.detector.metrology2phil) MFO (mmtbx.map_names attribute) midpoint() (in module mmtbx.kinemage.validation) miller_array_export_as_shelx_hklf() (in module iotbx.shelx.hklf) miller_array_in_original_setting() (mmtbx.density_modification.density_modification method) miller_arrays (mmtbx.command_line.load_model_and_data attribute) miller_arrays_as_cif_block (class in iotbx.cif) miller_indices (cctbx.miller.reindexing.assistant attribute) miller_indices_as_pdb_file() (cctbx.miller.set method) miller_set() (cctbx.crystal.symmetry method) (cctbx.xray.structure_factors.manager.managed_calculation_base method) (iotbx.xds.read_ascii.reader method) min (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) min() (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) (xfel.cxi.gfx.trials_plot.Run method) min_cross_distance() (cctbx.maptbx.peak_cluster_analysis method) (cctbx.maptbx.peak_search_parameters method) min_cubicle_edge() (cctbx.maptbx.peak_search_parameters method) min_default() (in module scitbx.array_family.flex) min_distance() (cctbx.sgtbx.harker.planes_cartesian method) (cctbx.xray.structure.structure method) min_distance_between_any_pair() (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) min_distance_between_any_pair_with_id() (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) min_distance_sym_equiv() (cctbx.crystal.special_position_settings method) (cctbx.maptbx.peak_search_parameters method) min_f_over_sigma() (cctbx.miller.array method) min_index() (scitbx.matrix.rec method) min_max_d_star_sq() (cctbx.miller.set method) min_max_indices() (cctbx.miller.set method) min_max_mean() (mmtbx.refinement.print_statistics.coordinate_shifts method) (scitbx.array_family.flex.double method) min_u_cart_eigenvalue() (cctbx.xray.structure.structure method) minimize (class in cctbx.merging.brehm_diederichs) minimize() (mmtbx.den.refinement.manager method) (mmtbx.refinement.adp_refinement.refine_adp method) minimize_divide (class in cctbx.merging.brehm_diederichs) minimize_wrapper_for_ramachandran() (in module mmtbx.refinement.geometry_minimization) minimize_wrapper_with_map (class in mmtbx.refinement.real_space.individual_sites) minimizer (class in mmtbx.refinement.anomalous_scatterer_groups) (class in mmtbx.refinement.occupancies) minimum_atom_group_occupancy() (mmtbx.disorder.analyze_model.disordered_segment method) minimum_cell() (cctbx.crystal.symmetry method) minimum_covering_sphere() (cctbx.crystal.direct_space_asu.direct_space_asu method) minimum_reduction (class in cctbx.uctbx.gruber_1973) (class in cctbx.uctbx.krivy_gruber_1976) minimum_reduction_mixin (class in cctbx.uctbx.reduction_base) minimum_resolution() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) minimum_wavelength_based_on_d_min() (cctbx.miller.set method) miscellaneous_features_section() (iotbx.pdb.ext.input method) misfit() (cctbx.symmetry_search.symmetrised_shifted_structure_factors method) missing_atoms (mmtbx.validation.molprobity.molprobity attribute) missing_geom (mmtbx.ions.atom_type_flags attribute) missing_hydrogen_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) missing_non_hydrogen_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) ml_aniso_absolute_scaling (class in mmtbx.scaling.absolute_scaling) ml_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests property) ml_iso_absolute_scaling (class in mmtbx.scaling.absolute_scaling) ml_map (mmtbx.map_names attribute) ml_murray_rust (class in mmtbx.scaling.twin_analyses) ml_murray_rust_with_ncs (class in mmtbx.scaling.twin_analyses) mmtbx module mmtbx.building module mmtbx.building.extend_sidechains module mmtbx.building.make_library module mmtbx.bulk_solvent module mmtbx.bulk_solvent.bulk_solvent_and_scaling module mmtbx.bulk_solvent.scaler module mmtbx.chemical_components module mmtbx.chemical_components.cif_parser module mmtbx.command_line module mmtbx.conformation_dependent_library module mmtbx.conformation_dependent_library.altloc_weighting module mmtbx.conformation_dependent_library.bond_angle_registry module mmtbx.conformation_dependent_library.cdl_database module mmtbx.conformation_dependent_library.rdl_database module mmtbx.conformation_dependent_library.tst_cdl module mmtbx.conformation_dependent_library.utils module mmtbx.den module mmtbx.den.plot_weights module mmtbx.den.refinement module mmtbx.density_modification module mmtbx.disorder module mmtbx.disorder.analyze_model module mmtbx.disorder.backbone module mmtbx.dynamics module mmtbx.dynamics.cartesian_dynamics module mmtbx.dynamics.constants module mmtbx.dynamics.ensemble_cd module mmtbx.dynamics.simulated_annealing module mmtbx.f_model module mmtbx.f_model_info module mmtbx.geometry module mmtbx.geometry.altloc module mmtbx.geometry.asa module mmtbx.geometry.clash module mmtbx.geometry.indexing module mmtbx.geometry.shared_types module mmtbx.geometry.sphere_surface_sampling module mmtbx.geometry.topology module mmtbx.geometry_restraints module mmtbx.geometry_restraints.c_beta module mmtbx.geometry_restraints.external module mmtbx.geometry_restraints.ramachandran module mmtbx.geometry_restraints.reference module mmtbx.hydrogens module mmtbx.hydrogens.build_hydrogens module mmtbx.hydrogens.find module mmtbx.ias module mmtbx.ions module mmtbx.ions.build module mmtbx.ions.environment module mmtbx.ions.geometry module mmtbx.ions.halides module mmtbx.ions.identify module mmtbx.ions.svm module mmtbx.ions.svm.dump_sites module mmtbx.ions.svm.utils module mmtbx.ions.utils module mmtbx.kinemage module mmtbx.kinemage.validation module mmtbx.ligands module mmtbx.ligands.xtal_screens module mmtbx.maps module mmtbx.maps.composite_omit_map module mmtbx.maps.fem module mmtbx.maps.fobs_minus_fobs_map module mmtbx.maps.kick module mmtbx.maps.superpose module mmtbx.maps.utils module mmtbx.masks module mmtbx.max_lik module mmtbx.max_lik.max_like_non_uniform module mmtbx.max_lik.maxlik module mmtbx.monomer_library module mmtbx.monomer_library.bondlength_defaults module mmtbx.monomer_library.cif_triage module mmtbx.monomer_library.cif_types module mmtbx.monomer_library.conformation_dependent_restraints module mmtbx.monomer_library.conv_v2_v3 module mmtbx.monomer_library.correct_hydrogen_geometries module mmtbx.monomer_library.glyco_chiral_values module mmtbx.monomer_library.glyco_utils module mmtbx.monomer_library.hydrogen_restrictions module mmtbx.monomer_library.idealized_aa module mmtbx.monomer_library.linking_mixins module mmtbx.monomer_library.linking_setup module mmtbx.monomer_library.linking_utils module mmtbx.monomer_library.pdb_interpretation module mmtbx.monomer_library.rna_sugar_pucker_analysis module mmtbx.monomer_library.rotamer_utils module mmtbx.monomer_library.server module mmtbx.ncs module mmtbx.ncs.ligands module mmtbx.ncs.ncs module mmtbx.ncs.ncs_search module mmtbx.ncs.ncs_utils module mmtbx.pdbtools module mmtbx.polygon module mmtbx.polygon.output module mmtbx.real_space module mmtbx.refinement module mmtbx.refinement.adp_refinement module mmtbx.refinement.anomalous_scatterer_groups module mmtbx.refinement.ensemble_refinement.ensemble_utils module mmtbx.refinement.geometry_minimization module mmtbx.refinement.group module mmtbx.refinement.inspect_tardy_trajectory module mmtbx.refinement.minimization module mmtbx.refinement.minimization_ncs_constraints module mmtbx.refinement.occupancies module mmtbx.refinement.orca module mmtbx.refinement.print_statistics module mmtbx.refinement.real_space module mmtbx.refinement.real_space.fit_residue module mmtbx.refinement.real_space.fit_water module mmtbx.refinement.real_space.individual_sites module mmtbx.refinement.real_space.rigid_body module mmtbx.refinement.real_space.weight module mmtbx.refinement.refinement_flags module mmtbx.refinement.rigid_body module mmtbx.refinement.select_best_starting_model module mmtbx.refinement.tardy module mmtbx.refinement.targets module mmtbx.refinement.weights_params module mmtbx.rotamer module mmtbx.rotamer.graphics module mmtbx.rotamer.n_dim_table module mmtbx.rotamer.ramachandran_eval module mmtbx.rotamer.rotamer_eval module mmtbx.rotamer.sidechain_angles module mmtbx.rsr module mmtbx.scaling module mmtbx.scaling.absence_likelihood module mmtbx.scaling.absences module mmtbx.scaling.absolute_scaling module mmtbx.scaling.basic_analyses module mmtbx.scaling.data_statistics module mmtbx.scaling.fa_estimation module mmtbx.scaling.fest module mmtbx.scaling.make_param module mmtbx.scaling.massage_twin_detwin_data module mmtbx.scaling.matthews module mmtbx.scaling.outlier_plots module mmtbx.scaling.outlier_rejection module mmtbx.scaling.pair_analyses module mmtbx.scaling.pre_scale module mmtbx.scaling.random_omit module mmtbx.scaling.relative_scaling module mmtbx.scaling.relative_wilson module mmtbx.scaling.remove_outliers module mmtbx.scaling.rip_scale module mmtbx.scaling.sad_scale module mmtbx.scaling.sigmaa_estimation module mmtbx.scaling.sir_scale module mmtbx.scaling.siras_scale module mmtbx.scaling.ta_alpha_beta_calc module mmtbx.scaling.thorough_outlier_test module mmtbx.scaling.twin_analyses module mmtbx.scaling.twmad_scale module mmtbx.scaling.xtriage module mmtbx.secondary_structure module mmtbx.secondary_structure.build module mmtbx.secondary_structure.proteins module mmtbx.secondary_structure.utils module mmtbx.solvent module mmtbx.solvent.ensemble_ordered_solvent module

mmtbx.solvent.ordered_solvent module mmtbx.tls module mmtbx.tls.command_line module mmtbx.tls.ladp module mmtbx.tls.tls_as_xyz module mmtbx.tls.tools module mmtbx.twinning module mmtbx.twinning.probabalistic_detwinning module mmtbx.twinning.twin_f_model module mmtbx.utils module mmtbx.utils.fab_elbow_angle module mmtbx.utils.rotatable_bonds module mmtbx.validation module mmtbx.validation.analyze_peptides module mmtbx.validation.cbetadev module mmtbx.validation.clashscore module mmtbx.validation.experimental module mmtbx.validation.graphics module mmtbx.validation.ligands module mmtbx.validation.model_properties module mmtbx.validation.molprobity module mmtbx.validation.molprobity.mp_geo module mmtbx.validation.ramalyze module mmtbx.validation.restraints module mmtbx.validation.rna_validate module mmtbx.validation.rotalyze module mmtbx.validation.sequence module mmtbx.validation.utils module mmtbx.validation.waters module mmtbx.wwpdb module mmtbx.wwpdb.rcsb_web_services module mmtbx.wwpdb.standard_geometry_cif module mmtbx.wwpdb.utils module mmtbx_res_alignment() (in module mmtbx.ncs.ncs_search) mod_average (class in xfel.cxi.cspad_ana.mod_average) mod_daq_status (class in xfel.cxi.cspad_ana.mod_daq_status) mod_dump (class in xfel.cxi.cspad_ana.mod_dump) mod_dump_bitmap (class in xfel.cxi.cspad_ana.mod_dump_bitmap) mod_event_info (class in xfel.cxi.cspad_ana.mod_event_info) mod_filter (class in xfel.cxi.cspad_ana.mod_filter) mod_hdf5 (class in xfel.cxi.cspad_ana.mod_hdf5) mod_hitfind (class in xfel.cxi.cspad_ana.mod_hitfind) mod_illumination_filter (class in xfel.cxi.cspad_ana.mod_illumination_filter) mod_mar (class in xfel.cxi.cspad_ana.mod_mar) mod_mod_id (class in mmtbx.monomer_library.cif_types) mod_param (class in xfel.cxi.cspad_ana.mod_param) mod_positive3() (in module cctbx.sgtbx.harker) mod_pulnix_dump (class in xfel.cxi.cspad_ana.mod_pulnix_dump) mod_radial_average (class in xfel.cxi.cspad_ana.mod_radial_average) mod_xes (class in xfel.cxi.cspad_ana.mod_xes) model (class in cctbx.euclidean_model_matching) (class in iotbx.pdb.hierarchy) Model (class in mmtbx.geometry.clash) model (mmtbx.validation.molprobity.molprobity attribute) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.restraint attribute) model() (iotbx.cif.reader method) (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) model_atom_counts() (iotbx.pdb.ext.input method) model_based_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method) model_building() (iotbx.map_model_manager.map_model_manager method) model_dict() (iotbx.map_model_manager.map_model_manager method) model_error_ml() (mmtbx.twinning.twin_f_model.twin_model_manager method) model_from_hierarchy() (iotbx.map_model_manager.map_model_manager method) model_from_sites_cart() (in module mmtbx.utils) (iotbx.map_model_manager.map_model_manager method) model_from_text() (iotbx.map_model_manager.map_model_manager method) model_id (iotbx.pdb.hierarchy.atom_with_labels property) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) model_id_list() (iotbx.map_model_manager.map_model_manager method) model_ids() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) model_indices() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) model_is_too_large() (in module cctbx.web.emma) model_matches (class in cctbx.euclidean_model_matching) model_sharpen() (iotbx.map_model_manager.map_model_manager method) model_statistics (class in mmtbx.validation.model_properties) model_statistics_geometry (mmtbx.validation.molprobity.molprobity attribute) model_statistics_geometry_result (mmtbx.validation.molprobity.molprobity attribute) model_stats (mmtbx.validation.molprobity.molprobity attribute) model_stats_new (mmtbx.validation.molprobity.molprobity attribute) models() (iotbx.map_model_manager.map_model_manager method) (iotbx.pdb.hierarchy.root method) models_size() (iotbx.pdb.hierarchy.root method) modify (class in mmtbx.pdbtools) modify_weights() (mmtbx.scaling.relative_wilson.relative_wilson method) module cctbx cctbx.adp_restraints cctbx.adp_restraints.energies cctbx.adp_restraints.flags cctbx.adptbx cctbx.array_family cctbx.array_family.flex cctbx.command_line cctbx.command_line.brehm_diederichs cctbx.command_line.cod_select_and_pickle cctbx.command_line.euclidean_model_matching cctbx.command_line.find_reticular_twin_laws cctbx.command_line.form_factor_query cctbx.command_line.precession_view cctbx.command_line.space_group_info cctbx.command_line.structure_factor_timings cctbx.command_line.subgroups cctbx.command_line.version cctbx.command_line.wavelength_units cctbx.covariance cctbx.crystal cctbx.crystal.burzlaff_zimmermann_dewolff cctbx.crystal.close_packing cctbx.crystal.coordination_sequences cctbx.crystal.direct_space_asu cctbx.crystal.distance_based_connectivity cctbx.crystal.find_best_cell cctbx.crystal.reindex cctbx.crystal_orientation cctbx.development cctbx.development.cns_density_modification cctbx.development.debug_utils cctbx.development.direct_or_fft cctbx.development.electron_density_sampling cctbx.development.fmt_utils cctbx.development.make_cns_input cctbx.development.make_settings cctbx.development.random_structure cctbx.development.run_shelx cctbx.development.run_shelx76 cctbx.development.space_group_option_parser cctbx.development.structure_factor_utils cctbx.dmtbx cctbx.eltbx cctbx.eltbx.attenuation_coefficient cctbx.eltbx.chemical_elements cctbx.eltbx.covalent_radii cctbx.eltbx.development cctbx.eltbx.development.combine_fits cctbx.eltbx.development.create_n_gaussian_raw_cpp cctbx.eltbx.development.e_scattering_plots cctbx.eltbx.development.format_gaussian_fits cctbx.eltbx.development.hydrogen_plots cctbx.eltbx.development.itvc_approx cctbx.eltbx.development.itvc_cross_validation cctbx.eltbx.development.itvc_fits cctbx.eltbx.development.itvc_section61_io cctbx.eltbx.development.kissel_fits cctbx.eltbx.development.kissel_io cctbx.eltbx.development.rez_rez_grant cctbx.eltbx.distance_based_connectivity cctbx.eltbx.e_scattering cctbx.eltbx.formula cctbx.eltbx.fp_fdp cctbx.eltbx.gaussian_fit cctbx.eltbx.henke cctbx.eltbx.icsd_radii cctbx.eltbx.neutron cctbx.eltbx.sasaki cctbx.eltbx.tiny_pse cctbx.eltbx.van_der_waals_radii cctbx.eltbx.wavelengths cctbx.eltbx.xray_scattering cctbx.euclidean_model_matching cctbx.examples cctbx.examples.adp_symmetry_constraints cctbx.examples.all_axes cctbx.examples.analyze_adp cctbx.examples.change_hand_p31 cctbx.examples.convert_ccp4_symop_lib cctbx.examples.cr2o3_consistency_checks cctbx.examples.cr2o3_primitive_cell cctbx.examples.exp_i_alpha_derivatives cctbx.examples.f_model_example cctbx.examples.fft_map_electron_density_around_atom cctbx.examples.find_distances_using_cpp_objects cctbx.examples.find_sys_abs_equiv_space_groups cctbx.examples.g_exp_i_alpha_derivatives cctbx.examples.g_exp_i_partial_derivatives cctbx.examples.getting_started cctbx.examples.hirshfeld_test cctbx.examples.le_page_1982_vs_lebedev_2005 cctbx.examples.lebedev_2005_perturbation cctbx.examples.list_non_principal_continuous_shifts cctbx.examples.location_part cctbx.examples.map_skewness cctbx.examples.maximum_subgroups cctbx.examples.miller_common_sets cctbx.examples.miller_transform cctbx.examples.neutron_structure_factors cctbx.examples.phase_o_phrenia cctbx.examples.quartz_structure cctbx.examples.random_f_calc cctbx.examples.random_puckers cctbx.examples.reduced_cell_two_folds cctbx.examples.site_symmetry_constraints cctbx.examples.site_symmetry_table cctbx.examples.space_group_matrices cctbx.examples.space_subgroups cctbx.examples.steve_collins cctbx.examples.structure_factor_calculus cctbx.examples.structure_factor_calculus.site_derivatives cctbx.examples.structure_factor_calculus.sites_derivatives cctbx.examples.structure_factor_calculus.sites_least_squares_derivatives cctbx.examples.structure_factor_calculus.u_star_derivatives cctbx.examples.structure_factor_derivatives cctbx.examples.structure_factor_derivatives_2 cctbx.examples.structure_factor_derivatives_3 cctbx.examples.structure_factor_derivatives_4 cctbx.examples.sub_group_graph cctbx.examples.symops_530 cctbx.examples.trigonal_r_vs_tetragonal_i cctbx.examples.unit_cell_minimizers cctbx.examples.unit_cell_refinement cctbx.french_wilson cctbx.geometry cctbx.geometry_restraints cctbx.geometry_restraints.energies cctbx.geometry_restraints.flags cctbx.geometry_restraints.lbfgs cctbx.geometry_restraints.manager cctbx.macro_mol cctbx.macro_mol.rotation_parameters cctbx.maptbx cctbx.maptbx.mem cctbx.maptbx.real_space_refinement_simple cctbx.masks cctbx.math_module cctbx.merging cctbx.merging.brehm_diederichs cctbx.miller cctbx.miller.display cctbx.miller.reindexing cctbx.multipolar cctbx.neutron cctbx.omz cctbx.omz.bfgs cctbx.omz.cif_refine cctbx.omz.cod_refine cctbx.omz.cod_select_and_pickle cctbx.omz.dev cctbx.omz.eval_iso_vs_refined cctbx.omz.pdb_dev cctbx.omz.tardy_adaptor cctbx.r_free_utils cctbx.run_examples cctbx.run_tests cctbx.sgtbx cctbx.sgtbx.bravais_types cctbx.sgtbx.cosets cctbx.sgtbx.direct_space_asu cctbx.sgtbx.direct_space_asu.check_redundancies cctbx.sgtbx.direct_space_asu.cut_plane cctbx.sgtbx.direct_space_asu.facet_analysis cctbx.sgtbx.direct_space_asu.plane_group_reference_table cctbx.sgtbx.direct_space_asu.proto cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table cctbx.sgtbx.direct_space_asu.reference_table cctbx.sgtbx.direct_space_asu.short_cuts cctbx.sgtbx.harker cctbx.sgtbx.lattice_symmetry cctbx.sgtbx.literal_description cctbx.sgtbx.plane_groups cctbx.sgtbx.pointgroup_tools cctbx.sgtbx.rational_matrices_point_groups cctbx.sgtbx.reticular_pg_tools cctbx.sgtbx.reticular_twin_laws cctbx.sgtbx.show_cosets cctbx.sgtbx.sub_lattice_tools cctbx.sgtbx.subgroups cctbx.sgtbx.symbol_confidence cctbx.sgtbx.sys_abs_equiv cctbx.source_generators cctbx.source_generators.eltbx cctbx.source_generators.eltbx.generate_henke_cpp cctbx.source_generators.eltbx.generate_sasaki_cpp cctbx.source_generators.flex_fwd_h cctbx.statistics cctbx.symmetry_search cctbx.translation_search cctbx.uctbx.determine_unit_cell cctbx.uctbx.gruber_1973 cctbx.uctbx.gruber_1973_table_1 cctbx.uctbx.krivy_gruber_1976 cctbx.uctbx.reduction_base cctbx.web cctbx.web.all_axes cctbx.web.asu_gallery cctbx.web.asu_gallery.guide_to_notation cctbx.web.asu_gallery.jv_asu cctbx.web.asu_gallery.jv_index cctbx.web.asu_gallery.jvx cctbx.web.asu_gallery.web_links cctbx.web.browse_settings cctbx.web.cgi_utils cctbx.web.change_basis cctbx.web.change_hand cctbx.web.change_setting cctbx.web.dispatcher cctbx.web.emma cctbx.web.explore_symmetry cctbx.web.frac_cart cctbx.web.io_utils cctbx.web.iotbx_cif_validate cctbx.web.lattice_symmetry cctbx.web.libtbx_help cctbx.web.multiple_cell cctbx.web.phase_o_phrenia cctbx.web.replay cctbx.web.shelx cctbx.web.structure_factors cctbx.web.structure_factors_pdb cctbx.web.wyckoff cctbx.xray cctbx.xray.ext cctbx.xray.minimization cctbx.xray.observation_types cctbx.xray.observations cctbx.xray.scatterer cctbx.xray.structure cctbx.xray.structure_factors cctbx.xray.structure_factors.from_scatterers cctbx.xray.structure_factors.from_scatterers_direct cctbx.xray.structure_factors.from_scatterers_direct_parallel cctbx.xray.structure_factors.from_scatterers_fft cctbx.xray.structure_factors.global_counters cctbx.xray.structure_factors.gradient_flags cctbx.xray.structure_factors.gradients cctbx.xray.structure_factors.gradients_base cctbx.xray.structure_factors.gradients_direct cctbx.xray.structure_factors.gradients_fft cctbx.xray.structure_factors.manager cctbx.xray.structure_factors.misc cctbx.xray.target_functors cctbx.xray.targets cctbx.xray.targets.r1 cctbx.xray.weighting_schemes dxtbx.model.beam dxtbx.model.crystal dxtbx.model.detector dxtbx.model.goniometer dxtbx.model.scan dxtbx.serialize.load dxtbx.serialize.xds iotbx.file_reader iotbx.map_manager iotbx.map_model_manager iotbx.reflection_file_reader iotbx.shelx iotbx.shelx.crystal_symmetry_from_ins iotbx.shelx.hklf iotbx.shelx.lexer iotbx.shelx.parsers iotbx.shelx.tokens iotbx.shelx.write_ins iotbx.shelx.writer iotbx.xds.integrate_hkl iotbx.xds.read_ascii iotbx.xds.spot_xds iotbx.xds.xds_inp iotbx.xds.xparm libtbx mmtbx mmtbx.building mmtbx.building.extend_sidechains mmtbx.building.make_library mmtbx.bulk_solvent mmtbx.bulk_solvent.bulk_solvent_and_scaling mmtbx.bulk_solvent.scaler mmtbx.chemical_components mmtbx.chemical_components.cif_parser mmtbx.command_line mmtbx.conformation_dependent_library mmtbx.conformation_dependent_library.altloc_weighting mmtbx.conformation_dependent_library.bond_angle_registry mmtbx.conformation_dependent_library.cdl_database mmtbx.conformation_dependent_library.rdl_database mmtbx.conformation_dependent_library.tst_cdl mmtbx.conformation_dependent_library.utils mmtbx.den mmtbx.den.plot_weights mmtbx.den.refinement mmtbx.density_modification mmtbx.disorder mmtbx.disorder.analyze_model mmtbx.disorder.backbone mmtbx.dynamics mmtbx.dynamics.cartesian_dynamics mmtbx.dynamics.constants mmtbx.dynamics.ensemble_cd mmtbx.dynamics.simulated_annealing mmtbx.f_model mmtbx.f_model_info mmtbx.geometry mmtbx.geometry.altloc mmtbx.geometry.asa mmtbx.geometry.clash mmtbx.geometry.indexing mmtbx.geometry.shared_types mmtbx.geometry.sphere_surface_sampling mmtbx.geometry.topology mmtbx.geometry_restraints mmtbx.geometry_restraints.c_beta mmtbx.geometry_restraints.external mmtbx.geometry_restraints.ramachandran mmtbx.geometry_restraints.reference mmtbx.hydrogens mmtbx.hydrogens.build_hydrogens mmtbx.hydrogens.find mmtbx.ias mmtbx.ions mmtbx.ions.build mmtbx.ions.environment mmtbx.ions.geometry mmtbx.ions.halides mmtbx.ions.identify mmtbx.ions.svm mmtbx.ions.svm.dump_sites mmtbx.ions.svm.utils mmtbx.ions.utils mmtbx.kinemage mmtbx.kinemage.validation mmtbx.ligands mmtbx.ligands.xtal_screens mmtbx.maps mmtbx.maps.composite_omit_map mmtbx.maps.fem mmtbx.maps.fobs_minus_fobs_map mmtbx.maps.kick mmtbx.maps.superpose mmtbx.maps.utils mmtbx.masks mmtbx.max_lik mmtbx.max_lik.max_like_non_uniform mmtbx.max_lik.maxlik mmtbx.monomer_library mmtbx.monomer_library.bondlength_defaults mmtbx.monomer_library.cif_triage mmtbx.monomer_library.cif_types mmtbx.monomer_library.conformation_dependent_restraints mmtbx.monomer_library.conv_v2_v3 mmtbx.monomer_library.correct_hydrogen_geometries mmtbx.monomer_library.glyco_chiral_values mmtbx.monomer_library.glyco_utils mmtbx.monomer_library.hydrogen_restrictions mmtbx.monomer_library.idealized_aa mmtbx.monomer_library.linking_mixins mmtbx.monomer_library.linking_setup mmtbx.monomer_library.linking_utils mmtbx.monomer_library.pdb_interpretation mmtbx.monomer_library.rna_sugar_pucker_analysis mmtbx.monomer_library.rotamer_utils mmtbx.monomer_library.server mmtbx.ncs mmtbx.ncs.ligands mmtbx.ncs.ncs mmtbx.ncs.ncs_search mmtbx.ncs.ncs_utils mmtbx.pdbtools mmtbx.polygon mmtbx.polygon.output mmtbx.real_space mmtbx.refinement mmtbx.refinement.adp_refinement mmtbx.refinement.anomalous_scatterer_groups mmtbx.refinement.ensemble_refinement.ensemble_utils mmtbx.refinement.geometry_minimization mmtbx.refinement.group mmtbx.refinement.inspect_tardy_trajectory mmtbx.refinement.minimization mmtbx.refinement.minimization_ncs_constraints mmtbx.refinement.occupancies mmtbx.refinement.orca mmtbx.refinement.print_statistics mmtbx.refinement.real_space mmtbx.refinement.real_space.fit_residue mmtbx.refinement.real_space.fit_water mmtbx.refinement.real_space.individual_sites mmtbx.refinement.real_space.rigid_body mmtbx.refinement.real_space.weight mmtbx.refinement.refinement_flags mmtbx.refinement.rigid_body mmtbx.refinement.select_best_starting_model mmtbx.refinement.tardy mmtbx.refinement.targets mmtbx.refinement.weights_params mmtbx.rotamer mmtbx.rotamer.graphics mmtbx.rotamer.n_dim_table mmtbx.rotamer.ramachandran_eval mmtbx.rotamer.rotamer_eval mmtbx.rotamer.sidechain_angles mmtbx.rsr mmtbx.scaling mmtbx.scaling.absence_likelihood mmtbx.scaling.absences mmtbx.scaling.absolute_scaling mmtbx.scaling.basic_analyses mmtbx.scaling.data_statistics mmtbx.scaling.fa_estimation mmtbx.scaling.fest mmtbx.scaling.make_param mmtbx.scaling.massage_twin_detwin_data mmtbx.scaling.matthews mmtbx.scaling.outlier_plots mmtbx.scaling.outlier_rejection mmtbx.scaling.pair_analyses mmtbx.scaling.pre_scale mmtbx.scaling.random_omit mmtbx.scaling.relative_scaling mmtbx.scaling.relative_wilson mmtbx.scaling.remove_outliers mmtbx.scaling.rip_scale mmtbx.scaling.sad_scale mmtbx.scaling.sigmaa_estimation mmtbx.scaling.sir_scale mmtbx.scaling.siras_scale mmtbx.scaling.ta_alpha_beta_calc mmtbx.scaling.thorough_outlier_test mmtbx.scaling.twin_analyses mmtbx.scaling.twmad_scale mmtbx.scaling.xtriage mmtbx.secondary_structure mmtbx.secondary_structure.build mmtbx.secondary_structure.proteins mmtbx.secondary_structure.utils mmtbx.solvent mmtbx.solvent.ensemble_ordered_solvent mmtbx.solvent.ordered_solvent mmtbx.tls mmtbx.tls.command_line mmtbx.tls.ladp mmtbx.tls.tls_as_xyz mmtbx.tls.tools mmtbx.twinning mmtbx.twinning.probabalistic_detwinning mmtbx.twinning.twin_f_model mmtbx.utils mmtbx.utils.fab_elbow_angle mmtbx.utils.rotatable_bonds mmtbx.validation mmtbx.validation.analyze_peptides mmtbx.validation.cbetadev mmtbx.validation.clashscore mmtbx.validation.experimental mmtbx.validation.graphics mmtbx.validation.ligands mmtbx.validation.model_properties mmtbx.validation.molprobity mmtbx.validation.molprobity.mp_geo mmtbx.validation.ramalyze mmtbx.validation.restraints mmtbx.validation.rna_validate mmtbx.validation.rotalyze mmtbx.validation.sequence mmtbx.validation.utils mmtbx.validation.waters mmtbx.wwpdb mmtbx.wwpdb.rcsb_web_services mmtbx.wwpdb.standard_geometry_cif mmtbx.wwpdb.utils scitbx.array_family.flex scitbx.lbfgs scitbx.lstbx.normal_eqns scitbx.lstbx.normal_eqns_solving scitbx.matrix xfel xfel.cftbx xfel.cftbx.detector xfel.cftbx.detector.cspad_cbf_tbx xfel.cftbx.detector.metrology2phil xfel.clustering.cluster xfel.clustering.cluster_groups xfel.clustering.singleframe xfel.command_line xfel.command_line.auto_submit xfel.command_line.brehm_diederichs xfel.command_line.cbf_average xfel.command_line.convert_gain_map xfel.command_line.convert_gain_map_cbf xfel.command_line.cxi_apply_metrology xfel.command_line.cxi_cspad_pinwheel xfel.command_line.cxi_diff xfel.command_line.cxi_display_metrology xfel.command_line.cxi_generate_circular_gain_mask xfel.command_line.cxi_index xfel.command_line.cxi_lsf xfel.command_line.cxi_merge xfel.command_line.cxi_optical2cbfheader xfel.command_line.cxi_pbs xfel.command_line.cxi_pickle2cbf xfel.command_line.cxi_plotcv xfel.command_line.cxi_psana xfel.command_line.cxi_pyana xfel.command_line.cxi_spots xfel.command_line.cxi_stream_to_pickle xfel.command_line.cxi_view xfel.command_line.cxi_xmerge xfel.command_line.histogram_finalise xfel.command_line.list_db_metadata xfel.command_line.make_mask xfel.command_line.metrology xfel.command_line.monitor_detectors xfel.command_line.monitor_trials xfel.command_line.overlay_spectra xfel.command_line.plot_to_subpixel xfel.command_line.postrefine xfel.command_line.print_pickle xfel.command_line.quadrants xfel.command_line.radial_average xfel.command_line.smooth_spectrum xfel.command_line.subtract_background xfel.command_line.trial_stats xfel.command_line.view_pixel_histograms xfel.command_line.xes_finalise xfel.command_line.xes_histograms xfel.cxi xfel.cxi.average_spots xfel.cxi.correction_vector_plot xfel.cxi.cspad_ana xfel.cxi.cspad_ana.average_tbx xfel.cxi.cspad_ana.common_mode xfel.cxi.cspad_ana.cspad_tbx xfel.cxi.cspad_ana.display_calib xfel.cxi.cspad_ana.histogram_finalise xfel.cxi.cspad_ana.hitfinder_tbx xfel.cxi.cspad_ana.mod_average xfel.cxi.cspad_ana.mod_daq_status xfel.cxi.cspad_ana.mod_dump xfel.cxi.cspad_ana.mod_dump_bitmap xfel.cxi.cspad_ana.mod_event_info xfel.cxi.cspad_ana.mod_filter xfel.cxi.cspad_ana.mod_hdf5 xfel.cxi.cspad_ana.mod_hitfind xfel.cxi.cspad_ana.mod_illumination_filter xfel.cxi.cspad_ana.mod_mar xfel.cxi.cspad_ana.mod_param xfel.cxi.cspad_ana.mod_pulnix_dump xfel.cxi.cspad_ana.mod_radial_average xfel.cxi.cspad_ana.mod_xes xfel.cxi.cspad_ana.parse_calib xfel.cxi.cspad_ana.pixel_histograms xfel.cxi.cspad_ana.xes_finalise xfel.cxi.cspad_ana.xes_histograms xfel.cxi.cxi_cc xfel.cxi.display_powder_arcs xfel.cxi.display_spots xfel.cxi.gfx xfel.cxi.gfx.status_plot xfel.cxi.gfx.trials_plot xfel.cxi.gfx.wx_detectors xfel.cxi.integrate_image_api xfel.cxi.strong_zulu xfel.cxi.util xfel.metrology xfel.metrology.flatfile xfel.metrology.legacy_scale xfel.metrology.mark0 xfel.metrology.mark1 xfel.metrology.mark10 xfel.metrology.mark3 xfel.metrology.quadrant xfel.mono_simulation xfel.mono_simulation.mono_treatment xfel.phil_preferences Molecule (class in mmtbx.geometry.topology) molecule (mmtbx.geometry.clash.SymmetryEquivalent property) molprobity (class in mmtbx.validation.molprobity) molprobity_flags() (in module mmtbx.validation.molprobity) molprobity_score() (in module mmtbx.validation.utils) (mmtbx.validation.molprobity.molprobity method) molprobity_table_labels (mmtbx.validation.entity attribute) molprobity_version_number (mmtbx.validation.molprobity.molprobity attribute) MolProbityParser (class in mmtbx.validation.molprobity) MolProbityTemplate (class in mmtbx.validation.molprobity) mon_lib_cif_loader (class in mmtbx.monomer_library.server) mon_lib_ener_lib_cif() (in module mmtbx.monomer_library.server) mon_lib_list_cif() (in module mmtbx.monomer_library.server) mon_lib_names (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) mon_lib_query() (in module mmtbx.rotamer.rotamer_eval) mon_lib_srv (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) monitor (class in mmtbx.refinement.minimization) (class in mmtbx.refinement.real_space.fit_residue) monitors (class in mmtbx.refinement) monomer (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) monomer_atom_dict (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) monomer_mapping (class in mmtbx.monomer_library.pdb_interpretation) monomer_mapping_summary (class in mmtbx.monomer_library.pdb_interpretation) MonomerLibraryServerError move_blank_altloc_atom_groups_to_front() (iotbx.pdb.hierarchy.residue_group method) move_solvent_to_the_end_of_atom_list() (mmtbx.solvent.ensemble_ordered_solvent.manager method) moving_average() (in module mmtbx.bulk_solvent.scaler) mp_reassemble() (in module cctbx.merging.brehm_diederichs) mpscore (mmtbx.validation.molprobity.summary attribute) ms_since_last_status_change() (xfel.cxi.cspad_ana.mod_event_info.laser_status method) mtz_object() (mmtbx.utils.guess_observation_type method) mu (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations property) multi_axis() (dxtbx.model.goniometer.GoniometerFactory static method) multi_axis_goniometer_from_phil() (dxtbx.model.goniometer.GoniometerFactory static method) multi_criterion_plot_mixin (class in mmtbx.validation.graphics) multi_criterion_view (class in mmtbx.validation.molprobity) MultiAxisGoniometer (class in dxtbx.model.goniometer) multiplicities() (cctbx.miller.set method) multiplicity() (cctbx.neutron.scatterer method) multipliers (cctbx.sgtbx.special_op_simplified_term attribute) multiscale() (cctbx.miller.array method) mum_dad (class in mmtbx.scaling.fa_estimation) (class in mmtbx.scaling.pair_analyses) mutable (class in libtbx) my_get_rot_trans() (in module mmtbx.ncs.ncs_search) my_selection() (in module mmtbx.ncs.ncs_search)

N

n (cctbx.sgtbx.direct_space_asu.cut_plane.cut attribute) (mmtbx.map_names attribute) n1_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.reduction_base method) n2_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.reduction_base method) n3_false_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.gruber_1973.minimum_reduction method) (cctbx.uctbx.reduction_base.reduction_base method) n3_true_action() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.reduction_base method) n_all (mmtbx.validation.model_properties.xray_structure_statistics attribute) n_allowed (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.rotalyze.rotalyze attribute) n_allowed_by_model (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.rotalyze.rotalyze attribute) n_aniso (mmtbx.validation.model_properties.xray_structure_statistics attribute) n_aniso_h (mmtbx.validation.model_properties.xray_structure_statistics attribute) n_as_s() (in module mmtbx.twinning.twin_f_model) n_asn_hd22 (mmtbx.utils.detect_hydrogen_nomenclature_problem attribute) n_atoms (mmtbx.maps.composite_omit_map.omit_box property) (mmtbx.maps.composite_omit_map.omit_regions property) (mmtbx.validation.model_properties.model_statistics attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.restraint attribute) n_atoms() (mmtbx.validation.atoms method) n_bad (mmtbx.validation.waters.waters attribute) n_below_fofc_cutoff (mmtbx.validation.ligands.ligand_validation attribute) n_below_two_fofc_cutoff (mmtbx.validation.ligands.ligand_validation attribute) n_bijvoet_pairs() (cctbx.miller.set method) n_boxes (mmtbx.maps.composite_omit_map.omit_regions property) n_cbeta_outliers() (mmtbx.disorder.analyze_model.disordered_segment method) n_chiral_by_model (mmtbx.validation.restraints.chiralities attribute) n_columns() (iotbx.cif.model.loop method) (scitbx.matrix.rec method) n_confs (mmtbx.validation.molprobity.residue_multi_criterion attribute) n_confs() (mmtbx.disorder.analyze_model.disordered_segment method) n_confs_max() (mmtbx.disorder.analyze_model.disordered_segment method) n_expected_atoms() (mmtbx.monomer_library.pdb_interpretation.source_info_server method) n_favored (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.rotalyze.rotalyze attribute) n_favored_by_model (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.rotalyze.rotalyze attribute) n_free (mmtbx.validation.experimental.data_statistics attribute) n_free_outer (mmtbx.validation.experimental.data_statistics attribute) n_grad_u_aniso() (cctbx.xray.structure.structure method) n_grad_u_iso() (cctbx.xray.structure.structure method) n_grid_points() (cctbx.maptbx.crystal_gridding method) n_handedness_by_model (mmtbx.validation.restraints.chiralities attribute) n_hbonds (mmtbx.validation.waters.water attribute) n_hd (mmtbx.validation.model_properties.xray_structure_statistics attribute) n_heavy (mmtbx.validation.waters.waters attribute) n_hydrogen (mmtbx.utils.detect_hydrogen_nomenclature_problem attribute) n_hydrogens (mmtbx.validation.model_properties.model_statistics attribute) n_iterations() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.reduction_base method) n_ligands (mmtbx.ncs.ligands.apply_ligand_ncs property) n_matches() (cctbx.euclidean_model_matching.delegating_model_matches method) n_max_iterations (scitbx.lstbx.normal_eqns_solving.iterations attribute) n_models (mmtbx.validation.model_properties.model_statistics attribute) n_ncs_oper() (mmtbx.ncs.ncs.ncs_group method) n_non_hd (mmtbx.validation.model_properties.xray_structure_statistics attribute) n_npd (mmtbx.validation.model_properties.xray_structure_statistics attribute) n_nuc (mmtbx.validation.model_properties.model_statistics attribute) n_other (mmtbx.utils.detect_hydrogen_nomenclature_problem attribute) n_outliers (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.clashscore.nqh_flips attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) (mmtbx.validation.rna_geometry attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) (mmtbx.validation.waters.waters attribute) n_outliers() (mmtbx.scaling.data_statistics.possible_outliers method) (mmtbx.scaling.relative_wilson.summary method) n_outliers_by_model (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.clashscore.nqh_flips attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) (mmtbx.validation.rna_geometry attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) (mmtbx.validation.waters.waters attribute) n_outliers_of_type() (mmtbx.disorder.analyze_model.disordered_segment method) n_pairs_best_match() (cctbx.euclidean_model_matching.delegating_model_matches method) n_parameters() (cctbx.xray.structure.structure method) n_partial_splits() (mmtbx.disorder.analyze_model.disordered_segment method) n_polymer (mmtbx.validation.model_properties.model_statistics attribute) n_problems (mmtbx.scaling.xtriage.summary property) n_protein (mmtbx.validation.model_properties.model_statistics attribute) n_pseudochiral_by_model (mmtbx.validation.restraints.chiralities attribute) n_real() (cctbx.maptbx.crystal_gridding method) n_refl (mmtbx.validation.experimental.data_statistics attribute) n_refl_outer (mmtbx.validation.experimental.data_statistics attribute) n_refl_refine (mmtbx.validation.experimental.data_statistics attribute) n_refl_refine_outer (mmtbx.validation.experimental.data_statistics attribute) n_reflections_by_sigi() (xfel.clustering.singleframe.SingleFrame method) n_res() (mmtbx.validation.graphics.residue_bin method) n_residues() (mmtbx.disorder.analyze_model.disordered_segment method) n_rotamer_changes() (mmtbx.disorder.analyze_model.disordered_segment method) n_rows() (iotbx.cif.model.loop method) (scitbx.matrix.rec method) n_tetrahedral_by_model (mmtbx.validation.restraints.chiralities attribute) n_tls_groups (mmtbx.validation.molprobity.pdb_header_info attribute) n_total (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.clashscore.nqh_flips attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) (mmtbx.validation.rna_geometry attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) (mmtbx.validation.waters.waters attribute) n_total_by_model (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.clashscore.nqh_flips attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) (mmtbx.validation.rna_geometry attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) (mmtbx.validation.waters.waters attribute)

n_type (mmtbx.validation.ramalyze.ramalyze attribute) n_undefined_multiplicities() (cctbx.xray.structure.structure method) n_unknown_type_symbols() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) n_waters (mmtbx.validation.model_properties.model_statistics attribute) n_z_test (class in mmtbx.scaling.twin_analyses) n_zero_b (mmtbx.validation.model_properties.xray_structure_statistics attribute) n_zero_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute) naive_fa_estimation (class in mmtbx.scaling.fa_estimation) naive_iterations (class in scitbx.lstbx.normal_eqns_solving) naive_iterations_with_damping (class in scitbx.lstbx.normal_eqns_solving) naive_iterations_with_damping_and_shift_limit (class in scitbx.lstbx.normal_eqns_solving) name (iotbx.pdb.hierarchy.atom property) (iotbx.shelx.tokens.atomname_token attribute) (mmtbx.ions.atom_type_flags attribute) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.waters.water attribute) name() (iotbx.cif.model.loop method) NamedRot (class in mmtbx.rotamer.rotamer_eval) names (mmtbx.rotamer.rotamer_eval.RotamerID attribute) ncs (class in mmtbx.ncs.ncs) ncs_averaging() (mmtbx.density_modification.density_modification method) ncs_cc() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) ncs_domain_pdb() (mmtbx.ncs.ncs.ncs_group method) ncs_from_import() (mmtbx.ncs.ncs.ncs method) ncs_from_pdb_input_BIOMT() (mmtbx.ncs.ncs.ncs method) ncs_group (class in mmtbx.ncs.ncs) ncs_grouping_and_group_dict() (in module mmtbx.ncs.ncs_search) ncs_groups() (mmtbx.ncs.ncs.ncs method) ncs_object() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) ncs_oper_in_first_group() (mmtbx.ncs.ncs.ncs method) ncs_read() (mmtbx.ncs.ncs.ncs method) nd() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) NDimTable (class in mmtbx.rotamer.n_dim_table) nearest_atom (mmtbx.validation.waters.water attribute) nearest_contact (mmtbx.validation.waters.water attribute) nearest_rotamer_sites_cart() (mmtbx.rotamer.rotamer_eval.RotamerEval method) neg (cctbx.omz.dev.shift_limit_pair attribute) negate_map_around_selected_atoms_except_selected_atoms() (in module mmtbx.refinement.real_space) nest_dict() (mmtbx.validation.atoms method) (mmtbx.validation.residue method) neutron_flag (mmtbx.refinement.print_statistics.stats_table attribute) neutron_line() (mmtbx.refinement.minimization.monitor method) neutron_refinement (mmtbx.fmodels attribute) neutron_scattering_dict (mmtbx.fmodels attribute) neutron_stats (mmtbx.validation.molprobity.molprobity attribute) new_format (mmtbx.scaling.xtriage.xtriage_analyses attribute) (mmtbx.scaling.xtriage.xtriage_summary attribute) new_if_defined() (in module mmtbx.monomer_library.cif_types) new_included_bonded_atoms() (cctbx.geometry_restraints.manager.manager method) new_including_isolated_sites() (cctbx.geometry_restraints.manager.manager method) new_outliers (mmtbx.validation.cbetadev.cbetadev attribute) newline() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) next() (cctbx.crystal.calculate_dihedrals method) (cctbx.maptbx.peak_cluster_analysis method) (cctbx.sgtbx.direct_space_asu.check_redundancies.color_server method) (mmtbx.monomer_library.rotamer_utils.rotamer_iterator method) (mmtbx.monomer_library.server.trivial_html_tag_filter method) next_cycle() (mmtbx.density_modification.density_modification method) next_permutation() (scitbx.array_family.flex.size_t method) next_site_cluster_analysis() (cctbx.maptbx.peak_cluster_analysis method) next_with_effective_resolution() (cctbx.maptbx.peak_cluster_analysis method) niggli_cell() (cctbx.crystal.symmetry method) nist_elements (class in cctbx.eltbx.attenuation_coefficient) NO_2FOFC_PEAK (mmtbx.ions.identify.AtomProperties attribute) NO_ANOM_PEAK (mmtbx.ions.identify.AtomProperties attribute) NO_GEOMETRY (mmtbx.ions.identify.AtomProperties attribute) node (class in cctbx.crystal.coordination_sequences) node_object (class in cctbx.sgtbx.pointgroup_tools) NOFIX() (in module cctbx.development.run_shelx) noise_filtered_map_coefficients() (mmtbx.maps.composite_omit_map.run method) nominal_tile_centers() (xfel.metrology.mark3.fit_translation2 method) non_crystallographic_asu_mappings() (in module cctbx.crystal.direct_space_asu) non_crystallographic_symmetry() (in module cctbx.crystal) non_hydrogen_atoms() (mmtbx.monomer_library.cif_types.comp_comp_id method) non_hydrogen_iselection (cctbx.omz.cif_refine.extract_from_cif_files attribute) (cctbx.omz.cod_select_and_pickle.cod_data attribute) non_hydrogen_selection (cctbx.omz.cif_refine.extract_from_cif_files attribute) (cctbx.omz.cod_select_and_pickle.cod_data attribute) non_linear_ls_mixin (class in scitbx.lstbx.normal_eqns) non_linear_ls_with_separable_scale_factor (in module scitbx.lstbx.normal_eqns) non_linear_ls_with_separable_scale_factor_BLAS_2 (class in scitbx.lstbx.normal_eqns) non_unit_occupancy_implies_min_distance_sym_equiv_zero() (cctbx.xray.structure.structure method) nonbonded_deviations() (cctbx.geometry_restraints.energies.energies method) nonbonded_distances() (cctbx.geometry_restraints.energies.energies method) nonbonded_energy_type_registry (class in mmtbx.monomer_library.pdb_interpretation) nonbonded_model_distances() (cctbx.geometry_restraints.manager.manager method) norm() (cctbx.miller.array method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) norm_1() (scitbx.array_family.flex.double method) norm_inf() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) norm_sq() (scitbx.matrix.rec method) norm_vec() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method) normal_matrix_packed_u() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) normalise_all() (mmtbx.scaling.fa_estimation.cns_fa_driver method) normalised_amplitudes (class in cctbx.miller) normalised_amplitudes() (cctbx.miller.array method) normalize() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method) (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method) (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method) (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method) (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method) (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method) (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method) (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method) (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method) (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method) (cctbx.miller.array method) (scitbx.matrix.rec method) normalize_atom_ids_in_place() (mmtbx.monomer_library.cif_types.comp_comp_id method) normalize_start_map() (cctbx.maptbx.mem.run method) normalized_angle_list() (mmtbx.monomer_library.cif_types.comp_comp_id method) normalized_bond_list() (in module mmtbx.monomer_library.cif_types) (mmtbx.monomer_library.cif_types.comp_comp_id method) normalized_rna_dna (mmtbx.monomer_library.cif_types.comp_comp_id attribute) norms() (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec3_double method) note() (mmtbx.ncs.ncs.ncs_group method) nproc() (iotbx.map_model_manager.map_model_manager method) nqh_flip (class in mmtbx.validation.clashscore) nqh_flips (class in mmtbx.validation.clashscore) (mmtbx.validation.molprobity.molprobity attribute) nucleic() (mmtbx.scaling.matthews.component class method) num_scan_points (dxtbx.model.goniometer.Goniometer property) number (iotbx.shelx.tokens.residue_token attribute) number() (cctbx.web.asu_gallery.jv_index.point_group_symbols method) number_from_string() (in module cctbx.web.change_basis) number_of_atoms_below_fofc_map_level() (mmtbx.building.local_density_quality method) number_of_atoms_below_two_fofc_map_level() (mmtbx.building.local_density_quality method) number_of_atoms_outside_density() (mmtbx.building.local_density_quality method) number_of_atoms_within_radius() (mmtbx.ions.identify.AtomProperties method) number_of_backbone_oxygens() (mmtbx.ions.identify.AtomProperties method) number_of_continuous_allowed_origin_shifts() (cctbx.sgtbx.space_group_info method) number_of_favored_ligand_residues() (mmtbx.ions.identify.AtomProperties method) number_of_wilson_outliers (mmtbx.scaling.xtriage.xtriage_analyses property) number_table() (in module mmtbx.scaling.matthews) nums_from_string() (in module cctbx.web.change_basis)

O

o3p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) o3p_perp_xyz (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) o_max (mmtbx.validation.model_properties.xray_structure_statistics attribute) o_mean (mmtbx.validation.model_properties.xray_structure_statistics attribute) o_min (mmtbx.validation.model_properties.xray_structure_statistics attribute) objective() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) objective_decrease_threshold (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations_encapsulated_eqns attribute) obliquity (class in mmtbx.scaling.twin_analyses) obs() (cctbx.xray.target_functors.unified_least_squares_residual method) obs_map() (in module mmtbx.hydrogens.find) observation_type() (cctbx.miller.array method) observed (cctbx.xray.weighting_schemes.shelx_weighting property) occ (iotbx.pdb.hierarchy.atom property) (mmtbx.ions.environment.atom_contact property) (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] occupancy (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) occupancy() (iotbx.pdb.hierarchy.atom_group method) occupancy_counts() (iotbx.pdb.hierarchy.root method) occupancy_groups_simple() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.root method) occupancy_mean (mmtbx.validation.ligands.ligand_validation attribute) occupancy_penalty_exp (class in cctbx.xray.minimization) occupancy_regroupping() (in module mmtbx.refinement.occupancies) occupancy_selections() (in module mmtbx.refinement.occupancies) offset_inside_cell() (in module mmtbx.ncs.ncs) offset_inside_zero_one() (in module mmtbx.ncs.ncs) omega_from_atoms() (in module mmtbx.rotamer) omegalyze (mmtbx.validation.molprobity.molprobity attribute) omit_box (class in mmtbx.maps.composite_omit_map) omit_box() (mmtbx.maps.composite_omit_map.run method) omit_region_results (class in mmtbx.maps.composite_omit_map) omit_regions (class in mmtbx.maps.composite_omit_map) on_new_space_group() (cctbx.examples.location_part.a_theorem_in_primitive_settings method) (cctbx.examples.location_part.symmetries_with_nonzero_location_parts method) on_new_symmetry() (cctbx.examples.location_part.a_theorem_in_primitive_settings method) (cctbx.examples.location_part.symmetries_with_both_nonzero_location_and_intrinsic_parts method) (cctbx.examples.location_part.symmetries_with_nonzero_location_parts method) one() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) one_gaussian_agarwal_1978 (class in cctbx.eltbx.xray_scattering) one_gaussian_approximation() (cctbx.maptbx.atom_curves method) one_gaussian_exact() (cctbx.maptbx.atom_curves method) one_lattice_slice() (cctbx.merging.brehm_diederichs.algorithm2 method) one_panel (class in xfel.metrology.quadrant) one_sensor (class in xfel.metrology.quadrant) one_water_correlation() (in module mmtbx.hydrogens.find) only_amide_hydrogen_split() (in module mmtbx.disorder.analyze_model) only_atom() (iotbx.pdb.hierarchy.atom_group method) (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue method) (iotbx.pdb.hierarchy.residue_group method) (iotbx.pdb.hierarchy.root method) only_atom_group() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue_group method) (iotbx.pdb.hierarchy.root method) only_chain() (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.root method) only_conformer() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.root method) only_model() (iotbx.pdb.hierarchy.root method) only_residue() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.root method) (mmtbx.building.box_build_refine_base method) only_residue_group() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.root method) OnPan() (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) OnSave() (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame method) OnSaveImage() (xfel.cxi.gfx.status_plot.StatusFrame method) OnSetRunNumber() (xfel.cxi.gfx.status_plot.StatusFrame method) OnTimeLockCheck() (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) OnTimer() (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame method) OnUpdate() (xfel.cxi.gfx.status_plot.StatusFrame method) OnZoom() (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) op (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute) open_rotarama_dlite() (in module mmtbx.rotamer.rotamer_eval)

oper_adds_offset() (mmtbx.ncs.ncs.ncs_group method) operation() (cctbx.sgtbx.harker.plane_fractional method) operator (mmtbx.scaling.twin_analyses.twin_law attribute) opposite_of_gradient() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) optimise_rectangle (class in xfel.metrology.flatfile) optimise_rectangle_2 (class in xfel.metrology.flatfile) optimise_rectangle_3 (class in xfel.metrology.flatfile) optimize_h() (in module mmtbx.utils) order() (iotbx.cif.model.loop method) order_check() (cctbx.crystal.find_best_cell.alternative_find_best_cell method) ordered_solvent_distribution (class in mmtbx.max_lik.max_like_non_uniform) origin() (mmtbx.twinning.twin_f_model.twin_model_manager method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) origin_is_zero() (iotbx.map_manager.map_manager method) origin_shift_grid_units() (mmtbx.utils.extract_box_around_model_and_map method) original_color_model (class in mmtbx.polygon.output) original_intensities_flag() (mmtbx.scaling.xtriage.xtriage_summary method) ortho() (scitbx.matrix.rec method) orthogonalizer (class in cctbx.web.asu_gallery.jv_asu) orthorhombic_unit_cell_around_centered_scatterers() (cctbx.xray.structure.structure method) other (mmtbx.validation.experimental.real_space attribute) out (mmtbx.scaling.printed_output attribute) out_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table) out_percent (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.rotalyze.rotalyze attribute) outer_loop() (mmtbx.maps.fem.run method) outer_product() (scitbx.matrix.rec method) outlier (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atoms attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.clash attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.entity attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.planarity attribute) (mmtbx.validation.restraints.restraint attribute) (mmtbx.validation.rna_validate.rna_angle attribute) (mmtbx.validation.rna_validate.rna_bond attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) outlier_manager (class in mmtbx.scaling.outlier_rejection) outlier_rejection (class in mmtbx.scaling.pair_analyses) outlier_selection() (mmtbx.twinning.twin_f_model.twin_model_manager method) (mmtbx.validation.validation method) outlier_threshold (mmtbx.validation.rotalyze.rotalyze attribute) outlier_type() (mmtbx.validation.restraints.chirality method) OutlierCellError outliers (mmtbx.validation.molprobity.residue_multi_criterion attribute) outliers_removed (mmtbx.validation.cbetadev.cbetadev attribute) output_header (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) output_image() (in module xfel.cxi.cspad_ana.xes_finalise) output_kinemage() (mmtbx.den.den_restraints method) output_matlab_form() (in module xfel.cxi.cspad_ana.xes_finalise) output_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise) overall_cc() (mmtbx.ncs.ncs.ncs method) overall_counts (class in iotbx.pdb.hierarchy) overall_counts() (iotbx.pdb.hierarchy.root method) overall_i_sig_i (mmtbx.scaling.xtriage.xtriage_analyses property) overall_isotropic_kb_estimate() (mmtbx.bulk_solvent.scaler.run method) overall_note() (mmtbx.ncs.ncs.ncs method) overall_rmsd() (mmtbx.ncs.ncs.ncs method) overall_rsc (mmtbx.validation.experimental.real_space attribute) overlap (mmtbx.validation.clashscore.clash attribute) overlap_predicate (class in mmtbx.geometry.indexing) overlap_predicate() (mmtbx.geometry.indexing.structure_indexer method) overwrite_from_phil() (dxtbx.model.detector.DetectorFactory static method)

P

p_distance_c1p_outbound_line (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) p_from_string() (in module cctbx.web.change_basis) p_perp_xyz (mmtbx.monomer_library.rna_sugar_pucker_analysis.evaluate attribute) p_solc_calc() (in module mmtbx.scaling.matthews) (mmtbx.scaling.matthews.p_vm_calculator method) p_value() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method) p_vm_calculator (class in mmtbx.scaling.matthews) pack() (mmtbx.refinement.group.group_minimizer method) (mmtbx.refinement.occupancies.minimizer method) (mmtbx.refinement.rigid_body.rigid_body_minimizer method) (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method) (mmtbx.scaling.relative_scaling.refinery method) (mmtbx.tls.tools.tls_from_uaniso_minimizer method) (mmtbx.tls.tools.tls_from_uiso_minimizer method) (mmtbx.tls.tools.tls_xray_target_minimizer method) pack_gradients() (in module cctbx.examples.g_exp_i_alpha_derivatives) (in module cctbx.examples.structure_factor_derivatives) (in module cctbx.examples.structure_factor_derivatives_2) (in module cctbx.examples.structure_factor_derivatives_3) (in module mmtbx.refinement.occupancies) pack_parameters() (in module cctbx.examples.g_exp_i_alpha_derivatives) (in module cctbx.examples.structure_factor_derivatives) pack_unpack() (in module mmtbx.refinement.occupancies) pack_variables() (cctbx.omz.dev.refinement method) packed() (cctbx.xray.structure_factors.gradients_base.gradients_base method) pai (mmtbx.ions.environment.ScatteringEnvironment attribute), [1] paint() (cctbx.command_line.precession_view.render_postscript method) pair() (cctbx.omz.dev.dynamic_shift_limit_site method) (cctbx.omz.dev.dynamic_shift_limit_u_iso method) pair_asu_table (cctbx.crystal.show_distances attribute) pair_asu_table() (cctbx.crystal.special_position_settings method) (cctbx.xray.structure.structure method) pair_generator() (cctbx.crystal.special_position_settings method) pair_proxies (class in cctbx.geometry_restraints) pair_proxies() (cctbx.geometry_restraints.manager.manager method) pair_sort_function() (in module cctbx.euclidean_model_matching) pair_sym_table_show() (cctbx.xray.structure.structure method) pair_sym_table_show_distances() (cctbx.xray.structure.structure method) pairs() (mmtbx.geometry.clash.ClashCollection method) (mmtbx.geometry.clash.ClashPoint method) parallel_map() (in module libtbx.easy_mp) parallelity_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) parallelity_deviations() (cctbx.geometry_restraints.energies.energies method) parallelity_proxy_registry (class in cctbx.geometry_restraints) parameter_based_model() (xfel.metrology.mark10.fit_translation4 method) (xfel.metrology.mark3.fit_translation2 method) parameter_based_model_one_frame_detail() (xfel.metrology.mark10.fit_translation4 method) parameter_map() (cctbx.xray.structure.structure method) parameter_nbonds (class in cctbx.development.make_cns_input) parameter_nonb (class in cctbx.development.make_cns_input) parameter_server (class in mmtbx.ions) parameter_vector_norm() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) parameters (class in cctbx.examples.g_exp_i_alpha_derivatives) (class in cctbx.examples.structure_factor_derivatives) params (mmtbx.command_line.load_model_and_data attribute) (mmtbx.ions.parameter_server attribute), [1] params_to_matrix() (cctbx.macro_mol.rotation_parameters.amore_alpha_beta_gamma method) (cctbx.macro_mol.rotation_parameters.amore_kappa_l_m_n method) (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fcalc_fobs method) (cctbx.macro_mol.rotation_parameters.ccp4_alpha_beta_gamma_fobs_fcalc method) (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fcalc_fobs method) (cctbx.macro_mol.rotation_parameters.ccp4_phi_omega_kappa_fobs_fcalc method) (cctbx.macro_mol.rotation_parameters.cns_axis_x_axis_y_axis_z_axis_kappa method) (cctbx.macro_mol.rotation_parameters.cns_psi_phi_kappa method) (cctbx.macro_mol.rotation_parameters.cns_theta1_theta2_theta3 method) (cctbx.macro_mol.rotation_parameters.cns_theta_plus_theta2_theta_minus method) parent() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_group method) (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.residue method) (iotbx.pdb.hierarchy.residue_group method) parse() (iotbx.shelx.parsers.crystal_symmetry_parser method) (iotbx.shelx.parsers.parser method) parse_lines() (iotbx.xds.xds_inp.reader method) parse_metrology() (in module xfel.metrology.flatfile) parse_options_loop_space_groups() (in module cctbx.development.debug_utils) parse_restraints() (iotbx.shelx.parsers.restraint_parser method) parse_smtbx_refinement_model() (in module iotbx.shelx) parse_version_1_tokens() (iotbx.xds.xparm.reader method) parse_version_2_tokens() (iotbx.xds.xparm.reader method) parser (class in iotbx.shelx.parsers) part_names() (scitbx.array_family.flex.complex_double static method) (scitbx.array_family.flex.vec3_double static method) partial_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute) partition_t (class in cctbx.sgtbx.cosets) parts() (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) pathsubst() (in module xfel.cxi.cspad_ana.cspad_tbx) patterson_map() (cctbx.miller.array method) patterson_symmetry() (cctbx.crystal.symmetry method) (cctbx.miller.array method) (cctbx.miller.set method) patterson_verdict (mmtbx.scaling.xtriage.xtriage_analyses property) patterson_verdict() (mmtbx.scaling.twin_analyses.twin_results_interpretation method) pbss (mmtbx.validation.ligands.ligand_validation attribute) pdb_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) pdb_element_charge_columns() (iotbx.pdb.hierarchy.atom method) pdb_file_names (mmtbx.command_line.load_model_and_data attribute) pdb_file_to_emma_model() (in module cctbx.web.emma) pdb_header_info (class in mmtbx.validation.molprobity) pdb_hierarchy (mmtbx.building.make_library.related_chain attribute) (mmtbx.command_line.load_model_and_data attribute) (mmtbx.validation.molprobity.molprobity attribute) pdb_id_str (mmtbx.ions.svm.svm_prediction attribute), [1] pdb_inp (mmtbx.command_line.load_model_and_data attribute) pdb_inp_from_multiple_files() (in module mmtbx.utils) pdb_label_columns() (iotbx.pdb.hierarchy.atom method) pdb_or_mmcif_string_info() (iotbx.pdb.hierarchy.root method) pdb_residue (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) pdb_residue_id_str (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) pdbx_align (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) pdbx_aromatic_flag (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) pdbx_leaving_atom_flag (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) pdbx_model_cartn_x_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) pdbx_model_cartn_y_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) pdbx_model_cartn_z_ideal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) pdbx_ordinal (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) pdbx_stereo_config (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) peak_cluster_analysis (class in cctbx.maptbx) peak_cluster_reduction() (in module cctbx.examples.phase_o_phrenia) peak_cutoff() (cctbx.maptbx.peak_search_parameters method) peak_list (class in cctbx.maptbx) peak_list() (cctbx.maptbx.peak_cluster_analysis method) peak_list_indices() (cctbx.maptbx.peak_cluster_analysis method) peak_search() (cctbx.maptbx.crystal_gridding_tags method) peak_search_level() (cctbx.maptbx.peak_search_parameters method) peak_search_parameters (class in cctbx.maptbx) peak_volume_estimate() (in module cctbx.maptbx) penalty_scores() (cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria method) pentagon_sites_cart() (in module cctbx.examples.random_puckers) per_frame_helper_factory() (xfel.mono_simulation.mono_treatment.refinement method) percent_allowed (mmtbx.validation.ramalyze.ramalyze property) (mmtbx.validation.rotalyze.rotalyze attribute) percent_favored (mmtbx.validation.ramalyze.ramalyze property) (mmtbx.validation.rotalyze.rotalyze attribute) percent_outliers (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.validation property) perform_least_squares_scaling() (mmtbx.scaling.fa_estimation.combined_scaling method) perform_local_scaling() (mmtbx.scaling.fa_estimation.combined_scaling method) perform_outlier_rejection() (mmtbx.scaling.fa_estimation.combined_scaling method) perms (cctbx.miller.reindexing.assistant attribute) permutation_generator() (in module scitbx.array_family.flex) permute_d_range() (cctbx.miller.array method) pgd_server (class in mmtbx.monomer_library.conformation_dependent_restraints) pH() (mmtbx.ligands.xtal_screens.solution method) pH_ (mmtbx.ligands.xtal_screens.solution attribute) phase_entropy() (cctbx.miller.array method) phase_error() (in module mmtbx.max_lik.maxlik) phase_errors() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method) (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method) (mmtbx.twinning.twin_f_model.twin_model_manager method) phase_errors_test() (mmtbx.twinning.twin_f_model.twin_model_manager method) phase_errors_work() (mmtbx.twinning.twin_f_model.twin_model_manager method) phase_integrals() (cctbx.miller.array method) phase_transfer() (cctbx.miller.array method) phased_translation_function_coeff() (cctbx.miller.array method) phaser_sad_llg (mmtbx.map_names attribute) phaser_sad_target_functor (class in mmtbx.refinement.targets) phases() (cctbx.miller.array method) (mmtbx.maps.map_coeffs_mtz_label_manager method) phi (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) phi_from_atoms() (in module mmtbx.rotamer) phi_from_sites() (in module mmtbx.rotamer) phi_min_max_mean() (mmtbx.validation.ramalyze.ramachandran_ensemble method) phi_psi_from_sites() (in module mmtbx.rotamer) phi_range() (mmtbx.validation.ramalyze.ramachandran_ensemble method) phi_sym_acceptance_cutoff (cctbx.symmetry_search.structure_factor_symmetry attribute) phi_sym_rejection_cutoff (cctbx.symmetry_search.structure_factor_symmetry attribute) phil_atom_selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) phil_atom_selection_multiple() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) phil_atom_selections_as_i_seqs() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) phil_atom_selections_as_i_seqs_multiple() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) phil_lego (class in mmtbx.scaling.make_param) pick_nicest_fit() (in module cctbx.eltbx.development.combine_fits) pixel_histograms (class in xfel.command_line.view_pixel_histograms) (class in xfel.cxi.cspad_ana.pixel_histograms) PixelFitError pixels() (xfel.command_line.view_pixel_histograms.pixel_histograms method) planarities (class in mmtbx.validation.restraints) (mmtbx.validation.restraints.combined attribute) planarity (class in mmtbx.validation.restraints) planarity_counters (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) planarity_deviations() (cctbx.geometry_restraints.energies.energies method) planarity_proxy_registry (class in cctbx.geometry_restraints) plane_atom_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute) plane_cartesian (class in cctbx.sgtbx.harker) plane_fractional (class in cctbx.sgtbx.harker) plane_group_table (class in cctbx.web.asu_gallery.jv_index) planes_cartesian (class in cctbx.sgtbx.harker) planes_fractional (class in cctbx.sgtbx.harker) plot() (xfel.command_line.view_pixel_histograms.pixel_histograms method) plot_energy() (in module xfel.cxi.cspad_ana.xes_finalise) plot_gaussians() (xfel.command_line.view_pixel_histograms.pixel_histograms method) plot_one_histogram() (xfel.command_line.view_pixel_histograms.pixel_histograms method) plot_overall_completeness() (in module xfel.command_line.cxi_merge) plot_range() (mmtbx.validation.graphics.multi_criterion_plot_mixin method) plot_samples() (cctbx.omz.dev.refinement method) plot_samples_ix() (cctbx.omz.dev.refinement method) plot_statistics (class in xfel.command_line.cxi_merge) plot_statistics_histograms() (xfel.command_line.cxi_merge.plot_statistics method) plot_unit_cell_histograms() (xfel.command_line.cxi_merge.plot_statistics method) plot_weights_pyplot() (in module mmtbx.den.plot_weights) plot_wilson() (xfel.clustering.singleframe.SingleFrame method) plotit() (in module mmtbx.scaling.outlier_plots) plus_minus (iotbx.shelx.tokens.atomname_token attribute) (iotbx.shelx.tokens.element_token attribute) plus_minus() (cctbx.merging.brehm_diederichs.minimize_divide method) point (class in cctbx.web.asu_gallery.jvx)

point_group_filter() (xfel.clustering.cluster.Cluster method) point_group_graph (class in cctbx.sgtbx.pointgroup_tools) point_group_symbols (class in cctbx.web.asu_gallery.jv_index) point_group_table (class in cctbx.web.asu_gallery.jv_index) point_in_polygon() (in module xfel.command_line.make_mask) point_inside_circle() (in module xfel.command_line.make_mask) points (mmtbx.geometry.asa.AccessibleSurfaceAreas property) pointSet (class in cctbx.web.asu_gallery.jvx) polarization_correction() (xfel.clustering.singleframe.SingleFrame method) polygon() (in module mmtbx.polygon) polygon_layout (class in mmtbx.polygon.output) polygon_stats (mmtbx.validation.molprobity.molprobity attribute) polygon_vertices() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) polymeric_type_filter() (in module mmtbx.wwpdb.rcsb_web_services) pool_map() (in module libtbx.easy_mp) pop_back() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) populate_bin_to_individual_k_mask_linear_interpolation() (mmtbx.bulk_solvent.scaler.run method) pos (cctbx.omz.dev.shift_limit_pair attribute) position (class in cctbx.euclidean_model_matching) positions() (cctbx.euclidean_model_matching.model method) positivity_constrained_density_modification (class in cctbx.maptbx) possible_cyclic_peptide() (in module mmtbx.monomer_library.linking_mixins) possible_outliers (class in mmtbx.scaling.data_statistics) possible_point_group_generators() (cctbx.symmetry_search.structure_factor_symmetry method) possible_symmetry (class in cctbx.symmetry_search) post_min_recalc() (xfel.metrology.mark1.fit_translation method) (xfel.metrology.mark3.fit_translation2 method) post_outlier_rejection() (in module xfel.mono_simulation.mono_treatment) post_query() (in module mmtbx.wwpdb.rcsb_web_services) post_report_query_with_pdb_list() (in module mmtbx.wwpdb.rcsb_web_services) postrefine_by_frame_mproc() (in module xfel.command_line.postrefine) potential_object (class in cctbx.omz.tardy_adaptor) (class in mmtbx.refinement.tardy) Pperp_distance (mmtbx.validation.rna_validate.rna_pucker attribute) pperp_outliers() (in module mmtbx.kinemage.validation) pprocess (class in cctbx.xray.structure_factors.from_scatterers_direct_parallel) pre_allocate_atom_groups() (iotbx.pdb.hierarchy.residue_group method) pre_allocate_atoms() (iotbx.pdb.hierarchy.atom_group method) pre_allocate_chains() (iotbx.pdb.hierarchy.model method) pre_allocate_models() (iotbx.pdb.hierarchy.root method) pre_allocate_residue_groups() (iotbx.pdb.hierarchy.chain method) pre_check() (in module cctbx.development.run_shelx) pre_get_predictions() (in module xfel.mono_simulation.mono_treatment) pre_scaler (class in mmtbx.scaling.pre_scale) predict_ion() (in module mmtbx.ions.svm) prefilter (class in mmtbx.building.extend_sidechains) prepare_f_obs_and_flags() (mmtbx.maps.fem.run method) prepare_for_minimization() (mmtbx.refinement.targets.phaser_sad_target_functor method) (mmtbx.refinement.targets.target_functor method) (mmtbx.twinning.twin_f_model.target_functor method) prepare_gaussians_symmetries_cell() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess method) prepare_miller_arrays_for_cuda() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess method) prepare_scattering_sites_for_cuda() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess method) prepare_target_functors_for_minimization() (mmtbx.fmodels method) preprocess_angles() (in module cctbx.macro_mol.rotation_parameters) primary_structure_section() (iotbx.pdb.ext.input method) prime_postrefine() (xfel.clustering.cluster.Cluster method) primitive_setting() (cctbx.crystal.symmetry method) (cctbx.sgtbx.space_group_info method) principal_axes_of_inertia() (cctbx.xray.structure.structure method) (in module cctbx.maptbx) (mmtbx.ions.identify.manager method) print_all_reflections_in_file() (mmtbx.max_lik.max_like_non_uniform.ordered_solvent_distribution method) print_apply() (in module mmtbx.monomer_library.linking_utils) print_atom() (in module mmtbx.hydrogens.find) print_atom_statisitics() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) print_banner() (in module mmtbx.scaling.fest) (in module mmtbx.scaling.xtriage) print_clashlist_old() (mmtbx.validation.clashscore.clashscore method) print_detailed_dynamics_stats() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) print_diagnostics() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess method) print_dict() (in module mmtbx.monomer_library.pdb_interpretation) print_diffs() (mmtbx.twinning.twin_f_model.twin_model_manager method) print_dynamics_stat() (mmtbx.dynamics.cartesian_dynamics.run method) print_filtered_cif() (in module mmtbx.monomer_library.server) print_ftp_info() (in module cctbx.source_generators.eltbx.generate_henke_cpp) (in module cctbx.source_generators.eltbx.generate_sasaki_cpp) print_grid() (in module mmtbx.conformation_dependent_library.utils) print_header() (in module cctbx.source_generators.eltbx.generate_henke_cpp) (in module cctbx.source_generators.eltbx.generate_sasaki_cpp) (in module mmtbx.utils) print_help() (in module mmtbx.scaling.remove_outliers) (in module mmtbx.scaling.xtriage) print_henke_cpp() (in module cctbx.source_generators.eltbx.generate_henke_cpp) print_list() (mmtbx.ncs.ncs.ncs_group method) print_programs_start_header() (in module mmtbx.utils) print_sasaki_cpp() (in module cctbx.source_generators.eltbx.generate_sasaki_cpp) print_scat() (in module mmtbx.hydrogens.find) print_scats() (in module mmtbx.hydrogens.find) print_step() (in module mmtbx.tls.tls_as_xyz) print_table() (xfel.metrology.mark0.correction_vectors method) (xfel.metrology.mark1.fit_translation method) (xfel.metrology.mark10.fit_translation4 method) (xfel.metrology.mark3.fit_translation2 method) print_table_2() (xfel.metrology.mark10.fit_translation4 method) print_table_block() (in module cctbx.source_generators.eltbx.generate_henke_cpp) (in module cctbx.source_generators.eltbx.generate_sasaki_cpp) print_ucs() (xfel.clustering.cluster.Cluster method) print_unit_translations() (xfel.metrology.mark10.fit_translation4 static method) printed_output (class in mmtbx.scaling) probable_pucker (mmtbx.validation.rna_validate.rna_pucker attribute) probe_clashscore_manager (class in mmtbx.validation.clashscore) (mmtbx.validation.clashscore.clashscore attribute) probe_file (mmtbx.validation.clashscore.clashscore attribute) probe_line_info (class in mmtbx.validation.clashscore) probe_type (mmtbx.validation.clashscore.clash attribute) process (class in mmtbx.monomer_library.pdb_interpretation) process() (cctbx.development.space_group_option_parser.space_group_option_parser method) (cctbx.geometry_restraints.angle_proxy_registry method) (cctbx.geometry_restraints.bond_simple_proxy_registry method) (cctbx.geometry_restraints.chirality_proxy_registry method) (cctbx.geometry_restraints.dihedral_proxy_registry method) (cctbx.geometry_restraints.parallelity_proxy_registry method) (cctbx.geometry_restraints.planarity_proxy_registry method) (cctbx.omz.cif_refine.extract_from_cif_files method) (cctbx.xray.structure_factors.global_counters.calls_and_accumulated_time method) (in module cctbx.omz.cod_refine) (in module cctbx.omz.pdb_dev) (mmtbx.rotamer.rotamer_eval.RotamerID method) (mmtbx.rotamer.sidechain_angles.PropertyFile method) process_altloc() (mmtbx.geometry.altloc.Aggregator method) (mmtbx.geometry.altloc.Inserter method) (mmtbx.geometry.asa.SeparateCheckerBuilder method) process_apply_cif_link() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_apply_cif_modification() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_atom_groups_for_linking_single_link() (in module mmtbx.monomer_library.linking_utils) process_BIOMT_records() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) process_break() (mmtbx.secondary_structure.proteins.find_helices_simple method) process_chem_comp_atom_buffer (class in mmtbx.wwpdb.standard_geometry_cif) process_chem_comps() (in module mmtbx.wwpdb.standard_geometry_cif) process_cif() (mmtbx.monomer_library.server.process_cif_mixin method) process_cif_mixin (class in mmtbx.monomer_library.server) process_cif_object() (mmtbx.monomer_library.server.process_cif_mixin method) process_command_line_args (class in mmtbx.utils) process_continue() (in module cctbx.omz.cod_refine) process_custom_links() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_custom_nonbonded_exclusions() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_custom_nonbonded_symmetry_exclusions() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geom_bond() (cctbx.omz.cif_refine.extract_from_cif_files method) process_geometry_restraints_edits() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geometry_restraints_edits_angle() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geometry_restraints_edits_bond() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geometry_restraints_edits_dihedral() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geometry_restraints_edits_parallelity() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geometry_restraints_edits_planarity() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geometry_restraints_remove() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geometry_restraints_scale() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_geostd_rna_dna() (mmtbx.monomer_library.server.server method) process_hydrogen_bonds() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) process_input_array() (cctbx.miller.display.scene method) process_MTRIX_records() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) process_nonbonded_for_links() (mmtbx.monomer_library.linking_mixins.linking_mixins method) process_occupancies_depending_on_free_variable() (iotbx.shelx.parsers.atom_parser method) process_outliers() (mmtbx.validation.molprobity.multi_criterion_view method) process_pdb_file_srv (class in mmtbx.utils) process_pdb_files() (mmtbx.utils.process_pdb_file_srv method) process_pdb_hierarchy (class in mmtbx.disorder.analyze_model) process_possible_constrained_occupancy() (iotbx.shelx.parsers.atom_parser method) process_possible_u_iso_constraints() (iotbx.shelx.parsers.atom_parser method) process_raw_probe_output() (mmtbx.validation.clashscore.probe_clashscore_manager method) process_regular() (mmtbx.geometry.altloc.Aggregator method) (mmtbx.geometry.altloc.Inserter method) (mmtbx.geometry.asa.SeparateCheckerBuilder method) process_residue_groups (class in mmtbx.disorder.analyze_model) processed_options_type (cctbx.development.space_group_option_parser.space_group_option_parser attribute) processed_pdb_file (mmtbx.command_line.load_model_and_data attribute) product() (scitbx.matrix.rec method) program (mmtbx.validation.molprobity.summary attribute) program_description (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) ProgramTemplate (class in libtbx.program_template) propagate_model_from_other() (iotbx.map_model_manager.map_model_manager method) PropertyFile (class in mmtbx.rotamer.sidechain_angles) propose() (mmtbx.scaling.absences.analyze_absences method) protein (mmtbx.validation.experimental.real_space attribute) protein() (mmtbx.scaling.matthews.component class method) protein_space_group_choices (class in mmtbx.scaling.absences) proxy_registry_base (class in cctbx.geometry_restraints) proxy_registry_process_result (class in cctbx.geometry_restraints) proxy_select() (mmtbx.den.den_restraints method) (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) pseudo_deep_copy() (mmtbx.fmodels method) psi (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) psi_from_atoms() (in module mmtbx.rotamer) psi_from_sites() (in module mmtbx.rotamer) psi_min_max_mean() (mmtbx.validation.ramalyze.ramachandran_ensemble method) pucker_dist (mmtbx.validation.rna_validate.rna_puckers attribute) pucker_perp_xyz (mmtbx.validation.rna_validate.rna_puckers attribute) pucker_states (mmtbx.validation.rna_validate.rna_puckers attribute) puckers (mmtbx.validation.rna_validate.rna_validation attribute) pure_statistical_weighting (class in cctbx.xray.weighting_schemes) push_back() (mmtbx.secondary_structure.proteins.find_helices_simple method) put_group_into_dict() (mmtbx.validation.clashscore.probe_clashscore_manager method) py_object (class in scitbx.array_family.flex) pyplot_label_axes() (in module xfel.command_line.smooth_spectrum)

Q

q_size (xfel.cxi.cspad_ana.parse_calib.Section attribute) Q_X() (in module cctbx.maptbx.mem) qrotate() (xfel.cxi.cspad_ana.parse_calib.Section method) quad() (xfel.command_line.convert_gain_map.fake_cspad_ElementV2 method) quadMask() (xfel.command_line.convert_gain_map.fake_config method) quadratic_interpolation_with_gradients() (scitbx.array_family.flex.double method) quality_factor() (cctbx.xray.structure_factors.manager.manager method) quality_factor_from_any() (in module cctbx.xray.structure_factors.misc)

quasi_normalize_structure_factors() (cctbx.miller.array method) quasi_normalized_as_normalized() (cctbx.miller.array method) quaternion_inverse() (scitbx.matrix.rec method) queue_entry() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method) queue_progress_entry() (xfel.cxi.cspad_ana.mod_hitfind.mod_hitfind method) quick() (cctbx.eltbx.gaussian_fit.fit_parameters method) quick_info() (cctbx.omz.cod_select_and_pickle.cod_data method) quote() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_with_labels method)

R

r1_factor() (cctbx.miller.array method) (cctbx.omz.dev.refinement method) (in module xfel.cxi.cxi_cc) r3_rotation_matrix_as_unit_quaternion() (scitbx.matrix.rec method) r3_rotation_matrix_as_x_y_z_angles() (scitbx.matrix.rec method) r_all() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.bulk_solvent.scaler.run method) (mmtbx.twinning.twin_f_model.twin_model_manager method) r_anom() (cctbx.miller.array method) r_factor() (in module cctbx.maptbx.mem) (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.bulk_solvent.scaler.run method) r_factors_in_resolution_bins() (mmtbx.twinning.twin_f_model.twin_model_manager method) r_free (mmtbx.maps.composite_omit_map.omit_region_results attribute) (mmtbx.refinement.select_best_starting_model.evaluate_model attribute) (mmtbx.validation.experimental.data_statistics attribute) (mmtbx.validation.molprobity.pdb_header_info attribute) (mmtbx.validation.molprobity.summary attribute) r_free() (mmtbx.refinement.select_best_starting_model.select_model method) (mmtbx.twinning.twin_f_model.twin_model_manager method) (mmtbx.validation.molprobity.molprobity method) r_free_flags (mmtbx.command_line.load_model_and_data attribute) r_free_flags() (mmtbx.twinning.twin_f_model.twin_model_manager method) r_free_flags_accumulation() (cctbx.miller.array method) r_free_outer (mmtbx.validation.experimental.data_statistics attribute) r_free_start (mmtbx.refinement.select_best_starting_model.evaluate_model attribute) r_frees (mmtbx.refinement.print_statistics.stats_table attribute) r_inv() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.reduction_base method) r_linear() (cctbx.miller.merge_equivalents method) r_meas() (cctbx.miller.merge_equivalents method) r_merge() (cctbx.miller.merge_equivalents method) r_overall_low_high() (mmtbx.twinning.twin_f_model.twin_model_manager method) r_pim() (cctbx.miller.merge_equivalents method) r_split() (in module xfel.cxi.cxi_cc) r_square() (cctbx.miller.merge_equivalents method) r_value() (mmtbx.scaling.relative_scaling.local_scaling_driver method) r_values (class in mmtbx.scaling.twin_analyses) r_values() (mmtbx.twinning.twin_f_model.twin_model_manager method) r_vs_r() (mmtbx.scaling.twin_analyses.r_values method) r_vs_r_classification() (mmtbx.scaling.twin_analyses.r_values method) r_work (mmtbx.maps.composite_omit_map.omit_region_results attribute) (mmtbx.refinement.select_best_starting_model.evaluate_model attribute) (mmtbx.validation.experimental.data_statistics attribute) (mmtbx.validation.molprobity.pdb_header_info attribute) (mmtbx.validation.molprobity.summary attribute) r_work() (mmtbx.bulk_solvent.scaler.run method) (mmtbx.refinement.select_best_starting_model.select_model method) (mmtbx.twinning.twin_f_model.twin_model_manager method) (mmtbx.validation.molprobity.molprobity method) r_work_in_lowest_resolution_bin() (mmtbx.twinning.twin_f_model.twin_model_manager method) r_work_outer (mmtbx.validation.experimental.data_statistics attribute) r_work_scale_k1_completeness_in_bins() (mmtbx.twinning.twin_f_model.twin_model_manager method) r_work_start (mmtbx.refinement.select_best_starting_model.evaluate_model attribute) r_works (mmtbx.refinement.print_statistics.stats_table attribute) radial_transverse_analysis() (xfel.metrology.mark10.fit_translation4 method) radius (mmtbx.density_modification.density_modification property) radius_adaptor() (in module mmtbx.geometry.asa) radius_for() (mmtbx.geometry.clash.Case method) rainbow_color_model (class in mmtbx.polygon.output) raise_chains_with_mix_of_proper_and_improper_alt_conf_if_necessary() (iotbx.pdb.hierarchy.overall_counts method) raise_duplicate_atom_labels_if_necessary() (iotbx.pdb.hierarchy.overall_counts method) raise_improper_alt_conf_if_necessary() (iotbx.pdb.hierarchy.overall_counts method) raise_residue_groups_with_multiple_resnames_using_same_altloc_if_necessary() (iotbx.pdb.hierarchy.overall_counts method) raise_uninterpretable() (in module cctbx.web.change_basis) raise_usage() (in module cctbx.command_line.wavelength_units) rama_allowed() (mmtbx.validation.molprobity.molprobity method) rama_favored (mmtbx.validation.molprobity.summary attribute) rama_favored() (mmtbx.validation.molprobity.molprobity method) rama_outliers (mmtbx.validation.molprobity.summary attribute) rama_outliers() (in module mmtbx.kinemage.validation) (mmtbx.validation.molprobity.molprobity method) rama_type (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) ramachandran (class in mmtbx.validation.ramalyze) ramachandran_ensemble (class in mmtbx.validation.ramalyze) ramachandran_manager (class in mmtbx.geometry_restraints.ramachandran) ramachandran_plot (class in mmtbx.rotamer.graphics) (class in mmtbx.validation.ramalyze) ramachandran_plot_data (class in mmtbx.geometry_restraints.ramachandran) ramachandran_plot_mixin (class in mmtbx.rotamer.graphics) (class in mmtbx.validation.ramalyze) RamachandranEval (class in mmtbx.rotamer.ramachandran_eval) ramalyze (class in mmtbx.validation.ramalyze) (mmtbx.validation.molprobity.molprobity attribute) ramalyze_type() (mmtbx.validation.ramalyze.ramachandran method) random_elements() (in module cctbx.development.random_structure) random_modify_adp_and_adp_flags() (in module cctbx.development.random_structure) random_modify_adp_and_adp_flags_2() (in module cctbx.development.random_structure) random_modify_fdp() (cctbx.development.random_structure.xray_structure method) random_modify_fp() (cctbx.development.random_structure.xray_structure method) random_modify_occupancy() (cctbx.development.random_structure.xray_structure method) random_modify_parameters() (cctbx.development.random_structure.xray_structure method) random_modify_site() (cctbx.development.random_structure.xray_structure method) (in module cctbx.development.random_structure) random_modify_u_iso() (cctbx.development.random_structure.xray_structure method) random_modify_u_star() (cctbx.development.random_structure.xray_structure method) random_omit_data (class in mmtbx.scaling.random_omit) random_origin_shift() (in module cctbx.development.debug_utils) random_phases_compatible_with_phase_restrictions() (cctbx.miller.set method) random_remove_sites_selection() (cctbx.xray.structure.structure method) random_rotate_ellipsoid() (in module cctbx.adptbx) random_selection() (in module scitbx.array_family.flex) random_shift_sites() (cctbx.xray.structure.structure method) random_site() (in module cctbx.development.random_structure) random_sites() (in module cctbx.development.random_structure) random_traceless_symmetry_constrained_b_cart() (in module cctbx.adptbx) random_u_cart() (in module cctbx.adptbx) random_velocities() (in module mmtbx.dynamics.cartesian_dynamics) (in module mmtbx.dynamics.ensemble_cd) random_weight_averaged_map_coefficients() (mmtbx.maps.kick.weighted_average method) randomize() (iotbx.map_manager.map_manager method) randomize_amplitude_and_phase() (cctbx.miller.array method) randomize_completeness() (in module mmtbx.maps.kick) randomize_completeness2() (in module mmtbx.maps.kick) randomize_new_velocities() (mmtbx.solvent.ensemble_ordered_solvent.manager method) randomize_phases() (cctbx.miller.array method) (in module cctbx.examples.map_skewness) randomize_struture_factors() (in module mmtbx.maps.kick) randomize_velocity() (mmtbx.solvent.ensemble_ordered_solvent.manager method) RascalMatch (class in mmtbx.geometry.topology) rat_rot_group (class in cctbx.sgtbx.rational_matrices_point_groups) (class in cctbx.sgtbx.reticular_pg_tools) ratio_cutoffs (mmtbx.polygon.output.renderer attribute) raw_data (mmtbx.command_line.load_model_and_data attribute) raw_flags (mmtbx.command_line.load_model_and_data attribute) raw_probe_line_info (class in mmtbx.validation.clashscore) re_apply_symmetry() (cctbx.xray.structure.structure method) read_all_mysql() (xfel.command_line.cxi_xmerge.xscaling_manager method) read_cif() (in module mmtbx.monomer_library.server) read_data() (xfel.metrology.mark0.correction_vectors method) read_file() (iotbx.xds.integrate_hkl.reader method) (iotbx.xds.spot_xds.reader method) (iotbx.xds.xds_inp.reader method) (iotbx.xds.xparm.reader method) read_input() (in module xfel.command_line.postrefine) read_map() (iotbx.map_model_manager.match_map_model_ncs method) read_model() (iotbx.map_model_manager.match_map_model_ncs method) read_ncs() (mmtbx.ncs.ncs.ncs method) read_ncs_file() (iotbx.map_model_manager.match_map_model_ncs method) read_optical_metrology_from_flat_file() (in module xfel.cftbx.detector.cspad_cbf_tbx) read_pickled_fits (class in cctbx.eltbx.development.format_gaussian_fits) read_scatterer() (in module cctbx.web.io_utils) read_structure() (in module cctbx.command_line.structure_factor_timings) read_table() (in module cctbx.eltbx.development.kissel_io) read_table6111() (in module cctbx.eltbx.development.itvc_section61_io) reader (class in iotbx.cif) (class in iotbx.shelx.hklf) (class in iotbx.xds.integrate_hkl) (class in iotbx.xds.read_ascii) (class in iotbx.xds.spot_xds) (class in iotbx.xds.xds_inp) (class in iotbx.xds.xparm) real_space (class in mmtbx.validation.experimental) (mmtbx.validation.molprobity.molprobity attribute) real_space_refine() (mmtbx.building.box_build_refine_base method) (mmtbx.refinement.real_space.fit_residue.run_with_minimization method) real_space_rigid_body_gradients_simple() (in module mmtbx.refinement.real_space.rigid_body) realign() (mmtbx.building.make_library.ensembler method) reassemble() (in module cctbx.merging.brehm_diederichs) rec (class in scitbx.matrix) recalc_hits() (xfel.cxi.gfx.trials_plot.Run method) reciprocal (cctbx.crystal_orientation.basis_type attribute) reciprocal_space_asu() (cctbx.sgtbx.space_group_info method) recolor_grid_points() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) reconstructed_amplitude (class in cctbx.xray.observation_types) record_type_counts() (iotbx.pdb.ext.input method) records_for_pdb_file() (mmtbx.secondary_structure.manager method) recurring_operators() (in module cctbx.sgtbx.reticular_pg_tools) red_color_model (class in mmtbx.polygon.output) reduce_for_tardy() (cctbx.geometry_restraints.manager.manager method) ReducingAccumulator (class in mmtbx.geometry.clash) reduction (class in cctbx.uctbx.gruber_1973) (class in cctbx.uctbx.krivy_gruber_1976) reduction_base (class in cctbx.uctbx.reduction_base) redundancies() (cctbx.miller.merge_equivalents method) ref_radii_asa_probe (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) ref_to_k_overall() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) ref_to_k_part() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) ref_to_k_sol() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) ref_to_twin_fraction() (mmtbx.twinning.twin_f_model.twin_fraction_object method) ref_to_u_part() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) ref_to_u_sol() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) ref_to_u_star() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) reference_dihedral_deviations() (cctbx.geometry_restraints.energies.energies method) reference_setting() (cctbx.sgtbx.space_group_info method) reference_setting_choices() (in module cctbx.sgtbx.pointgroup_tools) reference_space_group_infos() (in module cctbx.sgtbx) refinable_params_one_ncs_to_asu() (mmtbx.refinement.minimization_ncs_constraints.lbfgs method) refine (class in mmtbx.refinement.real_space.rigid_body) refine() (mmtbx.refinement.real_space.individual_sites.box_refinement_manager method) (mmtbx.refinement.real_space.individual_sites.diff_map method) (mmtbx.refinement.real_space.individual_sites.simple method) refine_adjusted_shift() (cctbx.euclidean_model_matching.match_refine method) refine_adp (class in mmtbx.refinement.adp_refinement) refine_all() (xfel.mono_simulation.mono_treatment.refinement2 method) refine_anomalous_substructure() (in module mmtbx.refinement.anomalous_scatterer_groups) (mmtbx.ions.identify.manager method) refine_groups (class in mmtbx.refinement.real_space.rigid_body) refine_mz (class in mmtbx.refinement.real_space.rigid_body) refine_oat() (mmtbx.solvent.ordered_solvent.manager method) refine_rotx_roty2() (xfel.mono_simulation.mono_treatment.refinement method) refinement (class in cctbx.omz.dev) (class in xfel.mono_simulation.mono_treatment) refinement2 (class in xfel.mono_simulation.mono_treatment) refinement_base (class in xfel.mono_simulation.mono_treatment) refinement_monitor (class in mmtbx.refinement.print_statistics) refinement_program (mmtbx.validation.molprobity.pdb_header_info attribute) refinery (class in cctbx.examples.unit_cell_minimizers) (class in cctbx.examples.unit_cell_refinement) (class in mmtbx.refinement.real_space.individual_sites) (class in mmtbx.scaling.relative_scaling) refit_residues() (in module mmtbx.building.extend_sidechains) reflection_intensity_equivalent_groups() (cctbx.sgtbx.space_group_info method) reflection_intensity_symmetry() (cctbx.crystal.symmetry method) (cctbx.miller.set method) region_density_correlation() (in module cctbx.maptbx) registry (cctbx.sgtbx.symmetry_equivalent_pair_interactions attribute) registry() (in module cctbx.xray.target_functors) regularize() (cctbx.miller.array method) regularize_model() (in module mmtbx.hydrogens.build_hydrogens) reindexing (class in mmtbx.scaling.pair_analyses) reindexing_operators (class in cctbx.crystal.reindex) rejected (cctbx.symmetry_search.possible_symmetry attribute) related_chain (class in mmtbx.building.make_library) relative_sd_on_edges() (in module cctbx.maptbx) relative_wilson (class in mmtbx.scaling.relative_wilson) remapped() (mmtbx.geometry.topology.GreedyMatch method) (mmtbx.geometry.topology.McGregorMatch method) (mmtbx.geometry.topology.RascalMatch method) remark_3_tls() (in module mmtbx.tls.tools) remark_section() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) remediate_mismatches() (in module cctbx.r_free_utils) remove_alt_confs() (iotbx.pdb.hierarchy.root method) remove_angles_in_place() (cctbx.geometry_restraints.manager.manager method) remove_anisotropy() (iotbx.map_model_manager.map_model_manager method) remove_atom() (iotbx.pdb.hierarchy.atom_group method) remove_atom_group() (iotbx.pdb.hierarchy.residue_group method) remove_atoms() (iotbx.pdb.hierarchy.root method) remove_c_beta_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) remove_chain() (iotbx.pdb.hierarchy.model method) remove_chi_torsion_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) remove_chiralities_in_place() (cctbx.geometry_restraints.manager.manager method) remove_clashing_atoms() (in module mmtbx.ncs.ligands) remove_common_isotropic_adp() (mmtbx.maps.fem.run method) remove_cone() (cctbx.miller.array method) remove_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method) remove_extra() (in module mmtbx.ncs.ncs) remove_far_atoms() (in module mmtbx.ncs.ncs_search) remove_hd() (iotbx.pdb.hierarchy.root method) remove_hetero() (iotbx.pdb.hierarchy.root method) remove_incomplete_main_chain_protein() (iotbx.pdb.hierarchy.root method) remove_items_from_selection() (in module mmtbx.ncs.ncs_utils) remove_labels() (iotbx.map_manager.map_manager method) remove_link() (mmtbx.monomer_library.linking_mixins.ResidueLinkClass method) remove_map_manager_by_id() (iotbx.map_model_manager.map_model_manager method) remove_model() (iotbx.pdb.hierarchy.root method) remove_model_by_id() (iotbx.map_model_manager.map_model_manager method) remove_model_outside_map() (iotbx.map_model_manager.map_model_manager method) remove_ncs_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method) remove_ncs_not_consistent_with_space_group_number() (in module mmtbx.ncs.ncs) remove_non_matching_pairs() (mmtbx.den.den_restraints method) remove_origin_shift_and_unit_cell_crystal_symmetry() (iotbx.map_model_manager.map_model_manager method) remove_outliers() (mmtbx.scaling.data_statistics.possible_outliers method) (mmtbx.scaling.pair_analyses.outlier_rejection method) (mmtbx.twinning.twin_f_model.twin_model_manager method) remove_parallelities_in_place() (cctbx.geometry_restraints.manager.manager method) remove_patterson_origin_peak() (cctbx.miller.array method) remove_planarities_in_place() (cctbx.geometry_restraints.manager.manager method) remove_point_group_and_its_super_groups_from_graph() (cctbx.sgtbx.pointgroup_tools.point_group_graph method) remove_quotes_from_chain_id() (in module mmtbx.ncs.ncs) remove_ramachandran_in_place() (cctbx.geometry_restraints.manager.manager method) remove_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) remove_reference_dihedral_manager() (cctbx.geometry_restraints.manager.manager method) remove_reference_dihedrals_in_place() (cctbx.geometry_restraints.manager.manager method) remove_residue_group() (iotbx.pdb.hierarchy.chain method) remove_residue_groups_with_atoms_on_special_positions_selective() (iotbx.pdb.hierarchy.root method) remove_secondary_structure_restraints() (cctbx.geometry_restraints.manager.manager method) remove_selections() (in module mmtbx.utils) remove_sidechain_atoms() (in module mmtbx.building) remove_single_quotes() (in module mmtbx.ncs.ncs) remove_site_with_most_neighbors() (in module iotbx.map_manager) remove_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method) remove_systematic_absences() (cctbx.miller.set method) remove_ter_or_break() (iotbx.pdb.hierarchy.root method) remove_tmp_files() (in module cctbx.omz.cod_refine) remove_user_supplied_restraints_in_place() (cctbx.geometry_restraints.manager.manager method) remove_zero_occupancy() (in module mmtbx.hydrogens.find) rename_angle() (in module mmtbx.monomer_library.conv_v2_v3) rename_atom() (in module mmtbx.monomer_library.conv_v2_v3) rename_bond() (in module mmtbx.monomer_library.conv_v2_v3) rename_chain_id() (iotbx.pdb.hierarchy.root method) rename_chir() (in module mmtbx.monomer_library.conv_v2_v3) rename_generic() (in module mmtbx.monomer_library.conv_v2_v3) rename_link_angle() (in module mmtbx.monomer_library.conv_v2_v3) rename_link_bond() (in module mmtbx.monomer_library.conv_v2_v3) rename_link_tor() (in module mmtbx.monomer_library.conv_v2_v3) rename_plan() (in module mmtbx.monomer_library.conv_v2_v3) rename_tor() (in module mmtbx.monomer_library.conv_v2_v3) rename_tree() (in module mmtbx.monomer_library.conv_v2_v3) render() (cctbx.miller.display.render_2d method) render_2d (class in cctbx.miller.display) render_pil (class in cctbx.command_line.precession_view) render_postscript (class in cctbx.command_line.precession_view) renderer (class in mmtbx.polygon.output) replace_scatterers() (cctbx.xray.structure.structure method) replace_site_symmetry() (cctbx.geometry_restraints.manager.manager method) replace_sites_cart() (cctbx.xray.structure.structure method) replace_sites_frac() (cctbx.xray.structure.structure method) report() (cctbx.development.structure_factor_utils.collector method) (cctbx.merging.brehm_diederichs.algorithm2 method) (mmtbx.monomer_library.pdb_interpretation.geometry_restraints_proxy_registries method) (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) report_fraction_of_negative_observations_if_any() (in module cctbx.omz.cif_refine) report_unknown_message() (mmtbx.monomer_library.pdb_interpretation.type_symbol_registry_base method) reprocess_pdb() (in module mmtbx.building) requires_experimental_phases() (mmtbx.refinement.targets.target_attributes method) res_type (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) resample_on_different_grid() (iotbx.map_manager.map_manager method) resAtomsToChi (mmtbx.rotamer.sidechain_angles.SidechainAngles attribute) reserve() (iotbx.pdb.hierarchy.af_shared_atom method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) reset() (mmtbx.building.extend_sidechains.conformation_scorer method) (mmtbx.monomer_library.rotamer_utils.rotamer_iterator method) (mmtbx.refinement.real_space.score method) (mmtbx.refinement.real_space.score3 method) (mmtbx.refinement.real_space.score4 method) (xfel.command_line.cxi_merge.scaling_manager method) reset_atom_i_seqs() (iotbx.pdb.hierarchy.root method) reset_cb_op() (cctbx.euclidean_model_matching.model method) reset_i_seq() (iotbx.pdb.hierarchy.af_shared_atom method) reset_i_seq_if_necessary() (iotbx.pdb.hierarchy.root method) reset_internals() (cctbx.geometry_restraints.manager.manager method) reset_max_error() (in module cctbx.eltbx.development.combine_fits) reset_scan_points() (dxtbx.model.goniometer.Goniometer method) reset_serial() (iotbx.pdb.hierarchy.af_shared_atom method) reset_solvent() (mmtbx.solvent.ensemble_ordered_solvent.manager method) reset_tmp() (iotbx.pdb.hierarchy.af_shared_atom method) reset_tmp_for_occupancy_groups_simple() (iotbx.pdb.hierarchy.af_shared_atom method) reshape() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) resid (mmtbx.validation.atom_base property) (mmtbx.validation.residue property) resid() (iotbx.pdb.hierarchy.atom_with_labels method) (iotbx.pdb.hierarchy.residue method) (iotbx.pdb.hierarchy.residue_group method) resid_str() (in module mmtbx.ncs.ligands) resid_to_pymol() (in module cctbx.geometry_restraints) residual (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.planarity attribute) (mmtbx.validation.restraints.restraint attribute) residual() (in module cctbx.examples.unit_cell_minimizers) (in module cctbx.examples.unit_cell_refinement) residue (class in iotbx.pdb.hierarchy) (class in mmtbx.validation) residue_altloc() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) residue_bfactor (class in mmtbx.validation.model_properties) residue_bin (class in mmtbx.validation.graphics) residue_binner (class in mmtbx.validation.graphics) residue_density_quality() (in module mmtbx.building) residue_dict() (in module mmtbx.monomer_library.idealized_aa) residue_evaluator (class in mmtbx.validation.rotalyze) residue_group (class in iotbx.pdb.hierarchy) (mmtbx.geometry.clash.SymmetryEquivalent property) residue_group_id_str() (mmtbx.validation.atom_base method) (mmtbx.validation.residue method) residue_group_is_linked_to_previous() (in module iotbx.map_model_manager) residue_group_proxy (class in mmtbx.disorder.analyze_model) residue_groups() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.root method) residue_groups_size() (iotbx.pdb.hierarchy.chain method) residue_id() (mmtbx.validation.residue method) residue_id_str() (in module mmtbx.monomer_library.pdb_interpretation) residue_monitor (class in mmtbx.refinement.real_space) residue_multi_criterion (class in mmtbx.validation.molprobity) residue_name (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) residue_name_plus_atom_names_interpreter() (iotbx.pdb.hierarchy.residue method) residue_number (iotbx.shelx.tokens.atomname_token attribute) (iotbx.shelx.tokens.element_token attribute) residue_occupancy (class in mmtbx.validation.model_properties) residue_real_space (class in mmtbx.validation.experimental) residue_token (class in iotbx.shelx.tokens) residue_type() (mmtbx.validation.ramalyze.ramachandran method) ResidueLinkClass (class in mmtbx.monomer_library.linking_mixins) residues (mmtbx.validation.graphics.residue_bin attribute) (mmtbx.validation.molprobity.multi_criterion_view attribute) residues() (iotbx.pdb.hierarchy.chain method) (iotbx.pdb.hierarchy.conformer method) residues_are_adjacent() (in module mmtbx.building) residues_in_common_list() (mmtbx.ncs.ncs.ncs_group method) residues_size() (iotbx.pdb.hierarchy.conformer method) resize() (mmtbx.polygon.output.renderer method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) resname (iotbx.pdb.hierarchy.atom_group property) (iotbx.pdb.hierarchy.atom_with_labels property) (iotbx.pdb.hierarchy.residue property) (mmtbx.disorder.analyze_model.atom_group_proxy attribute) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute)

resname() (mmtbx.ions.environment.atom_contact method) resolution() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) resolution_bin (class in mmtbx.twinning.twin_f_model) (class in xfel.command_line.cxi_merge) resolution_cut() (mmtbx.scaling.xtriage.xtriage_analyses method) resolution_dependent_r_values() (mmtbx.scaling.twin_analyses.r_values method) resolution_factor() (cctbx.maptbx.crystal_gridding method) resolution_filter() (cctbx.miller.set method) (in module mmtbx.wwpdb.rcsb_web_services) (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) (mmtbx.fmodels method) (mmtbx.twinning.twin_f_model.twin_model_manager method) resolution_filter_selection() (cctbx.miller.set method) resolution_limit_of_anomalous_signal() (mmtbx.scaling.xtriage.xtriage_analyses method) resolution_range() (cctbx.miller.set method) resolve_filter_map() (mmtbx.maps.fem.run method) resolve_partitions() (scitbx.matrix.rec method) resolve_unexpected() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) resseq (iotbx.pdb.hierarchy.atom_with_labels property) (iotbx.pdb.hierarchy.residue property) (iotbx.pdb.hierarchy.residue_group property) (mmtbx.disorder.analyze_model.residue_group_proxy attribute) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) resseq_as_int() (iotbx.pdb.hierarchy.atom_with_labels method) (iotbx.pdb.hierarchy.residue method) (iotbx.pdb.hierarchy.residue_group method) (mmtbx.validation.residue method) restrain_atoms() (mmtbx.building.box_build_refine_base method) restraint (class in mmtbx.validation.restraints) restraint_label (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) restraint_parser (class in iotbx.shelx.parsers) restraint_type (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) restraint_types (iotbx.shelx.parsers.restraint_parser attribute) restraint_validation (class in mmtbx.validation.restraints) restraints (mmtbx.validation.molprobity.molprobity attribute) restraints_show() (in module mmtbx.conformation_dependent_library) restraints_target_and_grads() (in module mmtbx.refinement.minimization_ncs_constraints) result_as_sf() (mmtbx.maps.composite_omit_map.run method) results (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.clashscore.nqh_flips attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) (mmtbx.validation.rna_geometry attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) (mmtbx.validation.waters.waters attribute) results() (mmtbx.building.make_library.extract_related_models method) ret_twin_law_info (class in cctbx.sgtbx.reticular_twin_laws) reticular_twin_laws (class in cctbx.sgtbx.reticular_twin_laws) return_best_cell() (cctbx.crystal.find_best_cell.alternative_find_best_cell method) return_best_xs() (cctbx.crystal.find_best_cell.alternative_find_best_cell method) return_change_of_basis_op_to_best_cell() (cctbx.crystal.find_best_cell.alternative_find_best_cell method) return_data() (mmtbx.scaling.massage_twin_detwin_data.massage_data method) return_likely_sg_and_cell() (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method) return_next_index() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method) return_next_left_over_set() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method) return_next_set() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method) return_next_sg() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method) return_point_groups() (mmtbx.scaling.twin_analyses.symmetry_issues method) return_unused() (cctbx.sgtbx.pointgroup_tools.edge_object method) return_used() (cctbx.sgtbx.pointgroup_tools.edge_object method) reverse_dict() (cctbx.sgtbx.pointgroup_tools.point_group_graph method) (in module cctbx.examples.maximum_subgroups) reversed() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) rfft() (cctbx.xray.structure_factors.manager.manager method) rho (cctbx.omz.bfgs.memory_element attribute) rho_stats() (in module cctbx.examples.fft_map_electron_density_around_atom) rhs (cctbx.sgtbx.direct_space_asu.cut_plane.cut_expression attribute) rigid_body_minimizer (class in mmtbx.refinement.rigid_body) rigid_body_shift_accumulator (class in mmtbx.refinement.rigid_body) rigid_bond_deviation() (cctbx.adp_restraints.energies.energies method) rigid_clusters_due_to_dihedrals_and_planes() (cctbx.geometry_restraints.manager.manager method) rigid_groups_from_pdb_chains() (in module mmtbx.refinement.rigid_body) rmb_color_model (class in mmtbx.polygon.output) rms() (cctbx.miller.array method) (in module mmtbx.density_modification) (scitbx.array_family.flex.double method) rms_angles (mmtbx.validation.molprobity.pdb_header_info attribute) rms_angles() (mmtbx.validation.molprobity.molprobity method) rms_bonds (mmtbx.validation.molprobity.pdb_header_info attribute) rms_bonds() (mmtbx.validation.molprobity.molprobity method) rms_deltas (mmtbx.validation.restraints.planarity attribute) rms_difference() (cctbx.xray.structure.structure method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) rms_filter() (cctbx.miller.array method) rms_length() (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) rmsd (mmtbx.disorder.backbone.backrub_residue attribute) rmsd_calculation() (mmtbx.refinement.orca.expand method) rmsd_calculator() (mmtbx.refinement.orca.expand method) rmsd_list() (mmtbx.ncs.ncs.ncs_group method) rmsd_of_matching_residues() (iotbx.map_model_manager.map_model_manager method) rmsds (mmtbx.validation.ligands.ligand_validation attribute) rmsds() (mmtbx.refinement.real_space.individual_sites.refinery method) (mmtbx.refinement.real_space.individual_sites.simple method) rna (mmtbx.validation.molprobity.molprobity attribute) rna_angle (class in mmtbx.validation.rna_validate) rna_angles (class in mmtbx.validation.rna_validate) rna_bond (class in mmtbx.validation.rna_validate) rna_bonds (class in mmtbx.validation.rna_validate) rna_geometry (class in mmtbx.validation) rna_pucker (class in mmtbx.validation.rna_validate) rna_pucker_ref (class in mmtbx.validation.rna_validate) rna_puckers (class in mmtbx.validation.rna_validate) rna_validation (class in mmtbx.validation.rna_validate) roiMask() (xfel.command_line.convert_gain_map.fake_config method) root (class in iotbx.pdb.hierarchy) (mmtbx.geometry.clash.SymmetryEquivalent property) root() (iotbx.pdb.hierarchy.residue method) rota_matrices() (mmtbx.ncs.ncs.ncs_group method) rota_matrices_inv() (mmtbx.ncs.ncs.ncs_group method) rota_outliers() (mmtbx.validation.molprobity.molprobity method) rotalyze (class in mmtbx.validation.rotalyze) (mmtbx.validation.molprobity.molprobity attribute) rotamer (class in mmtbx.validation.rotalyze) rotamer_ensemble (class in mmtbx.validation.rotalyze) rotamer_frequencies() (mmtbx.validation.rotalyze.rotamer_ensemble method) rotamer_info() (mmtbx.monomer_library.cif_types.comp_comp_id method) rotamer_info_master_phil() (in module mmtbx.monomer_library.rotamer_utils) rotamer_info_phil_str_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute) rotamer_iterator (class in mmtbx.monomer_library.rotamer_utils) rotamer_iterator() (mmtbx.monomer_library.cif_types.comp_comp_id method) (mmtbx.monomer_library.server.server method) rotamer_name (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) rotamer_outliers (mmtbx.validation.molprobity.summary attribute) rotamer_outliers() (in module mmtbx.kinemage.validation) rotamer_plot (class in mmtbx.rotamer.graphics) (class in mmtbx.validation.rotalyze) rotamer_plot_mixin (class in mmtbx.rotamer.graphics) (class in mmtbx.validation.rotalyze) RotamerEval (class in mmtbx.rotamer.rotamer_eval) RotamerID (class in mmtbx.rotamer.rotamer_eval) rotamersForAA (mmtbx.rotamer.sidechain_angles.SidechainAngles attribute) rotarama_plot_mixin (class in mmtbx.rotamer.graphics) (class in mmtbx.validation.graphics) rotatable() (in module mmtbx.hydrogens) rotate() (scitbx.matrix.rec method) rotate_2d() (scitbx.matrix.rec method) rotate_about_y() (mmtbx.ncs.ncs.ncs method) rotate_about_z() (mmtbx.ncs.ncs.ncs method) rotate_around_origin() (dxtbx.model.goniometer.Goniometer method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) rotate_matrices() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) rotate_point_around_axis() (in module scitbx.matrix) rotation() (mmtbx.refinement.rigid_body.manager method) rotation_angle() (scitbx.matrix.rec method) rotation_to_angles() (in module mmtbx.ncs.ncs_utils) rotations_translations_forward_euler() (mmtbx.ncs.ncs.ncs_group method) round() (mmtbx.ncs.ncs.ncs_group method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) round_occupancies_in_place() (iotbx.pdb.hierarchy.root method) round_to_ten() (in module mmtbx.conformation_dependent_library.utils) rows() (in module scitbx.array_family.flex) rplace() (in module xfel.cxi.cspad_ana.cspad_tbx) rsr_model (class in mmtbx.refinement.real_space) rt (class in scitbx.matrix) rt_for_rotation_around_axis_through() (scitbx.matrix.rec method) rt_from_string() (in module cctbx.web.change_basis) rt_mx (mmtbx.ions.environment.atom_contact attribute), [1] rt_mx_analysis() (in module cctbx.examples.all_axes) (in module cctbx.sgtbx.direct_space_asu.check_redundancies) (in module cctbx.web.explore_symmetry) rt_mx_analysis_header() (in module cctbx.web.explore_symmetry) rt_mx_as_rational() (in module cctbx.sgtbx.rational_matrices_point_groups) (in module cctbx.sgtbx.reticular_pg_tools) (in module cctbx.sgtbx.sub_lattice_tools) rt_mx_ji (cctbx.crystal.sym_pair attribute) rt_plus_unit_shifts() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) rt_times_grid_point() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) run (class in cctbx.maptbx.mem) (class in mmtbx.bulk_solvent.scaler) (class in mmtbx.dynamics.cartesian_dynamics) (class in mmtbx.dynamics.simulated_annealing) (class in mmtbx.maps.composite_omit_map) (class in mmtbx.maps.fem) (class in mmtbx.maps.kick) (class in mmtbx.refinement.real_space.fit_residue) (class in mmtbx.refinement.real_space.weight) Run (class in xfel.cxi.gfx.trials_plot) run() (in module cctbx.command_line.brehm_diederichs) (in module cctbx.command_line.euclidean_model_matching) (in module cctbx.command_line.find_reticular_twin_laws) (in module cctbx.command_line.form_factor_query) (in module cctbx.command_line.precession_view) (in module cctbx.command_line.space_group_info) (in module cctbx.command_line.structure_factor_timings) (in module cctbx.command_line.subgroups) (in module cctbx.command_line.version) (in module cctbx.command_line.wavelength_units) (in module cctbx.crystal.burzlaff_zimmermann_dewolff) (in module cctbx.development.cns_density_modification) (in module cctbx.development.direct_or_fft) (in module cctbx.development.electron_density_sampling) (in module cctbx.development.make_cns_input) (in module cctbx.development.make_settings) (in module cctbx.development.run_shelx) (in module cctbx.development.run_shelx76) (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp) (in module cctbx.eltbx.development.e_scattering_plots) (in module cctbx.eltbx.development.format_gaussian_fits) (in module cctbx.eltbx.development.hydrogen_plots) (in module cctbx.eltbx.development.itvc_approx) (in module cctbx.eltbx.development.itvc_cross_validation) (in module cctbx.eltbx.development.itvc_fits) (in module cctbx.eltbx.development.kissel_fits) (in module cctbx.eltbx.development.rez_rez_grant) (in module cctbx.examples.adp_symmetry_constraints) (in module cctbx.examples.all_axes) (in module cctbx.examples.analyze_adp) (in module cctbx.examples.change_hand_p31) (in module cctbx.examples.convert_ccp4_symop_lib) (in module cctbx.examples.fft_map_electron_density_around_atom) (in module cctbx.examples.find_distances_using_cpp_objects) (in module cctbx.examples.find_sys_abs_equiv_space_groups) (in module cctbx.examples.getting_started) (in module cctbx.examples.hirshfeld_test) (in module cctbx.examples.le_page_1982_vs_lebedev_2005) (in module cctbx.examples.lebedev_2005_perturbation) (in module cctbx.examples.list_non_principal_continuous_shifts) (in module cctbx.examples.location_part) (in module cctbx.examples.map_skewness) (in module cctbx.examples.miller_transform) (in module cctbx.examples.neutron_structure_factors) (in module cctbx.examples.quartz_structure) (in module cctbx.examples.random_f_calc) (in module cctbx.examples.random_puckers) (in module cctbx.examples.reduced_cell_two_folds) (in module cctbx.examples.site_symmetry_constraints) (in module cctbx.examples.space_group_matrices) (in module cctbx.examples.space_subgroups) (in module cctbx.examples.sub_group_graph) (in module cctbx.examples.symops_530) (in module cctbx.examples.trigonal_r_vs_tetragonal_i) (in module cctbx.examples.unit_cell_minimizers) (in module cctbx.examples.unit_cell_refinement) (in module cctbx.merging.brehm_diederichs) (in module cctbx.omz.cif_refine) (in module cctbx.omz.cod_refine) (in module cctbx.omz.cod_select_and_pickle) (in module cctbx.omz.eval_iso_vs_refined) (in module cctbx.omz.pdb_dev) (in module cctbx.run_examples) (in module cctbx.run_tests) (in module cctbx.sgtbx.cosets) (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table) (in module cctbx.sgtbx.rational_matrices_point_groups) (in module cctbx.sgtbx.reticular_pg_tools) (in module cctbx.sgtbx.show_cosets) (in module cctbx.source_generators.eltbx.generate_henke_cpp) (in module cctbx.source_generators.eltbx.generate_sasaki_cpp) (in module cctbx.source_generators.flex_fwd_h) (in module cctbx.web.all_axes) (in module cctbx.web.asu_gallery.jv_asu) (in module cctbx.web.asu_gallery.jvx) (in module cctbx.web.browse_settings) (in module cctbx.web.change_basis) (in module cctbx.web.change_hand) (in module cctbx.web.change_setting) (in module cctbx.web.dispatcher) (in module cctbx.web.emma) (in module cctbx.web.explore_symmetry) (in module cctbx.web.frac_cart) (in module cctbx.web.iotbx_cif_validate) (in module cctbx.web.lattice_symmetry) (in module cctbx.web.libtbx_help) (in module cctbx.web.multiple_cell) (in module cctbx.web.phase_o_phrenia) (in module cctbx.web.replay) (in module cctbx.web.shelx) (in module cctbx.web.structure_factors) (in module cctbx.web.structure_factors_pdb) (in module cctbx.web.wyckoff) (in module iotbx.reflection_file_reader) (in module mmtbx.chemical_components.cif_parser) (in module mmtbx.conformation_dependent_library) (in module mmtbx.conformation_dependent_library.altloc_weighting) (in module mmtbx.conformation_dependent_library.cdl_database) (in module mmtbx.conformation_dependent_library.rdl_database) (in module mmtbx.conformation_dependent_library.tst_cdl) (in module mmtbx.hydrogens.build_hydrogens) (in module mmtbx.hydrogens.find) (in module mmtbx.kinemage.validation) (in module mmtbx.maps.fobs_minus_fobs_map) (in module mmtbx.monomer_library.bondlength_defaults) (in module mmtbx.monomer_library.conv_v2_v3) (in module mmtbx.monomer_library.hydrogen_restrictions) (in module mmtbx.monomer_library.pdb_interpretation) (in module mmtbx.refinement.inspect_tardy_trajectory) (in module mmtbx.refinement.real_space.fit_water) (in module mmtbx.refinement.tardy) (in module mmtbx.scaling.fest) (in module mmtbx.scaling.make_param) (in module mmtbx.scaling.outlier_plots) (in module mmtbx.scaling.remove_outliers) (in module mmtbx.scaling.rip_scale) (in module mmtbx.scaling.sad_scale) (in module mmtbx.scaling.sir_scale) (in module mmtbx.scaling.siras_scale) (in module mmtbx.scaling.thorough_outlier_test) (in module mmtbx.scaling.twmad_scale) (in module mmtbx.scaling.xtriage) (in module mmtbx.tls.command_line) (in module mmtbx.tls.tls_as_xyz) (in module mmtbx.twinning.probabalistic_detwinning) (in module mmtbx.validation.molprobity.mp_geo) (in module scitbx.lbfgs) (in module xfel.command_line.auto_submit) (in module xfel.command_line.brehm_diederichs) (in module xfel.command_line.cbf_average) (in module xfel.command_line.convert_gain_map) (in module xfel.command_line.convert_gain_map_cbf) (in module xfel.command_line.cxi_cspad_pinwheel) (in module xfel.command_line.cxi_diff) (in module xfel.command_line.cxi_lsf) (in module xfel.command_line.cxi_merge) (in module xfel.command_line.cxi_pbs) (in module xfel.command_line.cxi_plotcv) (in module xfel.command_line.cxi_psana) (in module xfel.command_line.cxi_pyana) (in module xfel.command_line.cxi_xmerge) (in module xfel.command_line.list_db_metadata) (in module xfel.command_line.make_mask) (in module xfel.command_line.metrology) (in module xfel.command_line.overlay_spectra) (in module xfel.command_line.plot_to_subpixel) (in module xfel.command_line.radial_average) (in module xfel.command_line.smooth_spectrum) (in module xfel.command_line.subtract_background) (in module xfel.command_line.trial_stats) (in module xfel.command_line.view_pixel_histograms) (in module xfel.cxi.cspad_ana.xes_histograms) (in module xfel.cxi.gfx.trials_plot) (in module xfel.cxi.gfx.wx_detectors) (in module xfel.metrology.mark0) (in module xfel.metrology.mark1) (in module xfel.metrology.mark3) (libtbx.program_template.ProgramTemplate method) (mmtbx.maps.fobs_minus_fobs_map.launcher method) (mmtbx.maps.superpose.transform_maps method) (mmtbx.maps.utils.fast_maps_from_hkl_file method) (mmtbx.scaling.xtriage.launcher method) (mmtbx.secondary_structure.proteins.find_helices_simple method) (xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread method) run2 (class in mmtbx.refinement.geometry_minimization) run2() (in module mmtbx.chemical_components.cif_parser) run_all() (in module cctbx.examples.maximum_subgroups) run_and_time() (in module cctbx.eltbx.development.itvc_fits) (in module cctbx.eltbx.development.kissel_fits) run_anisotropic_scaling_as_class (class in iotbx.map_model_manager) run_apply() (in module mmtbx.conformation_dependent_library.tst_cdl) run_c_plus_plus() (in module scitbx.lbfgs) run_call_back() (in module cctbx.development.direct_or_fft) (in module cctbx.development.make_cns_input) (in module cctbx.development.run_shelx) (in module cctbx.development.run_shelx76) (in module mmtbx.scaling.thorough_outlier_test) run_cc() (in module xfel.cxi.cxi_cc) run_constrained (class in mmtbx.refinement.minimization) run_core_algorithm() (cctbx.merging.brehm_diederichs.algorithm2 method) run_correction_vector_plot() (in module xfel.cxi.correction_vector_plot) run_cycle_a() (xfel.metrology.mark10.fit_translation4 method) run_cycle_b() (xfel.metrology.mark10.fit_translation4 method) run_fit_rotatable() (in module mmtbx.hydrogens) run_fortran() (in module scitbx.lbfgs) run_fsc_as_class (class in iotbx.map_model_manager) run_implementation() (in module cctbx.web.emma) (in module cctbx.web.iotbx_cif_validate) run_interleaved_minimization() (mmtbx.dynamics.cartesian_dynamics.run method) run_ksdssp() (in module mmtbx.secondary_structure) run_ksdssp_direct() (in module mmtbx.secondary_structure) run_lbfgs() (mmtbx.refinement.adp_refinement.refine_adp method) run_lbfgs_raw() (cctbx.examples.unit_cell_minimizers.refinery method) run_lbfgsb() (cctbx.examples.unit_cell_minimizers.refinery method) run_molprobity_program() (in module mmtbx.validation.molprobity) run_multiprocess() (in module cctbx.merging.brehm_diederichs) run_one() (in module xfel.cxi.display_spots) run_one_index() (in module xfel.cxi.display_spots) run_one_index_core() (in module xfel.cxi.display_spots) run_probe_clashscore() (mmtbx.validation.clashscore.probe_clashscore_manager method) run_real_space_annealing() (in module mmtbx.building) run_reduce_with_timeout (class in mmtbx.utils) run_refinement() (in module cctbx.omz.dev) run_shelx() (in module cctbx.development.run_shelx) run_shelx76() (in module cctbx.development.run_shelx76) (in module cctbx.omz.cod_refine) run_shelxl() (in module cctbx.omz.cod_refine) run_simple() (in module mmtbx.bulk_solvent.scaler) run_single() (in module cctbx.examples.maximum_subgroups) run_smtbx_ls() (in module cctbx.omz.cod_refine) run_with_minimization (class in mmtbx.refinement.real_space.fit_residue) RunNumberEvent (class in xfel.cxi.gfx.status_plot)

S

s (cctbx.omz.bfgs.memory_element attribute) safe_atan2() (in module cctbx.macro_mol.rotation_parameters) safe_setup_binner() (cctbx.miller.set method) same_sensor_table() (xfel.metrology.mark10.fit_translation4 method) (xfel.metrology.mark3.fit_translation2 method) sample() (in module cctbx.examples.le_page_1982_vs_lebedev_2005) sample_asu() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) sample_e_pot() (in module cctbx.omz.tardy_adaptor) sample_operators (class in mmtbx.ncs.ligands) sample_standard_deviation() (scitbx.array_family.flex.double method) sampled_density_must_be_positive() (cctbx.xray.structure_factors.manager.manager method) sampled_model_density (class in mmtbx.real_space) sasaki_table (class in cctbx.source_generators.eltbx.generate_sasaki_cpp) save (class in iotbx.cif.model) save_best_model() (mmtbx.refinement.select_best_starting_model.select_model method) save_data_mtz() (mmtbx.command_line.load_model_and_data method) save_existing_group_info() (mmtbx.ncs.ncs.ncs method) save_ncs_group() (mmtbx.ncs.ncs.ncs method) save_oper() (mmtbx.ncs.ncs.ncs method) save_pdb_file() (mmtbx.refinement.print_statistics.coordinate_shifts method) save_png() (xfel.cxi.gfx.wx_detectors.DetectorPlot method) save_table_data() (mmtbx.validation.validation method) save_updated_data() (mmtbx.refinement.select_best_starting_model.select_model method) SaveImageEvent (class in xfel.cxi.gfx.status_plot) scale() (cctbx.miller.array method) (in module cctbx.maptbx.mem) scale_adp() (cctbx.xray.structure.structure method) scale_adps() (cctbx.xray.structure.structure method) scale_all() (xfel.command_line.cxi_merge.scaling_manager method) (xfel.command_line.cxi_xmerge.xscaling_manager method) scale_factor() (cctbx.miller.array method) (in module xfel.cxi.cxi_cc) scale_frame() (xfel.command_line.cxi_merge.scaling_manager method) scale_frame_by_mean_I_mproc() (in module xfel.command_line.postrefine) scale_frame_detail() (xfel.command_line.cxi_merge.scaling_manager method) scale_k1() (mmtbx.twinning.twin_f_model.twin_model_manager method) scale_k1_t() (mmtbx.twinning.twin_f_model.twin_model_manager method) scale_k1_w() (mmtbx.twinning.twin_f_model.twin_model_manager method) scale_k3_t() (mmtbx.twinning.twin_f_model.twin_model_manager method) scale_k3_w() (mmtbx.twinning.twin_f_model.twin_model_manager method) scale_matrix() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) scale_to() (in module mmtbx.ions.svm.utils) scaling_manager (class in xfel.command_line.cxi_merge) scaling_parameter_mask (class in mmtbx.twinning.twin_f_model) scaling_parameters_object (class in mmtbx.twinning.twin_f_model) scaling_result (class in xfel.command_line.cxi_merge) ScanFactory (class in dxtbx.model.scan) scat_data() (mmtbx.scaling.absolute_scaling.scattering_information method) scatter_env (mmtbx.ions.identify.ion_result attribute) scatterer (class in cctbx.neutron) (class in cctbx.xray.scatterer) scatterer_as_g_alpha() (in module cctbx.examples.structure_factor_derivatives_2) scatterer_as_list() (in module cctbx.examples.structure_factor_derivatives_2) (in module cctbx.examples.structure_factor_derivatives_3) scatterer_flags() (cctbx.xray.structure.structure method) scatterer_from_list() (in module cctbx.examples.structure_factor_derivatives_2) (in module cctbx.examples.structure_factor_derivatives_3) scatterers() (cctbx.neutron.structure method) (cctbx.xray.structure.structure method) scatterers_info() (in module mmtbx.hydrogens.find) scattering_dictionary_as_string() (cctbx.xray.structure.structure method) scattering_information (class in mmtbx.scaling.absolute_scaling) scattering_table() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) scattering_type() (mmtbx.ions.metal_parameters method) scattering_type_registry (class in mmtbx.monomer_library.pdb_interpretation) scattering_type_registry() (cctbx.xray.structure.structure method) scattering_type_registry_params (class in cctbx.xray.structure) scattering_types() (cctbx.xray.structure.structure method) scattering_types_counts_and_occupancy_sums() (cctbx.xray.structure.structure method) ScatteringEnvironment (class in mmtbx.ions.environment) scene (class in cctbx.miller.display) scitbx.array_family.flex module scitbx.lbfgs module scitbx.lstbx.normal_eqns module scitbx.lstbx.normal_eqns_solving module scitbx.matrix module score (class in mmtbx.refinement.real_space) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atoms attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.clash attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.entity attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.planarity attribute) (mmtbx.validation.restraints.restraint attribute) (mmtbx.validation.rna_validate.rna_angle attribute) (mmtbx.validation.rna_validate.rna_bond attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) score() (mmtbx.hydrogens.map_manager method) (mmtbx.refinement.adp_refinement.refine_adp method) score2 (class in mmtbx.refinement.real_space) score3 (class in mmtbx.refinement.real_space) score4 (class in mmtbx.refinement.real_space) score_atom() (mmtbx.solvent.ordered_solvent.maps method) score_format (mmtbx.validation.entity attribute) score_isigi() (mmtbx.scaling.absences.analyze_absences method) score_statistics() (mmtbx.validation.ramalyze.ramachandran_ensemble method) scores (mmtbx.ions.svm.svm_prediction attribute), [1] screen_name_ (mmtbx.ligands.xtal_screens.solution attribute) screen_number_ (mmtbx.ligands.xtal_screens.solution attribute) script() (cctbx.web.cgi_utils.server_info method) script_predict_methods_comparison() (in module cctbx.development.make_cns_input) script_vdw_energy() (in module cctbx.development.make_cns_input) script_xray_gradients() (in module cctbx.development.make_cns_input) sdb_file_to_emma_model() (in module cctbx.web.emma) sdb_files_as_xray_structures() (in module cctbx.web.phase_o_phrenia) search() (dxtbx.model.scan.ScanFactory static method) search_for_ncs() (mmtbx.monomer_library.pdb_interpretation.process method) search_ncs_relations() (in module mmtbx.ncs.ncs_search) sec_str_from_phil() (in module mmtbx.secondary_structure) second_moment() (cctbx.miller.array method) second_moment_of_intensities() (cctbx.miller.array method) second_moments_centric_acentric() (cctbx.miller.array method) secondary_structure_section() (iotbx.pdb.ext.input method) Section (class in xfel.cxi.cspad_ana.parse_calib) sections() (xfel.command_line.convert_gain_map.fake_config method) sections2phil() (in module xfel.cftbx.detector.metrology2phil) segid (iotbx.pdb.hierarchy.atom property) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) segments (mmtbx.disorder.analyze_model.process_pdb_hierarchy property) sel_all() (mmtbx.refinement.real_space.side_chain_fit_evaluator method) sel_backbone() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) sel_backbone_or_sidechain() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) sel_classification() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) sel_outliers() (mmtbx.refinement.real_space.side_chain_fit_evaluator method) sel_outliers_and_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method) sel_outliers_or_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method) sel_phosphate() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) sel_poormap() (mmtbx.refinement.real_space.side_chain_fit_evaluator method) sel_residues_within() (mmtbx.monomer_library.pdb_interpretation.selection_manager method) sel_ribose() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) sel_sidechain() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) sel_within() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) select() (cctbx.geometry_restraints.manager.manager method) (cctbx.miller.array method) (cctbx.miller.set method) (cctbx.sgtbx.literal_description.literal_description method) (cctbx.xray.scatterer.anomalous_scatterer_group method) (cctbx.xray.structure.structure method) (in module scitbx.array_family.flex) (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.root method) (mmtbx.masks.manager method) (mmtbx.refinement.adp_refinement.refine_adp method) (mmtbx.refinement.refinement_flags.manager method) (mmtbx.tls.tools.tls_groups method) (mmtbx.twinning.twin_f_model.twin_model_manager method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) select_acentric() (cctbx.miller.set method) select_and_transform() (mmtbx.scaling.pair_analyses.reindexing method) select_centric() (cctbx.miller.set method) select_color() (in module cctbx.web.asu_gallery.jv_asu) select_crystal_symmetry() (in module cctbx.crystal) select_detached() (mmtbx.refinement.refinement_flags.manager method) select_dict() (in module mmtbx.polygon) select_first_ncs_group() (mmtbx.ncs.ncs.ncs method) select_first_ncs_operator() (mmtbx.ncs.ncs.ncs method) select_good() (mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data method) select_indices() (cctbx.miller.array method) select_inplace() (cctbx.xray.structure.structure method) select_matching_segments() (iotbx.map_model_manager.map_model_manager method) select_model (class in mmtbx.refinement.select_best_starting_model) select_n_in_biggest_cluster() (in module iotbx.map_manager) select_one_water() (in module mmtbx.hydrogens.find) select_random_den_restraints() (mmtbx.den.den_restraints method) select_str() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method) select_sys_absent() (cctbx.miller.array method) selected_positions() (in module mmtbx.ncs.ncs_utils) selected_size (scitbx.array_family.flex.smart_selection property) selection (mmtbx.maps.composite_omit_map.omit_box attribute) (mmtbx.maps.composite_omit_map.omit_regions attribute) selection() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) (mmtbx.monomer_library.pdb_interpretation.selection_manager method) selection_around_to_negate() (in module mmtbx.refinement.real_space) selection_by_symmetry() (in module mmtbx.building.make_library) selection_manager (class in mmtbx.monomer_library.pdb_interpretation) selection_within() (cctbx.xray.structure.structure method) selector() (in module mmtbx.refinement.ensemble_refinement.ensemble_utils) send_insert_command() (xfel.cxi.correction_vector_plot.manage_sql method) sense_of_polygon() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) sensor() (dxtbx.model.detector.DetectorFactory static method) SeparateCheckerBuilder (class in mmtbx.geometry.asa) sequence (mmtbx.command_line.load_model_and_data attribute) (mmtbx.validation.molprobity.molprobity attribute) sequence() (iotbx.map_model_manager.map_model_manager method) sequence_as_cif_block() (mmtbx.validation.sequence.validation method) sequence_from_SEQRES() (iotbx.pdb.ext.input method) sequence_search() (in module mmtbx.wwpdb.rcsb_web_services) serial (iotbx.pdb.hierarchy.atom property) (mmtbx.maps.composite_omit_map.omit_box attribute) (mmtbx.maps.composite_omit_map.omit_region_results attribute) (mmtbx.maps.composite_omit_map.omit_regions attribute) serial_as_int() (iotbx.pdb.hierarchy.atom method) (iotbx.pdb.hierarchy.atom_with_labels method) server (class in mmtbx.ligands.xtal_screens) (class in mmtbx.monomer_library.server) server_info (class in cctbx.web.cgi_utils) set (class in cctbx.miller) set() (cctbx.miller.array method) set_adps_from_scatterers() (iotbx.pdb.hierarchy.af_shared_atom method) set_alignment() (mmtbx.validation.sequence.chain method) set_angles() (dxtbx.model.goniometer.MultiAxisGoniometer method) set_atomic_charge() (iotbx.pdb.hierarchy.root method) set_axes() (dxtbx.model.goniometer.MultiAxisGoniometer method) set_b() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_b_iso() (cctbx.xray.structure.structure method) set_charge() (iotbx.pdb.hierarchy.atom method) set_chemical_element_simple_if_necessary() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_classification() (mmtbx.monomer_library.cif_types.comp_comp_id method) set_color_model() (mmtbx.polygon.output.renderer method) set_colors() (mmtbx.polygon.output.histogram_layout method) set_components_of_global_origin() (cctbx.symmetry_search.possible_symmetry method) set_coordinates_from_hierarchy() (mmtbx.validation.residue method) set_crystal_symmetry_to_p1() (iotbx.map_manager.map_manager method) set_custom_inelastic_form_factors() (cctbx.xray.structure.structure method) set_element() (iotbx.pdb.hierarchy.atom method) set_element_and_charge_from_scattering_type_if_necessary() (iotbx.pdb.hierarchy.atom method) set_ensemble_b_factors_to_xyz_displacement() (in module mmtbx.disorder) set_experiment_type() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) set_external_energy_function() (cctbx.geometry_restraints.manager.manager method) set_fdp() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_fdps() (cctbx.xray.structure.structure method) set_file_type() (iotbx.file_reader.any_file_input method) set_fixed_rotation() (dxtbx.model.goniometer.Goniometer method) set_focus() (scitbx.array_family.flex.grid method) set_fp() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_fps() (cctbx.xray.structure.structure method) set_hetero() (iotbx.pdb.hierarchy.atom method) set_ias_name_and_predicted_position() (in module mmtbx.ias) set_ias_selection() (mmtbx.ias.manager method) set_inelastic_form_factors() (cctbx.xray.structure.structure method) set_info() (cctbx.miller.array method) (iotbx.map_model_manager.map_model_manager method) set_is_mask() (iotbx.map_manager.map_manager method) set_k_isotropic_exp() (mmtbx.bulk_solvent.scaler.run method) set_labels() (mmtbx.rotamer.graphics.ramachandran_plot_mixin method) (mmtbx.rotamer.graphics.rotamer_plot_mixin method) (mmtbx.validation.ramalyze.ramachandran_plot_mixin method) (mmtbx.validation.rotalyze.rotamer_plot_mixin method) set_ladp() (in module mmtbx.tls.ladp) set_log() (in module mmtbx.utils) (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) set_map_data() (iotbx.map_manager.map_manager method) set_map_id_lists() (iotbx.map_model_manager.map_model_manager method) set_map_manager() (iotbx.map_model_manager.map_model_manager method) set_map_to_value (class in mmtbx.utils) set_mean_zero_sd_one() (iotbx.map_manager.map_manager method) set_minimum_resolution() (iotbx.map_model_manager.map_model_manager method) set_model() (iotbx.map_model_manager.map_model_manager method) set_model_symmetries_and_shift_cart_to_match_map() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) set_multiprocessing() (iotbx.map_model_manager.map_model_manager method) set_name() (iotbx.map_model_manager.map_model_manager method) (iotbx.pdb.hierarchy.atom method) set_ncs_name() (mmtbx.ncs.ncs.ncs method) set_ncs_object() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) set_ncs_object_shift_cart_to_match_map() (iotbx.map_manager.map_manager method) set_nearby_empty_values() (in module iotbx.map_model_manager) set_non_unit_occupancy_implies_min_distance_sym_equiv_zero() (cctbx.xray.structure.structure method) set_observation_type() (cctbx.miller.array method) set_observation_type_xray_amplitude() (cctbx.miller.array method) set_observation_type_xray_intensity() (cctbx.miller.array method) set_occ() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_occupancies() (cctbx.xray.structure.structure method) set_original_origin_and_gridding() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.match_map_model_ncs method) set_original_origin_grid_units() (iotbx.map_model_manager.map_model_manager method) set_output_external_origin() (iotbx.map_manager.map_manager method) set_params() (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) set_peaks() (in module mmtbx.ias) set_program_name() (iotbx.map_manager.map_manager method) set_pseudo_ml_weights() (mmtbx.twinning.twin_f_model.twin_model_manager method) set_ramachandran_restraints() (cctbx.geometry_restraints.manager.manager method) set_random_seed() (in module scitbx.array_family.flex) set_refinable_parameters() (in module mmtbx.refinement.occupancies) set_resolution() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) set_rotation_axis() (dxtbx.model.goniometer.Goniometer method) set_rotation_axis_datum() (dxtbx.model.goniometer.Goniometer method) set_run_id() (xfel.cxi.gfx.wx_detectors.DetectorPlot method) (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame method) set_scatterer_flags() (cctbx.xray.structure.structure method) set_scattering_table() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) set_secondary_structure_restraints() (cctbx.geometry_restraints.manager.manager method) set_segid() (iotbx.pdb.hierarchy.atom method) set_selected() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) set_serial() (iotbx.pdb.hierarchy.atom method) set_setting_rotation() (dxtbx.model.goniometer.Goniometer method) set_setting_rotation_at_scan_points() (dxtbx.model.goniometer.Goniometer method) set_shift_cart() (mmtbx.ncs.ncs.ncs method) set_sigb() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_sigma_ratio() (mmtbx.scaling.fa_estimation.singh_ramasheshan_fa_estimate method) (mmtbx.scaling.pair_analyses.singh_ramasheshan_fa_estimate method) set_sigmas() (cctbx.miller.array method) set_sigocc() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_sigxyz() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_sites_cart() (cctbx.xray.structure.structure method) set_sites_frac() (cctbx.xray.structure.structure method) set_status() (in module mmtbx.ias) (mmtbx.ias.find_peak_at_bond method) (xfel.cxi.cspad_ana.mod_event_info.laser_status method) set_stop_file() (iotbx.map_model_manager.map_model_manager method) set_u_cart() (cctbx.xray.structure.structure method) set_u_iso() (cctbx.xray.structure.structure method) set_uij() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) set_unit_cell_crystal_symmetry() (iotbx.map_manager.map_manager method) set_unit_ncs() (mmtbx.ncs.ncs.ncs method) set_up_hitfinder() (xfel.cxi.cspad_ana.hitfinder_tbx.distl_hitfinder method) set_up_map_dict() (iotbx.map_model_manager.map_model_manager method) set_up_model_dict() (iotbx.map_model_manager.map_model_manager method) set_velocities() (mmtbx.dynamics.cartesian_dynamics.run method) (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) set_verbose() (iotbx.map_model_manager.map_model_manager method) set_watch_dir() (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame method) set_wrapping() (iotbx.map_manager.map_manager method) set_xyz() (iotbx.pdb.hierarchy.af_shared_atom method) (iotbx.pdb.hierarchy.atom method) settings() (in module cctbx.miller.display) setup_binner() (cctbx.miller.set method) setup_binner_counting_sorted() (cctbx.miller.set method) setup_binner_d_star_sq_bin_size() (cctbx.miller.set method) setup_binner_d_star_sq_step() (cctbx.miller.set method) setup_bulk_solvent_correction() (cctbx.omz.dev.refinement method) setup_colors() (cctbx.miller.display.render_2d method) setup_fft() (cctbx.xray.structure_factors.manager.manager method) setup_hexagonal_sampling (class in cctbx.crystal.close_packing) setup_ias_selection() (mmtbx.ias.manager method) setup_maps() (mmtbx.ncs.ligands.sample_operators method) setup_scattering_dictionaries() (in module mmtbx.utils) setup_test() (in module mmtbx.refinement.real_space) setValueAt() (mmtbx.rotamer.n_dim_table.NDimTable method) SFAC_DISP_UNIT() (in module cctbx.development.run_shelx) sfac_unit() (in module cctbx.development.run_shelx76) sgi_iterator (class in mmtbx.scaling.absences) sgtbx_rt_mx_as_matrix_rt() (in module cctbx.euclidean_model_matching) shake_adp() (cctbx.xray.structure.structure method) shake_adp_if_all_equal() (cctbx.xray.structure.structure method) shake_fdps() (cctbx.xray.structure.structure method) shake_fps() (cctbx.xray.structure.structure method) shake_occupancies() (cctbx.xray.structure.structure method) shake_sites_in_place() (cctbx.xray.structure.structure method) shake_transformations() (in module mmtbx.ncs.ncs_utils) shallow_copy() (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) shape_only() (cctbx.sgtbx.direct_space_asu.direct_space_asu method) shape_vertices() (cctbx.sgtbx.direct_space_asu.direct_space_asu method) (in module cctbx.sgtbx.direct_space_asu.facet_analysis) sharpen2() (in module cctbx.maptbx) shell_f_masks() (mmtbx.masks.manager method) shell_f_masks_twin() (mmtbx.masks.manager method) shelx_commands (iotbx.shelx.lexer.command_stream attribute) shelx_fvar_encoding() (cctbx.sgtbx.special_op_simplified method) shelx_weighting (class in cctbx.xray.weighting_schemes) shelxd() (in module iotbx.shelx.write_ins) shelxl_extinction_correction() (cctbx.miller.array method) shelxl_weights() (in module cctbx.omz.cod_refine) shelxl_weights_a_b() (in module cctbx.omz.cod_refine) shelxl_wght_ls (class in cctbx.xray.targets) shift_any_model_to_match() (iotbx.map_model_manager.map_model_manager method) shift_aware_rt (class in iotbx.map_manager) shift_aware_rt() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) shift_aware_rt_to_superpose_other() (iotbx.map_model_manager.map_model_manager method) shift_back() (mmtbx.utils.extract_box_around_model_and_map method) (mmtbx.utils.shift_origin method) shift_back_cart() (mmtbx.ncs.ncs.ncs method) shift_cart() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) (mmtbx.ncs.ncs.ncs method) shift_limit_pair (class in cctbx.omz.dev) shift_map_back() (mmtbx.utils.extract_box_around_model_and_map method) shift_map_coeffs_back() (mmtbx.utils.extract_box_around_model_and_map method) shift_model_to_match_map() (iotbx.map_manager.map_manager method) shift_model_to_match_original_map() (iotbx.map_model_manager.match_map_model_ncs method) shift_model_to_match_working_map() (iotbx.map_model_manager.match_map_model_ncs method) shift_ncs_object_to_match_map_and_return_new_ncs_object() (iotbx.map_manager.map_manager method) shift_ncs_to_match_original_map() (iotbx.map_model_manager.match_map_model_ncs method) shift_ncs_to_match_working_map() (iotbx.map_model_manager.match_map_model_ncs method) shift_occupancies() (cctbx.xray.structure.structure method) shift_origin (class in mmtbx.utils) shift_origin() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.match_map_model_ncs method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) shift_origin_if_needed() (in module cctbx.maptbx) shift_origin_to_match_original() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) shift_refinement (class in cctbx.symmetry_search) shift_sites_cart() (cctbx.geometry_restraints.manager.manager method) shift_sites_cart_back() (mmtbx.utils.extract_box_around_model_and_map method) shift_sites_in_place() (cctbx.xray.structure.structure method) shift_to_origin() (iotbx.pdb.hierarchy.root method) shift_us() (cctbx.xray.structure.structure method) shortcut() (in module mmtbx.hydrogens) shortcut_1() (in module mmtbx.ncs.ncs_search) show() (cctbx.adp_restraints.energies.energies method) (cctbx.adp_restraints.flags.flags method) (cctbx.eltbx.xray_scattering.fitted_gaussian method) (cctbx.euclidean_model_matching.euclidean_match_symmetry method) (cctbx.euclidean_model_matching.match_refine method) (cctbx.euclidean_model_matching.model method) (cctbx.geometry_restraints.energies.energies method) (cctbx.geometry_restraints.flags.flags method) (cctbx.maptbx.d99 method) (cctbx.maptbx.mem.run method) (cctbx.maptbx.spherical_variance_around_point method) (cctbx.masks.vdw_radii method) (cctbx.sgtbx.cosets.double_cosets method) (cctbx.sgtbx.cosets.left_decomposition method) (cctbx.sgtbx.lattice_symmetry.metric_subgroups method) (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method) (cctbx.sgtbx.pointgroup_tools.space_group_graph_from_cell_and_sg method) (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method) (cctbx.sgtbx.rational_matrices_point_groups.rat_rot_group method) (cctbx.sgtbx.reticular_pg_tools.rat_rot_group method) (cctbx.sgtbx.reticular_twin_laws.ret_twin_law_info method) (cctbx.sgtbx.reticular_twin_laws.reticular_twin_laws method) (cctbx.xray.structure.meaningful_site_cart_differences method) (in module cctbx.sgtbx.subgroups) (in module cctbx.xray.structure_factors.global_counters) (in module mmtbx.validation.analyze_peptides) (in module scitbx.array_family.flex) (iotbx.cif.model.block method) (iotbx.cif.model.cif method) (iotbx.cif.model.loop method) (iotbx.cif.model.save method) (iotbx.pdb.hierarchy.overall_counts method) (iotbx.pdb.hierarchy.root method) (iotbx.xds.xparm.writer method) (mmtbx.bulk_solvent.scaler.run method) (mmtbx.disorder.analyze_model.disordered_segment method) (mmtbx.disorder.analyze_model.process_pdb_hierarchy method) (mmtbx.disorder.analyze_model.process_residue_groups method) (mmtbx.disorder.backbone.backrub_residue method) (mmtbx.dynamics.simulated_annealing.run method) (mmtbx.ias.ias_counters method) (mmtbx.ions.atom_type_flags method) (mmtbx.ions.identify.ion_result method) (mmtbx.ions.svm.svm_prediction method) (mmtbx.maps.composite_omit_map.omit_box method) (mmtbx.maps.composite_omit_map.omit_regions method) (mmtbx.maps.fem.counter method) (mmtbx.monomer_library.cif_types.comp_comp_id method) (mmtbx.monomer_library.cif_types.looped_data method) (mmtbx.monomer_library.cif_types.mod_mod_id method) (mmtbx.refinement.adp_refinement.refine_adp method) (mmtbx.refinement.adp_refinement.weight_result method) (mmtbx.refinement.geometry_minimization.run2 method) (mmtbx.refinement.group.manager method) (mmtbx.refinement.minimization.monitor method) (mmtbx.refinement.occupancies.manager method) (mmtbx.refinement.print_statistics.refinement_monitor method) (mmtbx.refinement.real_space.cluster method) (mmtbx.refinement.real_space.fit_residue.monitor method) (mmtbx.refinement.real_space.rsr_model method) (mmtbx.refinement.real_space.side_chain_fit_evaluator method) (mmtbx.refinement.real_space.structure_monitor method) (mmtbx.refinement.real_space.weight.run method) (mmtbx.refinement.refinement_flags.manager method) (mmtbx.refinement.rigid_body.manager method) (mmtbx.refinement.rigid_body.rigid_body_shift_accumulator method) (mmtbx.refinement.select_best_starting_model.evaluate_model method) (mmtbx.refinement.select_best_starting_model.select_model method) (mmtbx.scaling.absences.absences_list method) (mmtbx.scaling.data_analysis method) (mmtbx.scaling.pair_analyses.f_double_prime_ratio method) (mmtbx.scaling.relative_scaling.ls_rel_scale_driver method) (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method) (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method) (mmtbx.scaling.xtriage_analysis method) (mmtbx.scaling.xtriage_output method) (mmtbx.secondary_structure.proteins.find_helices_simple method) (mmtbx.solvent.ensemble_ordered_solvent.manager method) (mmtbx.twinning.twin_f_model.scaling_parameters_object method) (mmtbx.twinning.twin_f_model.twin_fraction_object method) (mmtbx.twinning.twin_f_model.twin_model_manager method) (mmtbx.utils.experimental_data_target_and_gradients method) (mmtbx.validation.clashscore.clashscore method) (mmtbx.validation.clashscore.nqh_flips method) (mmtbx.validation.experimental.data_statistics method) (mmtbx.validation.experimental.real_space method) (mmtbx.validation.ligands.ligand_validation method) (mmtbx.validation.model_properties.model_statistics method) (mmtbx.validation.molprobity.molprobity method) (mmtbx.validation.molprobity.pdb_header_info method) (mmtbx.validation.molprobity.summary method) (mmtbx.validation.restraints.combined method) (mmtbx.validation.restraints.restraint_validation method) (mmtbx.validation.rna_geometry method) (mmtbx.validation.rna_validate.rna_validation method) (mmtbx.validation.sequence.validation method) (mmtbx.validation.validation method) (mmtbx.validation.waters.waters method)

show_all_possible_systematic_absences() (cctbx.miller.array method) show_all_pyplot() (xfel.command_line.cxi_merge.plot_statistics method) show_angles (class in cctbx.crystal) show_angles() (cctbx.xray.structure.structure method) show_array() (cctbx.miller.array method) show_atoms_outside_density() (mmtbx.building.local_density_quality method) show_bad_occupancy() (mmtbx.validation.model_properties.xray_structure_statistics method) show_basic_info() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method) show_bfactors() (mmtbx.validation.model_properties.xray_structure_statistics method) show_big_header() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_brief() (mmtbx.ions.identify.ion_result method) (mmtbx.ions.svm.svm_prediction method) show_cc_r1() (in module cctbx.omz.cod_refine) show_chain_resseq_ranges() (in module mmtbx.building) show_chains_with_mix_of_proper_and_improper_alt_conf() (iotbx.pdb.hierarchy.overall_counts method) show_completeness() (cctbx.miller.set method) show_comprehensive() (mmtbx.fmodels method) (mmtbx.twinning.twin_f_model.twin_model_manager method) show_comprehensive_summary() (cctbx.miller.array method) (cctbx.miller.set method) (cctbx.sgtbx.direct_space_asu.direct_space_asu method) show_consecutive_residue_groups_with_same_resid() (iotbx.pdb.hierarchy.overall_counts method) show_controls_default (xfel.cxi.gfx.status_plot.StatusFrame attribute) (xfel.cxi.gfx.trials_plot.TrialsPlotFrame attribute) (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame attribute) show_count_stats() (in module scitbx.array_family.flex) show_cpp() (in module cctbx.sgtbx.direct_space_asu.proto.generate_cpp_asu_table) show_current_r_factors_summary() (mmtbx.refinement.print_statistics.refinement_monitor method) show_current_scattering_statistics() (mmtbx.ions.identify.manager method) show_cycle_summary() (mmtbx.density_modification.density_modification method) show_den_opt_summary_cartesian() (mmtbx.den.refinement.manager method) show_den_opt_summary_torsion() (mmtbx.den.refinement.manager method) show_den_summary() (mmtbx.den.den_restraints method) show_dests() (cctbx.omz.dev.refinement method) show_differences_if_any() (in module cctbx.eltbx.development.itvc_cross_validation) show_dihedral_angles (class in cctbx.crystal) show_dihedral_angles() (cctbx.xray.structure.structure method) show_disagreeable_reflections() (cctbx.miller.array method) show_distances (class in cctbx.crystal) show_distances() (cctbx.xray.structure.structure method) show_duplicate_atom_labels() (iotbx.pdb.hierarchy.overall_counts method) show_errors() (iotbx.cif.reader method) show_essential() (mmtbx.twinning.twin_f_model.twin_model_manager method) show_fit() (in module cctbx.examples.unit_cell_minimizers) (in module cctbx.examples.unit_cell_refinement) show_fit_summary() (in module cctbx.eltbx.gaussian_fit) show_fom_phase_error_alpha_beta_in_bins() (mmtbx.twinning.twin_f_model.twin_model_manager method) show_group_generic() (in module cctbx.web.explore_symmetry) show_groups() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method) show_header() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_helper() (mmtbx.refinement.occupancies.manager method) show_histogram() (in module mmtbx.polygon) show_histograms() (xfel.command_line.cxi_merge.unit_cell_distribution method) show_improper_alt_conf() (iotbx.pdb.hierarchy.overall_counts method) show_input() (cctbx.sgtbx.lattice_symmetry.metric_subgroups method) show_input_symbol() (in module cctbx.web.io_utils) show_ion_results() (mmtbx.ions.identify.AtomProperties method) show_k_sol_b_sol_b_cart_target() (mmtbx.twinning.twin_f_model.twin_model_manager method) show_lines() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_literature_fits() (in module cctbx.eltbx.gaussian_fit) show_loop() (in module mmtbx.monomer_library.cif_types) show_loop_data() (mmtbx.monomer_library.cif_types.looped_data method) show_loop_header() (mmtbx.monomer_library.cif_types.looped_data method) show_map_stat() (in module cctbx.maptbx.mem) show_mean_data_over_sigma_along_a_b_c_star() (cctbx.miller.array method) show_old_output() (mmtbx.validation.cbetadev.cbetadev method) (mmtbx.validation.clashscore.clashscore method) (mmtbx.validation.restraints.restraint_validation method) (mmtbx.validation.validation method) show_overall_observations() (in module xfel.command_line.cxi_merge) show_paragraph_header() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_parameter_summary() (mmtbx.twinning.twin_f_model.twin_model_manager method) show_plot() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) (xfel.cxi.gfx.status_plot.StatusPlot method) (xfel.cxi.gfx.trials_plot.TrialsPlot method) (xfel.cxi.gfx.trials_plot.TrialsPlotFrame method) (xfel.cxi.gfx.wx_detectors.DetectorPlot method) (xfel.mono_simulation.mono_treatment.refinement method) show_plots_row() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method) show_preformatted_text() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_process_info() (in module mmtbx.refinement.print_statistics) show_properties() (mmtbx.ions.identify.AtomProperties method) show_r_free_flags_info() (cctbx.miller.array method) show_rejected_summary() (in module cctbx.french_wilson) show_residue_groups() (in module mmtbx.monomer_library.pdb_interpretation) show_residue_groups_with_multiple_resnames_using_same_altloc() (iotbx.pdb.hierarchy.overall_counts method) show_residues() (mmtbx.refinement.real_space.structure_monitor method) show_rigid_body_rotations_and_translations() (in module mmtbx.refinement.print_statistics) show_rms_info() (cctbx.omz.dev.refinement method) show_scatterer_flags_summary() (cctbx.xray.structure.structure method) show_scatterers() (cctbx.neutron.structure method) (cctbx.xray.structure.structure method) show_short() (mmtbx.fmodels method) (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method) (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method) show_simple() (mmtbx.validation.ligands.ligand_validation method) show_sizes_double() (in module scitbx.array_family.flex) show_sizes_int() (in module scitbx.array_family.flex) show_solution() (cctbx.sgtbx.sub_lattice_tools.compare_lattice method) show_sorted() (cctbx.geometry_restraints.manager.manager method) (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) show_special_position_shifts() (cctbx.xray.structure.structure method) show_sub_header() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_summary() (cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter method) (cctbx.crystal.symmetry method) (cctbx.miller.array method) (cctbx.miller.reindexing.assistant method) (cctbx.miller.set method) (cctbx.neutron.structure method) (cctbx.sgtbx.direct_space_asu.direct_space_asu method) (cctbx.sgtbx.space_group_info method) (cctbx.xray.scatterer.anomalous_scatterer_group method) (cctbx.xray.structure.structure method) (iotbx.file_reader.any_file_input method) (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) (mmtbx.ions.identify.water_result method) (mmtbx.masks.bulk_solvent method) (mmtbx.ncs.ligands.group_operators method) (mmtbx.ncs.ncs.ncs method) (mmtbx.scaling.relative_wilson.relative_wilson method) (mmtbx.secondary_structure.manager method) (mmtbx.validation.cbetadev.cbetadev method) (mmtbx.validation.clashscore.clashscore method) (mmtbx.validation.experimental.data_statistics method) (mmtbx.validation.experimental.real_space method) (mmtbx.validation.model_properties.xray_structure_statistics method) (mmtbx.validation.molprobity.molprobity method) (mmtbx.validation.ramalyze.ramalyze method) (mmtbx.validation.restraints.restraint_validation method) (mmtbx.validation.rna_validate.rna_angles method) (mmtbx.validation.rna_validate.rna_bonds method) (mmtbx.validation.rna_validate.rna_puckers method) (mmtbx.validation.rna_validate.rna_validation method) (mmtbx.validation.rotalyze.rotalyze method) (mmtbx.validation.sequence.chain method) (mmtbx.validation.validation method) (mmtbx.validation.waters.waters method) (scitbx.array_family.flex.grid method) (scitbx.array_family.flex.smart_selection method) show_summary_labelit_format() (cctbx.crystal.burzlaff_zimmermann_dewolff.LatticeCharacter method) show_symbols() (in module cctbx.web.explore_symmetry) show_symmetry_error() (in module mmtbx.command_line) show_table() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_targets() (mmtbx.fmodels method) (mmtbx.twinning.twin_f_model.twin_model_manager method) show_terms() (in module cctbx.crystal.coordination_sequences) show_text() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_text_columns() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) show_tiles() (in module xfel.command_line.radial_average) show_times() (in module mmtbx.refinement.adp_refinement) (in module mmtbx.refinement.group) (in module mmtbx.refinement.print_statistics) (in module mmtbx.tls.tools) show_tls (class in mmtbx.tls.tools) show_tls_one_group (class in mmtbx.tls.tools) show_u_statistics() (cctbx.xray.structure.structure method) show_unit_cell_histograms() (xfel.command_line.cxi_merge.scaling_manager method) show_unknown_scatterers() (cctbx.xray.structure_factors.from_scatterers_fft.from_scatterers_fft method) show_validation_results() (in module mmtbx.validation.ligands) show_verdict() (mmtbx.scaling.twin_analyses.twin_results_interpretation method) show_worrisome_shells() (mmtbx.scaling.data_statistics.wilson_scaling method) shrink_edge() (in module cctbx.web.asu_gallery.jv_asu) shrink_polygon() (in module cctbx.web.asu_gallery.jv_asu) side_chain_fit_evaluator (class in mmtbx.refinement.real_space) SidechainAngles (class in mmtbx.rotamer.sidechain_angles) sigb (iotbx.pdb.hierarchy.atom property) sigma (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.restraint attribute) (mmtbx.validation.rna_validate.rna_angle attribute) (mmtbx.validation.rna_validate.rna_bond attribute) sigma_as_weight() (in module cctbx.geometry_restraints) sigma_at_first_index() (cctbx.miller.array method) sigma_filter() (cctbx.miller.array method) sigma_gamma (mmtbx.scaling.absolute_scaling.gamma_protein attribute) sigma_miss() (in module mmtbx.max_lik.maxlik) sigmaa() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method) (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method) sigmaa_estimator (class in mmtbx.scaling.sigmaa_estimation) sigmaa_estimator_kernel_width_d_star_cubed() (in module mmtbx.scaling.sigmaa_estimation) (in module mmtbx.scaling.ta_alpha_beta_calc) sigmaa_model_error() (mmtbx.scaling.sigmaa_estimation.sigmaa_estimator method) (mmtbx.scaling.ta_alpha_beta_calc.ta_alpha_beta_calc method) sigmaa_object() (mmtbx.twinning.twin_f_model.twin_model_manager method) sigmaa_point_estimator (class in mmtbx.scaling.sigmaa_estimation) (class in mmtbx.scaling.ta_alpha_beta_calc) sigmas() (cctbx.miller.array method) sigmas_are_sensible() (cctbx.miller.array method) sign0() (in module cctbx.omz.dev) signal_to_noise_statistical() (in module xfel.command_line.subtract_background) significant_change_test() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.minimum_reduction_mixin method) significant_height_fraction() (cctbx.maptbx.peak_cluster_analysis method) (cctbx.maptbx.peak_search_parameters method) sigocc (iotbx.pdb.hierarchy.atom property) siguij_erase() (iotbx.pdb.hierarchy.atom method) siguij_is_defined() (iotbx.pdb.hierarchy.atom method) sigxyz (iotbx.pdb.hierarchy.atom property) simple (class in mmtbx.refinement.real_space.individual_sites) simple() (dxtbx.model.beam.BeamFactory static method) (dxtbx.model.detector.DetectorFactory static method) simple_and_slow() (in module cctbx.crystal.coordination_sequences) simple_directional() (dxtbx.model.beam.BeamFactory static method) simple_distance_predicate() (mmtbx.geometry.indexing.structure_indexer method) simple_edge_list() (cctbx.geometry_restraints.manager.manager method) simple_id() (mmtbx.validation.residue method) simple_shelx_weighting (class in cctbx.xray.weighting_schemes) simple_surface_calculation() (in module mmtbx.geometry.asa) sin_theta_over_lambda_sq() (cctbx.miller.set method) singh_ramasheshan_fa_estimate (class in mmtbx.scaling.fa_estimation) (class in mmtbx.scaling.pair_analyses) single_axis() (dxtbx.model.goniometer.GoniometerFactory static method) single_axis_goniometer_from_phil() (dxtbx.model.goniometer.GoniometerFactory static method) single_axis_reverse() (dxtbx.model.goniometer.GoniometerFactory static method) single_file() (dxtbx.model.scan.ScanFactory static method) single_peak_fit() (xfel.command_line.view_pixel_histograms.pixel_histograms method) single_reflection_histograms() (xfel.command_line.cxi_merge.scaling_manager static method) SingleFrame (class in xfel.clustering.singleframe) site_cart (mmtbx.ions.environment.atom_contact attribute), [1] site_cluster_analysis() (cctbx.crystal.special_position_settings method) (cctbx.maptbx.peak_cluster_analysis method) site_ideal() (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom method) site_symmetry() (cctbx.crystal.special_position_settings method) site_symmetry_ops_j (cctbx.sgtbx.symmetry_equivalent_pair_interactions attribute) site_symmetry_table() (cctbx.crystal.special_position_settings method) (cctbx.xray.structure.structure method) (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) sites() (cctbx.maptbx.peak_cluster_analysis method) sites_cart() (cctbx.xray.structure.structure method) (mmtbx.refinement.real_space.individual_sites.diff_map method) (mmtbx.refinement.real_space.individual_sites.simple method) (mmtbx.validation.atoms method) sites_cart_exact() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) sites_cart_used_for_pair_proxies() (cctbx.geometry_restraints.manager.manager method) sites_frac() (cctbx.xray.structure.structure method) sites_mod_positive() (cctbx.xray.structure.structure method) sites_mod_short() (cctbx.xray.structure.structure method) size() (cctbx.euclidean_model_matching.model method) (cctbx.miller.array method) (cctbx.miller.set method) (cctbx.web.asu_gallery.jvx.faceSet method) (cctbx.web.asu_gallery.jvx.lineSet method) (cctbx.web.asu_gallery.jvx.pointSet method) (iotbx.cif.model.loop method) (iotbx.pdb.hierarchy.af_shared_atom method) (mmtbx.geometry.topology.Molecule method) (scitbx.array_family.flex.bool method) (scitbx.array_family.flex.complex_double method) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.float method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) (scitbx.array_family.flex.size_t method) (scitbx.array_family.flex.std_string method) (scitbx.array_family.flex.sym_mat3_double method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.array_family.flex.vec3_int method) size_1d() (scitbx.array_family.flex.grid method) size_t (class in scitbx.array_family.flex) size_t_element_size (scitbx.array_family.flex.smart_selection attribute) sizeof_data() (iotbx.pdb.hierarchy.atom static method) skewness_calculation() (in module cctbx.examples.map_skewness) skip_event_flag() (in module xfel.cxi.cspad_ana) skip_if_non_linking() (in module mmtbx.monomer_library.linking_setup) slack (mmtbx.validation.restraints.bond attribute) slice() (cctbx.miller.set method) (in module cctbx.sgtbx.direct_space_asu.check_redundancies) slice_to_byte_str() (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) (scitbx.array_family.flex.long method) sliding_average() (in module xfel.command_line.view_pixel_histograms) slots_getstate_setstate (class in libtbx) slots_getstate_setstate_default_initializer (class in libtbx) smart_selection (class in scitbx.array_family.flex) smart_split_cif_line() (in module mmtbx.chemical_components.cif_parser) smooth() (mmtbx.bulk_solvent.scaler.run method) (mmtbx.max_lik.maxlik.alpha_beta_est_manager method) smooth_map() (in module cctbx.maptbx) smooth_mask (class in mmtbx.masks) snd() (mmtbx.twinning.probabalistic_detwinning.detwin method) soft_mask() (iotbx.map_manager.map_manager method) solc() (mmtbx.scaling.matthews.p_vm_calculator method) solution (class in mmtbx.ligands.xtal_screens) solve() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) (scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls method) solve_and_step_forward() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) (scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls method) solvent_adjust() (mmtbx.density_modification.density_modification method) solvent_flattening() (mmtbx.density_modification.density_modification method) solvent_flipping() (mmtbx.density_modification.density_modification method) solvent_fraction() (mmtbx.scaling.matthews.density_calculator method) Sorry_high_resolution_is_not_defined() (mmtbx.utils.fmodel_from_xray_structure method) sort() (cctbx.eltbx.xray_scattering.fitted_gaussian method) (cctbx.miller.set method) (cctbx.xray.structure.structure method) (iotbx.cif.model.block method) (iotbx.cif.model.cif method) (iotbx.cif.model.loop method) sort_atoms_in_place() (iotbx.pdb.hierarchy.atom_group method) (iotbx.pdb.hierarchy.root method) sort_atoms_permutation() (in module mmtbx.ions.utils) sort_by_file_type() (in module iotbx.file_reader) sort_by_z_translation() (mmtbx.ncs.ncs.ncs method) (mmtbx.ncs.ncs.ncs_group method) sort_chains_by_id() (iotbx.pdb.hierarchy.root method) sort_cosets() (cctbx.sgtbx.cosets.left_decomposition method) sort_cut_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method) sort_permutation() (cctbx.miller.array method) (cctbx.miller.set method) sort_redundancies() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) sort_triple() (in module cctbx.sgtbx.sub_lattice_tools) sorted() (in module scitbx.array_family.flex) sorted_as_c_h_then_by_increasing_atomic_number() (cctbx.eltbx.formula.formula method) sorted_by_map_value() (mmtbx.refinement.real_space.fit_residue.find_all_conformers method) sorted_cut_points() (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_with_cut_points method) source (cctbx.eltbx.xray_scattering.one_gaussian_agarwal_1978 attribute) (cctbx.eltbx.xray_scattering.two_gaussian_agarwal_1978 attribute) (cctbx.eltbx.xray_scattering.two_gaussian_agarwal_isaacs attribute) source_info (mmtbx.building.make_library.related_chain attribute) (mmtbx.monomer_library.cif_types.comp_comp_id attribute) source_info() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) source_info_server (class in mmtbx.monomer_library.pdb_interpretation) source_of_ncs_info() (mmtbx.ncs.ncs.ncs_group method) source_short (cctbx.eltbx.xray_scattering.one_gaussian_agarwal_1978 attribute) (cctbx.eltbx.xray_scattering.two_gaussian_agarwal_1978 attribute) (cctbx.eltbx.xray_scattering.two_gaussian_agarwal_isaacs attribute) space_group() (cctbx.crystal.symmetry method) (cctbx.maptbx.crystal_gridding method) (mmtbx.validation.molprobity.molprobity method) space_group_graph_from_cell_and_sg (class in cctbx.sgtbx.pointgroup_tools) space_group_info (class in cctbx.sgtbx) space_group_info() (cctbx.crystal.symmetry method) (cctbx.maptbx.crystal_gridding method) (mmtbx.refinement.select_best_starting_model.select_model method) (mmtbx.validation.molprobity.molprobity method) space_group_number() (cctbx.crystal.symmetry method) space_group_option_parser (class in cctbx.development.space_group_option_parser) space_group_processed_options (class in cctbx.development.space_group_option_parser) space_group_sets (cctbx.development.space_group_option_parser.space_group_option_parser attribute) spec_plot() (in module xfel.cxi.cspad_ana.xes_finalise) special_dispensation() (in module mmtbx.monomer_library.pdb_interpretation) special_op_simplified (class in cctbx.sgtbx) special_op_simplified_term (class in cctbx.sgtbx) special_op_simplifier() (in module cctbx.sgtbx) special_position_dict (class in mmtbx.monomer_library.pdb_interpretation) special_position_indices() (cctbx.neutron.structure method) (cctbx.xray.structure.structure method) special_position_settings (class in cctbx.crystal) special_position_settings() (cctbx.crystal.symmetry method) (cctbx.maptbx.peak_cluster_analysis method) (iotbx.pdb.ext.input method) special_position_settings_from_inp() (in module cctbx.web.io_utils) sphere_model_group_for() (mmtbx.geometry.clash.Case method) sphere_similarity_restraints (class in mmtbx.refinement.group) SphereModel (class in mmtbx.geometry.clash) SphereModelGroup (class in mmtbx.geometry.clash) spherical_variance_around_point (class in cctbx.maptbx) sphericity_by_heuristics() (in module cctbx.maptbx) split_array() (mmtbx.geometry_restraints.ramachandran.ramachandran_plot_data method) split_resolution_range() (in module mmtbx.refinement.rigid_body) split_rotamer_names() (in module mmtbx.validation.rotalyze) split_sigma_test() (in module xfel.cxi.cxi_cc) split_u() (in module mmtbx.tls.tools) split_up_map_and_model_by_boxes() (iotbx.map_model_manager.map_model_manager method) split_up_map_and_model_by_chain() (iotbx.map_model_manager.map_model_manager method) split_up_map_and_model_by_ncs_groups() (iotbx.map_model_manager.map_model_manager method) split_up_map_and_model_by_segment() (iotbx.map_model_manager.map_model_manager method) split_up_map_and_model_by_supplied_selections() (iotbx.map_model_manager.map_model_manager method) splitext() (in module iotbx.file_reader) spot_add() (in module xfel.cxi.average_spots) sqr (class in scitbx.matrix) srotate() (xfel.cxi.cspad_ana.parse_calib.Section method) standalone_check() (xfel.metrology.mark0.correction_vectors static method) standalone_copy() (iotbx.pdb.hierarchy.residue method) standard_deviation_of_the_sample() (scitbx.array_family.flex.double method) start_and_end_fom() (mmtbx.density_modification.density_modification method) start_local() (xfel.cxi.cspad_ana.mod_daq_status.StatusFrame_thread method) start_log_file() (mmtbx.command_line.load_model_and_data method) states (class in mmtbx.utils) statistical_mean() (cctbx.miller.array method) statistical_weighting (cctbx.xray.target_functors.least_squares_residual_for_amplitude attribute) statistics (class in cctbx.maptbx) statistics_in_resolution_bins() (mmtbx.twinning.twin_f_model.twin_model_manager method) stats (mmtbx.validation.cbetadev.cbetadev attribute) stats_table (class in mmtbx.refinement.print_statistics) status (xfel.cxi.cspad_ana.mod_event_info.laser_status property) status_change_timestamp (xfel.cxi.cspad_ana.mod_event_info.laser_status attribute) StatusFrame (class in xfel.cxi.gfx.status_plot) StatusFrame_thread (class in xfel.cxi.cspad_ana.mod_daq_status) StatusPlot (class in xfel.cxi.gfx.status_plot) std() (mmtbx.scaling.relative_wilson.relative_wilson method) std_string (class in scitbx.array_family.flex) step() (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.gruber_1973.reduction method) (cctbx.uctbx.krivy_gruber_1976.reduction method) (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) step_equations() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) step_forward() (scitbx.lstbx.normal_eqns.non_linear_ls_mixin method) (scitbx.lstbx.normal_eqns_solving.journaled_non_linear_ls method) step_i__compute_delta_L_r_dp() (in module mmtbx.tls.tls_as_xyz) step_i__get_dxdydz() (in module mmtbx.tls.tls_as_xyz) step_threshold (scitbx.lstbx.normal_eqns_solving.iterations attribute) steps (mmtbx.refinement.print_statistics.stats_table attribute) stop_global_motion() (mmtbx.dynamics.cartesian_dynamics.run method) (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) store_temperatures() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) str_ev() (in module cctbx.examples.all_axes) (in module cctbx.sgtbx.direct_space_asu.check_redundancies) (in module cctbx.sgtbx.literal_description) (in module cctbx.web.explore_symmetry) strain_tensor() (mmtbx.scaling.twin_analyses.twin_law_quality method) string_it() (mmtbx.scaling.twin_analyses.ml_murray_rust_with_ncs method) strip() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method) (scitbx.array_family.flex.std_string method) strip_model() (in module mmtbx.refinement.select_best_starting_model) strip_shelx_format_extension() (in module iotbx.file_reader) structure (class in cctbx.neutron) (class in cctbx.xray.structure) structure_factor (class in cctbx.examples.structure_factor_derivatives) (class in cctbx.examples.structure_factor_derivatives_2) (class in cctbx.examples.structure_factor_derivatives_3) (class in cctbx.examples.structure_factor_derivatives_4) structure_factor_symmetry (class in cctbx.symmetry_search) structure_factors (class in cctbx.examples.structure_factor_derivatives_2) (class in cctbx.examples.structure_factor_derivatives_3) (class in cctbx.examples.structure_factor_derivatives_4) structure_factors() (cctbx.neutron.structure method) (cctbx.xray.structure.structure method) (mmtbx.masks.bulk_solvent method) structure_factors_from_asu_map() (cctbx.miller.set method) structure_factors_from_map() (cctbx.miller.set method) structure_factors_from_scatterers() (cctbx.miller.set method) structure_from_inp() (in module cctbx.web.io_utils) structure_from_inp_pdb() (in module cctbx.web.io_utils) structure_indexer (class in mmtbx.geometry.indexing) structure_monitor (class in mmtbx.refinement.real_space) structure_seminvariants() (cctbx.sgtbx.space_group_info method) sub_super_point_group_relations (class in cctbx.sgtbx.pointgroup_tools) subgroups (class in cctbx.sgtbx.subgroups) subset() (mmtbx.geometry.topology.Compound method) subtract_background() (in module xfel.command_line.subtract_background) subtract_continuous_allowed_origin_shifts() (cctbx.crystal.symmetry method) (cctbx.sgtbx.space_group_info method) subtract_non_uniform_solvent_region_in_place() (mmtbx.masks.bulk_solvent method) subtract_tuples_int() (in module iotbx.map_manager) success() (mmtbx.refinement.select_best_starting_model.select_model method) suggest_likely_candidates() (mmtbx.scaling.absences.protein_space_group_choices method) suggest_new_space_groups() (mmtbx.scaling.twin_analyses.detect_pseudo_translations method) suites (mmtbx.validation.rna_validate.rna_validation attribute) sulfur_class() (in module mmtbx.monomer_library.linking_setup) sum() (cctbx.miller.array method) (in module scitbx.array_family.flex) (in module scitbx.matrix) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) sum_intensities() (xfel.command_line.cxi_merge.scaling_manager method) sum_sq() (cctbx.miller.array method) (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) summarize() (mmtbx.validation.molprobity.molprobity method) summarize_issues() (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method) (mmtbx.scaling.absolute_scaling.ml_iso_absolute_scaling method) (mmtbx.scaling.data_statistics.anomalous method) (mmtbx.scaling.data_statistics.data_strength_and_completeness method) (mmtbx.scaling.data_statistics.ice_ring_checker method) (mmtbx.scaling.data_statistics.possible_outliers method) (mmtbx.scaling.data_statistics.wilson_scaling method) (mmtbx.scaling.twin_analyses.twin_results_interpretation method) (mmtbx.scaling.xtriage.data_summary method) (mmtbx.scaling.xtriage.merging_statistics method) (mmtbx.scaling.xtriage.xtriage_analyses method) (mmtbx.scaling.xtriage_analysis method) summary (class in mmtbx.scaling.relative_wilson) (class in mmtbx.scaling.xtriage) (class in mmtbx.validation.molprobity) summary() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary method) (mmtbx.scaling.relative_wilson.relative_wilson method) superimpose_powder_arcs() (in module xfel.cxi.display_powder_arcs) superposed_map_manager_from_other() (iotbx.map_model_manager.map_model_manager method) surface (mmtbx.geometry.asa.AccessibleSurfaceResult property) svm_prediction (class in mmtbx.ions.svm) switch_rotamers() (in module mmtbx.utils) switch_to_neutron_scattering_dictionary() (cctbx.xray.structure.structure method) sym (class in scitbx.matrix) sym_equiv_sites() (cctbx.crystal.special_position_settings method) sym_mat3_double (class in scitbx.array_family.flex) sym_pair (class in cctbx.crystal) symbol() (cctbx.eltbx.attenuation_coefficient.nist_elements method) symbol_and_number() (cctbx.sgtbx.space_group_info method) symbol_list() (cctbx.eltbx.attenuation_coefficient.nist_elements method) symbol_table (class in cctbx.web.asu_gallery.jv_index) symm_space (iotbx.shelx.lexer.command_stream attribute) symmetries_with_both_nonzero_location_and_intrinsic_parts (class in cctbx.examples.location_part) symmetries_with_nonzero_location_parts (class in cctbx.examples.location_part) symmetrised_shifted_structure_factors (class in cctbx.symmetry_search) symmetrised_structure_factors() (cctbx.symmetry_search.structure_factor_symmetry method) symmetry (class in cctbx.crystal) (iotbx.shelx.tokens.atomname_token attribute) symmetry() (cctbx.crystal.find_best_cell.find_best_cell method) symmetry_agreement_factor() (cctbx.miller.array method) symmetry_equivalent_pair_interactions (class in cctbx.sgtbx) symmetry_flags() (cctbx.maptbx.crystal_gridding method) (cctbx.xray.structure_factors.manager.manager method) symmetry_issues (class in mmtbx.scaling.twin_analyses) symmetry_safe_sublattice_xs (class in cctbx.sgtbx.reticular_twin_laws) SymmetryEquivalent (class in mmtbx.geometry.clash) symop (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.waters.water attribute) sync_reference_dihedral_with_ncs() (cctbx.geometry_restraints.manager.manager method) sys_absent_flags() (cctbx.miller.set method) sys_absent_intensity_distribution (class in cctbx.statistics) szs() (mmtbx.refinement.refinement_flags.manager method)

T

t (mmtbx.scaling.twin_analyses.obliquity attribute) ta_alpha_beta_calc (class in mmtbx.scaling.ta_alpha_beta_calc) ta_harmonic_restraints() (cctbx.geometry_restraints.manager.manager method) table (cctbx.eltbx.van_der_waals_radii.vdw attribute) (cctbx.eltbx.xray_scattering.one_gaussian_agarwal_1978 attribute) (cctbx.eltbx.xray_scattering.two_gaussian_agarwal_1978 attribute) (cctbx.eltbx.xray_scattering.two_gaussian_agarwal_isaacs attribute) (class in cctbx.eltbx.development.kissel_io) (mmtbx.scaling.twin_analyses.britton_test property) (mmtbx.scaling.twin_analyses.h_test property) (mmtbx.scaling.twin_analyses.l_test property) (mmtbx.scaling.twin_analyses.ml_murray_rust property) (mmtbx.scaling.twin_analyses.n_z_test property) table6111 (class in cctbx.eltbx.development.itvc_section61_io) table6111_entry (class in cctbx.eltbx.development.itvc_section61_io) table_format_html() (in module cctbx.web.asu_gallery.jv_index) table_references (class in cctbx.source_generators.eltbx.generate_sasaki_cpp) tags() (cctbx.maptbx.crystal_gridding method) (cctbx.maptbx.crystal_gridding_tags method) tail() (in module cctbx.web.asu_gallery.jvx) tardy_model() (in module mmtbx.monomer_library.rotamer_utils) tardy_model_one_residue() (in module mmtbx.utils.rotatable_bonds) target (class in cctbx.xray.targets.r1) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint attribute) (mmtbx.validation.restraints.restraint_validation attribute) target() (mmtbx.refinement.group.target_and_grads method) (mmtbx.refinement.rigid_body.target_and_grads method) (mmtbx.scaling.relative_wilson.relative_wilson method) (mmtbx.twinning.twin_f_model.twin_model_manager method) (mmtbx.utils.experimental_data_target_and_gradients method) target_and_gradients() (mmtbx.den.den_restraints method) (mmtbx.fmodels method) (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) (mmtbx.refinement.group.sphere_similarity_restraints method) (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_geometry_minimization method) (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_real_space method) (mmtbx.refinement.minimization_ncs_constraints.target_function_and_grads_reciprocal_space method) target_and_grads (class in mmtbx.refinement.group) (class in mmtbx.refinement.rigid_body) target_attributes (class in mmtbx.refinement.targets) (class in mmtbx.twinning.twin_f_model) target_attributes() (mmtbx.twinning.twin_f_model.twin_model_manager method) target_f() (mmtbx.twinning.twin_f_model.twin_model_manager method) target_function_and_grads_geometry_minimization (class in mmtbx.refinement.minimization_ncs_constraints) target_function_and_grads_real_space (class in mmtbx.refinement.minimization_ncs_constraints) target_function_and_grads_reciprocal_space (class in mmtbx.refinement.minimization_ncs_constraints) target_function_is_invariant_under_allowed_origin_shifts() (mmtbx.refinement.targets.target_functor method) (mmtbx.twinning.twin_f_model.target_functor method) target_functions_are_invariant_under_allowed_origin_shifts() (mmtbx.fmodels method) target_functor (class in mmtbx.refinement.targets) (class in mmtbx.twinning.twin_f_model) target_functor() (mmtbx.twinning.twin_f_model.twin_model_manager method) target_functor_result_neutron() (mmtbx.fmodels method) target_functor_result_xray() (mmtbx.fmodels method) target_memory() (mmtbx.refinement.targets.phaser_sad_target_functor method) target_per_reflection() (mmtbx.refinement.targets.target_result method) target_result (class in mmtbx.refinement.targets) (class in mmtbx.twinning.twin_f_model) target_result_mixin (class in mmtbx.refinement.targets) target_test() (mmtbx.refinement.targets.target_result method) (mmtbx.twinning.twin_f_model.target_result method) target_work() (cctbx.xray.targets.r1.target method) (cctbx.xray.targets.shelxl_wght_ls method) (mmtbx.refinement.targets.target_result method) (mmtbx.twinning.twin_f_model.target_result method) tau (mmtbx.scaling.twin_analyses.obliquity attribute) (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations attribute) temperature_as_kinetic_energy() (in module mmtbx.dynamics) ter_indices() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) termination_parameters (class in scitbx.lbfgs) terms (cctbx.sgtbx.special_op_simplified attribute) test() (in module cctbx.sgtbx.harker) (in module mmtbx.scaling.absence_likelihood) (in module mmtbx.scaling.absences) test_all() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) test_average() (in module mmtbx.conformation_dependent_library.tst_cdl) test_call_back() (in module cctbx.sgtbx.harker) test_cdl_lookup() (in module mmtbx.conformation_dependent_library.tst_cdl) test_cis_trans_peptide() (in module mmtbx.conformation_dependent_library.tst_cdl) test_detwin() (in module mmtbx.twinning.probabalistic_detwinning) test_double_coset_decomposition() (in module cctbx.sgtbx.cosets) test_flag_value (mmtbx.command_line.load_model_and_data attribute) test_for_peptide() (mmtbx.monomer_library.cif_types.comp_comp_id method) test_for_rna_dna() (mmtbx.monomer_library.cif_types.comp_comp_id method) test_for_water() (mmtbx.monomer_library.cif_types.comp_comp_id method) test_lattice_translation_aware_left_decomposition() (in module cctbx.sgtbx.cosets) test_phi_psi_key() (in module mmtbx.conformation_dependent_library.tst_cdl) test_reassembly() (in module cctbx.merging.brehm_diederichs) test_res_type() (in module mmtbx.conformation_dependent_library.tst_cdl) test_threes_methods() (in module mmtbx.conformation_dependent_library.tst_cdl) test_utils (class in mmtbx.validation) tidy_us() (cctbx.xray.structure.structure method) tile_weight() (xfel.metrology.mark0.correction_vectors method) timings() (in module cctbx.command_line.structure_factor_timings) (in module cctbx.development.electron_density_sampling) title_section() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) tls_from_map() (iotbx.map_model_manager.map_model_manager method) tls_from_pdb_inp() (in module mmtbx.tls.tools) tls_from_u_cart() (in module mmtbx.tls.tools) tls_from_uaniso_minimizer (class in mmtbx.tls.tools) tls_from_uanisos() (in module mmtbx.tls.tools) tls_from_uiso_minimizer (class in mmtbx.tls.tools) tls_group (class in mmtbx.tls.tools) tls_groups (class in mmtbx.tls.tools) tls_refinement (class in mmtbx.tls.tools) tls_xray_grads (class in mmtbx.tls.tools)

tls_xray_target_minimizer (class in mmtbx.tls.tools) tmp (class in mmtbx.bulk_solvent.scaler) (iotbx.pdb.hierarchy.atom property) to_asu_map() (mmtbx.maps.composite_omit_map.run method) to_crystal() (in module dxtbx.serialize.xds) to_dict() (dxtbx.model.goniometer.Goniometer method) (dxtbx.model.goniometer.MultiAxisGoniometer method) to_imageset() (in module dxtbx.serialize.xds) to_list() (in module scitbx.array_family.flex) to_panda() (xfel.clustering.singleframe.SingleFrame method) to_pandas() (xfel.clustering.cluster.Cluster method) to_xds (class in dxtbx.serialize.xds) to_xray_structure() (in module mmtbx.geometry.clash) tolerance_positive_definite() (cctbx.xray.structure_factors.manager.manager method) too_few_coord (mmtbx.ions.atom_type_flags attribute) TOO_FEW_COORD (mmtbx.ions.identify.AtomProperties attribute) too_few_non_waters (mmtbx.ions.atom_type_flags attribute) TOO_FEW_NON_WATERS (mmtbx.ions.identify.AtomProperties attribute) too_many_coord (mmtbx.ions.atom_type_flags attribute) TOO_MANY_COORD (mmtbx.ions.identify.AtomProperties attribute) topology() (in module cctbx.development.make_cns_input) tor_list (mmtbx.monomer_library.cif_types.comp_comp_id attribute) torsion_search() (in module mmtbx.refinement.real_space) torsion_search_nested() (in module mmtbx.refinement.real_space) total_intensity_filter() (xfel.clustering.cluster.Cluster method) trace() (cctbx.macro_mol.rotation_parameters.matrix33 method) (scitbx.matrix.rec method) trace_atoms_in_map() (iotbx.map_manager.map_manager method) trace_polygon() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) track_all (scitbx.lstbx.normal_eqns_solving.iterations attribute) track_gradient (scitbx.lstbx.normal_eqns_solving.iterations attribute) track_step (scitbx.lstbx.normal_eqns_solving.iterations attribute) trajectory_output (class in mmtbx.refinement.print_statistics) trans_field() (in module mmtbx.monomer_library.conv_v2_v3) transfer_chains_from_other() (iotbx.pdb.hierarchy.model method) (iotbx.pdb.hierarchy.root method) transform_map_by_lsq_fit() (in module mmtbx.maps.superpose) transform_maps (class in mmtbx.maps.superpose) transform_model() (cctbx.euclidean_model_matching.delegating_model_matches method) transform_to_reference_setting() (cctbx.euclidean_model_matching.model method) translate() (cctbx.xray.structure.structure method) (xfel.cxi.cspad_ana.parse_calib.Section method) translation() (mmtbx.refinement.rigid_body.manager method) translational_shift() (cctbx.miller.array method) translations_orth() (mmtbx.ncs.ncs.ncs_group method) translations_orth_inv() (mmtbx.ncs.ncs.ncs_group method) transpose() (scitbx.matrix.rec method) transpose_multiply() (scitbx.array_family.flex.vec2_double method) (scitbx.array_family.flex.vec3_double method) (scitbx.matrix.rec method) TrialsPlot (class in xfel.cxi.gfx.trials_plot) TrialsPlotFrame (class in xfel.cxi.gfx.trials_plot) tricubic_interpolation() (scitbx.array_family.flex.double method) tricubic_interpolation_with_gradients() (scitbx.array_family.flex.double method) trim_res_limit() (xfel.clustering.singleframe.SingleFrame method) triplet_generator() (in module cctbx.dmtbx) trivial_html_tag_filter (class in mmtbx.monomer_library.server) truncate() (in module cctbx.maptbx) truncate_at_pdb_format_precision() (cctbx.xray.structure.structure method) truncate_to_poly() (iotbx.pdb.hierarchy.root method) truncate_to_poly_ala() (iotbx.pdb.hierarchy.root method) truncate_to_poly_gly() (iotbx.pdb.hierarchy.root method) truncate_with_roots() (in module mmtbx.maps.fem) try_all_readers() (in module iotbx.reflection_file_reader) try_all_types() (iotbx.file_reader.any_file_input method) try_den_weight_cartesian() (mmtbx.den.refinement.manager method) try_den_weight_torsion() (mmtbx.den.refinement.manager method) try_scale() (mmtbx.bulk_solvent.scaler.run method) try_weight() (mmtbx.refinement.adp_refinement.refine_adp method) tst_bravais_types() (in module cctbx.sgtbx.bravais_types) tst_build_edge_list() (in module cctbx.eltbx.distance_based_connectivity) tst_build_reticular_twin_laws() (in module cctbx.sgtbx.reticular_pg_tools) tst_centered_cells() (in module cctbx.sgtbx.sub_lattice_tools) tst_compare() (in module cctbx.sgtbx.rational_matrices_point_groups) (in module cctbx.sgtbx.reticular_pg_tools) (in module cctbx.sgtbx.sub_lattice_tools) tst_groups() (in module cctbx.sgtbx.rational_matrices_point_groups) (in module cctbx.sgtbx.reticular_pg_tools) tst_make_bigger_cell() (in module cctbx.sgtbx.sub_lattice_tools) tst_run_requiring_cns() (in module cctbx.development.make_cns_input) tst_sublattice() (in module cctbx.sgtbx.sub_lattice_tools) tube_number_ (mmtbx.ligands.xtal_screens.solution attribute) tune_up (class in mmtbx.refinement.real_space.fit_residue) twin_analyses (class in mmtbx.scaling.twin_analyses) twin_analyses_brief() (in module mmtbx.scaling.twin_analyses) twin_data() (cctbx.miller.array method) twin_fraction_object (class in mmtbx.twinning.twin_f_model) twin_fraction_scan() (mmtbx.twinning.twin_f_model.twin_model_manager method) twin_fraction_to_ref() (mmtbx.twinning.twin_f_model.twin_fraction_object method) twin_law (class in mmtbx.scaling.twin_analyses) (mmtbx.validation.experimental.data_statistics attribute) twin_law() (mmtbx.validation.molprobity.molprobity method) twin_law_dependent_twin_tests (class in mmtbx.scaling.twin_analyses) twin_law_quality (class in mmtbx.scaling.twin_analyses) twin_laws (class in mmtbx.scaling.twin_analyses) twin_model_manager (class in mmtbx.twinning.twin_f_model) twin_results_interpretation (class in mmtbx.scaling.twin_analyses) twin_test() (mmtbx.twinning.twin_f_model.twin_model_manager method) twin_type (mmtbx.scaling.twin_analyses.twin_law attribute) twmad_fa_driver (class in mmtbx.scaling.fa_estimation) two_fofc (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.waters.water attribute) two_fofc_map() (mmtbx.twinning.twin_f_model.twin_model_manager method) two_fofc_max (mmtbx.validation.ligands.ligand_validation attribute) two_fofc_mean (mmtbx.validation.ligands.ligand_validation attribute) two_fofc_min (mmtbx.validation.ligands.ligand_validation attribute) two_gaussian_agarwal_1978 (class in cctbx.eltbx.xray_scattering) two_gaussian_agarwal_isaacs (class in cctbx.eltbx.xray_scattering) two_theta() (cctbx.miller.set method) (dxtbx.model.detector.DetectorFactory static method) type (mmtbx.scaling.twin_analyses.obliquity attribute) type() (cctbx.sgtbx.space_group_info method) (cctbx.uctbx.gruber_1973.fast_minimum_reduction method) (cctbx.uctbx.reduction_base.gruber_parameterization method) type_conditions (class in cctbx.uctbx.gruber_1973_table_1) type_symbol (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute) type_symbol_registry_base (class in mmtbx.monomer_library.pdb_interpretation)

U

u (mmtbx.scaling.twin_analyses.obliquity attribute) u_base() (cctbx.xray.structure_factors.manager.manager method) u_cart() (mmtbx.twinning.twin_f_model.twin_model_manager method) u_cart_from_ensemble() (in module mmtbx.tls.tools) u_cart_from_tls() (in module mmtbx.tls.tools) u_index_as_r_index() (in module cctbx.sgtbx.direct_space_asu.check_redundancies) u_iso() (mmtbx.twinning.twin_f_model.twin_model_manager method) u_iso_as_u_cart() (mmtbx.twinning.twin_f_model.twin_model_manager method) u_part_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) u_sol() (mmtbx.twinning.twin_f_model.twin_model_manager method) u_sol_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) u_star() (mmtbx.bulk_solvent.bulk_solvent_and_scaling.bulk_solvent_and_scales method) (mmtbx.twinning.twin_f_model.twin_model_manager method) u_star_to_ref() (mmtbx.twinning.twin_f_model.scaling_parameters_object method) u_star_tolerance() (cctbx.crystal.special_position_settings method) u_tls_vs_u_ens (class in mmtbx.tls.tools) uc_feature_vector() (xfel.clustering.cluster.Cluster method) ucf() (in module mmtbx.refinement.select_best_starting_model) uij (iotbx.pdb.hierarchy.atom property) uij_erase() (iotbx.pdb.hierarchy.atom method) uij_is_defined() (iotbx.pdb.hierarchy.atom method) unexpected_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute) (mmtbx.monomer_library.pdb_interpretation.monomer_mapping_summary attribute) unified_least_squares_residual (class in cctbx.xray.target_functors) unique_resnames() (iotbx.pdb.hierarchy.residue_group method) unique_under_symmetry() (cctbx.miller.set method) unique_under_symmetry_selection() (cctbx.miller.set method) unit_cell (class in cctbx.uctbx) unit_cell() (cctbx.crystal.symmetry method) (cctbx.examples.unit_cell_minimizers.refinery method) (cctbx.examples.unit_cell_refinement.refinery method) (cctbx.maptbx.crystal_gridding method) (mmtbx.validation.molprobity.molprobity method) unit_cell_content() (cctbx.xray.structure.structure method) unit_cell_crystal_symmetry() (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) unit_cell_distribution (class in xfel.command_line.cxi_merge) unit_cell_geometry() (in module cctbx.web.asu_gallery.jv_asu) unit_cell_info() (in module xfel.clustering.cluster_groups) unit_cell_to_symetry_object() (in module xfel.command_line.cxi_stream_to_pickle) unit_crystal_symmetry() (in module cctbx.crystal) unit_quaternion_as_axis_and_angle() (scitbx.matrix.rec method) unit_quaternion_as_r3_rotation_matrix() (scitbx.matrix.rec method) unit_quaternion_product() (scitbx.matrix.rec method) unknown_residues_error_message (mmtbx.command_line.load_model_and_data attribute) unknown_residues_flag (mmtbx.command_line.load_model_and_data attribute) unknown_section() (iotbx.pdb.ext.input method) unmerged_i_obs (mmtbx.command_line.load_model_and_data attribute) unpack() (mmtbx.refinement.anomalous_scatterer_groups.minimizer method) (mmtbx.scaling.absolute_scaling.ml_aniso_absolute_scaling method) (mmtbx.scaling.relative_scaling.refinery method) unpack_x() (mmtbx.refinement.group.group_minimizer method) (mmtbx.refinement.occupancies.minimizer method) (mmtbx.refinement.rigid_body.rigid_body_minimizer method) (mmtbx.tls.tools.tls_from_uaniso_minimizer method) (mmtbx.tls.tools.tls_from_uiso_minimizer method) (mmtbx.tls.tools.tls_xray_target_minimizer method) unpicklable (class in libtbx) unpickle_miller_arrays() (in module iotbx.reflection_file_reader) unsure (cctbx.symmetry_search.possible_symmetry attribute) update() (iotbx.cif.model.block method) (mmtbx.building.extend_sidechains.conformation_scorer method) (mmtbx.fmodels method) (mmtbx.monomer_library.pdb_interpretation.cif_output_holder method) (mmtbx.refinement.real_space.rsr_model method) (mmtbx.refinement.real_space.score method) (mmtbx.refinement.real_space.score2 method) (mmtbx.refinement.real_space.score3 method) (mmtbx.refinement.real_space.score4 method) (mmtbx.refinement.real_space.structure_monitor method) (mmtbx.twinning.twin_f_model.twin_model_manager method)

update_all_scales() (mmtbx.fmodels method) (mmtbx.twinning.twin_f_model.twin_model_manager method) update_atom_nonbonded_type() (cctbx.geometry_restraints.manager.manager method) update_cdl_restraints() (mmtbx.refinement.geometry_minimization.run2 method) update_column() (iotbx.cif.model.loop method) update_coordinates() (mmtbx.building.box_build_refine_base method) update_core() (mmtbx.twinning.twin_f_model.twin_model_manager method) update_dests_using_bfgs_formula() (cctbx.omz.dev.refinement method) update_dihedral_ncs_restraints() (cctbx.geometry_restraints.manager.manager method) update_eq_distances() (mmtbx.den.den_restraints method) update_f_hydrogens() (mmtbx.twinning.twin_f_model.twin_model_manager method) update_f_mask() (mmtbx.twinning.twin_f_model.twin_model_manager method) update_fgc() (cctbx.omz.dev.refinement method) update_from_logs() (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame method) update_histograms() (in module xfel.cxi.cspad_ana.histogram_finalise) update_hit_rate() (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame method) update_internals_due_to_coordinates_change() (mmtbx.monomer_library.pdb_interpretation.build_all_chain_proxies method) update_maps() (mmtbx.ions.identify.manager method) update_metrics() (cctbx.maptbx.mem.run method) update_omit_map() (mmtbx.hydrogens.map_manager method) update_original_coordinates() (mmtbx.building.box_build_refine_base method) update_phi_psi_targets() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) update_phi_psi_targets_on_init() (mmtbx.geometry_restraints.ramachandran.ramachandran_manager method) update_plain_pair_sym_table() (cctbx.geometry_restraints.manager.manager method) update_plot() (xfel.cxi.cspad_ana.mod_daq_status.mod_daq_status method) update_ramachandran_restraints_phi_psi_targets() (cctbx.geometry_restraints.manager.manager method) update_restraints() (in module mmtbx.conformation_dependent_library) (in module mmtbx.conformation_dependent_library.altloc_weighting) (mmtbx.monomer_library.conformation_dependent_restraints.conformation_dependent_restraints method) update_sites_from_pdb_atoms() (mmtbx.building.box_build_refine_base method) update_skip_if_longer() (in module mmtbx.monomer_library.linking_setup) update_solvent_and_scale() (mmtbx.twinning.twin_f_model.twin_model_manager method) update_statistics() (mmtbx.refinement.real_space.rsr_model method) update_structure() (mmtbx.ions.identify.manager method) update_target_map() (mmtbx.refinement.real_space.individual_sites.box_refinement_manager method) update_weight() (cctbx.neutron.scatterer method) update_xray_structure() (mmtbx.fmodels method) (mmtbx.refinement.minimization_ncs_constraints.lbfgs method) (mmtbx.refinement.real_space.individual_sites.box_refinement_manager method) (mmtbx.twinning.twin_f_model.twin_model_manager method) (mmtbx.utils.experimental_data_target_and_gradients method) update_xray_structure_with_tls() (in module mmtbx.tls.tools) UpdateEvent (class in xfel.cxi.gfx.status_plot) updaterdl() (mmtbx.refinement.geometry_minimization.run2 method) upper() (scitbx.array_family.flex.std_string method) upper_bidiagonal() (in module scitbx.array_family.flex) usage() (in module mmtbx.kinemage.validation) (in module mmtbx.validation.analyze_peptides) use_alt_parallel (cctbx.xray.structure_factors.from_scatterers_direct_parallel.direct_summation_simple attribute) use_binner_of() (cctbx.miller.set method) use_binning() (cctbx.miller.set method) use_binning_of() (cctbx.miller.set method) use_multiplicities_as_weights() (cctbx.xray.target_functors.intensity_correlation method) use_segids_in_place_of_chainids() (in module mmtbx.validation.utils) use_sigmas_as_weights() (cctbx.xray.target_functors.least_squares_residual_for_amplitude method) use_u_aniso() (cctbx.xray.structure.structure method) use_u_iso() (cctbx.xray.structure.structure method) used_amber_restraints() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) used_cdl_restraints() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) used_omega_cdl_restraints() (iotbx.pdb.ext.input method) (iotbx.pdb.mmcif.cif_input method) user_callback() (xfel.cxi.display_spots.wrapper_of_callback method)

V

v2calib2sections() (in module xfel.cxi.cspad_ana.parse_calib) validate() (cctbx.source_generators.eltbx.generate_sasaki_cpp.sasaki_table method) (iotbx.cif.model.cif method) (libtbx.program_template.ProgramTemplate method) (mmtbx.refinement.targets.target_attributes method) validate_geometry_edits_params() (in module mmtbx.monomer_library.pdb_interpretation) validate_input_params() (in module mmtbx.command_line) validate_ion() (mmtbx.ions.identify.manager method) validate_ions() (mmtbx.ions.identify.manager method) validate_ligands() (in module mmtbx.validation.ligands) validate_params() (in module mmtbx.maps.fobs_minus_fobs_map) (in module mmtbx.scaling.xtriage) validate_phil() (in module xfel.command_line.metrology) validate_platform_resources() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.direct_summation_cuda_platform method) validate_the_inputs() (cctbx.xray.structure_factors.from_scatterers_direct_parallel.pprocess method) validation (class in mmtbx.validation) (class in mmtbx.validation.sequence) value() (in module mmtbx.ncs.ncs) value_at_closest_grid_point() (in module cctbx.maptbx) (scitbx.array_family.flex.double method) (scitbx.array_family.flex.int method) value_at_index() (cctbx.miller.array method) valueAt() (mmtbx.rotamer.n_dim_table.NDimTable method) variable_decoder (class in iotbx.shelx.parsers) vdw (class in cctbx.eltbx.van_der_waals_radii) vdw_radii (class in cctbx.masks) vdw_radii_from_xray_structure() (in module cctbx.masks)

vec2_double (class in scitbx.array_family.flex) vec3_double (class in scitbx.array_family.flex) vec3_int (class in scitbx.array_family.flex) vec3_rat_from_str() (in module cctbx.sgtbx) vector (mmtbx.ions.environment.atom_contact attribute), [1] vector_to_001_rotation() (scitbx.matrix.rec method) vectors() (xfel.cxi.correction_vector_plot.lines method) velocity_rescaling() (mmtbx.dynamics.cartesian_dynamics.run method) (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) verbose_iterations (scitbx.lstbx.normal_eqns_solving.iterations attribute) verify() (cctbx.examples.location_part.a_theorem_in_primitive_settings method) verify_asu_polygons() (in module cctbx.sgtbx.direct_space_asu.facet_analysis) verify_edge_segments() (cctbx.sgtbx.direct_space_asu.facet_analysis.consolidated_edges_with_cut_points method) verlet_leapfrog_integration() (mmtbx.dynamics.cartesian_dynamics.run method) (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) vertex (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute) vertex_geometry() (in module cctbx.web.asu_gallery.jv_asu) vertex_inclusive_flag (cctbx.sgtbx.direct_space_asu.facet_analysis.edge_segment attribute) very_bad_valence (mmtbx.ions.atom_type_flags attribute) VERY_BAD_VALENCES (mmtbx.ions.identify.AtomProperties attribute) view_raw_image() (in module xfel.command_line.quadrants) (in module xfel.cxi.display_spots) visualise_orientational_distribution() (xfel.clustering.cluster.Cluster method) vm() (mmtbx.scaling.matthews.density_calculator method) (mmtbx.scaling.matthews.p_vm_calculator method) vm_prop_table() (mmtbx.scaling.matthews.p_vm_calculator method) voxelizer() (mmtbx.geometry.clash.Case method)

W

w_from_string() (in module cctbx.web.change_basis) w_star() (mmtbx.twinning.twin_f_model.twin_model_manager method) warn() (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) warning_message() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) warnings() (iotbx.pdb.hierarchy.overall_counts method) water (class in mmtbx.validation.waters) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.model_statistics property) water_and_peaks (class in mmtbx.hydrogens.find) water_bond_angle() (in module mmtbx.hydrogens.find) water_in_tls_selections() (in module mmtbx.tls.tools) water_map_correlations() (in module mmtbx.hydrogens.find) water_result (class in mmtbx.ions.identify) water_selection() (mmtbx.ions.identify.manager method) waters (class in mmtbx.validation.waters) (mmtbx.validation.molprobity.molprobity attribute) wavelengeth (mmtbx.ions.environment.ScatteringEnvironment attribute) wavelength (mmtbx.ions.environment.ScatteringEnvironment attribute) (mmtbx.validation.experimental.data_statistics attribute) wavelength_parser (class in iotbx.shelx.parsers) wavelengths() (iotbx.shelx.hklf.reader method) web_to_models (class in cctbx.web.emma) weed_refined_matches() (in module cctbx.euclidean_model_matching) weight() (cctbx.neutron.scatterer method) weight_as_sigma() (in module cctbx.geometry_restraints) weight_result (class in mmtbx.refinement.adp_refinement) weighted_average (class in mmtbx.maps.kick) weighted_cc() (in module mmtbx.scaling.twin_analyses) weighted_histogram_slot_info (class in scitbx.array_family.flex) weighting() (cctbx.xray.target_functors.unified_least_squares_residual method) weights() (cctbx.xray.target_functors.intensity_correlation method) well_number_ (mmtbx.ligands.xtal_screens.solution attribute) whereIs() (mmtbx.rotamer.n_dim_table.NDimTable method) width (cctbx.omz.dev.dynamic_shift_limit_site attribute) width() (xfel.cxi.gfx.trials_plot.Run method) wilson_b (mmtbx.validation.experimental.data_statistics attribute) (mmtbx.validation.molprobity.molprobity attribute) wilson_b() (mmtbx.twinning.twin_f_model.twin_model_manager method) wilson_moments (class in mmtbx.scaling.twin_analyses) wilson_normalised_intensities (class in mmtbx.scaling.twin_analyses) wilson_plot (class in cctbx.statistics) wilson_plot() (cctbx.miller.array method) wilson_ratio() (cctbx.miller.array method) wilson_scaling (class in mmtbx.scaling.data_statistics) wing_cutoff() (cctbx.xray.structure_factors.manager.manager method) working_phil (mmtbx.command_line.load_model_and_data attribute) working_rt_info() (iotbx.map_manager.shift_aware_rt method) wrap_chis() (mmtbx.rotamer.rotamer_eval.RotamerID method) wrap_sym() (mmtbx.rotamer.rotamer_eval.RotamerID method) wrapbin() (mmtbx.rotamer.n_dim_table.NDimTable method) wrapper_of_callback (class in xfel.cxi.display_spots) wrapping() (iotbx.map_manager.map_manager method) write() (in module cctbx.development.make_cns_input) (in module iotbx.xds.xparm) (mmtbx.scaling.loggraph_output method) (mmtbx.scaling.printed_output method) (mmtbx.scaling.xtriage_output method) (mmtbx.utils.states method) write_as_xplor_map() (mmtbx.real_space.sampled_model_density method) write_atoms() (in module mmtbx.hydrogens.build_hydrogens) write_centroid_hierarchy() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) write_coot_script() (mmtbx.validation.molprobity.molprobity method) write_cspad_cbf() (in module xfel.cftbx.detector.cspad_cbf_tbx) write_data() (mmtbx.scaling.massage_twin_detwin_data.massage_data method) write_datasets() (mmtbx.scaling.random_omit.random_omit_data method)

write_file() (iotbx.xds.spot_xds.writer method) (iotbx.xds.xparm.writer method) write_fit_group() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp) write_geo_file() (cctbx.geometry_restraints.manager.manager method) write_header() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp) write_html() (in module cctbx.web.asu_gallery.guide_to_notation) (in module cctbx.web.asu_gallery.jv_index) write_labels() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp) write_map() (iotbx.map_manager.map_manager method) (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) write_map_coeffs() (in module mmtbx.maps.utils) (mmtbx.maps.utils.generate_water_omit_map method) write_map_file() (mmtbx.maps.fobs_minus_fobs_map.compute_fo_minus_fo_map method) (mmtbx.utils.shift_origin method) write_maps() (mmtbx.ncs.ligands.apply_ligand_ncs method) (mmtbx.ncs.ligands.get_final_maps_and_cc method) write_mc() (mmtbx.maps.kick.run method) write_mean_hierarchy() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method) write_mmcif_file() (iotbx.pdb.hierarchy.root method) write_model() (iotbx.map_model_manager.map_model_manager method) (iotbx.map_model_manager.match_map_model_ncs method) write_model_file() (mmtbx.utils.shift_origin method) write_module_info() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp) write_mtz() (cctbx.miller.array method) write_mtz_file() (cctbx.maptbx.mem.run method) (mmtbx.maps.compute_map_coefficients method) write_output_files() (mmtbx.maps.fem.run method) write_pdb() (mmtbx.ncs.ligands.apply_ligand_ncs method) write_pdb_file() (iotbx.pdb.ext.input method) (iotbx.pdb.hierarchy.root method) (mmtbx.ias.manager method) (mmtbx.maps.utils.generate_water_omit_map method) (mmtbx.tls.tls_as_xyz.ensemble_generator method) write_pdb_or_mmcif_file() (iotbx.pdb.hierarchy.root method) write_plot() (in module cctbx.eltbx.gaussian_fit) write_plots() (in module cctbx.eltbx.gaussian_fit) (mmtbx.validation.ramalyze.ramalyze method) write_shelx76_ls() (in module cctbx.development.run_shelx76) write_table() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp) write_tail() (in module cctbx.eltbx.development.create_n_gaussian_raw_cpp) write_tiff() (in module xfel.cxi.cspad_ana.cspad_tbx) write_to_file() (mmtbx.utils.fmodel_from_xray_structure method) write_xplor_map() (in module mmtbx.maps.utils) (mmtbx.utils.extract_box_around_model_and_map method) (mmtbx.utils.set_map_to_value method) write_xplor_map_file (class in mmtbx.maps) write_xplor_map_file() (in module mmtbx.maps.utils) writer (class in iotbx.xds.spot_xds) (class in iotbx.xds.xparm) WrongBravaisError wx_column_widths (mmtbx.validation.cbetadev.cbetadev attribute) (mmtbx.validation.clashscore.clashscore attribute) (mmtbx.validation.clashscore.nqh_flips attribute) (mmtbx.validation.experimental.real_space attribute) (mmtbx.validation.model_properties.xray_structure_statistics attribute) (mmtbx.validation.ramalyze.ramalyze attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) (mmtbx.validation.rna_validate.rna_angles attribute) (mmtbx.validation.rna_validate.rna_bonds attribute) (mmtbx.validation.rna_validate.rna_puckers attribute) (mmtbx.validation.rotalyze.rotalyze attribute) (mmtbx.validation.validation attribute) wyckoff_pair_generator (class in cctbx.development.random_structure) wyckoff_table() (cctbx.sgtbx.space_group_info method)

X

x (cctbx.omz.dev.xfgc_info attribute) x_values() (mmtbx.validation.graphics.residue_bin method) xds_detector_name() (in module dxtbx.serialize.xds) XDS_INP() (dxtbx.serialize.xds.to_xds method) xes_finalise (class in xfel.cxi.cspad_ana.xes_finalise) xes_from_histograms (class in xfel.cxi.cspad_ana.xes_histograms) xfel module xfel.cftbx module xfel.cftbx.detector module xfel.cftbx.detector.cspad_cbf_tbx module xfel.cftbx.detector.metrology2phil module xfel.clustering.cluster module xfel.clustering.cluster_groups module xfel.clustering.singleframe module xfel.command_line module xfel.command_line.auto_submit module xfel.command_line.brehm_diederichs module xfel.command_line.cbf_average module xfel.command_line.convert_gain_map module xfel.command_line.convert_gain_map_cbf module xfel.command_line.cxi_apply_metrology module xfel.command_line.cxi_cspad_pinwheel module xfel.command_line.cxi_diff module xfel.command_line.cxi_display_metrology module xfel.command_line.cxi_generate_circular_gain_mask module xfel.command_line.cxi_index module xfel.command_line.cxi_lsf module xfel.command_line.cxi_merge module xfel.command_line.cxi_optical2cbfheader module xfel.command_line.cxi_pbs module xfel.command_line.cxi_pickle2cbf module xfel.command_line.cxi_plotcv module xfel.command_line.cxi_psana module xfel.command_line.cxi_pyana module xfel.command_line.cxi_spots module xfel.command_line.cxi_stream_to_pickle module xfel.command_line.cxi_view module xfel.command_line.cxi_xmerge module xfel.command_line.histogram_finalise module xfel.command_line.list_db_metadata module xfel.command_line.make_mask module xfel.command_line.metrology module xfel.command_line.monitor_detectors module xfel.command_line.monitor_trials module xfel.command_line.overlay_spectra module xfel.command_line.plot_to_subpixel module xfel.command_line.postrefine module xfel.command_line.print_pickle module xfel.command_line.quadrants module xfel.command_line.radial_average module xfel.command_line.smooth_spectrum module xfel.command_line.subtract_background module xfel.command_line.trial_stats module xfel.command_line.view_pixel_histograms module xfel.command_line.xes_finalise module xfel.command_line.xes_histograms module xfel.cxi module xfel.cxi.average_spots module xfel.cxi.correction_vector_plot module xfel.cxi.cspad_ana module xfel.cxi.cspad_ana.average_tbx module xfel.cxi.cspad_ana.common_mode module xfel.cxi.cspad_ana.cspad_tbx module xfel.cxi.cspad_ana.display_calib module xfel.cxi.cspad_ana.histogram_finalise module xfel.cxi.cspad_ana.hitfinder_tbx module xfel.cxi.cspad_ana.mod_average module xfel.cxi.cspad_ana.mod_daq_status module xfel.cxi.cspad_ana.mod_dump module xfel.cxi.cspad_ana.mod_dump_bitmap module xfel.cxi.cspad_ana.mod_event_info module xfel.cxi.cspad_ana.mod_filter module xfel.cxi.cspad_ana.mod_hdf5 module

xfel.cxi.cspad_ana.mod_hitfind module xfel.cxi.cspad_ana.mod_illumination_filter module xfel.cxi.cspad_ana.mod_mar module xfel.cxi.cspad_ana.mod_param module xfel.cxi.cspad_ana.mod_pulnix_dump module xfel.cxi.cspad_ana.mod_radial_average module xfel.cxi.cspad_ana.mod_xes module xfel.cxi.cspad_ana.parse_calib module xfel.cxi.cspad_ana.pixel_histograms module xfel.cxi.cspad_ana.xes_finalise module xfel.cxi.cspad_ana.xes_histograms module xfel.cxi.cxi_cc module xfel.cxi.display_powder_arcs module xfel.cxi.display_spots module xfel.cxi.gfx module xfel.cxi.gfx.status_plot module xfel.cxi.gfx.trials_plot module xfel.cxi.gfx.wx_detectors module xfel.cxi.integrate_image_api module xfel.cxi.strong_zulu module xfel.cxi.util module xfel.metrology module xfel.metrology.flatfile module xfel.metrology.legacy_scale module xfel.metrology.mark0 module xfel.metrology.mark1 module xfel.metrology.mark10 module xfel.metrology.mark3 module xfel.metrology.quadrant module xfel.mono_simulation module xfel.mono_simulation.mono_treatment module xfel.phil_preferences module xfgc_info (class in cctbx.omz.dev) xparm_xds() (dxtbx.serialize.xds.to_xds method) xray_anomalous() (in module cctbx.development.make_cns_input) xray_declare() (in module cctbx.development.make_cns_input) xray_generate() (in module cctbx.development.make_cns_input) xray_gradients() (in module cctbx.development.make_cns_input) xray_grads() (mmtbx.dynamics.ensemble_cd.cartesian_dynamics method) xray_line() (mmtbx.refinement.minimization.monitor method) xray_mapresolution() (in module cctbx.development.make_cns_input) xray_method() (in module cctbx.development.make_cns_input) xray_predict() (in module cctbx.development.make_cns_input) xray_reflection() (in module cctbx.development.make_cns_input) xray_scattering_dict (mmtbx.fmodels attribute) xray_structure (cctbx.omz.cif_refine.extract_from_cif_files attribute) (cctbx.omz.cod_select_and_pickle.cod_data attribute) (class in cctbx.development.random_structure) (mmtbx.command_line.load_model_and_data attribute) (mmtbx.refinement.select_best_starting_model.evaluate_model attribute) xray_structure() (cctbx.crystal.special_position_settings method) (cctbx.xray.structure_factors.manager.managed_calculation_base method) (in module cctbx.development.make_cns_input) (iotbx.map_model_manager.map_model_manager method) (mmtbx.monomer_library.pdb_interpretation.process method) xray_structure_simple() (iotbx.pdb.ext.input method) xray_structure_statistics (class in mmtbx.validation.model_properties) xray_structures_from_processed_pdb_file (class in mmtbx.utils) xray_structures_simple() (iotbx.pdb.ext.input method) xray_symmetry() (in module cctbx.development.make_cns_input) xray_unit_cell() (in module cctbx.development.make_cns_input) xscaling_manager (class in xfel.command_line.cxi_xmerge) xtal6g() (in module cctbx.development.fmt_utils) xtal6g_list() (in module cctbx.development.fmt_utils) xtriage (mmtbx.validation.molprobity.molprobity attribute) xtriage_analyses (class in mmtbx.scaling.xtriage) xtriage_analysis (class in mmtbx.scaling) xtriage_output (class in mmtbx.scaling) xtriage_summary (class in mmtbx.scaling.xtriage) xy_plot_info() (cctbx.statistics.cumulative_intensity_distribution method) (cctbx.statistics.sys_absent_intensity_distribution method) (cctbx.statistics.wilson_plot method) xyz (iotbx.pdb.hierarchy.atom property) (mmtbx.disorder.backbone.backrub_residue attribute) (mmtbx.ions.identify.ion_result attribute) (mmtbx.validation.atom attribute) (mmtbx.validation.atom_info attribute) (mmtbx.validation.atoms attribute) (mmtbx.validation.cbetadev.cbeta attribute) (mmtbx.validation.clashscore.clash attribute) (mmtbx.validation.clashscore.nqh_flip attribute) (mmtbx.validation.entity attribute) (mmtbx.validation.experimental.residue_real_space attribute) (mmtbx.validation.model_properties.atom_bfactor attribute) (mmtbx.validation.model_properties.atom_occupancy attribute) (mmtbx.validation.model_properties.residue_bfactor attribute) (mmtbx.validation.model_properties.residue_occupancy attribute) (mmtbx.validation.molprobity.residue_multi_criterion attribute) (mmtbx.validation.ramalyze.c_alpha attribute) (mmtbx.validation.ramalyze.ramachandran attribute) (mmtbx.validation.ramalyze.ramachandran_ensemble attribute) (mmtbx.validation.residue attribute) (mmtbx.validation.restraints.angle attribute) (mmtbx.validation.restraints.bond attribute) (mmtbx.validation.restraints.chirality attribute) (mmtbx.validation.restraints.dihedral attribute) (mmtbx.validation.restraints.planarity attribute) (mmtbx.validation.restraints.restraint attribute) (mmtbx.validation.rna_validate.rna_angle attribute) (mmtbx.validation.rna_validate.rna_bond attribute) (mmtbx.validation.rna_validate.rna_pucker attribute) (mmtbx.validation.rotalyze.rotamer attribute) (mmtbx.validation.rotalyze.rotamer_ensemble attribute) (mmtbx.validation.waters.water attribute) xyz_center (mmtbx.validation.ligands.ligand_validation attribute) xyz_distance() (in module mmtbx.ncs.ligands) xyz_from_string() (in module cctbx.web.change_basis)

Y

y (cctbx.omz.bfgs.memory_element attribute)

Z

z_max (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) z_mean (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute)

z_min (mmtbx.validation.restraints.angles attribute) (mmtbx.validation.restraints.bonds attribute) (mmtbx.validation.restraints.chiralities attribute) (mmtbx.validation.restraints.dihedrals attribute) (mmtbx.validation.restraints.planarities attribute) (mmtbx.validation.restraints.restraint_validation attribute) zero() (cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria method) zero_below_threshold() (mmtbx.maps.fem.run method) zero_occ (mmtbx.validation.model_properties.xray_structure_statistics attribute) zero_penalty() (cctbx.crystal.burzlaff_zimmermann_dewolff.MetricCriteria method) zig_zag_fits() (in module cctbx.eltbx.gaussian_fit) zoom_info() (mmtbx.validation.entity method)