Index

_ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

_

__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)

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)
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)
action_callback() (mmtbx.refinement.wx_tardy_pdb.viewer method)
active_atoms (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)
active_indices (mmtbx.density_modification.density_modification attribute)
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.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.cablam.cablam_fingerprints.residue method)
(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_bridge() (mmtbx.secondary_structure.dssp.ladder 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_cycle() (mmtbx.density_modification.dm_stats 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_frame_shift() (xfel.cftbx.detector.cspad_cbf_tbx.cbf_wrapper method)
add_frame_specific_cbf_tables() (in module xfel.cftbx.detector.cspad_cbf_tbx)
add_gradients() (in module cctbx.xray.minimization)
add_harmonic_restraints() (mmtbx.refinement.ensemble_refinement.run_ensemble_refinement method)
add_hhh() (in module mmtbx.hydrogens.build_hydrogens)
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_lone_pairs_for_peptyde_o() (in module mmtbx.ias)
add_miller_array() (iotbx.cif.miller_arrays_as_cif_block 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)
(mmtbx.solvent.ordered_solvent.manager 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_probe_data() (in module mmtbx.cablam.cablam_training)
add_reference_coordinate_restraints_in_place() (cctbx.geometry_restraints.manager.manager method)
add_residue() (mmtbx.cablam.cablam_fingerprints.motif method)
(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_target_atom() (mmtbx.cablam.cablam_fingerprints.bond method)
add_tiles_to_cbf() (in module xfel.cftbx.detector.cspad_cbf_tbx)
add_to_instance() (mmtbx.cablam.cablam_fingerprints.motif_instance method)
add_to_validation_counts() (mmtbx.validation.ramalyze.ramalyze method)
add_water() (mmtbx.validation.experimental.real_space method)
add_wavelength_info() (mmtbx.scaling.make_param.phil_lego method)
address_split() (in module xfel.cxi.cspad_ana.cspad_tbx)
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)
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)
AlignCablamMeasures (class in mmtbx.cablam.cablam_align)
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 attribute)
all_with_effective_resolution() (cctbx.maptbx.peak_cluster_analysis method)
alpha() (in module mmtbx.secondary_structure.build)
alpha_310() (in module mmtbx.secondary_structure.build)
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)
alpha_pi() (in module mmtbx.secondary_structure.build)
alpha_selection() (mmtbx.secondary_structure.manager method)
alpha_selections() (mmtbx.secondary_structure.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 attribute)
(iotbx.pdb.hierarchy.atom_with_labels attribute)
(iotbx.pdb.hierarchy.conformer attribute)
(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.experimental.residue_real_space 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_angle attribute)
(mmtbx.validation.rna_validate.rna_bond attribute)
(mmtbx.validation.rna_validate.rna_pucker attribute)
(mmtbx.validation.rna_validate.rna_suite 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)
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_distances() (in module mmtbx.secondary_structure)
analyze_intensity_statistics() (cctbx.miller.array method)
(in module mmtbx.scaling.twin_analyses)
analyze_measurability (class in mmtbx.scaling.data_statistics)
analyze_pdb() (in module mmtbx.cablam.cablam_validate)
analyze_pdb_ca() (in module mmtbx.cablam.cablam_validate)
analyze_pdb_gui() (in module mmtbx.cablam.cablam_validate)
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_and_axis() (in module xfel.cftbx.detector.cspad_cbf_tbx)
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 attribute)
aniso_b_ratio (mmtbx.scaling.xtriage.xtriage_analyses attribute)
aniso_range_of_b (mmtbx.scaling.xtriage.xtriage_analyses attribute)
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)
ANOM_PEAK (mmtbx.ions.identify.AtomProperties attribute)
anomalous (class in mmtbx.scaling.data_statistics)
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_reflection_intensity_primitive_cell() (in module cctbx.sgtbx.subgroups)
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)
App (class in mmtbx.refinement.wx_tardy_pdb)
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)
(mmtbx.building.alternate_conformations.altloc_labeling.conformer 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_fixed_site() (cctbx.maptbx.peak_cluster_analysis method)
append_model() (iotbx.pdb.hierarchy.root method)
append_neighbours() (mmtbx.geometry.asa.SeparateCheckerBuilder static 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_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_metrology_from_matrices() (xfel.cftbx.detector.cspad_detector.CSPadDetector method)
apply_mod() (mmtbx.monomer_library.cif_types.comp_comp_id method)
(mmtbx.monomer_library.pdb_interpretation.monomer_mapping 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_params() (mmtbx.secondary_structure.manager 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_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_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 attribute)
arg() (cctbx.miller.array method)
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_atom_group() (mmtbx.building.alternate_conformations.single_residue.residue_trial method)
as_ave (mmtbx.refinement.print_statistics.stats_table attribute)
as_bool() (scitbx.array_family.flex.int method)
as_boost_rational() (scitbx.matrix.rec 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.validation.sequence.validation method)
as_cif_block_with_sequence() (iotbx.pdb.hierarchy.root method)
as_cif_input() (iotbx.pdb.hierarchy.root method)
as_cif_simple() (cctbx.miller.array method)
(cctbx.xray.structure.structure method)
as_clash_obj() (mmtbx.validation.clashscore.probe_line_info_storage 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_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_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_hkl() (in module cctbx.sgtbx.rational_matrices_point_groups)
(in module cctbx.sgtbx.reticular_pg_tools)
as_homogenous_transformation() (xfel.cftbx.detector.cspad_cbf_tbx.basis method)
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_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_long() (scitbx.array_family.flex.int method)
as_markup_for_kinemage() (mmtbx.validation.ramalyze.ramalyze method)
as_mat3() (scitbx.matrix.rec 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_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_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.matrix.rec 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_input() (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.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_pymol_cmd() (mmtbx.secondary_structure.dssp.hbond 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)
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)
as_str() (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.rna_validate.rna_suite 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)
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.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.rna_validate.rna_suite 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)
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.rsr_model method)
(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_chain_ids() (in module mmtbx.utils)
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)
assign_sec_struc() (in module mmtbx.cablam.cablam_validate)
assign_solvent_tls_groups() (mmtbx.refinement.ensemble_refinement.run_ensemble_refinement method)
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_ncs_converter (class in mmtbx.ncs)
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 attribute)
(mmtbx.ions.environment.ChemicalEnvironment attribute)
(mmtbx.ions.environment.atom_contact attribute)
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 attribute)
atom_group (class in iotbx.pdb.hierarchy)
(mmtbx.geometry.clash.SymmetryEquivalent attribute)
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 (mmtbx.building.alternate_conformations.altloc_labeling.conformer attribute)
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)
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_name_save (mmtbx.building.alternate_conformations.disorder_info attribute)
atom_names (mmtbx.building.alternate_conformations.disorder_info attribute)
atom_names_given (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)
atom_names_selection() (cctbx.xray.structure.structure method)
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.entity attribute)
(mmtbx.validation.experimental.residue_real_space attribute)
(mmtbx.validation.ligands.ligand_validation 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.bond 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.rna_validate.rna_suite 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.residue method)
atom_selections() (mmtbx.refinement.ensemble_refinement.run_ensemble_refinement method)
atom_type_flags (class in mmtbx.ions)
atom_types (mmtbx.ions.svm.svm_prediction attribute)
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 attribute)
(mmtbx.geometry.topology.Molecule attribute)
(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.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.bond 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.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_sites_cart() (in module mmtbx.refinement.orca)
average_suiteness (mmtbx.validation.rna_validate.rna_suites attribute)
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 attribute)
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)
(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.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_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)
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)
backbone_selection() (cctbx.xray.structure.structure method)
backrub_angle (mmtbx.disorder.backbone.backrub_residue attribute)
backrub_move() (in module mmtbx.utils)
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_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 (class in xfel.cftbx.detector.cspad_cbf_tbx)
basis_from_geo() (in module xfel.cftbx.detector.cspad_cbf_tbx)
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)
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() (in module mmtbx.secondary_structure.build)
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)
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.cablam.cablam_fingerprints)
(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 attribute)
(mmtbx.validation.restraints.combined attribute)
(mmtbx.validation.rna_validate.rna_validation attribute)
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)
bounding_box_mm() (xfel.cftbx.detector.cspad_detector.CSPadDetector 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)
brick() (cctbx.sgtbx.space_group_info method)
bridge (class in mmtbx.secondary_structure.dssp)
britton_frac (mmtbx.scaling.twin_analyses.twin_law_dependent_twin_tests attribute)
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_cycle() (in module mmtbx.building.alternate_conformations.single_residue)
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_superposition() (mmtbx.cablam.cablam_fingerprints.motif_instance method)
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)
ca_measures() (in module mmtbx.cablam.cablam_math)
cablam_align_wrapper() (in module mmtbx.cablam.cablam_align)
cablam_key() (in module mmtbx.cablam.cablam_res)
cablam_measures() (in module mmtbx.cablam.cablam_math)
cablam_multicrit_kin() (in module mmtbx.cablam.cablam_validate)
cablam_residues (class in mmtbx.cablam.cablam_align)
cablam_validation (class in mmtbx.cablam.cablam_validate)
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_chi_angles() (in module mmtbx.refinement.ensemble_refinement)
calculate_contents() (in module mmtbx.geometry.clash)
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_rmsd_smart() (in module mmtbx.secondary_structure.build)
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() (in module mmtbx.secondary_structure)
(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 attribute)
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)
CApseudos() (in module mmtbx.cablam.cablam_math)
carbonyl_oxygen_angle() (in module mmtbx.disorder.analyze_model)
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)
cbf_wrapper (class in xfel.cftbx.detector.cspad_cbf_tbx)
cc (mmtbx.validation.experimental.residue_real_space attribute)
(mmtbx.validation.ligands.ligand_validation attribute)
(mmtbx.validation.waters.water attribute)
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 attribute)
cc_one_half_sigma_tau() (cctbx.miller.array method)
cc_peak() (in module cctbx.maptbx)
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_kissel (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)
cctbx_xray_structure_from() (in module iotbx.shelx)
ccv() (in module cctbx.maptbx)
cell_equivalent_p1() (cctbx.crystal.symmetry method)
center() (in module xfel.cftbx.detector.cspad_cbf_tbx)
(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 attribute)
chain() (iotbx.pdb.hierarchy.atom method)
chain_id (iotbx.pdb.hierarchy.atom_with_labels attribute)
(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.experimental.residue_real_space 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_angle attribute)
(mmtbx.validation.rna_validate.rna_bond attribute)
(mmtbx.validation.rna_validate.rna_pucker attribute)
(mmtbx.validation.rna_validate.rna_suite attribute)
(mmtbx.validation.rotalyze.rotamer attribute)
(mmtbx.validation.rotalyze.rotamer_ensemble attribute)
(mmtbx.validation.waters.water attribute)
chain_residue_id() (mmtbx.ncs.ncs.ncs_group method)
chain_type (mmtbx.validation.model_properties.residue_occupancy attribute)
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_iso_level() (mmtbx.refinement.wx_tardy_pdb.draw_map 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 attribute)
(mmtbx.ions.environment.atom_contact attribute)
(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_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_duplicate_chain_ids() (in module mmtbx.utils)
check_for_motif() (in module mmtbx.cablam.cablam_fingerprints)
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_mask() (mmtbx.scaling.absences.absences 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_prolines() (in module mmtbx.cablam.cablam_validate)
check_protein() (in module mmtbx.cablam.cablam_fingerprints)
check_r1() (in module cctbx.development.run_shelx)
check_regression() (in module cctbx.development.structure_factor_utils)
check_resname() (mmtbx.cablam.cablam_fingerprints.residue method)
check_size() (cctbx.xray.structure_factors.gradients_base.gradients_base 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)
chemlex() (in module cctbx.eltbx.attenuation_coefficient)
chi_angles (mmtbx.refinement.ensemble_refinement.result attribute)
(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)
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_h_for_water() (in module mmtbx.hydrogens.find)
chunk_selections() (iotbx.pdb.hierarchy.root method)
cif (class in iotbx.cif.model)
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_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)
CleanupBeforeFrameClose() (mmtbx.refinement.wx_tardy_pdb.viewer method)
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_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)
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)
cmd (iotbx.shelx.lexer.command_stream attribute)
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_hd_exchangable() (in module mmtbx.utils)
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_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)
compact_simple_list() (in module dxtbx.serialize.dump)
compact_simple_lists() (in module dxtbx.serialize.dump)
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)
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_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.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.mark3.fit_translation2 method)
(xfel.mono_simulation.max_like.minimizer 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_negate_mask() (mmtbx.refinement.real_space.fit_residues.run 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)
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)
condense_simple_aligned_regions() (mmtbx.cablam.cablam_align.AlignCablamMeasures method)
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)
(class in mmtbx.building.alternate_conformations.altloc_labeling)
conformer_group (class in mmtbx.building.alternate_conformations.altloc_labeling)
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.mmcif.cif_input method)
connectivity_section() (iotbx.pdb.mmcif.cif_input method)
consecutive() (mmtbx.cablam.cablam_res.linked_residue 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.mmcif.cif_input method)
construct_linked_residues() (in module mmtbx.cablam.cablam_res)
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)
contacts_no_alts (mmtbx.ions.environment.ChemicalEnvironment attribute)
container_type (scitbx.matrix.rec attribute)
containment_predicate (class in mmtbx.geometry.indexing)
contains() (mmtbx.rotamer.rotamer_eval.NamedRot method)
contains_hbond() (mmtbx.secondary_structure.dssp.bridge 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.iterations attribute)
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_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.test_cdl)
convert_dict_to_gnuplot() (in module mmtbx.conformation_dependent_library.test_cdl)
convert_dict_to_kin2Dcont() (in module mmtbx.conformation_dependent_library.test_cdl)
convert_dict_to_scilab() (in module mmtbx.conformation_dependent_library.test_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_semet_to_met() (iotbx.pdb.hierarchy.root method)
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)
convert_to_numeric() (in module mmtbx.polygon)
convert_water_adp() (mmtbx.solvent.ordered_solvent.manager method)
converter_base (class in cctbx.macro_mol.rotation_parameters)
coord_geom (mmtbx.ions.atom_type_flags attribute)
coord_stats_for_atom_groups() (in module mmtbx.building.alternate_conformations)
coord_stats_with_flips() (in module mmtbx.building.alternate_conformations)
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)
COpseudodihedrals() (in module mmtbx.cablam.cablam_math)
copy() (cctbx.miller.array method)
(cctbx.miller.set method)
(iotbx.cif.model.cif method)
(iotbx.cif.model.loop 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.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_drifted_waters() (mmtbx.solvent.ordered_solvent.manager 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_non_hydrogen_atoms() (mmtbx.wwpdb.standard_geometry_cif.process_chem_comp_atom_buffer method)
count_occupancies() (mmtbx.refinement.refinement_flags.manager method)
count_outliers() (mmtbx.refinement.real_space.fit_residues.run 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() (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_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_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_target_functors() (mmtbx.fmodels method)
createFromText() (mmtbx.rotamer.n_dim_table.NDimTable static method)
cross() (in module mmtbx.cablam.cablam_math)
(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.dump)
(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.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.pdb.mmcif.cif_input method)
(iotbx.xds.read_ascii.reader method)
(mmtbx.refinement.tardy.potential_object method)
crystal_symmetry_from_cryst1() (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.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 (class in xfel.cftbx.detector.cspad_detector)
CsPadDetector() (in module xfel.cxi.cspad_ana.cspad_tbx)
CsPadElement() (in module xfel.cxi.cspad_ana.cspad_tbx)
csv_header() (in module mmtbx.cablam.cablam_training)
csv_print() (in module mmtbx.cablam.cablam_training)
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_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)
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)

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 attribute)
(mmtbx.ions.environment.ScatteringEnvironment attribute)
(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.iterations 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_and_flags_master_params() (in module mmtbx.utils)
data_as_f_obs() (mmtbx.utils.determine_data_and_flags method)
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_version (mmtbx.validation.rotalyze.rotalyze attribute)
datablock() (in module dxtbx.serialize.dump)
(in module dxtbx.serialize.load)
db() (cctbx.examples.exp_i_alpha_derivatives.least_squares method)
dbb() (cctbx.examples.exp_i_alpha_derivatives.least_squares method)
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.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_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.bond 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_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.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)
descriptor (mmtbx.wwpdb.standard_geometry_cif.chem_comp_atom attribute)
descriptor_for (mmtbx.geometry.topology.Molecule attribute)
descriptor_for() (mmtbx.geometry.clash.ASUContent method)
descriptors (mmtbx.geometry.topology.Compound attribute)
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_coords_as_image_coords() (xfel.cftbx.detector.generic_detector.GenericDetector method)
detector_coords_as_image_coords_float() (xfel.cftbx.detector.cspad_detector.CSPadDetector method)
(xfel.cftbx.detector.generic_detector.GenericDetector method)
DETECTOR_NORMAL (xfel.metrology.mark0.correction_vectors attribute)
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_data_and_flags (class in mmtbx.utils)
determine_experimental_phases() (in module mmtbx.utils)
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)
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_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 (mmtbx.refinement.ensemble_refinement.result attribute)
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)
disorder_info (class in mmtbx.building.alternate_conformations)
disordered_segment (class in mmtbx.disorder.analyze_model)
displace_panel_fast_slow() (xfel.cftbx.detector.cspad_detector.CSPadDetector method)
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)
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_move() (in module mmtbx.cablam.cablam_fingerprints)
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() (in module mmtbx.cablam.cablam_math)
(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_map (class in mmtbx.refinement.wx_tardy_pdb)
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)
draw_triangulation() (mmtbx.refinement.wx_tardy_pdb.draw_map method)
draw_unit_cell() (mmtbx.refinement.wx_tardy_pdb.draw_map method)
DrawGL() (mmtbx.refinement.wx_tardy_pdb.viewer method)
dssp (class in mmtbx.secondary_structure.dssp)
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)
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.dump (module)
dxtbx.serialize.load (module)
dxtbx.serialize.xds (module)
dxyz_save (mmtbx.building.alternate_conformations.disorder_info attribute)
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.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 attribute)
(iotbx.shelx.tokens.element_token attribute)
(mmtbx.ions.environment.atom_contact attribute)
(mmtbx.ions.identify.ion_result attribute)
(mmtbx.validation.atom attribute)
(mmtbx.validation.atom_info attribute)
(mmtbx.validation.waters.water attribute)
element_is_hydrogen() (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_view.mod_view 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_reduction() (mmtbx.refinement.ensemble_refinement.ensemble_utils.manager method)
ensemble_refinement_data (class in mmtbx.refinement.ensemble_refinement)
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 attribute)
entity (class in mmtbx.validation)
enumerate_reduced_cell_two_folds() (in module cctbx.examples.le_page_1982_vs_lebedev_2005)
env_detz() (in module xfel.cxi.cspad_ana.cspad_tbx)
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)
er_pickle (class in mmtbx.refinement.ensemble_refinement)
er_tls_manager (class in mmtbx.refinement.ensemble_refinement)
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_view.mod_view 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)
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_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)
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.dump)
(in module dxtbx.serialize.load)
experimental_data_target_and_gradients (class in mmtbx.utils)
explain_how_to_generate_array_of_r_free_flags() (in module 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)
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_and_superpose() (in module mmtbx.building.make_library)
extract_atoms_from_residue_group() (in module mmtbx.validation.cbetadev)
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_coordinates() (mmtbx.validation.sequence.chain method)
extract_cryst1_z_columns() (iotbx.pdb.mmcif.cif_input method)
extract_data() (mmtbx.utils.determine_data_and_flags method)
extract_element() (iotbx.pdb.hierarchy.af_shared_atom method)
extract_f_model_core_constants() (iotbx.pdb.mmcif.cif_input method)
extract_fdp() (iotbx.pdb.hierarchy.af_shared_atom method)
extract_flags() (mmtbx.utils.determine_data_and_flags 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.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_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_residue_groups() (mmtbx.validation.sequence.chain method)
extract_secondary_structure() (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.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.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() (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 attribute)
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_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)
fail_cis_or_trans_check() (in module mmtbx.cablam.cablam_fingerprints)
fail_forbidden_bond_check() (in module mmtbx.cablam.cablam_fingerprints)
fail_index_match() (in module mmtbx.cablam.cablam_fingerprints)
fail_required_bond_check() (in module mmtbx.cablam.cablam_fingerprints)
fail_residue_check() (in module mmtbx.cablam.cablam_fingerprints)
fails_cis_check() (in module mmtbx.cablam.cablam_training)
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_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)
fd_compute_functional_and_gradients() (xfel.mono_simulation.max_like.minimizer method)
fdp (iotbx.pdb.hierarchy.atom attribute)
fetch_ca_expectations() (in module mmtbx.cablam.cablam_validate)
fetch_cis_trans_proline() (in module mmtbx.cablam.cablam_validate)
fetch_fingerprints() (in module mmtbx.cablam.cablam_fingerprints)
fetch_labels() (iotbx.pdb.hierarchy.atom method)
(iotbx.pdb.hierarchy.atom_with_labels method)
fetch_motifs() (in module mmtbx.cablam.cablam_validate)
fetch_pdb_data() (in module mmtbx.wwpdb.utils)
fetch_peptide_expectations() (in module mmtbx.cablam.cablam_validate)
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 attribute)
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 attribute)
(mmtbx.validation.molprobity.molprobity attribute)
file_name() (iotbx.reflection_file_reader.any_reflection_file method)
file_object (iotbx.file_reader.any_file_input attribute)
file_server (iotbx.file_reader.any_file_input attribute)
file_type (iotbx.file_reader.any_file_input attribute)
file_type() (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_before_build() (in module mmtbx.building.alternate_conformations)
filter_database() (in module mmtbx.polygon)
filter_dicts() (mmtbx.validation.clashscore.probe_clashscore_manager method)
filter_histogram_of_key_value() (in module mmtbx.polygon)
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_solvent() (mmtbx.solvent.ordered_solvent.manager method)
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)
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)
finalize_and_save_data() (xfel.command_line.cxi_merge.scaling_manager method)
finalize_coords() (in module mmtbx.validation.molprobity.nqh_minimize)
finalize_model() (in module mmtbx.building.alternate_conformations)
finalize_target_and_gradients() (cctbx.adp_restraints.energies.energies method)
find_absent_indices() (cctbx.sgtbx.pointgroup_tools.find_compatible_space_groups method)
find_all_alternates (class in mmtbx.building.alternate_conformations.single_residue)
find_all_residue_stats() (in module mmtbx.cablam.cablam_validate)
find_alternate_residue() (in module mmtbx.building.alternate_conformations.single_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_bare_chains_with_segids() (in module mmtbx.utils)
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_ca_outliers() (in module mmtbx.cablam.cablam_validate)
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() (mmtbx.secondary_structure.dssp.dssp method)
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_left_over_symops() (cctbx.sgtbx.pointgroup_tools.sub_super_point_group_relations method)
find_logs() (xfel.cxi.gfx.wx_detectors.DetectorPlotFrame 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_ncs_in_hierarchy() (in module mmtbx.ncs.ncs_search)
find_ncs_operators() (in module mmtbx.ncs.ligands)
find_nearby_atoms() (in module mmtbx.ions.environment)
(mmtbx.ions.identify.manager method)
find_nearby_backbone_n() (mmtbx.secondary_structure.dssp.dssp method)
find_node() (in module cctbx.crystal.coordination_sequences)
find_nucleic_acids() (in module mmtbx.secondary_structure)
find_overlapping_selections() (in module mmtbx.utils)
find_partial_sec_struc() (in module mmtbx.cablam.cablam_validate)
find_peak() (mmtbx.ias.find_peak_at_bond method)
find_peak_at_bond (class in mmtbx.ias)
find_peaks() (mmtbx.solvent.ensemble_ordered_solvent.manager method)
(mmtbx.solvent.ordered_solvent.manager method)
find_peaks_2fofc() (mmtbx.solvent.ordered_solvent.manager method)
find_peptide_flips() (mmtbx.disorder.analyze_model.disordered_segment method)
find_peptide_outliers() (in module mmtbx.cablam.cablam_validate)
find_pure_altloc_ranges() (iotbx.pdb.hierarchy.chain method)
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_sheets() (mmtbx.secondary_structure.dssp.dssp method)
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)
find_whole_sec_struc() (in module mmtbx.cablam.cablam_validate)
FindSimilarCablamRegions (class in mmtbx.cablam.cablam_align)
finish_job() (in module mmtbx.maps.fobs_minus_fobs_map)
(in module mmtbx.scaling.xtriage)
(mmtbx.refinement.ensemble_refinement.result method)
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_action_callback() (mmtbx.refinement.wx_tardy_pdb.viewer method)
first_index() (cctbx.miller.set method)
first_moment_analysis (class in xfel.cxi.cspad_ana.xes_finalise)
firstalt() (mmtbx.cablam.cablam_res.linked_residue 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_chi1_simple() (in module mmtbx.building.alternate_conformations.single_residue)
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_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_side_chain() (mmtbx.refinement.real_space.fit_residue.run method)
fit_tls() (mmtbx.refinement.ensemble_refinement.run_ensemble_refinement method)
fit_translation (class in xfel.metrology.mark1)
fit_translation2 (class in xfel.metrology.mark3)
fit_water() (in module mmtbx.hydrogens.find)
fitted_gaussian (class in cctbx.eltbx.xray_scattering)
FIX() (in module cctbx.development.run_shelx)
fix_outliers (class in mmtbx.refinement.real_space.fit_residues)
fix_rotamer_outliers() (in module mmtbx.utils)
fixed_site_indices() (cctbx.maptbx.peak_cluster_analysis method)
fl (mmtbx.ions.atom_type_flags attribute)
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 attribute)
flags_as_r_free_flags() (mmtbx.utils.determine_data_and_flags method)
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.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_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 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)
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)
fofc_values (mmtbx.building.alternate_conformations.single_residue.residue_trial 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)
force_unique_chain_ids() (in module mmtbx.utils)
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() (dxtbx.model.scan.ScanFactory static method)
(mmtbx.map_names 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_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.conformer 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)
(mmtbx.validation.rna_validate.rna_suite 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)
fourier_filter() (in module xfel.command_line.smooth_spectrum)
fp (iotbx.pdb.hierarchy.atom attribute)
(mmtbx.ions.environment.ScatteringEnvironment attribute)
fpp (mmtbx.ions.environment.ScatteringEnvironment attribute)
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)
fragment_single_conformer_chain() (in module mmtbx.building.alternate_conformations)
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.GoniometerFactory 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_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)
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)
(xfel.mono_simulation.max_like.minimizer 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)
gamma (mmtbx.scaling.absolute_scaling.gamma_protein attribute)
gamma_nucleic (class in mmtbx.scaling.absolute_scaling)
gamma_protein (class in mmtbx.scaling.absolute_scaling)
general_positions_only() (cctbx.maptbx.peak_cluster_analysis method)
(cctbx.maptbx.peak_search_parameters method)
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_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_from_phil() (dxtbx.model.detector.DetectorFactory static method)
generate_inverse_matrix_up_to_order() (in module cctbx.sgtbx.sub_lattice_tools)
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_p1_box() (in module mmtbx.maps.superpose)
generate_protein_threes() (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_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_two_character_ids() (in module mmtbx.utils)
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)
GenericDetector (class in xfel.cftbx.detector.generic_detector)
geometry (class in cctbx.web.asu_gallery.jvx)
(mmtbx.ions.environment.ChemicalEnvironment attribute)
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_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_labels() (in module mmtbx.cablam.cablam_fingerprints)
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_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_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() (in module mmtbx.kinemage.validation)
get_angle_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)
get_angles_from_included_bonds() (in module mmtbx.monomer_library.linking_utils)
get_annotation() (mmtbx.secondary_structure.dssp.dssp method)
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_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_atoms_info() (in module mmtbx.validation)
get_atoms_str() (in module mmtbx.validation.molprobity.mp_geo)
get_average_cell_dimensions() (xfel.command_line.cxi_merge.unit_cell_distribution 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_beam_center_mm() (xfel.cftbx.detector.generic_detector.GenericDetector method)
get_beam_center_pixels_fast_slow() (xfel.cftbx.detector.generic_detector.GenericDetector 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() (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_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_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_chain_color() (in module mmtbx.kinemage.validation)
get_chain_selection() (in module mmtbx.cablam.cablam_align)
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_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_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_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_continuous_segments() (mmtbx.cablam.cablam_align.cablam_residues method)
get_converter_by_docstring() (in module cctbx.macro_mol.rotation_parameters)
get_converters() (in module cctbx.macro_mol.rotation_parameters)
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_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_custom_report_table() (in module mmtbx.wwpdb.rcsb_web_services)
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_den_atom_pairs() (mmtbx.den.den_restraints method)
get_detector() (dxtbx.serialize.xds.to_xds method)
get_diagonal_extend() (in module cctbx.web.asu_gallery.jv_asu)
get_difference_maps() (in module mmtbx.building)
get_dihedral() (in module mmtbx.validation.ramalyze)
get_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method)
get_distance2() (in module mmtbx.monomer_library.glyco_utils)
(in module mmtbx.monomer_library.linking_utils)
get_ebeam() (in module xfel.cxi.cspad_ana.cspad_tbx)
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_empty_ramachandran_proxies() (in module mmtbx.secondary_structure.build)
get_expected_count() (mmtbx.validation.cbetadev.cbetadev method)
get_experiment_type() (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_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_final_maps_and_cc (class in mmtbx.ncs.ligands)
get_flag_captions() (mmtbx.ions.atom_type_flags method)
get_flex_image() (xfel.cftbx.detector.cspad_detector.CSPadDetector method)
(xfel.cftbx.detector.generic_detector.GenericDetector 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_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_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() (in module mmtbx.secondary_structure.build)
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_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_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_initial_strand() (mmtbx.secondary_structure.dssp.ladder method)
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_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_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_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.test_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_for_build() (in module mmtbx.maps.utils)
get_map_gaussian_fit() (mmtbx.ions.identify.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_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_matching_sites_cart_in_both_h() (in module mmtbx.secondary_structure.build)
get_matthews_coeff() (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_measures() (mmtbx.cablam.cablam_align.FindSimilarCablamRegions method)
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.test_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_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_hangle_proxies() (cctbx.geometry_restraints.manager.manager method)
get_n_hbond_proxies() (cctbx.geometry_restraints.manager.manager method)
get_n_parallelity_bp_proxies() (cctbx.geometry_restraints.manager.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_reference_coordinate_proxies() (cctbx.geometry_restraints.manager.manager method)
get_n_reference_dihedral_proxies() (cctbx.geometry_restraints.manager.manager method)
get_n_stacking_proxies() (cctbx.geometry_restraints.manager.manager method)
get_n_turn() (mmtbx.secondary_structure.dssp.hbond method)
get_name() (in module mmtbx.chemical_components)
get_nconfs() (in module mmtbx.disorder.analyze_model)
get_ncs_from_text() (in module mmtbx.ncs.ncs)
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_next_strand() (mmtbx.secondary_structure.dssp.ladder method)
get_non_hydrogen_atom_indices() (in module mmtbx.building)
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_atoms() (in module mmtbx.rotamer)
(in module mmtbx.validation.ramalyze)
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)
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_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_panel_fast_slow() (xfel.cftbx.detector.cspad_detector.CSPadDetector method)
get_parallelity_proxies_without_user_supplied() (cctbx.geometry_restraints.manager.manager method)
get_partial_omit_map() (in module mmtbx.building.alternate_conformations)
get_pdb_chains() (mmtbx.utils.fab_elbow_angle.fab_elbow_angle method)
get_pdb_fields() (in module mmtbx.secondary_structure.dssp)
get_pdb_hierarchy() (in module mmtbx.secondary_structure)
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_psi_atoms() (in module mmtbx.rotamer)
get_phi_psi_indices() (in module mmtbx.rotamer)
get_phi_psi_residues_count() (mmtbx.validation.ramalyze.ramalyze method)
get_phil() (in module xfel.metrology.mark0)
get_pixel_intensity() (xfel.cftbx.detector.cspad_detector.CSPadDetector method)
(xfel.cftbx.detector.generic_detector.GenericDetector method)
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_point_in_plane() (cctbx.sgtbx.direct_space_asu.cut_plane.cut method)
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.mmcif.cif_input method)
get_projection_matrix() (in module xfel.cftbx.detector.metrology)
get_psana_corrected_data() (in module xfel.cftbx.detector.cspad_cbf_tbx)
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_flags() (mmtbx.utils.determine_data_and_flags method)
get_r_free_stats() (in module cctbx.r_free_utils)
get_r_rfree_sigma() (iotbx.pdb.mmcif.cif_input method)
get_r_t_matrices_from_structure() (in module mmtbx.secondary_structure.build)
get_r_value_total() (mmtbx.scaling.twin_analyses.symmetry_issues method)
get_range() (mmtbx.utils.extract_box_around_model_and_map method)
get_ranges() (mmtbx.validation.graphics.residue_binner method)
get_raw_data() (xfel.cftbx.detector.cspad_detector.CSPadDetector 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_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.secondary_structure.dssp.ladder method)
(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_restraint_values() (in module mmtbx.conformation_dependent_library)
get_restraints_loading_flags() (in module mmtbx.monomer_library.pdb_interpretation)
get_restraints_tg() (mmtbx.refinement.group.group_minimizer 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.rna_validate.rna_suites method)
(mmtbx.validation.rotalyze.rotalyze method)
(mmtbx.validation.validation method)
(mmtbx.validation.waters.waters method)
get_result_count() (mmtbx.validation.cbetadev.cbetadev method)
get_result_files() (mmtbx.refinement.ensemble_refinement.result method)
get_results() (libtbx.program_template.ProgramTemplate 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_rms_info() (cctbx.omz.dev.refinement method)
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)
get_rotamers() (mmtbx.rotamer.sidechain_angles.SidechainAngles method)
get_rotarama_data() (in module mmtbx.validation.utils)
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_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_sites() (mmtbx.building.box_build_refine_base method)
get_selection_gap() (in module mmtbx.building.alternate_conformations)
get_selection_strings() (mmtbx.den.den_restraints method)
get_selection_to_sites_map() (in module mmtbx.geometry_restraints.reference)
get_sequence_n_copies() (in module mmtbx.validation.sequence)
get_sequence_n_copies_from_files() (in module mmtbx.validation.sequence)
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_cc() (mmtbx.ncs.ligands.sample_operators method)
get_smiles() (in module mmtbx.chemical_components)
get_solvent_content() (iotbx.pdb.mmcif.cif_input method)
get_sorted_clashes() (in module mmtbx.building.alternate_conformations.altloc_labeling)
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_special_position_indices() (mmtbx.refinement.real_space.fit_residues.run method)
get_spectrum() (in module xfel.cxi.cspad_ana.xes_finalise)
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_strand_register() (mmtbx.secondary_structure.dssp.ladder method)
get_strict_valence_flag() (mmtbx.ions.identify.manager 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_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_u_cart() (in module mmtbx.tls.tools)
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_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)
getatomxyz() (mmtbx.cablam.cablam_res.linked_residue 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)
give_ca_kin() (in module mmtbx.cablam.cablam_validate)
give_kin() (in module mmtbx.cablam.cablam_validate)
give_points() (in module mmtbx.cablam.cablam_validate)
give_text() (in module mmtbx.cablam.cablam_validate)
glyco_link_class (class in mmtbx.monomer_library.glyco_utils)
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)
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_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.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.rna_validate.rna_suites 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.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.rna_validate.rna_suites 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 attribute)
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)
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_all_measures() (mmtbx.cablam.cablam_fingerprints.motif_instance 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_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)
hbond (class in mmtbx.secondary_structure.dssp)
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.rna_validate.rna_suite static method)
(mmtbx.validation.rotalyze.rotamer static method)
(mmtbx.validation.waters.water static method)
header_info (mmtbx.validation.molprobity.molprobity attribute)
heavy_selection() (cctbx.xray.structure.structure method)
heights() (cctbx.maptbx.peak_cluster_analysis method)
helix_or_sheet() (in module mmtbx.cablam.cablam_validate)
helix_or_sheet_res() (in module mmtbx.cablam.cablam_validate)
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 attribute)
heterogen_section() (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)
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)
HKLF() (in module cctbx.development.run_shelx)
hl_coeffs() (mmtbx.twinning.twin_f_model.twin_model_manager method)
hl_coeffs_in_original_setting (mmtbx.density_modification.density_modification attribute)
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)

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 attribute)
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 attribute)
(mmtbx.building.alternate_conformations.altloc_labeling.nb_clash attribute)
(mmtbx.ions.svm.svm_prediction attribute)
(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 attribute)
(iotbx.pdb.hierarchy.residue attribute)
(iotbx.pdb.hierarchy.residue_group attribute)
(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.experimental.residue_real_space 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_angle attribute)
(mmtbx.validation.rna_validate.rna_bond attribute)
(mmtbx.validation.rna_validate.rna_pucker attribute)
(mmtbx.validation.rna_validate.rna_suite attribute)
(mmtbx.validation.rotalyze.rotamer attribute)
(mmtbx.validation.rotalyze.rotamer_ensemble attribute)
(mmtbx.validation.waters.water attribute)
id (iotbx.pdb.hierarchy.chain attribute)
(iotbx.pdb.hierarchy.model attribute)
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.building.alternate_conformations.disorder_info attribute)
(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.entity method)
(mmtbx.validation.model_properties.atom_occupancy method)
(mmtbx.validation.residue method)
(mmtbx.validation.restraints.restraint method)
(mmtbx.validation.waters.water method)
id_str_i (mmtbx.building.alternate_conformations.altloc_labeling.nb_clash attribute)
id_str_j (mmtbx.building.alternate_conformations.altloc_labeling.nb_clash attribute)
id_str_no_atom_name() (mmtbx.validation.clashscore.clash method)
id_str_old() (mmtbx.validation.ramalyze.ramachandran method)
(mmtbx.validation.rotalyze.rotamer method)
id_to_str() (mmtbx.cablam.cablam_res.linked_residue method)
id_with_resname() (mmtbx.cablam.cablam_res.linked_residue 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_coords_as_detector_coords() (xfel.cftbx.detector.cspad_detector.CSPadDetector method)
(xfel.cftbx.detector.generic_detector.GenericDetector 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.dump)
(in module dxtbx.serialize.load)
imageset_from_string() (in module dxtbx.serialize.load)
imageset_to_string() (in module dxtbx.serialize.dump)
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)
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 attribute)
indices() (cctbx.miller.set method)
inflate() (mmtbx.refinement.refinement_flags.manager method)
info (iotbx.pdb.hierarchy.root attribute)
(mmtbx.validation.experimental.data_statistics attribute)
info() (cctbx.miller.array 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)
init_view_objects() (mmtbx.refinement.wx_tardy_pdb.App 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_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)
initialize_viewer_properties() (xfel.cftbx.detector.generic_detector.GenericDetector 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.hierarchy)
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_group (cctbx.miller.reindexing.assistant attribute)
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)
interpretation() (in module mmtbx.cablam.cablam_validate)
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() (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() (mmtbx.secondary_structure.dssp.bridge 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.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_approximately_helical() (in module mmtbx.secondary_structure.proteins)
is_atom_group_pair_linked() (in module mmtbx.monomer_library.linking_utils)
is_atom_pair_linked() (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_bridge() (mmtbx.secondary_structure.dssp.hbond method)
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_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_site() (mmtbx.ions.identify.AtomProperties method)
is_compatible_unit_cell() (cctbx.crystal.symmetry method)
is_complete() (mmtbx.cablam.cablam_fingerprints.motif_instance method)
is_complex_array() (cctbx.miller.array 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_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 attribute)
is_first_conformer_in_chain (mmtbx.monomer_library.pdb_interpretation.monomer_mapping attribute)
is_first_in_chain (iotbx.pdb.hierarchy.atom_with_labels attribute)
is_flags_good() (mmtbx.bulk_solvent.scaler.run 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_heavy_atom() (mmtbx.validation.waters.water method)
is_helical() (mmtbx.secondary_structure.dssp.hbond 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_identical_hierarchy() (iotbx.pdb.hierarchy.chain method)
(iotbx.pdb.hierarchy.model method)
(iotbx.pdb.hierarchy.residue_group 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_ladder() (mmtbx.secondary_structure.dssp.hbond 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_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_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_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_n_glyco_bond() (in module mmtbx.monomer_library.linking_utils)
is_na() (iotbx.pdb.hierarchy.chain method)
(iotbx.pdb.hierarchy.conformer method)
is_ncs_present() (mmtbx.ncs.asu_ncs_converter method)
is_negatively_charged_oxygen() (in module mmtbx.ions.halides)
is_niggli_cell() (cctbx.uctbx.reduction_base.gruber_parameterization method)
is_nonsence() (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_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_pure_main_conf (iotbx.pdb.hierarchy.residue attribute)
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_chain() (mmtbx.secondary_structure.dssp.hbond 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_self_clash() (mmtbx.geometry.clash.ClashingPair method)
is_similar() (mmtbx.validation.clashscore.probe_line_info_storage 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_symmetry() (cctbx.crystal.symmetry 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_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_summary attribute)
is_unusual() (mmtbx.monomer_library.pdb_interpretation.monomer_mapping method)
is_useful() (cctbx.omz.cod_select_and_pickle.cod_data method)
is_valid_index() (scitbx.array_family.flex.grid method)
is_validation_outlier() (in module mmtbx.building.alternate_conformations)
is_water() (mmtbx.monomer_library.cif_types.comp_comp_id method)
is_water_last() (mmtbx.solvent.ensemble_ordered_solvent.manager method)
(mmtbx.solvent.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)
(scitbx.array_family.flex.bool method)
iso_b_wilson (mmtbx.scaling.xtriage.xtriage_analyses attribute)
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)
(mmtbx.building.alternate_conformations.altloc_labeling.nb_clash 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_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)
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_frame() (in module mmtbx.cablam.cablam_training)
kin_header() (in module mmtbx.cablam.cablam_training)
kin_print() (in module mmtbx.cablam.cablam_training)
kin_print_by_instance() (in module mmtbx.cablam.cablam_training)
kin_print_by_instance_header() (in module mmtbx.cablam.cablam_training)
kin_print_probe() (in module mmtbx.cablam.cablam_training)
kin_print_probe_annote() (in module mmtbx.cablam.cablam_training)
kin_print_probe_header() (in module mmtbx.cablam.cablam_training)
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.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_running_average() (mmtbx.refinement.ensemble_refinement.run_ensemble_refinement method)
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 attribute)
l_test_mean_l_squared (mmtbx.scaling.xtriage.xtriage_analyses attribute)
label (mmtbx.building.alternate_conformations.altloc_labeling.conformer attribute)
(mmtbx.building.alternate_conformations.refined_fragment attribute)
(mmtbx.ions.atom_type_flags attribute)
(mmtbx.validation.rna_validate.rna_angles attribute)
(mmtbx.validation.rna_validate.rna_bonds attribute)
(mmtbx.validation.rna_validate.rna_puckers attribute)
(mmtbx.validation.rna_validate.rna_suites attribute)
label_regex_selection() (cctbx.xray.structure.structure method)
label_selection() (cctbx.xray.structure.structure method)
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)
ladder (class in mmtbx.secondary_structure.dssp)
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)
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.refinement.ensemble_refinement)
(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)
leave_all_available_entries() (in module mmtbx.polygon)
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)
libtbx.phil.command_line (module)
ligand_validation (class in mmtbx.validation.ligands)
ligands (mmtbx.validation.model_properties.model_statistics attribute)
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)
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 attribute)
(iotbx.pdb.hierarchy.residue_group attribute)
linked_residue (class in mmtbx.cablam.cablam_res)
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_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_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_density_quality (class in mmtbx.building)
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_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_binned_completeness (class in mmtbx.scaling.data_statistics)
log_binning() (cctbx.miller.set method)
log_out (mmtbx.refinement.ensemble_refinement.trial attribute)
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)
(mmtbx.refinement.real_space.fit_residues.run 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 attribute)
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 attribute)
magnification() (mmtbx.ncs.ncs.ncs method)
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.itvc_kissel)
(in module cctbx.eltbx.development.kissel_fits)
(in module cctbx.eltbx.development.kissel_io)
(in module xfel.cxi.average_spots)
main_chain_selection() (cctbx.xray.structure.structure method)
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_box() (mmtbx.building.alternate_conformations.rsr_fragments_base method)
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_pickle() (in module mmtbx.cablam.cablam_fingerprints)
make_point() (in module cctbx.web.asu_gallery.jvx)
make_polarized_beam() (dxtbx.model.beam.BeamFactory static method)
make_probe_data() (in module mmtbx.cablam.cablam_training)
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_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)
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)
manager_from_pdb_file() (in module mmtbx.secondary_structure)
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_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_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 attribute)
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_detector_to_basis_dict() (in module xfel.cftbx.detector.cspad_cbf_tbx)
map_inside_unit_cell() (mmtbx.ncs.ncs.ncs method)
(mmtbx.ncs.ncs.ncs_group method)
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)
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)
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_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)
massage_data (class in mmtbx.scaling.massage_twin_detwin_data)
master_params() (in module mmtbx.dynamics.simulated_annealing)
(in module mmtbx.refinement.geometry_minimization)
(in module mmtbx.solvent.ensemble_ordered_solvent)
(in module mmtbx.solvent.ordered_solvent)
match_bijvoet_mates() (cctbx.miller.set method)
match_dihedral_to_name() (in module mmtbx.validation.utils)
match_dod() (in module mmtbx.hydrogens.find)
match_indices() (cctbx.miller.set 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_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)
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)
matrix_swap_columns_in_place() (scitbx.array_family.flex.double method)
(scitbx.array_family.flex.int method)
matrix_swap_rows_in_place() (scitbx.array_family.flex.double method)
(scitbx.array_family.flex.int 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)
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.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_atom_conformers() (in module mmtbx.building.alternate_conformations)
max_distance_between_conformers() (mmtbx.disorder.analyze_model.disordered_segment method)
(mmtbx.disorder.analyze_model.process_pdb_hierarchy method)
max_distance_over_u (mmtbx.building.alternate_conformations.disorder_info attribute)
max_element_length() (scitbx.array_family.flex.std_string method)
max_estimated_twin_fraction (mmtbx.scaling.xtriage.xtriage_analyses attribute)
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 (mmtbx.building.alternate_conformations.disorder_info attribute)
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.iterations 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.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_data_and_guess_space_groups() (in module mmtbx.scaling.twin_analyses)
merge_dict() (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_residue_groups() (iotbx.pdb.hierarchy.chain 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)
metrology_as_transformation_matrices() (in module xfel.cftbx.detector.metrology)
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_array_symmetry_safety_check() (in module mmtbx.utils)
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.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)
(class in xfel.mono_simulation.max_like)
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_wavelength_based_on_d_min() (cctbx.miller.set 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 attribute)
ml_iso_absolute_scaling (class in mmtbx.scaling.absolute_scaling)
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.alternate_conformations (module)
mmtbx.building.alternate_conformations.altloc_labeling (module)
mmtbx.building.alternate_conformations.single_residue (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.cablam (module)
mmtbx.cablam.cablam_align (module)
mmtbx.cablam.cablam_fingerprints (module)
mmtbx.cablam.cablam_math (module)
mmtbx.cablam.cablam_res (module)
mmtbx.cablam.cablam_training (module)
mmtbx.cablam.cablam_validate (module)
mmtbx.cablam.fingerprints (module)
mmtbx.cablam.fingerprints.antiparallel_beta (module)
mmtbx.cablam.fingerprints.antiparallel_beta_bridge (module)
mmtbx.cablam.fingerprints.how_to (module)
mmtbx.cablam.fingerprints.parallel_beta (module)
mmtbx.cablam.fingerprints.regular_helix_definitions (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.test_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.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 (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_residues (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.refinement.wx_tardy_pdb (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.dssp (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.twinning.twin_map_utils (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.molprobity.nqh_minimize (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_view (class in xfel.cxi.cspad_ana.mod_view)
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.restraints.bond attribute)
(mmtbx.validation.restraints.restraint attribute)
model() (iotbx.cif.reader method)
model_based_outliers() (mmtbx.scaling.outlier_rejection.outlier_manager method)
model_error_ml() (mmtbx.twinning.twin_f_model.twin_model_manager method)
model_id (iotbx.pdb.hierarchy.atom_with_labels attribute)
model_ids() (iotbx.pdb.mmcif.cif_input method)
model_indices() (iotbx.pdb.mmcif.cif_input method)
model_is_too_large() (in module cctbx.web.emma)
model_matches (class in cctbx.euclidean_model_matching)
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)
models() (iotbx.pdb.hierarchy.root method)
models_size() (iotbx.pdb.hierarchy.root method)
modify_weights() (mmtbx.scaling.relative_wilson.relative_wilson method)
Molecule (class in mmtbx.geometry.topology)
molecule (mmtbx.geometry.clash.SymmetryEquivalent attribute)
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)
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)
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
motif (class in mmtbx.cablam.cablam_fingerprints)
motif_chunk (class in mmtbx.cablam.cablam_validate)
motif_guess (class in mmtbx.cablam.cablam_validate)
motif_instance (class in mmtbx.cablam.cablam_fingerprints)
motif_value (class in mmtbx.cablam.cablam_validate)
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)
(mmtbx.solvent.ordered_solvent.manager method)
moving_average() (in module mmtbx.bulk_solvent.scaler)
mp_id() (mmtbx.cablam.cablam_res.linked_residue method)
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_file (mmtbx.refinement.ensemble_refinement.result attribute)
(mmtbx.refinement.ensemble_refinement.trial attribute)
mtz_object() (mmtbx.utils.guess_observation_type method)
mu (scitbx.lstbx.normal_eqns_solving.levenberg_marquardt_iterations attribute)
multi_axis() (dxtbx.model.goniometer.GoniometerFactory static method)
multi_axis_goniometer_from_phil() (dxtbx.model.goniometer.GoniometerFactory static method)
multi_conformer_selection() (in module mmtbx.building.alternate_conformations)
multi_criterion_plot_mixin (class in mmtbx.validation.graphics)
multi_criterion_view (class in mmtbx.validation.molprobity)
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)
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)
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_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_atoms (mmtbx.maps.composite_omit_map.omit_box attribute)
(mmtbx.maps.composite_omit_map.omit_regions attribute)
(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 attribute)
n_cbeta_outliers() (mmtbx.disorder.analyze_model.disordered_segment method)
n_columns() (iotbx.cif.model.loop method)
(scitbx.matrix.rec method)
n_confs (mmtbx.building.alternate_conformations.disorder_info attribute)
(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_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_hbonds (mmtbx.validation.waters.water attribute)
n_hd (mmtbx.validation.model_properties.xray_structure_statistics attribute)
n_heavy (mmtbx.validation.waters.waters attribute)
n_hydrogens (mmtbx.validation.model_properties.model_statistics attribute)
n_incomplete (mmtbx.validation.rna_validate.rna_suites 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 attribute)
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_outliers (mmtbx.validation.cbetadev.cbetadev attribute)
(mmtbx.validation.clashscore.clashscore attribute)
(mmtbx.validation.experimental.real_space attribute)
(mmtbx.validation.model_properties.xray_structure_statistics attribute)
(mmtbx.validation.ramalyze.ramalyze attribute)
(mmtbx.validation.restraints.restraint_validation attribute)
(mmtbx.validation.rna_validate.rna_puckers attribute)
(mmtbx.validation.rna_validate.rna_suites 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_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 attribute)
n_protein (mmtbx.validation.model_properties.model_statistics 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_suites (mmtbx.validation.rna_validate.rna_suites 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.experimental.real_space attribute)
(mmtbx.validation.model_properties.xray_structure_statistics attribute)
(mmtbx.validation.ramalyze.ramalyze attribute)
(mmtbx.validation.restraints.restraint_validation attribute)
(mmtbx.validation.rna_validate.rna_puckers attribute)
(mmtbx.validation.rna_validate.rna_suites attribute)
(mmtbx.validation.rotalyze.rotalyze attribute)
(mmtbx.validation.validation attribute)
(mmtbx.validation.waters.waters attribute)
n_triaged (mmtbx.validation.rna_validate.rna_suites 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 attribute)
(iotbx.shelx.tokens.atomname_token attribute)
(mmtbx.ions.atom_type_flags attribute)