Index

_

_DatabaseReader (class in ccdc.io)

_DatabaseWriter (class in ccdc.io) _mogul_version() (in module ccdc.conformer)

A

abbreviated_name (ccdc.entry.Journal attribute) abbreviated_translated_name (ccdc.entry.Journal attribute) absolute_angle_tolerance (ccdc.search.ReducedCellSearch.Settings attribute) ACC() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) acceptor (ccdc.search.QueryAtom attribute) acceptor_atom_type (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAcceptor attribute) acceptor_atom_type() (ccdc.molecule.Molecule.HBondCriterion method) acceptor_label (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity attribute) acceptor_range (ccdc.cavity.CavityDatabase.Settings attribute) accessible_surface_area (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom attribute) activity_column (ccdc.descriptors.StatisticalDescriptors.RankStatistics attribute) add_all_identifiers() (ccdc.search.TextNumericSearch method) add_all_text() (ccdc.search.TextNumericSearch method) add_analogue() (ccdc.search.TextNumericSearch method) add_angle_constraint() (ccdc.search.SubstructureSearch method) add_angle_measurement() (ccdc.search.SubstructureSearch method) add_atom() (ccdc.molecule.Molecule method) (ccdc.search.QuerySubstructure method) add_atom_property_constraint() (ccdc.search.SubstructureSearch method) add_atom_property_measurement() (ccdc.search.SubstructureSearch method) add_atoms() (ccdc.molecule.Molecule method) add_author() (ccdc.search.TextNumericSearch method) add_binary_transform_constraint() (ccdc.search.SubstructureSearch method) add_binary_transform_measurement() (ccdc.search.SubstructureSearch method) add_bioactivity() (ccdc.search.TextNumericSearch method) add_bond() (ccdc.molecule.Molecule method) (ccdc.search.QuerySubstructure method) add_bonds() (ccdc.molecule.Molecule method) add_ccdc_number() (ccdc.search.TextNumericSearch method) add_centroid() (ccdc.search.SubstructureSearch method) add_citation() (ccdc.search.TextNumericSearch method) add_cofactor() (ccdc.protein.Protein method) add_color() (ccdc.search.TextNumericSearch method) add_compound_name() (ccdc.search.TextNumericSearch method) add_connected_element_count() (ccdc.search.QueryAtom method) add_constant_value_measurement() (ccdc.search.SubstructureSearch method) add_constraint() (ccdc.docking.Docker.Settings method) (ccdc.docking.Docker.Settings.ProteinFileInfo method) add_disorder() (ccdc.search.TextNumericSearch method) add_distance_constraint() (ccdc.pharmacophore.Pharmacophore.Query method) (ccdc.search.SubstructureSearch method) add_distance_measurement() (ccdc.search.SubstructureSearch method) add_doi() (ccdc.search.TextNumericSearch method) add_dummy_point() (ccdc.search.SubstructureSearch method) add_feature() (ccdc.pharmacophore.Pharmacophore.Query method) add_feature_definition() (ccdc.pharmacophore.Pharmacophore.FeatureDatabase method) add_group() (ccdc.molecule.Molecule method) (ccdc.search.SubstructureSearch method) add_habit() (ccdc.search.TextNumericSearch method) add_hit() (ccdc.search.SubstructureSearch.HitProcessor method) add_hydrogens() (ccdc.molecule.Molecule method) (ccdc.protein.Protein method) add_identifier() (ccdc.search.TextNumericSearch method) add_ligand() (ccdc.protein.Protein method) add_ligand_file() (ccdc.docking.Docker.Settings method) add_molecule() (ccdc.molecule.Molecule method) add_peptide_sequence() (ccdc.search.TextNumericSearch method) add_phase_transition() (ccdc.search.TextNumericSearch method) add_plane() (ccdc.search.SubstructureSearch method) add_plane_angle_constraint() (ccdc.search.SubstructureSearch method) add_plane_angle_measurement() (ccdc.search.SubstructureSearch method) add_point_plane_distance_constraint() (ccdc.search.SubstructureSearch method) add_point_plane_distance_measurement() (ccdc.search.SubstructureSearch method) add_polymorph() (ccdc.search.TextNumericSearch method) add_protein_atom_type_constraint() (ccdc.search.QueryAtom method) add_protein_file() (ccdc.docking.Docker.Settings method) add_solvent() (ccdc.search.TextNumericSearch method) add_source() (ccdc.search.TextNumericSearch method) add_sphere() (ccdc.pharmacophore.Pharmacophore.Feature method) add_substructure() (ccdc.search.SubstructureSearch method) add_synonym() (ccdc.search.TextNumericSearch method) add_torsion_angle_constraint() (ccdc.search.SubstructureSearch method) add_torsion_angle_measurement() (ccdc.search.SubstructureSearch method) add_unary_transform_constraint() (ccdc.search.SubstructureSearch method) add_unary_transform_measurement() (ccdc.search.SubstructureSearch method) add_value() (ccdc.utilities.Histogram method) add_values() (ccdc.utilities.Histogram method) add_vector() (ccdc.search.SubstructureSearch method) add_vector_angle_constraint() (ccdc.search.SubstructureSearch method)

add_vector_angle_measurement() (ccdc.search.SubstructureSearch method) add_vector_plane_angle_constraint() (ccdc.search.SubstructureSearch method) add_vector_plane_angle_measurement() (ccdc.search.SubstructureSearch method) advice_comment (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) advice_comment() (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FittingData method) akaike_information_criterion (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) aligned_molecule (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox attribute) aliphatic_range (ccdc.cavity.CavityDatabase.Settings attribute) all_atoms_have_sites (ccdc.molecule.Molecule attribute) all_bond_types() (ccdc.molecule.Bond.BondType static method) allow_artificial_inversion (ccdc.crystal.PackingSimilarity.Settings attribute) allow_molecular_differences (ccdc.crystal.PackingSimilarity.Settings attribute) allow_overlaps (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition attribute) amino_acid_code (ccdc.cavity.Cavity.Feature attribute) analogue (ccdc.entry.Entry attribute) analyse (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) analyse_angle() (ccdc.conformer.GeometryAnalyser method) analyse_bond() (ccdc.conformer.GeometryAnalyser method) analyse_fitting_data() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) analyse_ligand() (ccdc.interaction.InteractionMapAnalysis method) analyse_molecule() (ccdc.conformer.GeometryAnalyser method) analyse_protein() (ccdc.interaction.InteractionMapAnalysis method) analyse_ring() (ccdc.conformer.GeometryAnalyser method) analyse_small_molecule() (ccdc.interaction.InteractionMapAnalysis method) analyse_torsion() (ccdc.conformer.GeometryAnalyser method) angle (ccdc.molecule.Molecule.HBond attribute) angle_tolerance (ccdc.crystal.PackingSimilarity.Settings attribute) (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) (ccdc.molecule.Molecule.HBondCriterion attribute) angles (ccdc.utilities.ApplicationInterface attribute) annotate() (ccdc.pharmacophore.Pharmacophore.FeatureDatabase method) annotation_keys (ccdc.pharmacophore.Pharmacophore.FeatureDatabase attribute) annotations (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.Entry attribute) (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) apolar_shell_correction (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) ApplicationInterface (class in ccdc.utilities) ApplicationInterface.CmdParser (class in ccdc.utilities) apply_quaternion() (ccdc.molecule.Molecule method) apply_rule (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition attribute) area (ccdc.descriptors.CrystalDescriptors.Morphology.Facet attribute) area_under_roc_curve (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) aromatic (ccdc.search.QueryAtom attribute) aromatic_range (ccdc.cavity.CavityDatabase.Settings attribute) assign_bond_types() (ccdc.molecule.Molecule method) assign_bonds() (ccdc.crystal.Crystal method) assign_partial_charges() (ccdc.molecule.Molecule method) asymmetric_unit_molecule (ccdc.crystal.Crystal attribute) atom (ccdc.cavity.Cavity.Feature attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom attribute) Atom (class in ccdc.molecule) atom() (ccdc.molecule.Molecule method) Atom.DisplacementParameters (class in ccdc.molecule) atom_angle() (ccdc.descriptors.MolecularDescriptors static method) atom_centroid() (ccdc.descriptors.MolecularDescriptors static method) atom_distance() (ccdc.descriptors.MolecularDescriptors static method) atom_indices (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) atom_labels (ccdc.conformer.GeometryAnalyser.Analysis attribute) (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) atom_plane() (ccdc.descriptors.MolecularDescriptors static method) atom_torsion_angle() (ccdc.descriptors.MolecularDescriptors static method) atom_vector() (ccdc.descriptors.MolecularDescriptors static method) atomic_number (ccdc.molecule.Atom attribute) atomic_symbol (ccdc.molecule.Atom attribute) atomic_weight (ccdc.molecule.Atom attribute) atoms (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) (ccdc.molecule.Bond attribute) (ccdc.molecule.Molecule attribute) (ccdc.molecule.Molecule.Contact attribute) (ccdc.molecule.Molecule.HBond attribute) (ccdc.protein.Protein.BindingSite attribute) (ccdc.protein.Protein.Nucleotide attribute) (ccdc.protein.Protein.Residue attribute) (ccdc.search.QueryBond attribute) (ccdc.search.QuerySubstructure attribute) atoms_on_special_positions() (ccdc.crystal.Crystal method) atoms_within_range() (ccdc.descriptors.MolecularDescriptors.AtomDistanceSearch method) AUC() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) autoscale (ccdc.docking.Docker.Settings attribute) average_connectivity_index() (ccdc.descriptors.MolecularDescriptors.ConnectivityIndices method) average_density (ccdc.interaction.InteractionLibrary.InteractionData attribute)

B

backbone_atoms (ccdc.protein.Protein.Residue attribute) background_color (ccdc.diagram.DiagramGenerator.Settings attribute) BEDROC() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) best_hit (ccdc.screening.Screener.ScreenHitList attribute) bias_conformer_selection (ccdc.screening.Screener.Settings attribute) bin_width (ccdc.utilities.Histogram attribute) bioactivity (ccdc.entry.Entry attribute) Bond (class in ccdc.molecule) bond() (ccdc.molecule.Molecule method) Bond.BondType (class in ccdc.molecule) bond_length (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) (ccdc.search.QueryBond attribute) bond_length() (ccdc.descriptors.MolecularDescriptors static method) bond_polymeric (ccdc.search.QueryBond attribute)

bond_smallest_ring (ccdc.search.QueryBond attribute) bond_type (ccdc.molecule.Bond attribute) bond_unfused_unbridged_ring (ccdc.search.QueryBond attribute) bonds (ccdc.molecule.Atom attribute) (ccdc.molecule.Molecule attribute) (ccdc.molecule.Ring attribute) (ccdc.search.QuerySubstructure attribute) bounding_box (ccdc.cavity.Cavity attribute) (ccdc.descriptors.CrystalDescriptors.Morphology attribute) (ccdc.utilities.Grid attribute) bounding_sphere (ccdc.pharmacophore.Pharmacophore.Query attribute) bounds (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity attribute) burial (ccdc.cavity.Cavity.Feature attribute) by_abbreviated_name() (ccdc.entry.JournalList method) by_full_name() (ccdc.entry.JournalList method)

C

c_alpha (ccdc.protein.Protein.Residue attribute) c_beta (ccdc.protein.Protein.Residue attribute) c_terminus (ccdc.protein.Protein.Residue attribute) calculate() (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Parameter method) calculate_connolly_surface (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) calculate_contour_surface (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) calculate_propensities() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) calculated_density (ccdc.crystal.Crystal attribute) (ccdc.entry.Entry attribute) cancel() (ccdc.search.SubstructureSearch.HitProcessor method) carbonyl_oxygen (ccdc.protein.Protein.Residue attribute) cavities() (ccdc.cavity.CavityDatabase method) (ccdc.interaction.InteractionMapAnalysis method) Cavity (class in ccdc.cavity) cavity() (ccdc.cavity.CavityDatabase method) Cavity.CavityDistanceHistograms (class in ccdc.cavity) Cavity.CavityGraphComparison (class in ccdc.cavity) Cavity.FastCavityGraphComparison (class in ccdc.cavity) Cavity.Feature (class in ccdc.cavity) cavity_atoms (ccdc.protein.Protein attribute) cavity_distance_histogram_sets() (ccdc.cavity.CavityDatabase method) cavity_distance_histograms() (ccdc.cavity.Cavity method) (ccdc.cavity.CavityDatabase method) cavity_origin (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) cavity_radius (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) cavity_residues (ccdc.protein.Protein attribute) CavityDatabase (class in ccdc.cavity) CavityDatabase.Settings (class in ccdc.cavity) ccdc.cavity (module) ccdc.conformer (module) ccdc.crystal (module) ccdc.descriptors (module) ccdc.diagram (module) ccdc.docking (module) ccdc.entry (module) ccdc.interaction (module) ccdc.io (module) ccdc.molecule (module) ccdc.pharmacophore (module) ccdc.protein (module) ccdc.screening (module) ccdc.search (module) ccdc.utilities (module) ccdc_logo (ccdc.utilities.ApplicationInterface attribute) ccdc_number (ccdc.entry.Entry attribute) cell_angles (ccdc.crystal.Crystal attribute) (ccdc.crystal.Crystal.ReducedCell attribute) cell_lengths (ccdc.crystal.Crystal attribute) (ccdc.crystal.Crystal.ReducedCell attribute) cell_volume (ccdc.crystal.Crystal attribute) central_group_atoms() (ccdc.interaction.InteractionLibrary.InteractionHit method) central_group_name (ccdc.interaction.InteractionLibrary.InteractionData attribute) central_groups() (ccdc.interaction.InteractionLibrary.ContactGroup method) centre_molecule() (ccdc.crystal.Crystal method) centre_of_geometry (ccdc.descriptors.CrystalDescriptors.Morphology attribute) (ccdc.descriptors.CrystalDescriptors.Morphology.Facet attribute) centre_of_geometry() (ccdc.molecule.Molecule method) centroid_atoms() (ccdc.search.SubstructureSearch.SubstructureHit method) centroid_objects() (ccdc.search.SubstructureSearch.SubstructureHit method) chain (ccdc.cavity.Cavity.Feature attribute) chain_identifier (ccdc.protein.Protein.Residue attribute) chain_label (ccdc.molecule.Atom attribute) chains (ccdc.protein.Protein attribute) change_group() (ccdc.molecule.Molecule method) check_bond_count (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings attribute) check_bond_polymeric (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings attribute) check_bond_type (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings attribute) check_charge (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings attribute) check_element (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings attribute) check_hydrogen_count (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings attribute) chemical_name (ccdc.entry.Entry attribute) chemical_name_as_html (ccdc.entry.Entry attribute) chirality (ccdc.molecule.Atom attribute) classification_measure (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) classification_measure_threshold (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) clear() (ccdc.search.QuerySubstructure method) (ccdc.search.TextNumericSearch method) clear_annotations() (ccdc.pharmacophore.Pharmacophore.FeatureDatabase method) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.Entry method) clear_constraints() (ccdc.docking.Docker.Settings method) (ccdc.docking.Docker.Settings.ProteinFileInfo method) clear_ligand_files() (ccdc.docking.Docker.Settings method) clear_protein_files() (ccdc.docking.Docker.Settings method) clique_rmsd (ccdc.cavity.Cavity.CavityGraphComparison attribute) close() (ccdc.io._DatabaseReader method) (ccdc.io._DatabaseWriter method) (ccdc.utilities.HTMLReport method) cluster_number (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) code (ccdc.protein.Protein.Nucleotide attribute) coefficient (ccdc.search.SimilaritySearch attribute) (ccdc.search.SimilaritySearch.Settings attribute) coefficients (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) cofactors (ccdc.protein.Protein attribute) (ccdc.protein.Protein.BindingSite attribute) color (ccdc.entry.Entry attribute) colour (ccdc.pharmacophore.Pharmacophore.Feature attribute) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.DatabaseInfo attribute) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition attribute) CombinedSearch (class in ccdc.search) CombinedSearch.CombinedHit (class in ccdc.search) CombinedSearch.Settings (class in ccdc.search) commandline_parser (ccdc.utilities.ApplicationInterface attribute)

compare() (ccdc.cavity.Cavity method) (ccdc.crystal.PackingSimilarity method) (ccdc.utilities.Histogram method) compare_cells() (ccdc.search.ReducedCellSearch method) complete_proteins (ccdc.pharmacophore.Pharmacophore.Search.Settings attribute) complete_small_molecules (ccdc.pharmacophore.Pharmacophore.Search.Settings attribute) component_label (ccdc.pharmacophore.Pharmacophore.Feature attribute) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition attribute) components (ccdc.molecule.Molecule attribute) conf_file (ccdc.docking.Docker.Settings attribute) confidence_interval (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient attribute) ConformerGenerator (class in ccdc.conformer) ConformerHit (class in ccdc.conformer) ConformerHitList (class in ccdc.conformer) ConformerSettings (class in ccdc.conformer) connected (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings attribute) connectivity_index() (ccdc.descriptors.MolecularDescriptors.ConnectivityIndices method) ConnserSubstructure (class in ccdc.search) conquest_path (ccdc.utilities.ApplicationInterface attribute) constraint_atoms() (ccdc.search.SubstructureSearch.SubstructureHit method) constraint_objects() (ccdc.search.SubstructureSearch.SubstructureHit method) constraint_values() (ccdc.pharmacophore.Pharmacophore.SearchHit method) constraints (ccdc.docking.Docker.Settings attribute) (ccdc.docking.Docker.Settings.ProteinFileInfo attribute) contact_group_atoms() (ccdc.interaction.InteractionLibrary.InteractionHit method) contact_group_name (ccdc.interaction.InteractionLibrary.InteractionData attribute) contact_groups() (ccdc.interaction.InteractionLibrary.CentralGroup method) contact_network() (ccdc.crystal.Crystal method) contacts() (ccdc.crystal.Crystal method) (ccdc.molecule.Molecule method) contains_unknown_bonds (ccdc.molecule.Molecule attribute) contract() (ccdc.utilities.Grid method) coordinates (ccdc.cavity.Cavity.Feature attribute) (ccdc.descriptors.CrystalDescriptors.Morphology.Facet attribute) (ccdc.interaction.InteractionMapAnalysis.Results.Hotspot attribute) (ccdc.molecule.Atom attribute) coordination_count (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions.Observation attribute) coordination_models_path (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Settings attribute) copy() (ccdc.molecule.Molecule method) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition method) (ccdc.protein.Protein method) (ccdc.utilities.Grid method) copy_settings() (ccdc.docking.Docker method) corners (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox attribute) count_grid() (ccdc.utilities.Grid method) count_neighbours() (ccdc.utilities.Grid method) create() (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.Creator method) cross() (ccdc.descriptors.GeometricDescriptors.Vector method) cross_references (ccdc.entry.Entry attribute) crystal (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) (ccdc.entry.Entry attribute) (ccdc.interaction.InteractionLibrary.InteractionHit attribute) (ccdc.search.Search.SearchHit attribute) Crystal (class in ccdc.crystal) crystal() (ccdc.io._DatabaseReader method) Crystal.Contact (class in ccdc.crystal) Crystal.HBond (class in ccdc.crystal) Crystal.MillerIndices (class in ccdc.crystal) Crystal.ReducedCell (class in ccdc.crystal) crystal_system (ccdc.crystal.Crystal attribute) CrystalDescriptors (class in ccdc.descriptors) CrystalDescriptors.GraphSetSearch (class in ccdc.descriptors) CrystalDescriptors.GraphSetSearch.GraphSet (class in ccdc.descriptors) CrystalDescriptors.GraphSetSearch.Settings (class in ccdc.descriptors) CrystalDescriptors.HBondCoordination (class in ccdc.descriptors) CrystalDescriptors.HBondCoordination.Predictions (class in ccdc.descriptors) CrystalDescriptors.HBondCoordination.Predictions.Observation (class in ccdc.descriptors) CrystalDescriptors.HBondCoordination.Settings (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.FittingData (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.FittingData.FittingDataEntry (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.FunctionalGroup (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.HBond (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.HBondAcceptor (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.HBondAtom (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.HBondDonor (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.HBondGrouping (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.InterPropensity (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.IntraPropensity (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.Model (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.Model.Coefficient (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.Model.Parameter (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.Propensity (class in ccdc.descriptors) CrystalDescriptors.HBondPropensities.Settings (class in ccdc.descriptors) CrystalDescriptors.Morphology (class in ccdc.descriptors) CrystalDescriptors.Morphology.Facet (class in ccdc.descriptors) CrystalDescriptors.Morphology.OrientedBoundingBox (class in ccdc.descriptors) CrystalDescriptors.PowderPattern (class in ccdc.descriptors) CrystalDescriptors.PowderPattern.Settings (class in ccdc.descriptors) CrystalDescriptors.PowderPattern.TickMark (class in ccdc.descriptors) CrystalDescriptors.PowderPattern.Wavelength (class in ccdc.descriptors) CrystalReader (class in ccdc.io) crystals() (ccdc.io._DatabaseReader method) CrystalWriter (class in ccdc.io) csd_defined_probes (ccdc.interaction.InteractionMapAnalysis.CommonSettings attribute) csd_directory() (in module ccdc.io) csd_version() (in module ccdc.io) current_entry (ccdc.utilities.ApplicationInterface attribute) custom_grid_bounding_box (ccdc.interaction.InteractionMapAnalysis.CommonSettings attribute) cyclic (ccdc.search.QueryAtom attribute) (ccdc.search.QueryBond attribute) cyclic_bonds (ccdc.search.QueryAtom attribute) cysteine_sulphur (ccdc.protein.Protein.Residue attribute)

D

d_min (ccdc.conformer.GeometryAnalyser.Analysis attribute) da_distance (ccdc.molecule.Molecule.HBond attribute) database_name (ccdc.entry.Entry attribute) database_path (ccdc.utilities.ApplicationInterface attribute) databases (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Settings attribute) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase attribute) days_remaining (ccdc.utilities.Licence attribute) decorate() (ccdc.utilities.Timer method) default_csd_filters() (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.Creator.StructureDatabase static method) default_feature_database() (ccdc.pharmacophore.Pharmacophore static method) default_feature_database_location() (ccdc.pharmacophore.Pharmacophore static method) degree (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) deposition_date (ccdc.entry.Entry attribute) description (ccdc.pharmacophore.Pharmacophore.Feature attribute) descriptor (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) detect_cavities (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) detect_cavity_from_residues (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) detect_hotspots (ccdc.interaction.InteractionMapAnalysis.CommonSettings attribute) detect_intra_hbonds (ccdc.diagram.DiagramGenerator.Settings attribute) detect_ligand_bonds() (ccdc.protein.Protein method) deuterium_is_hydrogen (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings attribute) DiagramGenerator (class in ccdc.diagram) DiagramGenerator.Settings (class in ccdc.diagram) dilate() (ccdc.utilities.Grid method) disorder_details (ccdc.entry.Entry attribute) disordered_molecule (ccdc.crystal.Crystal attribute) (ccdc.entry.Entry attribute) displacement_parameters (ccdc.molecule.Atom attribute) distance (ccdc.descriptors.GeometricDescriptors.Plane attribute) (ccdc.interaction.InteractionLibrary.InteractionHit attribute) distance() (ccdc.cavity.Cavity.Feature method) distance_range (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) (ccdc.molecule.Molecule.HBondCriterion attribute) (ccdc.pharmacophore.Pharmacophore.Query.DistanceConstraint attribute) distance_tolerance (ccdc.crystal.PackingSimilarity.Settings attribute) distances (ccdc.utilities.ApplicationInterface attribute) distribution (ccdc.conformer.GeometryAnalyser.Analysis attribute) distributions_pruned (ccdc.conformer.ConformerHitList attribute) diverse_solutions (ccdc.docking.Docker.Settings attribute) dock() (ccdc.docking.Docker method) (ccdc.docking.Docker.InteractiveResults method)

dock_status() (ccdc.docking.Docker method) Docker (class in ccdc.docking) Docker.InteractiveResults (class in ccdc.docking) Docker.LigandPreparation (class in ccdc.docking) Docker.LigandPreparation.Settings (class in ccdc.docking) Docker.Results (class in ccdc.docking) Docker.Results.DockedLigand (class in ccdc.docking) Docker.Results.DockedLigand.HBond (class in ccdc.docking) Docker.Results.DockedLigandReader (class in ccdc.docking) Docker.Settings (class in ccdc.docking) Docker.Settings.BindingSite (class in ccdc.docking) Docker.Settings.BindingSiteFromAtom (class in ccdc.docking) Docker.Settings.BindingSiteFromLigand (class in ccdc.docking) Docker.Settings.BindingSiteFromListOfAtoms (class in ccdc.docking) Docker.Settings.BindingSiteFromListOfResidues (class in ccdc.docking) Docker.Settings.BindingSiteFromPoint (class in ccdc.docking) Docker.Settings.BindingSiteFromResidue (class in ccdc.docking) Docker.Settings.Constraint (class in ccdc.docking) Docker.Settings.DistanceConstraint (class in ccdc.docking) Docker.Settings.HBondConstraint (class in ccdc.docking) Docker.Settings.LigandFileInfo (class in ccdc.docking) Docker.Settings.ProteinFileInfo (class in ccdc.docking) Docker.Settings.ProteinHBondConstraint (class in ccdc.docking) Docker.Settings.RegionConstraint (class in ccdc.docking) Docker.Settings.ScaffoldMatchConstraint (class in ccdc.docking) Docker.Settings.SubstructureConstraint (class in ccdc.docking) Docker.Settings.TemplateSimilarityConstraint (class in ccdc.docking) docking_log (ccdc.docking.Docker.Results attribute) donor (ccdc.search.QueryAtom attribute) donor_acceptor_range (ccdc.cavity.CavityDatabase.Settings attribute) donor_atom_type (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondDonor attribute) donor_atom_type() (ccdc.molecule.Molecule.HBondCriterion method) donor_label (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity attribute) donor_range (ccdc.cavity.CavityDatabase.Settings attribute) dot() (ccdc.descriptors.GeometricDescriptors.Vector method) drop_all_tables() (ccdc.cavity.CavityDatabase method) drugbank_database_dir() (ccdc.cavity.CavityDatabase static method) dummy_point_atoms() (ccdc.search.SubstructureSearch.SubstructureHit method) dummy_point_objects() (ccdc.search.SubstructureSearch.SubstructureHit method)

E

early_termination (ccdc.docking.Docker.Settings attribute) edge_labels (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) edges (ccdc.descriptors.CrystalDescriptors.Morphology.Facet attribute) EF() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) eissn (ccdc.entry.Journal attribute) element_coloring (ccdc.diagram.DiagramGenerator.Settings attribute) element_pair_count() (ccdc.descriptors.MolecularDescriptors.AtomPairDistanceDescriptorCalculator method) end_value (ccdc.utilities.Histogram attribute) end_year (ccdc.entry.Journal attribute) enough_hits (ccdc.conformer.GeometryAnalyser.Analysis attribute) entries() (ccdc.io._DatabaseReader method) entry (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) (ccdc.interaction.InteractionLibrary.InteractionHit attribute) (ccdc.search.Search.SearchHit attribute) Entry (class in ccdc.entry)

entry() (ccdc.io._DatabaseReader method) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase method) Entry.CrossReference (class in ccdc.entry) EntryReader (class in ccdc.io) EntryWriter (class in ccdc.io) equation (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) error_file() (ccdc.interaction.InteractionMapAnalysis.Results method) error_log (ccdc.docking.Docker.Results attribute) esd (ccdc.descriptors.CrystalDescriptors.PowderPattern attribute) estimate (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient attribute) excluded_volume_envelop (ccdc.screening.Screener.Settings attribute) excluded_volume_penalty (ccdc.screening.Screener.Settings attribute) exit_with_error() (ccdc.utilities.ApplicationInterface method) explicit_polar_hydrogens (ccdc.diagram.DiagramGenerator.Settings attribute) extrema (ccdc.utilities.Grid attribute)

F

facets (ccdc.descriptors.CrystalDescriptors.Morphology attribute) fatal() (ccdc.utilities.Logger method) feature_database (ccdc.pharmacophore.Pharmacophore.Search attribute) feature_definitions (ccdc.pharmacophore.Pharmacophore.FeatureDatabase attribute) feature_point1 (ccdc.pharmacophore.Pharmacophore.Query.DistanceConstraint attribute) feature_point2 (ccdc.pharmacophore.Pharmacophore.Query.DistanceConstraint attribute) feature_points() (ccdc.pharmacophore.Pharmacophore.PointGenerator method) (ccdc.pharmacophore.Pharmacophore.SearchHit method) features (ccdc.cavity.Cavity attribute) (ccdc.pharmacophore.Pharmacophore.Query attribute) features_by_atom_distance() (ccdc.cavity.Cavity method) features_by_distance() (ccdc.cavity.Cavity method) features_by_residues() (ccdc.cavity.Cavity method) features_by_type() (ccdc.cavity.Cavity method) features_from_atoms() (ccdc.pharmacophore.Pharmacophore.FeatureDefinition method) few_hits (ccdc.conformer.GeometryAnalyser.Analysis attribute) few_hits_threshold (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) file_name (ccdc.docking.Docker.Settings.ProteinFileInfo attribute) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.DatabaseInfo attribute) file_path (ccdc.utilities.ApplicationInterface attribute) FileLogger (class in ccdc.utilities) files (ccdc.utilities.Licence attribute) fitness() (ccdc.docking.Docker.Results.DockedLigand method) fitness_function (ccdc.docking.Docker.Settings attribute) fitting_data (ccdc.descriptors.CrystalDescriptors.HBondPropensities attribute) fitting_points_cluster_radius (ccdc.screening.Screener.Settings attribute) fitting_points_file (ccdc.docking.Docker.Settings attribute) fitting_points_threshold (ccdc.screening.Screener.Settings attribute) flexible_rings (ccdc.conformer.ConformerHitList attribute) flood_fill() (ccdc.utilities.Grid method) font_family (ccdc.diagram.DiagramGenerator.Settings attribute) font_italic (ccdc.diagram.DiagramGenerator.Settings attribute) font_size (ccdc.diagram.DiagramGenerator.Settings attribute) font_weight (ccdc.diagram.DiagramGenerator.Settings attribute) force_constraints (ccdc.docking.Docker.Settings attribute) foreground_color (ccdc.diagram.DiagramGenerator.Settings attribute) formal_charge (ccdc.molecule.Atom attribute) (ccdc.molecule.Molecule attribute) (ccdc.search.QueryAtom attribute) formal_valency (ccdc.search.QueryAtom attribute) format_time() (ccdc.utilities.Timer static method) formula (ccdc.crystal.Crystal attribute) (ccdc.entry.Entry attribute) (ccdc.molecule.Molecule attribute) (ccdc.protein.Protein.BindingSite attribute) fractional_coordinates (ccdc.molecule.Atom attribute)

fractional_uncertainties (ccdc.molecule.Atom attribute) fragment_identifier() (ccdc.conformer.GeometryAnalyser method) fragment_label (ccdc.conformer.GeometryAnalyser.Analysis attribute) frequencies (ccdc.utilities.Histogram attribute) from_crystal() (ccdc.descriptors.CrystalDescriptors.PowderPattern static method) from_dict() (ccdc.utilities.Grid method) from_entry() (ccdc.protein.Protein static method) from_file() (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FittingData static method) (ccdc.descriptors.CrystalDescriptors.Morphology static method) (ccdc.docking.Docker.Settings static method) (ccdc.interaction.InteractionMapAnalysis.ProteinSettings static method) (ccdc.interaction.InteractionMapAnalysis.SmallMoleculeSettings static method) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase static method) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition static method) (ccdc.pharmacophore.Pharmacophore.Query static method) (ccdc.protein.Protein static method) (ccdc.utilities.Grid static method) from_growth_rates() (ccdc.descriptors.CrystalDescriptors.Morphology static method) from_molecule() (ccdc.entry.Entry static method) from_pdb_file() (ccdc.cavity.Cavity static method) from_points() (ccdc.descriptors.GeometricDescriptors.Plane static method) (ccdc.descriptors.GeometricDescriptors.Vector static method) from_rotation_and_translation() (ccdc.molecule.Molecule.Transformation static method) from_SMARTS_definitions() (ccdc.pharmacophore.Pharmacophore.FeatureDefinition static method) from_string() (ccdc.crystal.Crystal static method) (ccdc.entry.Entry static method) (ccdc.molecule.Molecule static method) (ccdc.search.ConnserSubstructure static method) (ccdc.utilities.UncertainValue static method) from_vector() (ccdc.utilities.Grid method) from_xml() (ccdc.cavity.Cavity static method) (ccdc.search.ReducedCellSearch static method) (ccdc.search.SimilaritySearch static method) (ccdc.search.SubstructureSearch static method) (ccdc.search.TextNumericSearch static method) from_xml_file() (ccdc.cavity.Cavity static method) (ccdc.search.ReducedCellSearch static method) (ccdc.search.SimilaritySearch static method) (ccdc.search.SubstructureSearch static method) (ccdc.search.TextNumericSearch static method) from_xye_file() (ccdc.descriptors.CrystalDescriptors.PowderPattern static method) full_name (ccdc.entry.Journal attribute) full_width_at_half_maximum (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings attribute) functional_group_identifier (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom attribute) functional_groups_of_hbond() (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions method) fuse_rings() (ccdc.molecule.Molecule method)

G

generalisation (ccdc.conformer.GeometryAnalyser.Settings attribute) generalised (ccdc.conformer.GeometryAnalyser.Analysis attribute) generate() (ccdc.conformer.ConformerGenerator method) generate_hbond_groupings() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) GeometricDescriptors (class in ccdc.descriptors) GeometricDescriptors.Plane (class in ccdc.descriptors) GeometricDescriptors.Sphere (class in ccdc.descriptors) GeometricDescriptors.Vector (class in ccdc.descriptors) GeometryAnalyser (class in ccdc.conformer) GeometryAnalyser.Analysis (class in ccdc.conformer) GeometryAnalyser.AnalysisHit (class in ccdc.conformer) GeometryAnalyser.Settings (class in ccdc.conformer) GeometryAnalyser.Settings.GeometrySettings (class in ccdc.conformer) get_cavities_by_ligand() (ccdc.cavity.CavityDatabase method) get_cavities_by_pdb_code() (ccdc.cavity.CavityDatabase method)

get_cavity_by_name() (ccdc.cavity.CavityDatabase method) get_cavity_identifiers_by_ligand() (ccdc.cavity.CavityDatabase method) get_ccdc_logo() (ccdc.utilities.ApplicationInterface method) get_diagnostic_info() (ccdc.utilities.ApplicationInterface method) get_info_for_cavity() (ccdc.cavity.CavityDatabase method) get_ligands_by_cavity_identifier() (ccdc.cavity.CavityDatabase method) get_ligands_by_pdb_code() (ccdc.cavity.CavityDatabase method) get_number_of_cavities() (ccdc.cavity.CavityDatabase method) get_number_of_ligands() (ccdc.cavity.CavityDatabase method) Grid (class in ccdc.utilities) grid_spacing (ccdc.interaction.InteractionMapAnalysis.CommonSettings attribute) GridEnsemble (class in ccdc.utilities) group_atoms() (ccdc.search.SubstructureSearch.SubstructureHit method) group_by_index() (ccdc.interaction.InteractionLibrary.ContactGroupLibrary method) group_objects() (ccdc.search.SubstructureSearch.SubstructureHit method)

H

habit (ccdc.entry.Entry attribute) has_3d_coordinates (ccdc.search.QueryAtom attribute) (ccdc.search.Search.Settings attribute) has_3d_structure (ccdc.entry.Entry attribute) has_disorder (ccdc.crystal.Crystal attribute) (ccdc.entry.Entry attribute) hbond_atoms() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) hbond_network() (ccdc.crystal.Crystal method) hbonds (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) hbonds() (ccdc.crystal.Crystal method) (ccdc.molecule.Molecule method) heaviest_component (ccdc.molecule.Molecule attribute) heaviest_element (ccdc.conformer.GeometryAnalyser.Settings attribute) heavy_atoms (ccdc.molecule.Molecule attribute) highlight_color (ccdc.diagram.DiagramGenerator.Settings attribute)

histogram (ccdc.interaction.InteractionLibrary.InteractionData attribute) Histogram (class in ccdc.utilities) histogram() (ccdc.conformer.GeometryAnalyser.Analysis method) histogram_reference_points (ccdc.cavity.CavityDatabase.Settings attribute) histograms (ccdc.cavity.Cavity.CavityDistanceHistograms attribute) hit_identifiers (ccdc.conformer.GeometryAnalyser.Analysis attribute) hit_molecules (ccdc.conformer.GeometryAnalyser.Analysis attribute) hits (ccdc.conformer.GeometryAnalyser.Analysis attribute) (ccdc.interaction.InteractionLibrary.InteractionData attribute) hkl (ccdc.crystal.Crystal.MillerIndices attribute) hotspots() (ccdc.interaction.InteractionMapAnalysis.Results method) hotspots_min_value (ccdc.interaction.InteractionMapAnalysis.CommonSettings attribute) hotspots_ncycles (ccdc.interaction.InteractionMapAnalysis.CommonSettings attribute) hotspots_refine (ccdc.interaction.InteractionMapAnalysis.CommonSettings attribute) html_report() (ccdc.utilities.ApplicationInterface method) HTMLReport (class in ccdc.utilities)

I

ideal_bond_length (ccdc.molecule.Bond attribute) identifier (ccdc.cavity.Cavity attribute) (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) (ccdc.crystal.Crystal attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FittingData.FittingDataEntry attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FunctionalGroup attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Parameter attribute) (ccdc.entry.Entry attribute) (ccdc.interaction.InteractionLibrary.InteractionHit attribute) (ccdc.molecule.Molecule attribute) (ccdc.pharmacophore.Pharmacophore.Feature attribute) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.Entry attribute) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition attribute) (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) (ccdc.protein.Protein.Nucleotide attribute) (ccdc.protein.Protein.Residue attribute) (ccdc.search.Search.SearchHit attribute) (ccdc.utilities.ApplicationInterface attribute) identifier() (ccdc.io._DatabaseReader method) identifiers (ccdc.entry.Entry.CrossReference attribute) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase attribute) ignore_bond_counts (ccdc.crystal.PackingSimilarity.Settings attribute) ignore_bond_types (ccdc.crystal.PackingSimilarity.Settings attribute) ignore_hydrogen_counts (ccdc.crystal.PackingSimilarity.Settings attribute) ignore_hydrogen_positions (ccdc.crystal.PackingSimilarity.Settings attribute) ignore_hydrogens (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings attribute) ignore_line_numbers() (ccdc.utilities.Logger method) ignore_smallest_components (ccdc.crystal.PackingSimilarity.Settings attribute) image() (ccdc.diagram.DiagramGenerator method) image_height (ccdc.diagram.DiagramGenerator.Settings attribute) image_url (ccdc.entry.Journal attribute) image_width (ccdc.diagram.DiagramGenerator.Settings attribute) impose_upper_limits (ccdc.conformer.GeometryAnalyser.Settings attribute) include_hydrogens (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings attribute) index (ccdc.molecule.Atom attribute) (ccdc.search.QueryAtom attribute) indices_at_value() (ccdc.utilities.Grid method) input_h2a_file (ccdc.utilities.ApplicationInterface attribute) input_m2a_file (ccdc.utilities.ApplicationInterface attribute) input_mol2_file (ccdc.utilities.ApplicationInterface attribute) input_pdb_file (ccdc.utilities.ApplicationInterface attribute) integral() (ccdc.descriptors.CrystalDescriptors.PowderPattern method) intensity (ccdc.descriptors.CrystalDescriptors.PowderPattern attribute) interaction_data() (ccdc.interaction.InteractionLibrary.CentralGroup method) (ccdc.interaction.InteractionLibrary.ContactGroup method) interaction_library_contact_atoms() (ccdc.search.ConnserSubstructure method) InteractionLibrary (class in ccdc.interaction) InteractionLibrary.CentralGroup (class in ccdc.interaction) InteractionLibrary.CentralGroupLibrary (class in ccdc.interaction) InteractionLibrary.ContactGroup (class in ccdc.interaction) InteractionLibrary.ContactGroupLibrary (class in ccdc.interaction) InteractionLibrary.FunctionalGroupHit (class in ccdc.interaction) InteractionLibrary.InteractionData (class in ccdc.interaction) InteractionLibrary.InteractionHit (class in ccdc.interaction) InteractionMapAnalysis (class in ccdc.interaction)

InteractionMapAnalysis.CommonSettings (class in ccdc.interaction) InteractionMapAnalysis.ProteinSettings (class in ccdc.interaction) InteractionMapAnalysis.Results (class in ccdc.interaction) InteractionMapAnalysis.Results.Hotspot (class in ccdc.interaction) InteractionMapAnalysis.SmallMoleculeSettings (class in ccdc.interaction) interface_file (ccdc.utilities.ApplicationInterface attribute) intermolecular (ccdc.crystal.Crystal.Contact attribute) (ccdc.crystal.Crystal.HBond attribute) (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) (ccdc.molecule.Molecule.Contact attribute) (ccdc.molecule.Molecule.HBondCriterion attribute) international_coden (ccdc.entry.Journal attribute) intra_only (ccdc.pharmacophore.Pharmacophore.Query attribute) inverse() (ccdc.molecule.Molecule.Transformation method) is_3d (ccdc.molecule.Molecule attribute) is_acceptor (ccdc.molecule.Atom attribute) is_acceptor() (ccdc.molecule.Molecule.HBondCriterion method) is_acidic (ccdc.protein.Protein.Residue attribute) is_aromatic (ccdc.molecule.Ring attribute) is_baseline (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient attribute) is_basic (ccdc.protein.Protein.Residue attribute) is_centrosymmetric (ccdc.crystal.Crystal attribute) is_chiral (ccdc.molecule.Atom attribute) is_conjugated (ccdc.molecule.Bond attribute) is_cyclic (ccdc.molecule.Atom attribute) (ccdc.molecule.Bond attribute) is_donor (ccdc.molecule.Atom attribute) is_donor() (ccdc.molecule.Molecule.HBondCriterion method) is_fully_conjugated (ccdc.molecule.Ring attribute) is_fused (ccdc.molecule.Ring attribute) is_hydrophilic (ccdc.protein.Protein.Residue attribute) is_hydrophobic (ccdc.protein.Protein.Residue attribute) is_in_line_of_sight (ccdc.molecule.Molecule.Contact attribute) (ccdc.molecule.Molecule.HBond attribute) is_in_line_of_sight() (ccdc.molecule.Atom method) is_in_protein (ccdc.molecule.Atom attribute) is_intermolecular (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity attribute) is_journal_valid() (ccdc.search.TextNumericSearch method) is_metal (ccdc.molecule.Atom attribute) is_normalised (ccdc.search.ReducedCellSearch.Settings attribute) is_observed (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity attribute) is_organic (ccdc.entry.Entry attribute) (ccdc.molecule.Molecule attribute) is_organometallic (ccdc.entry.Entry attribute) (ccdc.molecule.Molecule attribute) is_polymeric (ccdc.entry.Entry attribute) (ccdc.molecule.Molecule attribute) is_powder_study (ccdc.entry.Entry attribute) is_rotatable (ccdc.molecule.Bond attribute) is_sohncke (ccdc.crystal.Crystal attribute) is_spiro (ccdc.molecule.Atom attribute) is_systematically_absent (ccdc.descriptors.CrystalDescriptors.PowderPattern.TickMark attribute) is_valid (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions attribute) islands() (ccdc.utilities.Grid method) isotropic_equivalent (ccdc.molecule.Atom.DisplacementParameters attribute) issn (ccdc.entry.Journal attribute) items() (ccdc.molecule.Molecule.HBondCriterion.HBondAtomTypes method)

J

Journal (class in ccdc.entry) JournalList (class in ccdc.entry)

journals (ccdc.io._DatabaseReader attribute) (ccdc.search.TextNumericSearch attribute)

K

kekulize() (ccdc.molecule.Molecule method) key (ccdc.pharmacophore.Pharmacophore.AnnotationFilter attribute)

keys() (ccdc.molecule.Molecule.HBondCriterion.HBondAtomTypes method) known_cofactor_codes() (ccdc.protein.Protein static method)

L

label (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions.Observation attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom attribute) (ccdc.molecule.Atom attribute) label_match (ccdc.search.QueryAtom attribute) label_set (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) label_to_atom_index() (ccdc.search.SMARTSSubstructure method) language_name (ccdc.entry.Journal attribute) largest_clique_size (ccdc.cavity.Cavity.FastCavityGraphComparison attribute) largest_ring_size (ccdc.molecule.Molecule attribute) lattice_centring (ccdc.crystal.Crystal attribute) length (ccdc.descriptors.GeometricDescriptors.Vector attribute) (ccdc.molecule.Bond attribute) (ccdc.molecule.Molecule.Contact attribute) (ccdc.molecule.Molecule.HBond attribute) level (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) Licence (class in ccdc.utilities) ligand_files (ccdc.docking.Docker.Settings attribute) ligand_identifiers (ccdc.cavity.Cavity attribute) ligand_log() (ccdc.docking.Docker.Results method) ligand_range (ccdc.cavity.CavityDatabase.Settings attribute)

ligands (ccdc.cavity.Cavity attribute) (ccdc.docking.Docker.Results attribute) (ccdc.docking.Docker.Settings attribute) (ccdc.protein.Protein attribute) (ccdc.protein.Protein.BindingSite attribute) limit_identifier_list (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Settings attribute) line_width (ccdc.diagram.DiagramGenerator.Settings attribute) local_density (ccdc.conformer.GeometryAnalyser.Analysis attribute) local_density_threshold (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) local_density_tolerance (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) lock_torsion() (ccdc.conformer.ConformerGenerator static method) log_file() (ccdc.interaction.InteractionMapAnalysis.Results method) log_file_name (ccdc.utilities.ApplicationInterface attribute) log_likelihood (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) log_likelihood_test_p_value (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) logfile (ccdc.cavity.CavityDatabase.Settings attribute) Logger (class in ccdc.utilities) logp_hydrophobic_attenuation_a (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) logp_hydrophobic_attenuation_b (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) lower_quartile (ccdc.conformer.GeometryAnalyser.Analysis attribute)

M

major_length (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox attribute) make_absolute_file_names() (ccdc.docking.Docker.Settings method) make_complex() (ccdc.docking.Docker.Results method) make_fitting_data() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) masked_set() (ccdc.utilities.Grid method) match_abbreviated_name() (ccdc.entry.JournalList method) match_atom() (ccdc.search.QuerySubstructure method) match_atoms() (ccdc.interaction.InteractionLibrary.FunctionalGroupHit method) (ccdc.search.SubstructureSearch.SubstructureHit method) match_components() (ccdc.search.SubstructureSearch.SubstructureHit method) match_entire_packing_shell (ccdc.crystal.PackingSimilarity.Settings attribute) match_fitting_data() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) match_full_name() (ccdc.entry.JournalList method) match_molecule() (ccdc.search.QuerySubstructure method) match_substructures() (ccdc.search.SubstructureSearch.SubstructureHit method) match_symmetry_operators() (ccdc.search.SubstructureSearch.SubstructureHit method) matches() (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FunctionalGroup method) max_chain_size (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) max_conformers (ccdc.conformer.ConformerSettings attribute) max_discrete_chain_size (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) max_distance (ccdc.interaction.InteractionLibrary.InteractionData attribute) max_hit_rmsd (ccdc.pharmacophore.Pharmacophore.Search.Settings attribute) max_hit_structures (ccdc.cavity.CavityDatabase.Settings attribute) (ccdc.pharmacophore.Pharmacophore.Search.Settings attribute) (ccdc.search.Search.Settings attribute) max_hit_structures() (ccdc.search.CombinedSearch static method) max_hits_per_structure (ccdc.pharmacophore.Pharmacophore.Search.Settings attribute) (ccdc.search.SubstructureSearch.Settings attribute) max_log_probability (ccdc.conformer.ConformerHitList attribute) max_product_graph_size (ccdc.cavity.CavityDatabase.Settings attribute) max_r_factor (ccdc.search.Search.Settings attribute) max_ring_size (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) max_unusual_torsions (ccdc.conformer.ConformerSettings attribute) max_value_of_neighbours() (ccdc.utilities.Grid method) maximum (ccdc.conformer.GeometryAnalyser.Analysis attribute) maximum_feature_distance (ccdc.pharmacophore.Pharmacophore.Query attribute) mean (ccdc.conformer.GeometryAnalyser.Analysis attribute) mean_value_of_neighbours() (ccdc.utilities.Grid method) measurement_atoms() (ccdc.search.SubstructureSearch.SubstructureHit method) measurement_objects() (ccdc.search.SubstructureSearch.SubstructureHit method) median (ccdc.conformer.GeometryAnalyser.Analysis attribute) median_length (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox attribute) melting_point (ccdc.entry.Entry attribute) metal_range (ccdc.cavity.CavityDatabase.Settings attribute) metals (ccdc.protein.Protein attribute) (ccdc.protein.Protein.BindingSite attribute) miller_indices (ccdc.descriptors.CrystalDescriptors.Morphology.Facet attribute) (ccdc.descriptors.CrystalDescriptors.PowderPattern.TickMark attribute)

miller_indices() (ccdc.crystal.Crystal method) min_cavity_buriedness (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) min_cavity_volume (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) min_distance (ccdc.interaction.InteractionLibrary.InteractionData attribute) min_log_probability (ccdc.conformer.ConformerHitList attribute) min_obs_exact (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) min_obs_generalised (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) min_relevance (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute) min_value_of_neighbours() (ccdc.utilities.Grid method) minimise() (ccdc.conformer.MoleculeMinimiser method) minimised_molecule (ccdc.conformer.ConformerHitList attribute) minimum (ccdc.conformer.GeometryAnalyser.Analysis attribute) minor_length (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox attribute) modules (ccdc.utilities.Licence attribute) molecular_shell() (ccdc.crystal.Crystal method) molecular_similarity_threshold (ccdc.crystal.PackingSimilarity.Settings attribute) molecular_volume (ccdc.molecule.Molecule attribute) molecular_weight (ccdc.molecule.Molecule attribute) MolecularDescriptors (class in ccdc.descriptors) MolecularDescriptors.AdjacencyMatrixDescriptorCalculator (class in ccdc.descriptors) MolecularDescriptors.AtomDistanceSearch (class in ccdc.descriptors) MolecularDescriptors.AtomPairDistanceDescriptorCalculator (class in ccdc.descriptors) MolecularDescriptors.ConnectivityIndices (class in ccdc.descriptors) MolecularDescriptors.MaximumCommonSubstructure (class in ccdc.descriptors) MolecularDescriptors.MaximumCommonSubstructure.Settings (class in ccdc.descriptors) MolecularDescriptors.PrincipleAxesAlignedBox (class in ccdc.descriptors) molecule (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) (ccdc.crystal.Crystal attribute) (ccdc.entry.Entry attribute) (ccdc.interaction.InteractionLibrary.InteractionHit attribute) (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) (ccdc.search.Search.SearchHit attribute) (ccdc.search.SimilaritySearch attribute) Molecule (class in ccdc.molecule) molecule() (ccdc.io._DatabaseReader method) Molecule.Contact (class in ccdc.molecule) Molecule.HBond (class in ccdc.molecule) Molecule.HBondCriterion (class in ccdc.molecule) Molecule.HBondCriterion.HBondAtomTypes (class in ccdc.molecule) Molecule.Transformation (class in ccdc.molecule) MoleculeMinimiser (class in ccdc.conformer) MoleculeReader (class in ccdc.io) molecules() (ccdc.io._DatabaseReader method) MoleculeSubstructure (class in ccdc.search) MoleculeWriter (class in ccdc.io) must_have_elements (ccdc.search.Search.Settings attribute) must_not_have_elements (ccdc.search.Search.Settings attribute)

N

n_cliques (ccdc.cavity.Cavity.CavityGraphComparison attribute) n_entries (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.DatabaseInfo attribute) n_flexible_rings_in_molecule (ccdc.conformer.ConformerHitList attribute) n_flexible_rings_sampled (ccdc.conformer.ConformerHitList attribute) n_flexible_rings_with_no_observations (ccdc.conformer.ConformerHitList attribute) n_matched_rotamers (ccdc.conformer.ConformerHitList attribute) n_matches (ccdc.cavity.Cavity.CavityGraphComparison attribute) n_rotamers_in_molecule (ccdc.conformer.ConformerHitList attribute) n_rotamers_sampled (ccdc.conformer.ConformerHitList attribute) n_rotamers_with_no_observations (ccdc.conformer.ConformerHitList attribute) n_terminus (ccdc.protein.Protein.Residue attribute) n_threads (ccdc.pharmacophore.Pharmacophore.Search.Settings attribute) nacceptors (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) name (ccdc.entry.Journal attribute) (ccdc.interaction.InteractionLibrary.CentralGroup attribute) (ccdc.interaction.InteractionLibrary.FunctionalGroupHit attribute) nbins (ccdc.utilities.Histogram attribute) ncentral_atoms (ccdc.interaction.InteractionLibrary.InteractionData attribute) ncontact_atoms (ccdc.interaction.InteractionLibrary.InteractionData attribute) ncontacts (ccdc.interaction.InteractionLibrary.InteractionData attribute) ncontacts_in_range() (ccdc.interaction.InteractionLibrary.InteractionData method) ndonors (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) neighbours (ccdc.molecule.Atom attribute) nflexible_atoms (ccdc.interaction.InteractionLibrary.InteractionData attribute) nhits (ccdc.conformer.GeometryAnalyser.Analysis attribute) nimplicit_hydrogens (ccdc.search.QueryAtom attribute) nitems() (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FittingData method) nlone_pairs (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom attribute)

nmatch_molecule() (ccdc.search.QuerySubstructure method) nmatched_molecules (ccdc.crystal.PackingSimilarity.Comparison attribute) nmolecules (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) no_disorder (ccdc.search.Search.Settings attribute) no_errors (ccdc.search.Search.Settings attribute) no_hits (ccdc.conformer.GeometryAnalyser.Analysis attribute) no_ions (ccdc.search.Search.Settings attribute) no_metals (ccdc.search.Search.Settings attribute) no_powder (ccdc.search.Search.Settings attribute) normal (ccdc.descriptors.GeometricDescriptors.Plane attribute) normalise_atom_order() (ccdc.molecule.Molecule method) normalise_hydrogens() (ccdc.molecule.Molecule method) normalise_labels() (ccdc.molecule.Molecule method) normalised_score (ccdc.conformer.ConformerHit attribute) not_polymeric (ccdc.search.Search.Settings attribute) noverflow (ccdc.utilities.Histogram attribute) nsteps (ccdc.utilities.Grid attribute) nucleic_acid_identifier (ccdc.protein.Protein.Nucleotide attribute) nucleic_acids (ccdc.protein.Protein attribute) nucleotides (ccdc.protein.Protein attribute) (ccdc.protein.Protein.BindingSite attribute) (ccdc.protein.Protein.NucleicAcid attribute) null_deviance (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) null_deviance_degrees_of_freedom (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) num_bonds (ccdc.search.QueryAtom attribute) num_hydrogens (ccdc.search.QueryAtom attribute) nunderflow (ccdc.utilities.Histogram attribute) nvalues (ccdc.utilities.Histogram attribute) nvdw_contacts (ccdc.interaction.InteractionLibrary.InteractionData attribute)

O

observed (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions attribute) occupancy (ccdc.molecule.Atom attribute) one_letter_code (ccdc.protein.Protein.Nucleotide attribute) (ccdc.protein.Protein.Residue attribute) only_organic (ccdc.search.Search.Settings attribute) only_organometallic (ccdc.search.Search.Settings attribute) open_output_folder() (ccdc.utilities.ApplicationInterface method) options (ccdc.utilities.ApplicationInterface attribute) order (ccdc.crystal.Crystal.MillerIndices attribute) organometallic_filter (ccdc.conformer.GeometryAnalyser.Settings attribute) oriented_bounding_box (ccdc.descriptors.CrystalDescriptors.Morphology attribute) original_molecule (ccdc.conformer.ConformerHitList attribute) output_base (ccdc.utilities.ApplicationInterface attribute) output_c2m_file (ccdc.utilities.ApplicationInterface attribute) output_csv_file (ccdc.utilities.ApplicationInterface attribute) output_directory (ccdc.docking.Docker.Settings attribute) (ccdc.screening.Screener.Settings attribute) output_directory_path (ccdc.utilities.ApplicationInterface attribute) output_file (ccdc.docking.Docker.Settings attribute) output_file_name() (ccdc.utilities.ApplicationInterface method)

output_format (ccdc.docking.Docker.Settings attribute) output_gcd_file (ccdc.utilities.ApplicationInterface attribute) output_gold_conf_file (ccdc.utilities.ApplicationInterface attribute) output_html_file (ccdc.utilities.ApplicationInterface attribute) output_mol2_file (ccdc.utilities.ApplicationInterface attribute) output_morphology_file (ccdc.utilities.ApplicationInterface attribute) output_pdb_file (ccdc.utilities.ApplicationInterface attribute) output_progress_file (ccdc.utilities.ApplicationInterface attribute) output_sdf_file (ccdc.utilities.ApplicationInterface attribute) output_tsv_file (ccdc.utilities.ApplicationInterface attribute) overflow (ccdc.utilities.Histogram attribute) overlay() (ccdc.descriptors.MolecularDescriptors static method) overlay_convergence_tolerance (ccdc.protein.Protein.ChainSuperposition.Settings attribute) overlay_minimum_cycles (ccdc.protein.Protein.ChainSuperposition.Settings attribute) overlay_molecules() (ccdc.crystal.PackingSimilarity.Comparison method) overlay_rmsd (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) overlay_rmsd_and_rmsd_tanimoto() (ccdc.descriptors.MolecularDescriptors static method) overlay_rmsds_and_transformation() (ccdc.descriptors.MolecularDescriptors static method) overlay_transformation (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) overlay_weighting_factor (ccdc.protein.Protein.ChainSuperposition.Settings attribute) overwrite_existing_image (ccdc.diagram.DiagramGenerator.Settings attribute)

P

p_value (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient attribute) packing (ccdc.pharmacophore.Pharmacophore.Query attribute) packing() (ccdc.crystal.Crystal method) packing_coefficient (ccdc.crystal.Crystal attribute) packing_shell() (ccdc.crystal.Crystal method) packing_shell_size (ccdc.crystal.PackingSimilarity.Comparison attribute) (ccdc.crystal.PackingSimilarity.Settings attribute) PackingSimilarity (class in ccdc.crystal) PackingSimilarity.Comparison (class in ccdc.crystal) PackingSimilarity.Settings (class in ccdc.crystal) parameter_directory (ccdc.screening.Screener.Settings attribute) parameters (ccdc.pharmacophore.Pharmacophore.PointGenerator attribute) parse_commandline() (ccdc.utilities.ApplicationInterface method) partial_charge (ccdc.molecule.Atom attribute) path_length_range (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) (ccdc.molecule.Molecule.HBondCriterion attribute) peptide_sequence (ccdc.entry.Entry attribute) percent_length_tolerance (ccdc.search.ReducedCellSearch.Settings attribute) percentile() (ccdc.conformer.GeometryAnalyser.Analysis method) perform_regression() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) period (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet attribute) permutational_equivalence (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition attribute) perpendicular_distance (ccdc.descriptors.CrystalDescriptors.Morphology.Facet attribute) Pharmacophore (class in ccdc.pharmacophore) Pharmacophore.AnnotationFilter (class in ccdc.pharmacophore) Pharmacophore.AnyCentroidPointGenerator (class in ccdc.pharmacophore) Pharmacophore.DummyPointGenerator (class in ccdc.pharmacophore) Pharmacophore.ExcludedVolume (class in ccdc.pharmacophore) Pharmacophore.Feature (class in ccdc.pharmacophore) Pharmacophore.FeatureDatabase (class in ccdc.pharmacophore) Pharmacophore.FeatureDatabase.Creator (class in ccdc.pharmacophore) Pharmacophore.FeatureDatabase.Creator.Settings (class in ccdc.pharmacophore) Pharmacophore.FeatureDatabase.Creator.StructureDatabase (class in ccdc.pharmacophore) Pharmacophore.FeatureDatabase.DatabaseInfo (class in ccdc.pharmacophore) Pharmacophore.FeatureDatabase.Entry (class in ccdc.pharmacophore) Pharmacophore.FeatureDefinition (class in ccdc.pharmacophore) Pharmacophore.LinearPointGenerator (class in ccdc.pharmacophore) Pharmacophore.NonPlanarCentroidPointGenerator (class in ccdc.pharmacophore) Pharmacophore.NormalPointGenerator (class in ccdc.pharmacophore) Pharmacophore.PlanarCentroidPointGenerator (class in ccdc.pharmacophore) Pharmacophore.PlanarNormalPointGenerator (class in ccdc.pharmacophore) Pharmacophore.PointGenerator (class in ccdc.pharmacophore) Pharmacophore.PointPointGenerator (class in ccdc.pharmacophore) Pharmacophore.Query (class in ccdc.pharmacophore) Pharmacophore.Query.DistanceConstraint (class in ccdc.pharmacophore) Pharmacophore.Search (class in ccdc.pharmacophore) Pharmacophore.Search.Settings (class in ccdc.pharmacophore) Pharmacophore.SearchHit (class in ccdc.pharmacophore) Pharmacophore.SMARTSDefinition (class in ccdc.pharmacophore) Pharmacophore.TetrahedralPointGenerator (class in ccdc.pharmacophore) Pharmacophore.TrigonalPointGenerator (class in ccdc.pharmacophore) phase_transition (ccdc.entry.Entry attribute) pi_range (ccdc.cavity.CavityDatabase.Settings attribute) plane (ccdc.crystal.Crystal.MillerIndices attribute) (ccdc.descriptors.CrystalDescriptors.Morphology.Facet attribute) plane_angle() (ccdc.descriptors.GeometricDescriptors.Plane method) plane_atoms() (ccdc.search.SubstructureSearch.SubstructureHit method) plane_distance() (ccdc.descriptors.GeometricDescriptors.Plane method) plane_objects() (ccdc.search.SubstructureSearch.SubstructureHit method)

plane_vector1 (ccdc.descriptors.GeometricDescriptors.Plane attribute) plane_vector2 (ccdc.descriptors.GeometricDescriptors.Plane attribute) point_angle() (ccdc.descriptors.GeometricDescriptors static method) point_distance() (ccdc.cavity.Cavity.Feature method) (ccdc.descriptors.GeometricDescriptors static method) (ccdc.descriptors.GeometricDescriptors.Plane method) point_generator_names (ccdc.pharmacophore.Pharmacophore.FeatureDefinition attribute) point_generators (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition attribute) point_group_analysis() (ccdc.descriptors.MolecularDescriptors static method) point_torsion_angle() (ccdc.descriptors.GeometricDescriptors static method) points (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) polar_shell_correction (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) polymer_expansion() (ccdc.crystal.Crystal method) polymorph (ccdc.entry.Entry attribute) populate_all() (ccdc.cavity.CavityDatabase method) powder_filter (ccdc.conformer.GeometryAnalyser.Settings attribute) PPV() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) precision (ccdc.molecule.Atom.DisplacementParameters attribute) (ccdc.utilities.UncertainValue attribute) (ccdc.utilities.Uncertainty attribute) predict() (ccdc.descriptors.CrystalDescriptors.HBondCoordination method) predictions_for_label() (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions method) predictive_error (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity attribute) prepare() (ccdc.docking.Docker.LigandPreparation method) pressure (ccdc.entry.Entry attribute) previous_identifier (ccdc.entry.Entry attribute) probability (ccdc.conformer.ConformerHit attribute) (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions.Observation attribute) product_graph_size (ccdc.cavity.Cavity.FastCavityGraphComparison attribute) program_executable_path (ccdc.utilities.ApplicationInterface attribute) program_path (ccdc.utilities.ApplicationInterface attribute) progress() (ccdc.utilities.Timer static method) propensities (ccdc.descriptors.CrystalDescriptors.HBondPropensities attribute) propensity (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity attribute) proper (ccdc.crystal.Crystal.MillerIndices attribute) protein (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) Protein (class in ccdc.protein) Protein.BindingSite (class in ccdc.protein) Protein.BindingSiteFromAtom (class in ccdc.protein) Protein.BindingSiteFromListOfAtoms (class in ccdc.protein) Protein.BindingSiteFromListOfResidues (class in ccdc.protein) Protein.BindingSiteFromMolecule (class in ccdc.protein) Protein.BindingSiteFromPoint (class in ccdc.protein) Protein.BindingSiteFromResidue (class in ccdc.protein) Protein.Chain (class in ccdc.protein) Protein.ChainSuperposition (class in ccdc.protein) Protein.ChainSuperposition.Settings (class in ccdc.protein) Protein.NucleicAcid (class in ccdc.protein) Protein.Nucleotide (class in ccdc.protein) Protein.Residue (class in ccdc.protein) protein_atom_type (ccdc.molecule.Atom attribute) protein_files (ccdc.docking.Docker.Settings attribute) protein_log (ccdc.docking.Docker.Results attribute) protein_vector (ccdc.cavity.Cavity.Feature attribute) proteins (ccdc.docking.Docker.Results attribute) (ccdc.docking.Docker.Settings attribute) publication (ccdc.entry.Entry attribute) publications (ccdc.entry.Entry attribute) publisher_name (ccdc.entry.Journal attribute)

Q

queries (ccdc.search.TextNumericSearch attribute) QueryAtom (class in ccdc.search)

QueryBond (class in ccdc.search) QuerySubstructure (class in ccdc.search)

R

r_factor (ccdc.entry.Entry attribute) radiation_source (ccdc.entry.Entry attribute) read_feature_definitions() (ccdc.pharmacophore.Pharmacophore static method) read_xml() (ccdc.search.ReducedCellSearch method) (ccdc.search.SimilaritySearch method) (ccdc.search.SubstructureSearch method) (ccdc.search.TextNumericSearch method) read_xml_file() (ccdc.search.ReducedCellSearch method) (ccdc.search.SimilaritySearch method) (ccdc.search.SubstructureSearch method) (ccdc.search.TextNumericSearch method) reduced_cell (ccdc.crystal.Crystal attribute) ReducedCellSearch (class in ccdc.search) ReducedCellSearch.CrystalQuery (class in ccdc.search) ReducedCellSearch.Query (class in ccdc.search) ReducedCellSearch.Settings (class in ccdc.search) ReducedCellSearch.XMLFileQuery (class in ccdc.search) ReducedCellSearch.XMLQuery (class in ccdc.search) reference_ligand_file (ccdc.docking.Docker.Settings attribute) relative_area() (ccdc.descriptors.CrystalDescriptors.Morphology method) relative_density (ccdc.interaction.InteractionLibrary.InteractionData attribute) remarks (ccdc.entry.Entry attribute) remove() (ccdc.io._DatabaseWriter method) remove_all_metals() (ccdc.protein.Protein method) remove_all_waters() (ccdc.protein.Protein method) remove_atom() (ccdc.molecule.Molecule method) remove_atoms() (ccdc.molecule.Molecule method) remove_bond() (ccdc.molecule.Molecule method) remove_bonds() (ccdc.molecule.Molecule method) remove_chain() (ccdc.protein.Protein method) remove_cofactor() (ccdc.protein.Protein method) remove_group() (ccdc.molecule.Molecule method) remove_hydrogens() (ccdc.molecule.Molecule method) (ccdc.protein.Protein method) remove_ligand() (ccdc.protein.Protein method) remove_metal() (ccdc.protein.Protein method) remove_metal_bonds() (ccdc.protein.Protein method) remove_nucleic_acid() (ccdc.protein.Protein method)

remove_nucleotide() (ccdc.protein.Protein method) remove_partial_charges() (ccdc.molecule.Molecule method) remove_residue() (ccdc.protein.Protein method) remove_unknown_atoms() (ccdc.molecule.Molecule method) remove_water() (ccdc.protein.Protein method) report() (ccdc.utilities.Timer method) require_hydrogens (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) (ccdc.molecule.Molecule.HBondCriterion attribute) rescore_function (ccdc.docking.Docker.Settings attribute) reset() (ccdc.search.ReducedCellSearch.Settings method) (ccdc.utilities.Logger class method) residual_deviance (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) residual_deviance_degrees_of_freedom (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model attribute) residue (ccdc.cavity.Cavity.Feature attribute) residue_label (ccdc.molecule.Atom attribute) residues (ccdc.protein.Protein attribute) (ccdc.protein.Protein.BindingSite attribute) (ccdc.protein.Protein.Chain attribute) results (ccdc.docking.Docker attribute) return_type (ccdc.diagram.DiagramGenerator.Settings attribute) rfactor_filter (ccdc.conformer.GeometryAnalyser.Settings attribute) RIE() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) Ring (class in ccdc.molecule) ring_centroid() (ccdc.descriptors.MolecularDescriptors static method) ring_plane() (ccdc.descriptors.MolecularDescriptors static method) rings (ccdc.molecule.Atom attribute) (ccdc.molecule.Bond attribute) (ccdc.molecule.Molecule attribute) rmsd (ccdc.cavity.Cavity.CavityGraphComparison attribute) (ccdc.crystal.PackingSimilarity.Comparison attribute) rmsd() (ccdc.conformer.ConformerHit method) (ccdc.descriptors.MolecularDescriptors static method) ROC() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) rotamers (ccdc.conformer.ConformerHitList attribute) rotamers_with_no_observations (ccdc.conformer.ConformerHitList attribute) rotate() (ccdc.molecule.Molecule method) rotate_torsions (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) rotation (ccdc.molecule.Molecule.Transformation attribute)

S

sampling_limit_reached (ccdc.conformer.ConformerHitList attribute) save_binding_site_atoms (ccdc.docking.Docker.Settings attribute) save_files (ccdc.screening.Screener.Settings attribute) scale_factor (ccdc.descriptors.CrystalDescriptors.Morphology attribute) (ccdc.descriptors.CrystalDescriptors.PowderPattern.Wavelength attribute) schema_version (ccdc.pharmacophore.Pharmacophore.FeatureDatabase attribute) scope (ccdc.entry.Entry.CrossReference attribute) score (ccdc.cavity.Cavity.CavityGraphComparison attribute) (ccdc.cavity.Cavity.FastCavityGraphComparison attribute) (ccdc.screening.Screener.ScreenHitList.ScreenHit attribute) score_molecule() (ccdc.utilities.Grid method) score_parameter_file (ccdc.docking.Docker.Settings attribute) scores (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity attribute) scoring_term() (ccdc.docking.Docker.Results.DockedLigand method) screen() (ccdc.screening.Screener method) Screener (class in ccdc.screening) Screener.ScreenHitList (class in ccdc.screening) Screener.ScreenHitList.ScreenHit (class in ccdc.screening) Screener.Settings (class in ccdc.screening) script_name (ccdc.utilities.ApplicationInterface attribute) Search (class in ccdc.search) search() (ccdc.cavity.CavityDatabase method) (ccdc.descriptors.CrystalDescriptors.GraphSetSearch method) (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure method) (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition method) (ccdc.pharmacophore.Pharmacophore.Search method) (ccdc.search.Search method) (ccdc.search.SubstructureSearch.HitProcessor method) Search.SearchHit (class in ccdc.search) Search.Settings (class in ccdc.search) search_molecule() (ccdc.search.SimilaritySearch method) second_wavelength (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings attribute) seed_file (ccdc.docking.Docker.Settings attribute) selected_atoms (ccdc.utilities.ApplicationInterface attribute) selected_indices (ccdc.utilities.ApplicationInterface attribute) self_returning_walk() (ccdc.descriptors.MolecularDescriptors.AdjacencyMatrixDescriptorCalculator method) self_returning_walk_ln() (ccdc.descriptors.MolecularDescriptors.AdjacencyMatrixDescriptorCalculator method) sequence (ccdc.protein.Protein attribute) (ccdc.protein.Protein.Chain attribute) (ccdc.protein.Protein.NucleicAcid attribute) sequence_alignment_tool (ccdc.protein.Protein.ChainSuperposition.Settings attribute) sequence_search_tool (ccdc.protein.Protein.ChainSuperposition.Settings attribute) set_acceptor_type() (ccdc.molecule.Molecule.HBondCriterion method) set_bond_length() (ccdc.molecule.Molecule method) set_ccdc_log_level() (ccdc.utilities.Logger method) set_ccdc_minimum_log_level() (ccdc.utilities.Logger method) set_coordinates() (ccdc.molecule.Molecule method) set_custom_grid_from_grid() (ccdc.interaction.InteractionMapAnalysis.CommonSettings method) set_donor_type() (ccdc.molecule.Molecule.HBondCriterion method) set_formal_charges() (ccdc.molecule.Molecule method) set_hostname() (ccdc.docking.Docker.Settings method) set_log_level() (ccdc.utilities.Logger method) set_output_file() (ccdc.utilities.Logger method) set_query() (ccdc.search.ReducedCellSearch method) set_residue_by_component() (ccdc.molecule.Molecule method) set_sphere() (ccdc.utilities.Grid method) set_target() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) set_torsion_angle() (ccdc.molecule.Molecule method) set_valence_angle() (ccdc.molecule.Molecule method) set_value() (ccdc.utilities.Grid method) shortest_path() (ccdc.molecule.Molecule method) shortest_path_atoms() (ccdc.molecule.Molecule method) shortest_path_bonds() (ccdc.molecule.Molecule method) show_fitting_data_counts() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) show_highest_similarity_result (ccdc.crystal.PackingSimilarity.Settings attribute) show_script_error() (ccdc.utilities.ApplicationInterface method) shrink_symbols (ccdc.diagram.DiagramGenerator.Settings attribute) sidechain_atoms (ccdc.protein.Protein.Residue attribute) significance_code (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient attribute) similarity() (ccdc.descriptors.CrystalDescriptors.PowderPattern method)

similarity_score (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) SimilaritySearch (class in ccdc.search) SimilaritySearch.Settings (class in ccdc.search) SimilaritySearch.SimilarityHit (class in ccdc.search) simple_search() (ccdc.entry.JournalList method) skip_proteins (ccdc.pharmacophore.Pharmacophore.Search.Settings attribute) skip_when_identifiers_equal (ccdc.crystal.PackingSimilarity.Settings attribute) slice() (ccdc.utilities.Grid method) slicing() (ccdc.crystal.Crystal method) small_molecule (ccdc.pharmacophore.Pharmacophore.SearchHit attribute) smallest_ring (ccdc.search.QueryAtom attribute) smallest_ring_size (ccdc.molecule.Molecule attribute) SMARTS (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition attribute) smarts (ccdc.search.SMARTSSubstructure attribute) SMARTSSubstructure (class in ccdc.search) smiles (ccdc.molecule.Molecule attribute) solvent (ccdc.entry.Entry attribute) solvent_accessible_surface() (ccdc.molecule.Atom method) solvent_filter (ccdc.conformer.GeometryAnalyser.Settings attribute) sort_order (ccdc.search.SimilaritySearch.Settings attribute) source (ccdc.entry.Entry attribute) (ccdc.interaction.InteractionMapAnalysis.ProteinSettings attribute) source_name (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) spacegroup_number_and_setting (ccdc.crystal.Crystal attribute) spacegroup_symbol (ccdc.crystal.Crystal attribute) spacing (ccdc.utilities.Grid attribute) spheres (ccdc.pharmacophore.Pharmacophore.Feature attribute) standard_deviation (ccdc.conformer.GeometryAnalyser.Analysis attribute) standard_error (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient attribute) standardise_aromatic_bonds() (ccdc.molecule.Molecule method) standardise_delocalised_bonds() (ccdc.molecule.Molecule method) start (ccdc.cavity.CavityDatabase.Settings attribute) start_value (ccdc.utilities.Histogram attribute) start_year (ccdc.entry.Journal attribute) state (ccdc.entry.Journal attribute) StatisticalDescriptors (class in ccdc.descriptors) StatisticalDescriptors.RankStatistics (class in ccdc.descriptors) store_atom_types (ccdc.screening.Screener.Settings attribute) strength (ccdc.molecule.Molecule.Contact attribute) sub_grid() (ccdc.utilities.Grid method) subcavity() (ccdc.cavity.Cavity method) SubstructureSearch (class in ccdc.search) SubstructureSearch.HitProcessor (class in ccdc.search) SubstructureSearch.Settings (class in ccdc.search) SubstructureSearch.SubstructureHit (class in ccdc.search) SubstructureSearch.SubstructureHitList (class in ccdc.search) summary() (ccdc.conformer.GeometryAnalyser.Settings method) (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings method) (ccdc.interaction.InteractionMapAnalysis.CommonSettings method) (ccdc.interaction.InteractionMapAnalysis.ProteinSettings method) (ccdc.interaction.InteractionMapAnalysis.SmallMoleculeSettings method) super_grid() (ccdc.utilities.Grid static method) superimpose() (ccdc.search.SubstructureSearch.SubstructureHitList method) superimpose_conformers_onto_reference (ccdc.conformer.ConformerSettings attribute) superpose() (ccdc.protein.Protein.ChainSuperposition method) superposition_atoms (ccdc.protein.Protein.ChainSuperposition.Settings attribute) surface_depths (ccdc.cavity.Cavity.Feature attribute) surface_points (ccdc.cavity.Cavity.Feature attribute) surface_vector (ccdc.cavity.Cavity.Feature attribute) sybyl_type (ccdc.molecule.Atom attribute) (ccdc.molecule.Bond attribute) symmetric_molecule() (ccdc.crystal.Crystal method) symmetry_operator_description() (ccdc.crystal.Crystal static method) symmetry_operators (ccdc.crystal.Crystal attribute) (ccdc.crystal.Crystal.Contact attribute) (ccdc.crystal.Crystal.HBond attribute) symmetry_rotation() (ccdc.crystal.Crystal static method) symmetry_translation() (ccdc.crystal.Crystal static method) synonyms (ccdc.entry.Entry attribute) synonyms_as_html (ccdc.entry.Entry attribute)

T

target_hbond_grouping() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) temperature (ccdc.entry.Entry attribute) temperature_factor (ccdc.molecule.Atom.DisplacementParameters attribute) test() (ccdc.search.Search.Settings method) text (ccdc.entry.Entry.CrossReference attribute) TextNumericSearch (class in ccdc.search) TextNumericSearch.TextNumericHit (class in ccdc.search) TextNumericSearch.TextNumericSearchSettings (class in ccdc.search) three_cubed_packing (ccdc.pharmacophore.Pharmacophore.Search.Settings attribute) three_letter_code (ccdc.protein.Protein.Residue attribute) threshold (ccdc.search.SimilaritySearch attribute) (ccdc.search.SimilaritySearch.Settings attribute) tick_marks (ccdc.descriptors.CrystalDescriptors.PowderPattern attribute) Timer (class in ccdc.utilities) Timer.Manager (class in ccdc.utilities) to_csv() (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions method) to_dict() (ccdc.utilities.Grid method) to_pymol_file() (ccdc.cavity.Cavity method) to_string() (ccdc.crystal.Crystal method) (ccdc.entry.Entry method) (ccdc.molecule.Molecule method) to_vector() (ccdc.utilities.Grid method) to_xml() (ccdc.cavity.Cavity method)

to_xml_file() (ccdc.cavity.Cavity method) topological_charge_autocorrelation_index() (ccdc.descriptors.MolecularDescriptors.AdjacencyMatrixDescriptorCalculator method) torsion_angle (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) torsion_angles (ccdc.utilities.ApplicationInterface attribute) torsion_distribution_file (ccdc.docking.Docker.Settings attribute) transform() (ccdc.molecule.Molecule method) transformation_matrix (ccdc.cavity.Cavity.CavityGraphComparison attribute) translate() (ccdc.molecule.Molecule method) translated_name (ccdc.entry.Journal attribute) translation (ccdc.molecule.Molecule.Transformation attribute) two_theta (ccdc.descriptors.CrystalDescriptors.PowderPattern attribute) (ccdc.descriptors.CrystalDescriptors.PowderPattern.TickMark attribute) two_theta_maximum (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings attribute) two_theta_minimum (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings attribute) two_theta_step (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings attribute) type (ccdc.cavity.Cavity.Feature attribute) (ccdc.conformer.GeometryAnalyser.Analysis attribute) (ccdc.crystal.Crystal.Contact attribute) (ccdc.crystal.Crystal.HBond attribute) (ccdc.entry.Entry.CrossReference attribute) (ccdc.molecule.Atom.DisplacementParameters attribute) (ccdc.molecule.Molecule.Contact attribute) (ccdc.molecule.Molecule.HBond attribute)

U

uncertainties (ccdc.molecule.Atom.DisplacementParameters attribute) uncertainty (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity attribute) (ccdc.utilities.UncertainValue attribute) (ccdc.utilities.Uncertainty attribute) Uncertainty (class in ccdc.utilities)

UncertainValue (class in ccdc.utilities) unfused_unbridged_ring (ccdc.search.QueryAtom attribute) unusual (ccdc.conformer.GeometryAnalyser.Analysis attribute) update_progress() (ccdc.utilities.ApplicationInterface method) upper_quartile (ccdc.conformer.GeometryAnalyser.Analysis attribute) url (ccdc.entry.Journal attribute)

V

valence_angle (ccdc.conformer.GeometryAnalyser.AnalysisHit attribute) value (ccdc.conformer.GeometryAnalyser.Analysis attribute) (ccdc.interaction.InteractionMapAnalysis.Results.Hotspot attribute) (ccdc.pharmacophore.Pharmacophore.AnnotationFilter attribute) (ccdc.utilities.UncertainValue attribute) value() (ccdc.utilities.Grid method) value_at_point() (ccdc.utilities.Grid method) values (ccdc.molecule.Atom.DisplacementParameters attribute) vdw_corrected (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) (ccdc.molecule.Molecule.HBondCriterion attribute) vdw_radius (ccdc.molecule.Atom attribute)

vector_angle() (ccdc.descriptors.GeometricDescriptors.Plane method) vector_atoms() (ccdc.search.SubstructureSearch.SubstructureHit method) vector_objects() (ccdc.search.SubstructureSearch.SubstructureHit method) verbose (ccdc.cavity.CavityDatabase.Settings attribute) void_volume() (ccdc.crystal.Crystal method) volume (ccdc.cavity.Cavity attribute) (ccdc.crystal.Crystal.ReducedCell attribute) (ccdc.descriptors.CrystalDescriptors.Morphology attribute) (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox attribute) (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox attribute) volume_range (ccdc.cavity.CavityDatabase.Settings attribute)

W

waters (ccdc.protein.Protein attribute) (ccdc.protein.Protein.BindingSite attribute) wavelength (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings attribute) (ccdc.descriptors.CrystalDescriptors.PowderPattern.Wavelength attribute) which (ccdc.pharmacophore.Pharmacophore.Query.DistanceConstraint attribute) with_ligands (ccdc.cavity.CavityDatabase.Settings attribute) working_directory (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Settings attribute) (ccdc.interaction.InteractionMapAnalysis.CommonSettings attribute) working_directory_path (ccdc.utilities.ApplicationInterface attribute) write() (ccdc.cavity.Cavity method) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FittingData method) (ccdc.descriptors.CrystalDescriptors.Morphology method) (ccdc.interaction.InteractionLibrary.InteractionData method) (ccdc.interaction.InteractionMapAnalysis.CommonSettings method) (ccdc.interaction.InteractionMapAnalysis.ProteinSettings method) (ccdc.io.CrystalWriter method) (ccdc.io.EntryWriter method) (ccdc.io.MoleculeWriter method) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase method) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition method) (ccdc.pharmacophore.Pharmacophore.Query method) (ccdc.utilities.Grid method) (ccdc.utilities.HTMLReport method)

write_c2m_file() (ccdc.search.SubstructureSearch.SubstructureHitList method) write_crystal() (ccdc.io._DatabaseWriter method) write_entry() (ccdc.io._DatabaseWriter method) write_figure() (ccdc.utilities.HTMLReport method) write_figure_data() (ccdc.utilities.HTMLReport method) write_footer() (ccdc.utilities.HTMLReport method) write_molecule() (ccdc.io._DatabaseWriter method) write_options (ccdc.docking.Docker.Settings attribute) write_paragraph() (ccdc.utilities.HTMLReport method) write_raw_file() (ccdc.descriptors.CrystalDescriptors.PowderPattern method) write_report() (ccdc.utilities.ApplicationInterface method) (ccdc.utilities.HTMLReport method) write_report_header() (ccdc.utilities.HTMLReport method) write_section_header() (ccdc.utilities.HTMLReport method) write_xml() (ccdc.search.QuerySubstructure method) write_xye_file() (ccdc.descriptors.CrystalDescriptors.PowderPattern method)

X

x_vector (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox attribute)

Y

y_vector (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox attribute)

Z

z_prime (ccdc.crystal.Crystal attribute) z_score (ccdc.conformer.GeometryAnalyser.Analysis attribute) z_value (ccdc.crystal.Crystal attribute) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient attribute)

z_vector (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox attribute) zscore_threshold (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings attribute)