Index

_

_DatabaseReader (class in ccdc.io)

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

A

abbreviated_name (ccdc.entry.Journal property) abbreviated_translated_name (ccdc.entry.Journal property) absolute_angle_tolerance (ccdc.search.ReducedCellSearch.Settings property) ACC() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) acceptor (ccdc.search.QueryAtom property) acceptor_atom (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondObservation property) (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) acceptor_atom_type (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAcceptor property) acceptor_atom_type() (ccdc.molecule.Molecule.HBondCriterion method) acceptor_component (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) acceptor_functional_group_name (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) acceptor_label (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) acceptor_range (ccdc.cavity.CavityDatabase.Settings attribute) acceptor_rank (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) accessible_surface_area (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAcceptor property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondDonor property) activity_column (ccdc.descriptors.StatisticalDescriptors.RankStatistics property) 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_crystal_rotamer() (ccdc.docking.Docker.Settings.RotamerLibrary method) add_default_rotamers() (ccdc.docking.Docker.Settings.RotamerLibrary 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_free_rotamer() (ccdc.docking.Docker.Settings.RotamerLibrary method) add_group() (ccdc.molecule.Molecule method) (ccdc.search.SubstructureSearch method) add_habit() (ccdc.search.TextNumericSearch method) add_heat_capacity_notes() (ccdc.search.TextNumericSearch method) add_heat_of_fusion_notes() (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_rotamer() (ccdc.docking.Docker.Settings.RotamerLibrary method) add_rotamer_library() (ccdc.docking.Docker.Settings method) (ccdc.docking.Docker.Settings.ProteinFileInfo method) add_solubility_notes() (ccdc.search.TextNumericSearch method) add_solvent() (ccdc.entry.SolubilityMeasurement method) (ccdc.search.TextNumericSearch method) add_source() (ccdc.search.TextNumericSearch method) add_spacegroup_symbol() (ccdc.search.TextNumericSearch method) add_specific_fixed_rotatable_bond() (ccdc.docking.Docker.Settings 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) add_water_file() (ccdc.docking.Docker.Settings method) advice_comment (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) advice_comment() (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FittingData method) akaike_information_criterion (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) aligned_molecule (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox property) aliphatic_range (ccdc.cavity.CavityDatabase.Settings attribute) all_atoms_have_sites (ccdc.molecule.Molecule property) all_bond_types() (ccdc.molecule.Bond.BondType static method) allow_artificial_inversion (ccdc.crystal.PackingSimilarity.Settings property) allow_molecular_differences (ccdc.crystal.PackingSimilarity.Settings property) allow_overlaps (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition property) amino_acid_code (ccdc.cavity.Cavity.Feature property) analogue (ccdc.entry.Entry property) analyse (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) 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_surface() (ccdc.interaction.InteractionMapAnalysis method) analyse_torsion() (ccdc.conformer.GeometryAnalyser method) angle (ccdc.docking.Docker.Settings.RotamerAngleRange property) (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondObservation property) (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) (ccdc.molecule.Molecule.HBond property) angle_tolerance (ccdc.crystal.PackingSimilarity.Settings property) (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings property) (ccdc.molecule.Molecule.HBondCriterion property) angle_unusual (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) angles (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) (ccdc.utilities.ApplicationInterface property) annotate() (ccdc.pharmacophore.Pharmacophore.FeatureDatabase method) annotation_keys (ccdc.pharmacophore.Pharmacophore.FeatureDatabase property) annotations (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.Entry property) (ccdc.pharmacophore.Pharmacophore.SearchHit property) apolar_shell_correction (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) ApplicationInterface (class in ccdc.utilities) ApplicationInterface.CmdParser (class in ccdc.utilities) apply_quaternion() (ccdc.molecule.Molecule method) apply_rule (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition property) are_labels_pdb_compliant() (ccdc.protein.Protein method) area (ccdc.descriptors.CrystalDescriptors.Morphology.Facet property) (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) area_under_roc_curve (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) aromatic (ccdc.search.QueryAtom property) aromatic_bonds (ccdc.particle.Surface.Descriptors property) aromatic_range (ccdc.cavity.CavityDatabase.Settings attribute) as_dict() (ccdc.particle.SlipPlanes method) (ccdc.particle.SlipPlanes.SlipPlane method) 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 property) atom (ccdc.cavity.Cavity.Feature property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAcceptor property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondDonor property) 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_index (ccdc.docking.Docker.Settings.WaterFileInfo property) atom_indices (ccdc.conformer.GeometryAnalyser.AnalysisHit property) (ccdc.docking.Docker.Results.DockedLigand.ProteinRotatedTorsion property) atom_labels (ccdc.conformer.GeometryAnalyser.Analysis property) (ccdc.conformer.GeometryAnalyser.AnalysisHit property) atom_match (ccdc.descriptors.MolecularDescriptors.Overlay property) atom_plane() (ccdc.descriptors.MolecularDescriptors static method) atom_surface_node_contacts (ccdc.particle.Surface property) atom_torsion_angle() (ccdc.descriptors.MolecularDescriptors static method) atom_vector() (ccdc.descriptors.MolecularDescriptors static method) atomic_number (ccdc.molecule.Atom property) atomic_symbol (ccdc.molecule.Atom property) atomic_weight (ccdc.molecule.Atom property) atoms (ccdc.conformer.GeometryAnalyser.AnalysisHit property) (ccdc.molecule.Bond property) (ccdc.molecule.Molecule property) (ccdc.molecule.Molecule.Contact property) (ccdc.molecule.Molecule.HBond property) (ccdc.protein.Protein.BindingSite property) (ccdc.protein.Protein.Nucleotide property) (ccdc.protein.Protein.Residue property) (ccdc.search.QueryBond property) (ccdc.search.QuerySubstructure property) atoms_on_special_positions() (ccdc.crystal.Crystal method) atoms_within_range() (ccdc.descriptors.MolecularDescriptors.AtomDistanceSearch method) attachment_energy (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) AUC() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) autoscale (ccdc.docking.Docker.Settings property) average_connectivity_index() (ccdc.descriptors.MolecularDescriptors.ConnectivityIndices method) average_density (ccdc.interaction.InteractionLibrary.InteractionData property)

B

backbone_atoms (ccdc.protein.Protein.Residue property) background_color (ccdc.diagram.DiagramGenerator.Settings property) BEDROC() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) best_hit (ccdc.screening.Screener.ScreenHitList property) BFDH_form (ccdc.csp.prediction.Prediction property) BFDHMorphology (class in ccdc.morphology) bias_conformer_selection (ccdc.screening.Screener.Settings property) bin_width (ccdc.utilities.Histogram property) binding_site (ccdc.docking.Docker.Settings property) bioactivity (ccdc.entry.Entry property) Bond (class in ccdc.molecule) bond() (ccdc.molecule.Molecule method) Bond.BondType (class in ccdc.molecule) bond_length (ccdc.conformer.GeometryAnalyser.AnalysisHit property) (ccdc.search.QueryBond property) bond_length() (ccdc.descriptors.MolecularDescriptors static method) bond_polymeric (ccdc.search.QueryBond property) bond_smallest_ring (ccdc.search.QueryBond property)

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

C

c_alpha (ccdc.protein.Protein.Residue property) c_beta (ccdc.protein.Protein.Residue property) c_terminus (ccdc.protein.Protein.Residue property) calculate() (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Parameter method) (ccdc.morphology.VisualHabit method) calculate_connolly_surface (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) calculate_contour_surface (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) calculate_propensities() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) calculated_density (ccdc.crystal.Crystal property) (ccdc.csp.prediction.Prediction property) (ccdc.entry.Entry property) cancel() (ccdc.search.SubstructureSearch.HitProcessor method) carbonyl_oxygen (ccdc.protein.Protein.Residue property) 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 property) 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 property) cavity_radius (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) cavity_residues (ccdc.protein.Protein property) CavityDatabase (class in ccdc.cavity) CavityDatabase.Settings (class in ccdc.cavity) ccdc.cavity module ccdc.conformer module ccdc.crystal module ccdc.csp.csd_landscape_generator module ccdc.csp.database module ccdc.csp.prediction module ccdc.descriptors module ccdc.diagram module ccdc.docking module ccdc.entry module ccdc.interaction module ccdc.io module ccdc.molecule module ccdc.morphology module ccdc.particle module ccdc.pharmacophore module ccdc.protein module ccdc.screening module ccdc.search module ccdc.utilities module ccdc_logo (ccdc.utilities.ApplicationInterface property) ccdc_number (ccdc.entry.Entry property) cell_angles (ccdc.crystal.Crystal property) (ccdc.crystal.Crystal.ReducedCell property) cell_lengths (ccdc.crystal.Crystal property) (ccdc.crystal.Crystal.ReducedCell property) cell_volume (ccdc.crystal.Crystal property) central_group_atoms() (ccdc.interaction.InteractionLibrary.InteractionHit method) central_group_name (ccdc.interaction.InteractionLibrary.InteractionData property) central_groups() (ccdc.interaction.InteractionLibrary.ContactGroup method) centre_molecule() (ccdc.crystal.Crystal method) centre_of_geometry (ccdc.descriptors.CrystalDescriptors.Morphology property) (ccdc.descriptors.CrystalDescriptors.Morphology.Facet property) (ccdc.morphology.BFDHMorphology property) (ccdc.morphology.VisualHabitMorphology property) (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) 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 property) chain_identifier (ccdc.protein.Protein.Residue property) chain_label (ccdc.molecule.Atom property) chains (ccdc.protein.Protein property) change_group() (ccdc.molecule.Molecule method) check_bond_count (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings property) check_bond_polymeric (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings property) check_bond_type (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings property) check_charge (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings property) check_element (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings property) check_hydrogen_count (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings property) chemical_name (ccdc.entry.Entry property) chemical_name_as_html (ccdc.entry.Entry property) chi_number (ccdc.docking.Docker.Results.DockedLigand.ProteinRotatedTorsion property) chirality (ccdc.molecule.Atom property) classification_energy_relative (ccdc.csp.prediction.Prediction property) classification_measure (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) classification_measure_threshold (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) 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) clear_rotamer_libraries() (ccdc.docking.Docker.Settings method) (ccdc.docking.Docker.Settings.ProteinFileInfo method) clear_water_files() (ccdc.docking.Docker.Settings method) clique_rmsd (ccdc.cavity.Cavity.CavityGraphComparison property) close() (ccdc.io._DatabaseReader method) (ccdc.io._DatabaseWriter method) (ccdc.utilities.HTMLReport method) cluster_number (ccdc.pharmacophore.Pharmacophore.SearchHit property) code (ccdc.protein.Protein.Nucleotide property) coefficient (ccdc.search.SimilaritySearch property) (ccdc.search.SimilaritySearch.Settings property)

coefficients (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) cofactors (ccdc.protein.Protein property) (ccdc.protein.Protein.BindingSite property) color (ccdc.entry.Entry property) colour (ccdc.pharmacophore.Pharmacophore.Feature property) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.DatabaseInfo property) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition property) 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 property) complete_small_molecules (ccdc.pharmacophore.Pharmacophore.Search.Settings property) complex_conjugate() (ccdc.descriptors.GeometricDescriptors.Quaternion method) component_label (ccdc.pharmacophore.Pharmacophore.Feature property) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition property) components (ccdc.molecule.Molecule property) conf_file (ccdc.docking.Docker.Settings property) confidence_interval (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient property) 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 property) 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 property) (ccdc.docking.Docker.Settings.ProteinFileInfo property) contact_group_atoms() (ccdc.interaction.InteractionLibrary.InteractionHit method) contact_group_name (ccdc.interaction.InteractionLibrary.InteractionData property) 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 property) contract() (ccdc.utilities.Grid method) convergence_limiting_radius (ccdc.morphology.VisualHabit.Settings property) coordinates (ccdc.cavity.Cavity.Feature property) (ccdc.descriptors.CrystalDescriptors.Morphology.Facet property) (ccdc.interaction.InteractionMapAnalysis.Results.Hotspot property) (ccdc.molecule.Atom property) (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) coordination_count (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions.Observation property) coordination_models_path (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Settings property) copy() (ccdc.descriptors.GeometricDescriptors.Quaternion method) (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 property) count() (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions.Observation method) 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_reference() (ccdc.csp.database.CspDatabase method) cross_references (ccdc.entry.Entry property) crystal (ccdc.conformer.GeometryAnalyser.AnalysisHit property) (ccdc.csp.prediction.Prediction property) (ccdc.entry.Entry property) (ccdc.interaction.InteractionLibrary.InteractionHit property) (ccdc.search.Search.SearchHit property) 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 property) 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) CSDLandscapeGenerator (class in ccdc.csp.csd_landscape_generator) CSDLandscapeGenerator.GeneratedEntry (class in ccdc.csp.csd_landscape_generator) CSDLandscapeGenerator.Settings (class in ccdc.csp.csd_landscape_generator) CspDatabase (class in ccdc.csp.database) CspDatabase.LandscapeSummary (class in ccdc.csp.database) current_entry (ccdc.utilities.ApplicationInterface property) custom_grid_bounding_box (ccdc.interaction.InteractionMapAnalysis.CommonSettings property) cyclic (ccdc.search.QueryAtom property) (ccdc.search.QueryBond property) cyclic_bonds (ccdc.search.QueryAtom property) cysteine_sulphur (ccdc.protein.Protein.Residue property)

D

d_min (ccdc.conformer.GeometryAnalyser.Analysis property) d_spacing (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) da_distance (ccdc.molecule.Molecule.HBond property) database_file (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.Settings property) database_name (ccdc.entry.Entry property) database_path (ccdc.utilities.ApplicationInterface attribute) databases (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Settings property) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase property) days_remaining (ccdc.utilities.Licence property) 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 property) deposition_date (ccdc.entry.Entry property) description (ccdc.pharmacophore.Pharmacophore.Feature property) descriptor (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet property) descriptors (ccdc.particle.Surface property) detect_cavities (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) detect_cavity (ccdc.docking.Docker.Settings property) detect_cavity_from_residues (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) detect_hotspots (ccdc.interaction.InteractionMapAnalysis.CommonSettings property) detect_internal_hydrogen_bonds (ccdc.docking.Docker.Settings property) detect_intra_hbonds (ccdc.diagram.DiagramGenerator.Settings attribute) detect_ligand_bonds() (ccdc.protein.Protein method) deuterium_is_hydrogen (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings property) DiagramGenerator (class in ccdc.diagram) DiagramGenerator.Settings (class in ccdc.diagram) dilate() (ccdc.utilities.Grid method) disorder_details (ccdc.entry.Entry property) disordered_molecule (ccdc.crystal.Crystal property) (ccdc.entry.Entry property) displacement_parameters (ccdc.molecule.Atom property) distance (ccdc.descriptors.GeometricDescriptors.Plane property) (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondObservation property) (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) (ccdc.interaction.InteractionLibrary.InteractionHit property) distance() (ccdc.cavity.Cavity.Feature method) distance_range (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings property) (ccdc.molecule.Molecule.HBondCriterion property) (ccdc.pharmacophore.Pharmacophore.Query.DistanceConstraint property) distance_tolerance (ccdc.crystal.PackingSimilarity.Settings property) distance_unusual (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) distances (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) (ccdc.utilities.ApplicationInterface property) distribution (ccdc.conformer.GeometryAnalyser.Analysis property) distributions_pruned (ccdc.conformer.ConformerHitList property) diverse_solutions (ccdc.docking.Docker.Settings property) dock() (ccdc.docking.Docker method) (ccdc.docking.Docker.InteractiveResults method) dock_status() (ccdc.docking.Docker method) docked_waters (ccdc.docking.Docker.Results.DockedLigand property) 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.DockedLigand.ProteinRotatedTorsion (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.PharmacophoreConstraint (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.Rotamer (class in ccdc.docking) Docker.Settings.RotamerAngleRange (class in ccdc.docking) Docker.Settings.RotamerLibrary (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) Docker.Settings.WaterFileInfo (class in ccdc.docking) docking_log (ccdc.docking.Docker.Results property) donor (ccdc.search.QueryAtom property) donor_acceptor_range (ccdc.cavity.CavityDatabase.Settings attribute) donor_atom (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondObservation property) (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) donor_atom_type (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondDonor property) donor_atom_type() (ccdc.molecule.Molecule.HBondCriterion method) donor_component (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) donor_functional_group_name (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) donor_label (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) donor_range (ccdc.cavity.CavityDatabase.Settings attribute) donor_rank (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) 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 property) edge_labels (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet property) edges (ccdc.descriptors.CrystalDescriptors.Morphology.Facet property) (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) EF() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) eissn (ccdc.entry.Journal property) electrostatic (ccdc.morphology.VisualHabit.Results.LatticeEnergy property) electrostatic_correction (ccdc.morphology.VisualHabit.Settings property) element_coloring (ccdc.diagram.DiagramGenerator.Settings property) element_pair_count() (ccdc.descriptors.MolecularDescriptors.AtomPairDistanceDescriptorCalculator method) end_value (ccdc.utilities.Histogram property) end_year (ccdc.entry.Journal property) energy (ccdc.docking.Docker.Settings.Rotamer property) enough_hits (ccdc.conformer.GeometryAnalyser.Analysis property) entries() (ccdc.io._DatabaseReader method) entry (ccdc.conformer.GeometryAnalyser.AnalysisHit property) (ccdc.csp.prediction.Prediction property) (ccdc.interaction.InteractionLibrary.InteractionHit property) (ccdc.search.Search.SearchHit property)

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 property) error_file() (ccdc.interaction.InteractionMapAnalysis.Results method) error_log (ccdc.docking.Docker.Results property) esd (ccdc.descriptors.CrystalDescriptors.PowderPattern property) estimate (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient property) excluded_volume_envelop (ccdc.screening.Screener.Settings property) excluded_volume_penalty (ccdc.screening.Screener.Settings property) exit_with_error() (ccdc.utilities.ApplicationInterface method) experimental_refcodes (ccdc.csp.database.CspDatabase.LandscapeSummary property) explicit_polar_hydrogens (ccdc.diagram.DiagramGenerator.Settings attribute) extrema (ccdc.utilities.Grid property) ez_stereochemistry (ccdc.molecule.Bond property)

F

facets (ccdc.descriptors.CrystalDescriptors.Morphology property) (ccdc.morphology.BFDHMorphology property) (ccdc.morphology.VisualHabitMorphology property) fatal() (ccdc.utilities.Logger method) feature_database (ccdc.pharmacophore.Pharmacophore.Search property) feature_definitions (ccdc.pharmacophore.Pharmacophore.FeatureDatabase property) feature_point1 (ccdc.pharmacophore.Pharmacophore.Query.DistanceConstraint property) feature_point2 (ccdc.pharmacophore.Pharmacophore.Query.DistanceConstraint property) feature_points() (ccdc.pharmacophore.Pharmacophore.PointGenerator method) (ccdc.pharmacophore.Pharmacophore.SearchHit method) features (ccdc.cavity.Cavity property) (ccdc.pharmacophore.Pharmacophore.Query property) 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 property) few_hits_threshold (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) file_name (ccdc.docking.Docker.Settings.ProteinFileInfo property) (ccdc.docking.Docker.Settings.WaterFileInfo property) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.DatabaseInfo property) file_path (ccdc.utilities.ApplicationInterface property) FileLogger (class in ccdc.utilities) files (ccdc.utilities.Licence property) filter_smarts (ccdc.pharmacophore.Pharmacophore.ExcludedVolume property) final_angle (ccdc.docking.Docker.Results.DockedLigand.ProteinRotatedTorsion property) fitness() (ccdc.docking.Docker.Results.DockedLigand method) fitness_function (ccdc.docking.Docker.Settings property) fitting_data (ccdc.descriptors.CrystalDescriptors.HBondPropensities property) fitting_points_cluster_radius (ccdc.screening.Screener.Settings property) fitting_points_file (ccdc.docking.Docker.Settings property) fitting_points_threshold (ccdc.screening.Screener.Settings property) fix_all_protein_rotatable_bonds (ccdc.docking.Docker.Settings property) fix_ligand_rotatable_bonds (ccdc.docking.Docker.Settings property) flexible_rings (ccdc.conformer.ConformerHitList property) flip_amide_bonds (ccdc.docking.Docker.Settings property) flip_free_corners (ccdc.docking.Docker.Settings property) flip_planar_nitrogen (ccdc.docking.Docker.Settings property) flip_pyramidal_nitrogen (ccdc.docking.Docker.Settings property) flood_fill() (ccdc.utilities.Grid method) font_family (ccdc.diagram.DiagramGenerator.Settings property) font_italic (ccdc.diagram.DiagramGenerator.Settings property) font_size (ccdc.diagram.DiagramGenerator.Settings property) font_weight (ccdc.diagram.DiagramGenerator.Settings property) force_constraints (ccdc.docking.Docker.Settings property) foreground_color (ccdc.diagram.DiagramGenerator.Settings property) formal_charge (ccdc.molecule.Atom property) (ccdc.molecule.Molecule property) (ccdc.search.QueryAtom property) formal_valency (ccdc.search.QueryAtom property) format (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.Settings property) format_time() (ccdc.utilities.Timer static method) formatted_melting_point_range (ccdc.entry.Entry property) formatted_melting_point_text (ccdc.entry.Entry property) formula (ccdc.crystal.Crystal property) (ccdc.entry.Entry property) (ccdc.molecule.Molecule property) (ccdc.protein.Protein.BindingSite property) fractional_coordinates (ccdc.molecule.Atom property)

fractional_uncertainties (ccdc.molecule.Atom property) fragment_identifier() (ccdc.conformer.GeometryAnalyser method) fragment_label (ccdc.conformer.GeometryAnalyser.Analysis property) free_energy_id (ccdc.csp.prediction.Prediction property) free_energy_method (ccdc.csp.prediction.Prediction property) free_energy_relative (ccdc.csp.prediction.Prediction property) frequencies (ccdc.utilities.Histogram property) from_cif() (ccdc.csp.prediction.Prediction static method) from_crystal() (ccdc.descriptors.CrystalDescriptors.PowderPattern static method) from_dict() (ccdc.utilities.Grid method) from_dimensions() (ccdc.descriptors.GeometricDescriptors.Quaternion static method) from_entry() (ccdc.protein.Protein static method) from_euler_angles() (ccdc.descriptors.GeometricDescriptors.Quaternion 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.interaction.InteractionMapAnalysis.SurfaceSettings static method) (ccdc.morphology.BFDHMorphology static method) (ccdc.morphology.VisualHabitMorphology 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) (ccdc.morphology.BFDHMorphology static method) (ccdc.morphology.VisualHabitMorphology 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_vector_and_angle() (ccdc.descriptors.GeometricDescriptors.Quaternion static 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 property) full_width_at_half_maximum (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings property) functional_group_identifier (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAcceptor property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondDonor property) functional_groups_of_hbond() (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions method) fuse_rings() (ccdc.molecule.Molecule method)

G

generalisation (ccdc.conformer.GeometryAnalyser.Settings property) generalised (ccdc.conformer.GeometryAnalyser.Analysis property) generate() (ccdc.conformer.ConformerGenerator method) (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator method) generate_hbond_groupings() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) GeometricDescriptors (class in ccdc.descriptors) GeometricDescriptors.Plane (class in ccdc.descriptors) GeometricDescriptors.Quaternion (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 property) (ccdc.interaction.InteractionMapAnalysis.SurfaceSettings property) 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

h_bond (ccdc.morphology.VisualHabit.Results.LatticeEnergy property) h_bond_attraction (ccdc.morphology.VisualHabit.Results.LatticeEnergy property) h_bond_repulsion (ccdc.morphology.VisualHabit.Results.LatticeEnergy property) h_bonded (ccdc.particle.SlipPlanes.SlipPlane property) habit (ccdc.entry.Entry property) has_3d_coordinates (ccdc.search.QueryAtom property) (ccdc.search.Search.Settings property) has_3d_structure (ccdc.entry.Entry property) has_charged_atoms (ccdc.molecule.Molecule property) has_disorder (ccdc.crystal.Crystal property) (ccdc.entry.Entry property) hb_acceptors (ccdc.particle.Surface.AtomProperties property) (ccdc.particle.Surface.Descriptors property) hb_donors (ccdc.particle.Surface.AtomProperties property) (ccdc.particle.Surface.Descriptors property) hbond_atoms() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) hbond_count (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) hbond_dimensionality (ccdc.particle.SlipPlanes property) hbond_inter_frequency (ccdc.csp.database.CspDatabase.LandscapeSummary property) hbond_intra_frequency (ccdc.csp.database.CspDatabase.LandscapeSummary property) hbond_network() (ccdc.crystal.Crystal method) hbonds (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet property) hbonds() (ccdc.crystal.Crystal method) (ccdc.molecule.Molecule method) heat_capacity (ccdc.entry.Entry property)

heat_capacity_notes (ccdc.entry.Entry property) heat_of_fusion (ccdc.entry.Entry property) heat_of_fusion_notes (ccdc.entry.Entry property) heaviest_component (ccdc.molecule.Molecule property) heaviest_element (ccdc.conformer.GeometryAnalyser.Settings property) heavy_atoms (ccdc.molecule.Molecule property) highlight_color (ccdc.diagram.DiagramGenerator.Settings property) histogram (ccdc.interaction.InteractionLibrary.InteractionData property) Histogram (class in ccdc.utilities) histogram() (ccdc.conformer.GeometryAnalyser.Analysis method) histogram_reference_points (ccdc.cavity.CavityDatabase.Settings attribute) histograms (ccdc.cavity.Cavity.CavityDistanceHistograms property) hit_identifiers (ccdc.conformer.GeometryAnalyser.Analysis property) hit_molecules (ccdc.conformer.GeometryAnalyser.Analysis property) hits (ccdc.conformer.GeometryAnalyser.Analysis property) (ccdc.interaction.InteractionLibrary.InteractionData property) hkl (ccdc.crystal.Crystal.MillerIndices property) hotspots() (ccdc.interaction.InteractionMapAnalysis.Results method) hotspots_min_value (ccdc.interaction.InteractionMapAnalysis.CommonSettings property) hotspots_ncycles (ccdc.interaction.InteractionMapAnalysis.CommonSettings property) hotspots_refine (ccdc.interaction.InteractionMapAnalysis.CommonSettings property) html_report() (ccdc.utilities.ApplicationInterface method) HTMLReport (class in ccdc.utilities) hydrogen_bonds (ccdc.csp.prediction.Prediction property) HydrogenBondStatisticsSearch (class in ccdc.interaction) HydrogenBondStatisticsSearch.HydrogenBondObservation (class in ccdc.interaction) HydrogenBondStatisticsSearch.HydrogenBondStatistics (class in ccdc.interaction) HydrogenBondStatisticsSearch.Settings (class in ccdc.interaction)

I

ideal_bond_length (ccdc.molecule.Bond property) identifier (ccdc.cavity.Cavity property) (ccdc.conformer.GeometryAnalyser.AnalysisHit property) (ccdc.crystal.Crystal property) (ccdc.csp.prediction.Prediction property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FittingData.FittingDataEntry property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FunctionalGroup property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAcceptor property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondDonor property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Parameter property) (ccdc.entry.Entry property) (ccdc.interaction.InteractionLibrary.InteractionHit property) (ccdc.molecule.Molecule property) (ccdc.pharmacophore.Pharmacophore.Feature property) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase.Entry property) (ccdc.pharmacophore.Pharmacophore.FeatureDefinition property) (ccdc.pharmacophore.Pharmacophore.SearchHit property) (ccdc.protein.Protein.Nucleotide property) (ccdc.protein.Protein.Residue property) (ccdc.search.Search.SearchHit property) (ccdc.utilities.ApplicationInterface attribute) identifier() (ccdc.io._DatabaseReader method) identifiers (ccdc.entry.Entry.CrossReference property) (ccdc.pharmacophore.Pharmacophore.FeatureDatabase property) ignore_bond_counts (ccdc.crystal.PackingSimilarity.Settings property) ignore_bond_types (ccdc.crystal.PackingSimilarity.Settings property) ignore_hydrogen_counts (ccdc.crystal.PackingSimilarity.Settings property) ignore_hydrogen_positions (ccdc.crystal.PackingSimilarity.Settings property) ignore_hydrogens (ccdc.descriptors.MolecularDescriptors.MaximumCommonSubstructure.Settings property) ignore_line_numbers() (ccdc.utilities.Logger method) ignore_smallest_components (ccdc.crystal.PackingSimilarity.Settings property) image() (ccdc.diagram.DiagramGenerator method) image_height (ccdc.diagram.DiagramGenerator.Settings property) image_url (ccdc.entry.Journal property) image_width (ccdc.diagram.DiagramGenerator.Settings property) impose_upper_limits (ccdc.conformer.GeometryAnalyser.Settings property) improper (ccdc.docking.Docker.Settings.Rotamer property) improper_angle (ccdc.docking.Docker.Settings.Rotamer property) include_hydrogens (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings property) index (ccdc.molecule.Atom property) (ccdc.search.QueryAtom property) index() (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions.Observation method) indices_at_value() (ccdc.utilities.Grid method) input_angle (ccdc.docking.Docker.Results.DockedLigand.ProteinRotatedTorsion property) input_h2a_file (ccdc.utilities.ApplicationInterface property) input_m2a_file (ccdc.utilities.ApplicationInterface property) input_melting_point_range (ccdc.entry.Entry property) input_melting_point_text (ccdc.entry.Entry property) 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 property) 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) InteractionMapAnalysis.SurfaceSettings (class in ccdc.interaction) interface_file (ccdc.utilities.ApplicationInterface attribute) intermolecular (ccdc.crystal.Crystal.Contact property) (ccdc.crystal.Crystal.HBond property) (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings property) (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) (ccdc.molecule.Molecule.Contact property) (ccdc.molecule.Molecule.HBondCriterion property) international_coden (ccdc.entry.Journal property) intra_only (ccdc.pharmacophore.Pharmacophore.Query property) inverse() (ccdc.molecule.Molecule.Transformation method) invert() (ccdc.descriptors.GeometricDescriptors.Quaternion method) is_3d (ccdc.molecule.Molecule property) is_acceptor (ccdc.molecule.Atom property) is_acceptor() (ccdc.molecule.Molecule.HBondCriterion method) is_acceptor_bifurcated (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) is_acidic (ccdc.protein.Protein.Residue property) is_aromatic (ccdc.molecule.Ring property) is_baseline (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient property) is_basic (ccdc.protein.Protein.Residue property) is_centrosymmetric (ccdc.crystal.Crystal property) is_chiral (ccdc.molecule.Atom property) is_conjugated (ccdc.molecule.Bond property) is_cyclic (ccdc.molecule.Atom property) (ccdc.molecule.Bond property) is_donor (ccdc.molecule.Atom property) is_donor() (ccdc.molecule.Molecule.HBondCriterion method) is_donor_bifurcated (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) is_fully_conjugated (ccdc.molecule.Ring property) is_fused (ccdc.molecule.Ring property) is_hydrophilic (ccdc.protein.Protein.Residue property) is_hydrophobic (ccdc.protein.Protein.Residue property) is_in_line_of_sight (ccdc.molecule.Molecule.Contact property) (ccdc.molecule.Molecule.HBond property) is_in_line_of_sight() (ccdc.molecule.Atom method) is_in_protein (ccdc.molecule.Atom property) is_intermolecular (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) is_journal_valid() (ccdc.search.TextNumericSearch method) is_metal (ccdc.molecule.Atom property) is_normalised (ccdc.search.ReducedCellSearch.Settings property) is_observed (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) is_organic (ccdc.entry.Entry property) (ccdc.molecule.Molecule property) is_organometallic (ccdc.entry.Entry property) (ccdc.molecule.Molecule property) is_polymeric (ccdc.entry.Entry property) (ccdc.molecule.Molecule property) is_powder_study (ccdc.entry.Entry property) is_rotatable (ccdc.molecule.Bond property) is_sohncke (ccdc.crystal.Crystal property) is_spiro (ccdc.molecule.Atom property) is_systematically_absent (ccdc.descriptors.CrystalDescriptors.PowderPattern.TickMark property) is_valid (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions property) islands() (ccdc.utilities.Grid method) isotropic_equivalent (ccdc.molecule.Atom.DisplacementParameters property) issn (ccdc.entry.Journal property) items() (ccdc.molecule.Molecule.HBondCriterion.HBondAtomTypes method)

J

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

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

K

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

keys() (ccdc.molecule.Molecule.HBondCriterion.HBondAtomTypes method) known_cofactor_codes() (ccdc.protein.Protein static method) kurtosis (ccdc.particle.Surface.Descriptors property)

L

label (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions.Observation property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAcceptor property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondAtom property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.HBondDonor property) (ccdc.molecule.Atom property) label_match (ccdc.search.QueryAtom property) label_set (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet property) label_to_atom_index() (ccdc.search.SMARTSSubstructure method) landscape (ccdc.csp.prediction.Prediction property) landscape_names (ccdc.csp.database.CspDatabase property) landscape_summary() (ccdc.csp.database.CspDatabase method) language_name (ccdc.entry.Journal property) largest_clique_size (ccdc.cavity.Cavity.FastCavityGraphComparison property) largest_ring_size (ccdc.molecule.Molecule property) lattice_centring (ccdc.crystal.Crystal property) lattice_energy (ccdc.morphology.VisualHabit.Results property) length (ccdc.descriptors.GeometricDescriptors.Vector property) (ccdc.molecule.Bond property) (ccdc.molecule.Molecule.Contact property) (ccdc.molecule.Molecule.HBond property) level (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) Licence (class in ccdc.utilities) ligand_files (ccdc.docking.Docker.Settings property)

ligand_identifiers (ccdc.cavity.Cavity property) ligand_log() (ccdc.docking.Docker.Results method) ligand_range (ccdc.cavity.CavityDatabase.Settings attribute) ligands (ccdc.cavity.Cavity property) (ccdc.docking.Docker.Results property) (ccdc.docking.Docker.Settings property) (ccdc.protein.Protein property) (ccdc.protein.Protein.BindingSite property) limit_identifier_list (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Settings property) line_width (ccdc.diagram.DiagramGenerator.Settings property) local_density (ccdc.conformer.GeometryAnalyser.Analysis property) local_density_threshold (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) local_density_tolerance (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) 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 property) log_likelihood_test_p_value (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) logfile (ccdc.cavity.CavityDatabase.Settings attribute) Logger (class in ccdc.utilities) logp_hydrophobic_attenuation_a (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) logp_hydrophobic_attenuation_b (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) lower_quartile (ccdc.conformer.GeometryAnalyser.Analysis property) lowest_energy_prediction_name (ccdc.csp.database.CspDatabase.LandscapeSummary property)

M

major_length (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox property) make_absolute_file_names() (ccdc.docking.Docker.Settings method) make_complex() (ccdc.docking.Docker.Results method) make_fitting_data() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) march_dollase_preferred_orientation (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings property) 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) match_entire_packing_shell (ccdc.crystal.PackingSimilarity.Settings property) match_fitting_data() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) match_full_name() (ccdc.entry.JournalList method) match_molecule() (ccdc.search.QuerySubstructure method) match_template_conformations (ccdc.docking.Docker.Settings property) matched_refcode (ccdc.csp.prediction.Prediction property) matches() (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FunctionalGroup method) matching_prediction_names (ccdc.csp.database.CspDatabase.LandscapeSummary property) max (ccdc.entry.SolubilityMeasurement.Solubility property) max_0K_relative_energy (ccdc.csp.database.CspDatabase.LandscapeSummary property) max_chain_size (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) max_conformers (ccdc.conformer.ConformerSettings attribute) max_delta (ccdc.docking.Docker.Settings.RotamerAngleRange property) max_discrete_chain_size (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings attribute) max_distance (ccdc.descriptors.MolecularDescriptors.Overlay property) (ccdc.interaction.InteractionLibrary.InteractionData property) max_hit_rmsd (ccdc.pharmacophore.Pharmacophore.Search.Settings property) max_hit_structures (ccdc.cavity.CavityDatabase.Settings attribute) (ccdc.pharmacophore.Pharmacophore.Search.Settings property) (ccdc.search.Search.Settings property) max_hit_structures() (ccdc.search.CombinedSearch static method) max_hits_per_structure (ccdc.pharmacophore.Pharmacophore.Search.Settings property) (ccdc.search.SubstructureSearch.Settings property) max_log_probability (ccdc.conformer.ConformerHitList property) max_product_graph_size (ccdc.cavity.CavityDatabase.Settings attribute) max_r_factor (ccdc.search.Search.Settings property) 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 property) maximum_feature_distance (ccdc.pharmacophore.Pharmacophore.Query property) mean (ccdc.conformer.GeometryAnalyser.Analysis property) 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 property) median_length (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox property) melting_point (ccdc.entry.Entry property) melting_point_default_units (ccdc.entry.Entry property) melting_point_display_string (ccdc.entry.Entry property) metal_range (ccdc.cavity.CavityDatabase.Settings attribute) metals (ccdc.protein.Protein property) (ccdc.protein.Protein.BindingSite property) mid_plane (ccdc.particle.SlipPlanes.SlipPlane property) miller_indices (ccdc.descriptors.CrystalDescriptors.Morphology.Facet property) (ccdc.descriptors.CrystalDescriptors.PowderPattern.TickMark property) (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) (ccdc.particle.Surface property) miller_indices() (ccdc.crystal.Crystal method) min (ccdc.entry.SolubilityMeasurement.Solubility property) min_cavity_buriedness (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) min_cavity_volume (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) min_delta (ccdc.docking.Docker.Settings.RotamerAngleRange property) min_distance (ccdc.interaction.InteractionLibrary.InteractionData property) min_log_probability (ccdc.conformer.ConformerHitList property) min_obs_exact (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) min_obs_generalised (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) min_relevance (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property) min_value_of_neighbours() (ccdc.utilities.Grid method) minimise() (ccdc.conformer.MoleculeMinimiser method) minimised_molecule (ccdc.conformer.ConformerHitList property)

minimum (ccdc.conformer.GeometryAnalyser.Analysis property) minor_length (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox property) module ccdc.cavity ccdc.conformer ccdc.crystal ccdc.csp.csd_landscape_generator ccdc.csp.database ccdc.csp.prediction ccdc.descriptors ccdc.diagram ccdc.docking ccdc.entry ccdc.interaction ccdc.io ccdc.molecule ccdc.morphology ccdc.particle ccdc.pharmacophore ccdc.protein ccdc.screening ccdc.search ccdc.utilities utilities.csp.create_shape_database.create_shape_database utilities.csp.csp_cross_reference.csp_cross_reference utilities.csp.delete_csp_landscape.delete_csp_landscape utilities.csp.import_csp_landscape.import_csp_landscape modules (ccdc.utilities.Licence property) molecular_shape_average (ccdc.csp.prediction.Prediction property) molecular_shape_descriptor_average_max (ccdc.csp.database.CspDatabase.LandscapeSummary property) molecular_shape_descriptor_average_min (ccdc.csp.database.CspDatabase.LandscapeSummary property) molecular_shape_descriptor_difference_max (ccdc.csp.database.CspDatabase.LandscapeSummary property) molecular_shape_descriptor_difference_min (ccdc.csp.database.CspDatabase.LandscapeSummary property) molecular_shape_difference (ccdc.csp.prediction.Prediction property) molecular_shell() (ccdc.crystal.Crystal method) molecular_similarity_threshold (ccdc.crystal.PackingSimilarity.Settings property) molecular_volume (ccdc.molecule.Molecule property) molecular_weight (ccdc.molecule.Molecule property) 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.Overlay (class in ccdc.descriptors) MolecularDescriptors.PrincipleAxesAlignedBox (class in ccdc.descriptors) molecule (ccdc.conformer.GeometryAnalyser.AnalysisHit property) (ccdc.crystal.Crystal property) (ccdc.csp.prediction.Prediction property) (ccdc.descriptors.MolecularDescriptors.Overlay property) (ccdc.entry.Entry property) (ccdc.interaction.InteractionLibrary.InteractionHit property) (ccdc.pharmacophore.Pharmacophore.SearchHit property) (ccdc.search.Search.SearchHit property) (ccdc.search.SimilaritySearch property) 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) morphology (ccdc.morphology.VisualHabit.Results property) must_have_elements (ccdc.search.Search.Settings property) must_not_have_elements (ccdc.search.Search.Settings property)

N

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

no_errors (ccdc.search.Search.Settings property) no_hits (ccdc.conformer.GeometryAnalyser.Analysis property) no_ions (ccdc.search.Search.Settings property) no_metals (ccdc.search.Search.Settings property) no_powder (ccdc.search.Search.Settings property) nodes (ccdc.particle.Surface.Topology property) normal (ccdc.descriptors.GeometricDescriptors.Plane property) normalise_atom_order() (ccdc.molecule.Molecule method) normalise_hydrogens() (ccdc.molecule.Molecule method) normalise_labels() (ccdc.molecule.Molecule method) (ccdc.protein.Protein method) normalised_score (ccdc.conformer.ConformerHit property) not_polymeric (ccdc.search.Search.Settings property) notes (ccdc.entry.SolubilityMeasurement property) noverflow (ccdc.utilities.Histogram property) nsteps (ccdc.utilities.Grid property) nstructures (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.Settings property) nthreads (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.Settings property) nucleic_acid_identifier (ccdc.protein.Protein.Nucleotide property) nucleic_acids (ccdc.protein.Protein property) nucleotides (ccdc.protein.Protein property) (ccdc.protein.Protein.BindingSite property) (ccdc.protein.Protein.NucleicAcid property) null_deviance (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) null_deviance_degrees_of_freedom (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) num_bonds (ccdc.search.QueryAtom property) num_hydrogens (ccdc.search.QueryAtom property) num_threads (ccdc.interaction.InteractionMapAnalysis.CommonSettings property) number_exp_matches (ccdc.csp.database.CspDatabase.LandscapeSummary property) number_of_torsions (ccdc.docking.Docker.Settings.RotamerLibrary property) number_predictions_0K (ccdc.csp.database.CspDatabase.LandscapeSummary property) number_simulated_T_non_zero (ccdc.csp.database.CspDatabase.LandscapeSummary property) nunderflow (ccdc.utilities.Histogram property) nvalues (ccdc.utilities.Histogram property) nvdw_contacts (ccdc.interaction.InteractionLibrary.InteractionData property)

O

observations (ccdc.interaction.HydrogenBondStatisticsSearch.HydrogenBondStatistics property) observed (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions property) occupancy (ccdc.molecule.Atom property) offset (ccdc.particle.SlipPlanes.SlipPlane property) (ccdc.particle.Surface property) one_letter_code (ccdc.protein.Protein.Nucleotide property) (ccdc.protein.Protein.Residue property) only_organic (ccdc.search.Search.Settings property) only_organometallic (ccdc.search.Search.Settings property) open_output_folder() (ccdc.utilities.ApplicationInterface method) optimisation_energy_model (ccdc.csp.prediction.Prediction property) optimisation_energy_model_definition (ccdc.csp.prediction.Prediction property) options (ccdc.utilities.ApplicationInterface attribute) order (ccdc.crystal.Crystal.MillerIndices property) organometallic_filter (ccdc.conformer.GeometryAnalyser.Settings property) orientation (ccdc.particle.SlipPlanes.SlipPlane property) oriented_bounding_box (ccdc.descriptors.CrystalDescriptors.Morphology property) (ccdc.morphology.BFDHMorphology property) (ccdc.morphology.VisualHabitMorphology property) original_molecule (ccdc.conformer.ConformerHitList property) 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 property) (ccdc.screening.Screener.Settings property)

output_directory_path (ccdc.utilities.ApplicationInterface attribute) output_file (ccdc.docking.Docker.Settings property) output_file_name() (ccdc.utilities.ApplicationInterface method) output_format (ccdc.docking.Docker.Settings property) 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 property) 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 property) overlay_rmsds_and_transformation() (ccdc.descriptors.MolecularDescriptors static method) overlay_transformation (ccdc.pharmacophore.Pharmacophore.SearchHit property) 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 property) packing (ccdc.pharmacophore.Pharmacophore.Query property) packing() (ccdc.crystal.Crystal method) packing_coefficient (ccdc.crystal.Crystal property) (ccdc.csp.prediction.Prediction property) packing_coefficient_max (ccdc.csp.database.CspDatabase.LandscapeSummary property) packing_coefficient_min (ccdc.csp.database.CspDatabase.LandscapeSummary property) packing_shell() (ccdc.crystal.Crystal method) packing_shell_size (ccdc.crystal.PackingSimilarity.Comparison property) (ccdc.crystal.PackingSimilarity.Settings property) PackingSimilarity (class in ccdc.crystal) PackingSimilarity.Comparison (class in ccdc.crystal) PackingSimilarity.Settings (class in ccdc.crystal) parameter_directory (ccdc.screening.Screener.Settings property) parameters (ccdc.pharmacophore.Pharmacophore.PointGenerator property) parse_commandline() (ccdc.utilities.ApplicationInterface method) partial_charge (ccdc.molecule.Atom property) path_length_range (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings property) (ccdc.molecule.Molecule.HBondCriterion property) peptide_sequence (ccdc.entry.Entry property) percent_length_tolerance (ccdc.search.ReducedCellSearch.Settings property) percentage_area (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) percentile() (ccdc.conformer.GeometryAnalyser.Analysis method) perform_regression() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) period (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.GraphSet property) periodic_vectors (ccdc.particle.Surface property) permutational_equivalence (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition property) perpendicular_distance (ccdc.descriptors.CrystalDescriptors.Morphology.Facet property) (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) perpendicular_slip_planes (ccdc.particle.SlipPlanes.SlipPlane property) 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 property) pi_range (ccdc.cavity.CavityDatabase.Settings attribute) plane (ccdc.crystal.Crystal.MillerIndices property) (ccdc.descriptors.CrystalDescriptors.Morphology.Facet property) (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) 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 property)

plane_vector2 (ccdc.descriptors.GeometricDescriptors.Plane property) 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 property) point_generators (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition property) point_group_analysis() (ccdc.descriptors.MolecularDescriptors static method) point_torsion_angle() (ccdc.descriptors.GeometricDescriptors static method) points (ccdc.pharmacophore.Pharmacophore.SearchHit property) polar_shell_correction (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) polymer_expansion() (ccdc.crystal.Crystal method) polymorph (ccdc.entry.Entry property) populate_all() (ccdc.cavity.CavityDatabase method) potential (ccdc.morphology.VisualHabit.Settings property) powder_filter (ccdc.conformer.GeometryAnalyser.Settings property) PPV() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) precision (ccdc.molecule.Atom.DisplacementParameters property) (ccdc.utilities.Uncertainty property) (ccdc.utilities.UncertainValue property) predict() (ccdc.descriptors.CrystalDescriptors.HBondCoordination method) Prediction (class in ccdc.csp.prediction) prediction() (ccdc.csp.database.CspDatabase method) prediction_identifiers() (ccdc.csp.database.CspDatabase method) predictions_for_label() (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions method) predictive_error (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) prepare() (ccdc.docking.Docker.LigandPreparation method) pressure (ccdc.entry.Entry property) previous_identifier (ccdc.entry.Entry property) probability (ccdc.conformer.ConformerHit property) (ccdc.descriptors.CrystalDescriptors.HBondCoordination.Predictions.Observation property) product_graph_size (ccdc.cavity.Cavity.FastCavityGraphComparison property) program_executable_path (ccdc.utilities.ApplicationInterface property) program_path (ccdc.utilities.ApplicationInterface attribute) progress() (ccdc.utilities.Timer static method) projected_area (ccdc.particle.Surface.Descriptors property) propensities (ccdc.descriptors.CrystalDescriptors.HBondPropensities property) propensity (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) proper (ccdc.crystal.Crystal.MillerIndices property) protein (ccdc.pharmacophore.Pharmacophore.SearchHit property) 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 property) protein_files (ccdc.docking.Docker.Settings property) protein_log (ccdc.docking.Docker.Results property) protein_rotated_torsions() (ccdc.docking.Docker.Results.DockedLigand method) protein_vector (ccdc.cavity.Cavity.Feature property) proteins (ccdc.docking.Docker.Results property) (ccdc.docking.Docker.Settings property) publication (ccdc.entry.Entry property) publications (ccdc.entry.Entry property) publisher_name (ccdc.entry.Journal property)

Q

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

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

R

r_factor (ccdc.entry.Entry property) radiation_source (ccdc.entry.Entry property) 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 property) 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) refcode_match (ccdc.csp.prediction.Prediction property) refcode_match_rmsd (ccdc.csp.prediction.Prediction property) reference_ligand_file (ccdc.docking.Docker.Settings property) relative_area() (ccdc.descriptors.CrystalDescriptors.Morphology method) (ccdc.morphology.BFDHMorphology method) (ccdc.morphology.VisualHabitMorphology method) relative_density (ccdc.interaction.InteractionLibrary.InteractionData property) relative_score (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.GeneratedEntry property) remarks (ccdc.entry.Entry property) remove() (ccdc.io._DatabaseWriter method) (ccdc.io.EntryWriter 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_rotamer() (ccdc.docking.Docker.Settings.RotamerLibrary method) remove_rotamers() (ccdc.docking.Docker.Settings.RotamerLibrary method)

remove_specific_fixed_rotatable_bond() (ccdc.docking.Docker.Settings method) remove_unknown_atoms() (ccdc.molecule.Molecule method) remove_water() (ccdc.protein.Protein method) repeat_distance (ccdc.particle.SlipPlanes.SlipPlane property) report() (ccdc.utilities.Timer method) require_hydrogens (ccdc.descriptors.CrystalDescriptors.GraphSetSearch.Settings property) (ccdc.molecule.Molecule.HBondCriterion property) rescore_function (ccdc.docking.Docker.Settings property) reset() (ccdc.search.ReducedCellSearch.Settings method) (ccdc.utilities.Logger class method) residual_deviance (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) residual_deviance_degrees_of_freedom (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model property) residue (ccdc.cavity.Cavity.Feature property) residue_label (ccdc.molecule.Atom property) residues (ccdc.protein.Protein property) (ccdc.protein.Protein.BindingSite property) (ccdc.protein.Protein.Chain property) results (ccdc.docking.Docker property) return_type (ccdc.diagram.DiagramGenerator.Settings property) rfactor_filter (ccdc.conformer.GeometryAnalyser.Settings property) 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 property) (ccdc.molecule.Bond property) (ccdc.molecule.Molecule property) rmsd (ccdc.cavity.Cavity.CavityGraphComparison property) (ccdc.crystal.PackingSimilarity.Comparison property) (ccdc.descriptors.MolecularDescriptors.Overlay property) (ccdc.particle.Surface.Descriptors property) rmsd() (ccdc.conformer.ConformerHit method) (ccdc.descriptors.MolecularDescriptors static method) rmsd_tanimoto (ccdc.descriptors.MolecularDescriptors.Overlay property) ROC() (ccdc.descriptors.StatisticalDescriptors.RankStatistics method) rotamer_libraries (ccdc.docking.Docker.Settings.ProteinFileInfo property) rotamer_libraries() (ccdc.docking.Docker.Settings method) rotamer_library() (ccdc.docking.Docker.Settings method) rotamers (ccdc.conformer.ConformerHitList property) rotamers() (ccdc.docking.Docker.Settings.RotamerLibrary method) rotamers_with_no_observations (ccdc.conformer.ConformerHitList property) rotatable_bond_override_file (ccdc.docking.Docker.Settings property) rotate() (ccdc.descriptors.GeometricDescriptors.Quaternion method) (ccdc.molecule.Molecule method) rotate_carboxylic_hydroxyl_groups (ccdc.docking.Docker.Settings property) rotate_torsions (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) rotation (ccdc.molecule.Molecule.Transformation property) rotation_matrix() (ccdc.descriptors.GeometricDescriptors.Quaternion method) rugosity (ccdc.particle.Surface.Descriptors property)

S

sampling_limit_reached (ccdc.conformer.ConformerHitList property) save_binding_site_atoms (ccdc.docking.Docker.Settings property) save_files (ccdc.screening.Screener.Settings property) save_lone_pairs (ccdc.docking.Docker.Settings property) scale_factor (ccdc.descriptors.CrystalDescriptors.Morphology property) (ccdc.descriptors.CrystalDescriptors.PowderPattern.Wavelength property) (ccdc.morphology.BFDHMorphology property) (ccdc.morphology.VisualHabitMorphology property) schema_version (ccdc.pharmacophore.Pharmacophore.FeatureDatabase property) scope (ccdc.entry.Entry.CrossReference property) score (ccdc.cavity.Cavity.CavityGraphComparison property) (ccdc.cavity.Cavity.FastCavityGraphComparison property) (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.GeneratedEntry property) (ccdc.screening.Screener.ScreenHitList.ScreenHit property) score_molecule() (ccdc.utilities.Grid method) score_parameter_file (ccdc.docking.Docker.Settings property) scores (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) 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.interaction.HydrogenBondStatisticsSearch method) (ccdc.pharmacophore.Pharmacophore.Search method) (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition 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 property) seed_file (ccdc.docking.Docker.Settings property) selected_atoms (ccdc.utilities.ApplicationInterface property) selected_indices (ccdc.utilities.ApplicationInterface property) self_returning_walk() (ccdc.descriptors.MolecularDescriptors.AdjacencyMatrixDescriptorCalculator method) self_returning_walk_ln() (ccdc.descriptors.MolecularDescriptors.AdjacencyMatrixDescriptorCalculator method) separation_threshold() (ccdc.particle.SlipPlanes method) sequence (ccdc.protein.Protein property) (ccdc.protein.Protein.Chain property) (ccdc.protein.Protein.NucleicAcid property) 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_flip_planar_nitrogen() (ccdc.docking.Docker.Settings method) set_formal_charges() (ccdc.molecule.Molecule method) set_hostname() (ccdc.docking.Docker.Settings method) set_improper() (ccdc.docking.Docker.Settings.RotamerLibrary 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_separation_threshold() (ccdc.particle.SlipPlanes 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) shape_database_location (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.Settings property) 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 property) show_script_error() (ccdc.utilities.ApplicationInterface method) shrink_symbols (ccdc.diagram.DiagramGenerator.Settings attribute) sidechain_atoms (ccdc.protein.Protein.Residue property) significance_code (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient property) similarity() (ccdc.descriptors.CrystalDescriptors.PowderPattern method) similarity_score (ccdc.conformer.GeometryAnalyser.AnalysisHit property) SimilaritySearch (class in ccdc.search) SimilaritySearch.Settings (class in ccdc.search) SimilaritySearch.SimilarityHit (class in ccdc.search) simple_search() (ccdc.entry.JournalList method) simulation_temperature (ccdc.csp.prediction.Prediction property) skewness (ccdc.particle.Surface.Descriptors property) skip_proteins (ccdc.pharmacophore.Pharmacophore.Search.Settings property)

skip_when_identifiers_equal (ccdc.crystal.PackingSimilarity.Settings property) slab (ccdc.particle.Surface property) slab_molecules (ccdc.particle.Surface property) slab_separation (ccdc.particle.SlipPlanes.SlipPlane property) slice() (ccdc.utilities.Grid method) slicing() (ccdc.crystal.Crystal method) slicing_plane_distance (ccdc.particle.Surface property) SlipPlanes (class in ccdc.particle) SlipPlanes.SlipPlane (class in ccdc.particle) small_molecule (ccdc.pharmacophore.Pharmacophore.SearchHit property) smallest_ring (ccdc.search.QueryAtom property) smallest_ring_size (ccdc.molecule.Molecule property) SMARTS (ccdc.pharmacophore.Pharmacophore.SMARTSDefinition property) smarts (ccdc.search.SMARTSSubstructure property) SMARTSSubstructure (class in ccdc.search) smiles (ccdc.molecule.Molecule property) sohncke_only (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.Settings property) solubility (ccdc.entry.SolubilityMeasurement property) solubility_data (ccdc.entry.Entry property) solubility_unit (ccdc.entry.SolubilityMeasurement property) SolubilityMeasurement (class in ccdc.entry) SolubilityMeasurement.Solubility (class in ccdc.entry) solvate_all (ccdc.docking.Docker.Settings property) solvent (ccdc.entry.Entry property) solvent_accessible_surface() (ccdc.molecule.Atom method) solvent_filter (ccdc.conformer.GeometryAnalyser.Settings property) solvents (ccdc.entry.SolubilityMeasurement property) sort_atoms_by_residue() (ccdc.protein.Protein method) sort_order (ccdc.search.SimilaritySearch.Settings property) source (ccdc.entry.Entry property) (ccdc.interaction.InteractionMapAnalysis.ProteinSettings property) source_name (ccdc.conformer.GeometryAnalyser.AnalysisHit property) spacegroup_frequency (ccdc.csp.database.CspDatabase.LandscapeSummary property) spacegroup_number_and_setting (ccdc.crystal.Crystal property) spacegroup_symbol (ccdc.crystal.Crystal property) spacing (ccdc.utilities.Grid property) specific_fixed_rotatable_bonds (ccdc.docking.Docker.Settings property) spheres (ccdc.pharmacophore.Pharmacophore.Feature property) square() (ccdc.descriptors.GeometricDescriptors.Quaternion method) standard_deviation (ccdc.conformer.GeometryAnalyser.Analysis property) standard_error (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient property) 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 property) start_year (ccdc.entry.Journal property) state (ccdc.entry.Journal property) StatisticalDescriptors (class in ccdc.descriptors) StatisticalDescriptors.RankStatistics (class in ccdc.descriptors) store_atom_types (ccdc.screening.Screener.Settings property) strength (ccdc.molecule.Molecule.Contact property) sub_grid() (ccdc.utilities.Grid method) subcavity() (ccdc.cavity.Cavity method) Subsets (class in ccdc.io) 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 (class in ccdc.particle) Surface.AtomProperties (class in ccdc.particle) Surface.Descriptors (class in ccdc.particle) Surface.Topology (class in ccdc.particle) surface_area (ccdc.particle.Surface.Descriptors property) surface_atoms (ccdc.particle.Surface property) surface_depths (ccdc.cavity.Cavity.Feature property) surface_energy (ccdc.morphology.VisualHabitMorphology.VisualHabitFacet property) surface_node_atom_contacts (ccdc.particle.Surface property) surface_points (ccdc.cavity.Cavity.Feature property) surface_vector (ccdc.cavity.Cavity.Feature property) sybyl_type (ccdc.molecule.Atom property) (ccdc.molecule.Bond property) symmetric_molecule() (ccdc.crystal.Crystal method) symmetry_operator_description() (ccdc.crystal.Crystal static method) symmetry_operators (ccdc.crystal.Crystal property) (ccdc.crystal.Crystal.Contact property) (ccdc.crystal.Crystal.HBond property) symmetry_rotation() (ccdc.crystal.Crystal static method) symmetry_translation() (ccdc.crystal.Crystal static method) synonyms (ccdc.entry.Entry property) synonyms_as_html (ccdc.entry.Entry property)

T

target_hbond_grouping() (ccdc.descriptors.CrystalDescriptors.HBondPropensities method) temperature (ccdc.entry.Entry property) (ccdc.entry.SolubilityMeasurement property) temperature_factor (ccdc.molecule.Atom.DisplacementParameters property) temperature_unit (ccdc.entry.SolubilityMeasurement property) test() (ccdc.search.Search.Settings method) text (ccdc.entry.Entry.CrossReference property) 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 property) three_letter_code (ccdc.protein.Protein.Residue property) threshold (ccdc.search.SimilaritySearch property) (ccdc.search.SimilaritySearch.Settings property) tick_marks (ccdc.descriptors.CrystalDescriptors.PowderPattern property) 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)

topology (ccdc.particle.Surface property) torsion_angle (ccdc.conformer.GeometryAnalyser.AnalysisHit property) torsion_angles (ccdc.utilities.ApplicationInterface property) torsion_distribution_file (ccdc.docking.Docker.Settings property) total (ccdc.morphology.VisualHabit.Results.LatticeEnergy property) total_number_predictions (ccdc.csp.database.CspDatabase.LandscapeSummary property) transform() (ccdc.molecule.Molecule method) transformation (ccdc.descriptors.MolecularDescriptors.Overlay property) transformation_matrix (ccdc.cavity.Cavity.CavityGraphComparison property) translate() (ccdc.molecule.Molecule method) translated_name (ccdc.entry.Journal property) translation (ccdc.molecule.Molecule.Transformation property) triangles (ccdc.particle.Surface.Topology property) two_theta (ccdc.descriptors.CrystalDescriptors.PowderPattern property) (ccdc.descriptors.CrystalDescriptors.PowderPattern.TickMark property) two_theta_maximum (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings property) two_theta_minimum (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings property) two_theta_step (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings property) type (ccdc.cavity.Cavity.Feature property) (ccdc.conformer.GeometryAnalyser.Analysis property) (ccdc.crystal.Crystal.Contact property) (ccdc.crystal.Crystal.HBond property) (ccdc.docking.Docker.Results.DockedLigand.ProteinRotatedTorsion property) (ccdc.entry.Entry.CrossReference property) (ccdc.molecule.Atom.DisplacementParameters property) (ccdc.molecule.Molecule.Contact property) (ccdc.molecule.Molecule.HBond property)

U

uncertainties (ccdc.molecule.Atom.DisplacementParameters property) uncertainty (ccdc.descriptors.CrystalDescriptors.HBondPropensities.InterPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.IntraPropensity property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Propensity property) (ccdc.utilities.Uncertainty property) (ccdc.utilities.UncertainValue property) Uncertainty (class in ccdc.utilities) UncertainValue (class in ccdc.utilities) unfused_unbridged_ring (ccdc.search.QueryAtom property) unsatisfied_hb_donors (ccdc.particle.Surface.AtomProperties property) (ccdc.particle.Surface.Descriptors property) unusual (ccdc.conformer.GeometryAnalyser.Analysis property) update_progress() (ccdc.utilities.ApplicationInterface method) update_rotamer_library() (ccdc.docking.Docker.Settings method) (ccdc.docking.Docker.Settings.ProteinFileInfo method)

upper_quartile (ccdc.conformer.GeometryAnalyser.Analysis property) url (ccdc.entry.Journal property) use_internal_ligand_energy_offset (ccdc.docking.Docker.Settings property) use_rotatable_bond_override_file (ccdc.docking.Docker.Settings property) use_torsion_angle_distributions (ccdc.docking.Docker.Settings property) utilities.csp.create_shape_database.create_shape_database module utilities.csp.csp_cross_reference.csp_cross_reference module utilities.csp.delete_csp_landscape.delete_csp_landscape module utilities.csp.import_csp_landscape.import_csp_landscape module

V

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

VisualHabit (class in ccdc.morphology) VisualHabit.Results (class in ccdc.morphology) VisualHabit.Results.LatticeEnergy (class in ccdc.morphology) VisualHabit.Settings (class in ccdc.morphology) VisualHabitMorphology (class in ccdc.morphology) VisualHabitMorphology.VisualHabitFacet (class in ccdc.morphology) void_percent (ccdc.csp.prediction.Prediction property) void_volume (ccdc.csp.prediction.Prediction property) void_volume() (ccdc.crystal.Crystal method) void_volume_max (ccdc.csp.database.CspDatabase.LandscapeSummary property) void_volume_min (ccdc.csp.database.CspDatabase.LandscapeSummary property) volume (ccdc.cavity.Cavity property) (ccdc.crystal.Crystal.ReducedCell property) (ccdc.descriptors.CrystalDescriptors.Morphology property) (ccdc.descriptors.CrystalDescriptors.Morphology.OrientedBoundingBox property) (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox property) (ccdc.morphology.BFDHMorphology property) (ccdc.morphology.VisualHabitMorphology property) volume_range (ccdc.cavity.CavityDatabase.Settings attribute)

W

water_files (ccdc.docking.Docker.Settings property) waters (ccdc.docking.Docker.Settings property) (ccdc.protein.Protein property) (ccdc.protein.Protein.BindingSite property) wavelength (ccdc.descriptors.CrystalDescriptors.PowderPattern.Settings property) (ccdc.descriptors.CrystalDescriptors.PowderPattern.Wavelength property) which (ccdc.pharmacophore.Pharmacophore.Query.DistanceConstraint property) with_ligands (ccdc.cavity.CavityDatabase.Settings attribute) working_directory (ccdc.csp.csd_landscape_generator.CSDLandscapeGenerator.Settings property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Settings property) (ccdc.interaction.InteractionMapAnalysis.CommonSettings property) working_directory_path (ccdc.utilities.ApplicationInterface attribute) write() (ccdc.cavity.Cavity method) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.FittingData method) (ccdc.descriptors.CrystalDescriptors.Morphology method) (ccdc.docking.Docker.Settings 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.morphology.BFDHMorphology method) (ccdc.morphology.VisualHabitMorphology 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 property) 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 property)

Y

y_vector (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox property)

Z

z_prime (ccdc.crystal.Crystal property) z_prime_frequency (ccdc.csp.database.CspDatabase.LandscapeSummary property) z_score (ccdc.conformer.GeometryAnalyser.Analysis property)

z_value (ccdc.crystal.Crystal property) (ccdc.descriptors.CrystalDescriptors.HBondPropensities.Model.Coefficient property) z_vector (ccdc.descriptors.MolecularDescriptors.PrincipleAxesAlignedBox property) zscore_threshold (ccdc.conformer.GeometryAnalyser.Settings.GeometrySettings property)