Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A a (cosmolkit.BioCrystalCell attribute) A (cosmolkit.ResidueCode attribute) A2G (cosmolkit.ResidueCode attribute) AA (cosmolkit.ResidueInfoKind attribute) AAD (cosmolkit.ResidueInfoKind attribute) ABA (cosmolkit.ResidueCode attribute) AC (cosmolkit.Element attribute) ACA (cosmolkit.ResidueCode attribute) access (cosmolkit.MoleculeOpSpec attribute) accession_code (cosmolkit.BioEntityDbRef attribute) accession_index (cosmolkit.BioSiftsUnpResidue attribute) ACE (cosmolkit.ResidueCode attribute) ACN (cosmolkit.ResidueCode attribute) ACT (cosmolkit.ResidueCode attribute) actual (cosmolkit.ForceFieldError property) (cosmolkit.MmffForceFieldError property) actual() (cosmolkit.PropertyValueError method) ACY (cosmolkit.ResidueCode attribute) add_2d_conformer() (cosmolkit.MoleculeBuilder method) add_3d_conformer() (cosmolkit.MoleculeBuilder method) add_3d_conformer_() (cosmolkit.Molecule method) add_3d_conformer_with_params_() (cosmolkit.Molecule method) add_atom() (cosmolkit.MoleculeBuilder method) add_bond() (cosmolkit.MoleculeBuilder method) add_coords (cosmolkit.AddHsParams property) add_hydrogens_() (cosmolkit.Molecule method) add_hydrogens_with_params_() (cosmolkit.Molecule method) add_residue_info (cosmolkit.AddHsParams property) add_stereo_group() (cosmolkit.MoleculeBuilder method) add_substance_group() (cosmolkit.MoleculeBuilder method) AddHsParams (class in cosmolkit) AddHsParams() (class) AddHsParams.[Symbol․dispose]() (AddHsParams method) AddHsParams.addCoords (AddHsParams attribute) AddHsParams.addResidueInfo (AddHsParams attribute) AddHsParams.explicitOnly (AddHsParams attribute) AddHsParams.free() (AddHsParams method) AddHsParams.onlyOnAtoms (AddHsParams attribute) AddHsParams.skipQueries (AddHsParams attribute) AddHsParamsOptions() (interface) AddHsParamsOptions.addCoords? (AddHsParamsOptions attribute) AddHsParamsOptions.addResidueInfo? (AddHsParamsOptions attribute) AddHsParamsOptions.explicitOnly? (AddHsParamsOptions attribute) AddHsParamsOptions.onlyOnAtoms? (AddHsParamsOptions attribute) AddHsParamsOptions.skipQueries? (AddHsParamsOptions attribute) additional_output() (cosmolkit.BatchFingerprintOutput method) ADJUST_HS (cosmolkit.SanitizeOperations attribute) AdjustHs (cosmolkit.SanitizeStage attribute) ADP (cosmolkit.ResidueCode attribute) AG (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) Agent (cosmolkit.ReactionRole attribute) agent_template() (cosmolkit.Reaction method) agent_templates() (cosmolkit.Reaction method) AGM (cosmolkit.ResidueCode attribute) AIB (cosmolkit.ResidueCode attribute) AL (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) ALA (cosmolkit.ResidueCode attribute) ALC (cosmolkit.ResidueCode attribute) align_conformers_() (cosmolkit.Molecule method) align_conformers_with_params_() (cosmolkit.Molecule method) align_loops (cosmolkit.BioMmcifWriteParams property) align_pairs (cosmolkit.BioMmcifWriteParams property) align_to_() (cosmolkit.Molecule method) align_to_with_params_() (cosmolkit.Molecule method) alignment_transform_to() (cosmolkit.Molecule method) alignment_transform_to_with_params() (cosmolkit.Molecule method) AlignmentAtomMap (class in cosmolkit) AlignmentAtomMap() (class) AlignmentAtomMap.[Symbol․dispose]() (AlignmentAtomMap method) AlignmentAtomMap.free() (AlignmentAtomMap method) AlignmentAtomMap.new() (AlignmentAtomMap method) AlignmentAtomMap.probeAtom (AlignmentAtomMap attribute) AlignmentAtomMap.referenceAtom (AlignmentAtomMap attribute) AlignmentError AlignmentError() (class) AlignmentError.[Symbol․dispose]() (AlignmentError method) AlignmentError.cause (AlignmentError attribute) AlignmentError.domain (AlignmentError attribute) AlignmentError.free() (AlignmentError method) AlignmentError.kind (AlignmentError attribute) AlignmentError.message (AlignmentError attribute) AlignmentParameters (class in cosmolkit) AlignmentParameters() (class) AlignmentParameters.[Symbol․dispose]() (AlignmentParameters method) AlignmentParameters.atomMap (AlignmentParameters attribute) AlignmentParameters.free() (AlignmentParameters method) AlignmentParameters.maxIterations (AlignmentParameters attribute) AlignmentParameters.new() (AlignmentParameters method) AlignmentParameters.probeConformerId (AlignmentParameters attribute) AlignmentParameters.referenceConformerId (AlignmentParameters attribute) AlignmentParameters.reflect (AlignmentParameters attribute) AlignmentParameters.weights (AlignmentParameters attribute) AlignmentParametersOptions() (interface) AlignmentParametersOptions.atomMap? (AlignmentParametersOptions attribute) AlignmentParametersOptions.maxIterations? (AlignmentParametersOptions attribute) AlignmentParametersOptions.probeConformerId? (AlignmentParametersOptions attribute) AlignmentParametersOptions.referenceConformerId? (AlignmentParametersOptions attribute) AlignmentParametersOptions.reflect? (AlignmentParametersOptions attribute) AlignmentParametersOptions.weights? (AlignmentParametersOptions attribute) AlignmentResult (class in cosmolkit) AlignmentResult() (class) AlignmentResult.[Symbol․dispose]() (AlignmentResult method) AlignmentResult.atomMap() (AlignmentResult method) AlignmentResult.free() (AlignmentResult method) AlignmentResult.rmsd() (AlignmentResult method) AlignmentResult.transform() (AlignmentResult method) AlignmentTransform (class in cosmolkit) AlignmentTransform() (class) AlignmentTransform.[Symbol․dispose]() (AlignmentTransform method) AlignmentTransform.free() (AlignmentTransform method) AlignmentTransform.matrix() (AlignmentTransform method) ALL (cosmolkit.CxSmilesFields attribute) (cosmolkit.SanitizeOperations attribute) all_bonds_explicit (cosmolkit.RandomSmilesWriteParams property) (cosmolkit.SmilesWriteParams property) ALL_BUT_COORDS (cosmolkit.CxSmilesFields attribute) all_conformer_best_rmsds() (cosmolkit.Molecule method) all_conformer_best_rmsds_with_params() (cosmolkit.Molecule method) all_groups (cosmolkit.BioMmcifWriteParams property) all_hydrogens_explicit (cosmolkit.RandomSmilesWriteParams property) (cosmolkit.SmilesWriteParams property) AllConformerRmsdParameters (class in cosmolkit) AllConformerRmsdParameters() (class) AllConformerRmsdParameters.[Symbol․dispose]() (AllConformerRmsdParameters method) AllConformerRmsdParameters.atomMaps (AllConformerRmsdParameters attribute) AllConformerRmsdParameters.free() (AllConformerRmsdParameters method) AllConformerRmsdParameters.ignoreHydrogens (AllConformerRmsdParameters attribute) AllConformerRmsdParameters.maxMatches (AllConformerRmsdParameters attribute) AllConformerRmsdParameters.new() (AllConformerRmsdParameters method) AllConformerRmsdParameters.numThreads (AllConformerRmsdParameters attribute) AllConformerRmsdParameters.symmetrizeConjugatedTerminalGroups (AllConformerRmsdParameters attribute) AllConformerRmsdParameters.weights (AllConformerRmsdParameters attribute) AllConformerRmsdParametersOptions() (interface) AllConformerRmsdParametersOptions.atomMaps? (AllConformerRmsdParametersOptions attribute) AllConformerRmsdParametersOptions.ignoreHydrogens? (AllConformerRmsdParametersOptions attribute) AllConformerRmsdParametersOptions.maxMatches? (AllConformerRmsdParametersOptions attribute) AllConformerRmsdParametersOptions.numThreads? (AllConformerRmsdParametersOptions attribute) AllConformerRmsdParametersOptions.symmetrizeConjugatedTerminalGroups? (AllConformerRmsdParametersOptions attribute) AllConformerRmsdParametersOptions.weights? (AllConformerRmsdParametersOptions attribute) allocate_atom_counts() (cosmolkit.FingerprintAdditionalOutput method) allocate_atom_to_bits() (cosmolkit.FingerprintAdditionalOutput method) allocate_atoms_per_bit() (cosmolkit.FingerprintAdditionalOutput method) allocate_bit_info_map() (cosmolkit.FingerprintAdditionalOutput method) allocate_bit_paths() (cosmolkit.FingerprintAdditionalOutput method) AllocationFailed (cosmolkit.InchiErrorKind attribute) allow_cxsmiles (cosmolkit.ReactionParseParams property) (cosmolkit.SmartsParseParams property) (cosmolkit.SmilesParseParams property) allow_nontetrahedral (cosmolkit.PotentialStereoParams property) alpha (cosmolkit.BioCrystalCell attribute) altloc (cosmolkit.AtomAddress attribute) altloc() (cosmolkit.BioAtomRow method) (cosmolkit.ProteinAtomRef method) AltLocLabel (class in cosmolkit) AltLocLabel() (class) AltLocLabel.[Symbol․dispose]() (AltLocLabel method) AltLocLabel.free() (AltLocLabel method) AltLocLabel.value() (AltLocLabel method) AltLocRequest (class in cosmolkit) AltLocRequest() (class) AltLocRequest.[Symbol․dispose]() (AltLocRequest method) AltLocRequest.Any (AltLocRequest attribute) AltLocRequest.Exact() (AltLocRequest method) AltLocRequest.free() (AltLocRequest method) ALY (cosmolkit.ResidueCode attribute) AM (cosmolkit.Element attribute) AminoAcid (cosmolkit.ResidueKind attribute) aniso_b (cosmolkit.BioRefinementInfo attribute) AnisotropicU (cosmolkit.BioMmcifReadStage attribute) Any (cosmolkit.AltLocRequest attribute) (cosmolkit.BioAsu attribute) (cosmolkit.McsAtomComparator attribute) (cosmolkit.McsBondComparator attribute) AnyHeavyAtom (cosmolkit.McsAtomComparator attribute) AnyPolymer (cosmolkit.SubstanceGroupKind attribute) apply_reaction() (cosmolkit.Molecule method) apply_reaction_() (cosmolkit.Molecule method) apply_reaction_with_params() (cosmolkit.Molecule method) apply_reaction_with_params_() (cosmolkit.Molecule method) approx() (cosmolkit.BioTransform method) AR (cosmolkit.Element attribute) ARG (cosmolkit.ResidueCode attribute) AROMATIC (cosmolkit.BondOrder attribute) aromatic_matches_conjugated (cosmolkit.SubstructMatchParams property) aromatic_matches_single_or_double (cosmolkit.SubstructMatchParams property) AromaticityError AromaticityError() (class) AromaticityError.[Symbol․dispose]() (AromaticityError method) AromaticityError.cause (AromaticityError attribute) AromaticityError.domain (AromaticityError attribute) AromaticityError.free() (AromaticityError method) AromaticityError.kind (AromaticityError attribute) AromaticityError.message (AromaticityError attribute) AromaticityModel (class in cosmolkit) (None attribute) AromaticityModel.Custom (AromaticityModel attribute) AromaticityModel.Mdl (AromaticityModel attribute) AromaticityModel.Mmff94 (AromaticityModel attribute) AromaticityModel.Rdkit (AromaticityModel attribute) AromaticityModel.Simple (AromaticityModel attribute) AromaticityParams (class in cosmolkit) AromaticityParams() (class) AromaticityParams.[Symbol․dispose]() (AromaticityParams method) AromaticityParams.free() (AromaticityParams method) AromaticityParams.model (AromaticityParams attribute) AromaticityParamsOptions() (interface) AromaticityParamsOptions.model? (AromaticityParamsOptions attribute) AS (cosmolkit.Element attribute) as_bio_structure() (cosmolkit.Protein method) as_bool() (cosmolkit.PropertyValue method) as_bytes() (cosmolkit.AtomName method) as_dict() (cosmolkit.BatchError method) as_double() (cosmolkit.PropertyValue method) as_int() (cosmolkit.PropertyValue method) as_int_vector() (cosmolkit.PropertyValue method) as_str() (cosmolkit.AtomName method) as_string() (cosmolkit.PropertyValue method) as_uint() (cosmolkit.PropertyValue method) asa (cosmolkit.LabuteAsaContributions attribute) ASN (cosmolkit.ResidueCode attribute) ASP (cosmolkit.ResidueCode attribute) Assemblies (cosmolkit.BioMmcifReadStage attribute) assemblies() (cosmolkit.BioStructure method) assembly (cosmolkit.BioMmcifWriteParams property) assign_aromaticity_() (cosmolkit.Molecule method) assign_aromaticity_with_params_() (cosmolkit.Molecule method) assign_chiral_tags_from_structure_() (cosmolkit.Molecule method) assign_chiral_tags_from_structure_with_params_() (cosmolkit.Molecule method) assign_cip_labels_() (cosmolkit.Molecule method) assign_cip_labels_with_options_() (cosmolkit.Molecule method) assign_radicals_() (cosmolkit.Molecule method) assign_ring_families_() (cosmolkit.Molecule method) assign_ring_families_with_params_() (cosmolkit.Molecule method) assign_rings_() (cosmolkit.Molecule method) assign_valence_() (cosmolkit.Molecule method) assign_valence_with_params_() (cosmolkit.Molecule method) asu (cosmolkit.BioConnection attribute) ASX (cosmolkit.ResidueCode attribute) AT (cosmolkit.Element attribute) Atom (class in cosmolkit) atom (cosmolkit.LigandRef attribute) (cosmolkit.ReactionValidationIssue attribute) (cosmolkit.RingStereoRelation attribute) Atom (cosmolkit.SdfPropertyListTarget attribute) Atom() (class) atom() (cosmolkit.Molecule method) (cosmolkit.TautomerMoleculeView method) Atom.[Symbol․dispose]() (Atom method) Atom.atomicNumber() (Atom method) Atom.atomMap() (Atom method) Atom.chiralTag() (Atom method) Atom.chiralTagCode() (Atom method) Atom.chiralTagName() (Atom method) Atom.cipDescriptor() (Atom method) Atom.cipNeighborOrder() (Atom method) Atom.cipRank() (Atom method) Atom.element() (Atom method) Atom.explicitHydrogens() (Atom method) Atom.formalCharge() (Atom method) Atom.free() (Atom method) Atom.hybridization() (Atom method) Atom.id() (Atom method) Atom.isAromatic() (Atom method) Atom.isotope() (Atom method) Atom.noImplicit() (Atom method) Atom.radicalElectrons() (Atom method) Atom.templateAttachmentOrder() (Atom method) atom_bits (cosmolkit.TopologicalFingerprintOutput attribute) (cosmolkit.TopologicalFingerprintOutputRequest property) atom_bits() (cosmolkit.TopologicalFingerprintResult method) atom_by_altloc() (cosmolkit.BioStructure method) atom_comparator (cosmolkit.McsParameters property) atom_compare_parameters (cosmolkit.McsParameters property) atom_contributions (cosmolkit.LabuteAsaContributions attribute) atom_count (cosmolkit.McsResult attribute) atom_counts (cosmolkit.LayeredFingerprintParams property) atom_counts() (cosmolkit.BatchFingerprintAdditionalOutput method) (cosmolkit.FingerprintAdditionalOutput method) (cosmolkit.LayeredFingerprintResult method) atom_degree() (cosmolkit.TautomerMoleculeView method) atom_index (cosmolkit.ForceFieldError property) (cosmolkit.MmffForceFieldError property) atom_indices (cosmolkit.ConformerAlignmentParameters property) atom_invariants (cosmolkit.TopologicalFingerprintParams property) atom_invariants_generator (cosmolkit.AtomPairFingerprintParams property) (cosmolkit.TopologicalTorsionFingerprintParams property) ATOM_LABELS (cosmolkit.CxSmilesFields attribute) atom_map (cosmolkit.AlignmentParameters property) atom_map() (cosmolkit.AlignmentResult method) (cosmolkit.Atom method) (cosmolkit.QueryAtom method) atom_mapping() (cosmolkit.MatchResult method) atom_maps (cosmolkit.AllConformerRmsdParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.CoordinateRmsdParameters property) atom_match (cosmolkit.SubstructMatchParams property) atom_metadata() (cosmolkit.Molecule method) (cosmolkit.TautomerMoleculeView method) ATOM_OCTAHEDRAL (cosmolkit.PotentialStereoType attribute) atom_order() (cosmolkit.CompiledQuery method) atom_pair() (cosmolkit.MorganAtomInvariantsGenerator static method) atom_pairs() (cosmolkit.MatchResult method) atom_position() (cosmolkit.BioStructure method) atom_properties (cosmolkit.SubstructMatchParams property) atom_property() (cosmolkit.Molecule method) atom_property_string() (cosmolkit.Molecule method) ATOM_PROPS (cosmolkit.CxSmilesFields attribute) atom_ranks (cosmolkit.PotentialStereoResult attribute) ATOM_SQUAREPLANAR (cosmolkit.PotentialStereoType attribute) atom_symbols (cosmolkit.FragmentCxSmilesWriteParams property) (cosmolkit.FragmentSmilesWriteParams property) ATOM_TETRAHEDRAL (cosmolkit.PotentialStereoType attribute) atom_to_bits() (cosmolkit.BatchFingerprintAdditionalOutput method) (cosmolkit.FingerprintAdditionalOutput method) ATOM_TRIGONALBIPYRAMIDAL (cosmolkit.PotentialStereoType attribute) atom_type (cosmolkit.BioMmcifWriteParams property) atom_type() (cosmolkit.MmffAtomProperties method) (cosmolkit.MmffProperties method) atom_types() (cosmolkit.AtomPairsParameters static method) AtomAddress (class in cosmolkit) AtomAddress() (class) AtomAddress.[Symbol․dispose]() (AtomAddress method) AtomAddress.altloc (AtomAddress attribute) AtomAddress.chainName (AtomAddress attribute) AtomAddress.free() (AtomAddress method) AtomAddress.logicalAtomName (AtomAddress attribute) AtomAddress.residue (AtomAddress attribute) AtomCodeExplanation (class in cosmolkit) AtomCodeExplanation() (class) AtomCodeExplanation.[Symbol․dispose]() (AtomCodeExplanation method) AtomCodeExplanation.branchCount() (AtomCodeExplanation method) AtomCodeExplanation.chirality() (AtomCodeExplanation method) AtomCodeExplanation.free() (AtomCodeExplanation method) AtomCodeExplanation.fromCode() (AtomCodeExplanation method) AtomCodeExplanation.piElectrons() (AtomCodeExplanation method) AtomCodeExplanation.symbol() (AtomCodeExplanation method) AtomCodeExplanationError AtomCodeExplanationError() (class) AtomCodeExplanationError.[Symbol․dispose]() (AtomCodeExplanationError method) AtomCodeExplanationError.cause (AtomCodeExplanationError attribute) AtomCodeExplanationError.code (AtomCodeExplanationError attribute) AtomCodeExplanationError.domain (AtomCodeExplanationError attribute) AtomCodeExplanationError.free() (AtomCodeExplanationError method) AtomCodeExplanationError.kind (AtomCodeExplanationError attribute) AtomCodeExplanationError.message (AtomCodeExplanationError attribute) atomic_number() (cosmolkit.Atom method) (cosmolkit.Element method) (cosmolkit.ElementInfo method) (cosmolkit.ProteinAtomRef method) (cosmolkit.QueryAtom method) atomic_weight() (cosmolkit.ElementInfo method) AtomMetadata (class in cosmolkit) AtomMetadata() (class) AtomMetadata.[Symbol․dispose]() (AtomMetadata method) AtomMetadata.degree() (AtomMetadata method) AtomMetadata.explicitValence() (AtomMetadata method) AtomMetadata.free() (AtomMetadata method) AtomMetadata.implicitHydrogens() (AtomMetadata method) AtomMetadata.totalHydrogens() (AtomMetadata method) AtomMetadata.totalValence() (AtomMetadata method) AtomName (class in cosmolkit) AtomName() (class) AtomName.[Symbol․dispose]() (AtomName method) AtomName.asBytes() (AtomName method) AtomName.asStr() (AtomName method) AtomName.free() (AtomName method) AtomName.fromAscii() (AtomName method) AtomPairAtomCodeResult (class in cosmolkit) AtomPairAtomCodeResult() (class) AtomPairAtomCodeResult.[Symbol․dispose]() (AtomPairAtomCodeResult method) AtomPairAtomCodeResult.code (AtomPairAtomCodeResult attribute) AtomPairAtomCodeResult.free() (AtomPairAtomCodeResult method) AtomPairAtomCodeResult.molecule (AtomPairAtomCodeResult attribute) AtomPairAtomInvariantsGenerator (class in cosmolkit) AtomPairAtomInvariantsGenerator() (class) AtomPairAtomInvariantsGenerator.[Symbol․dispose]() (AtomPairAtomInvariantsGenerator method) AtomPairAtomInvariantsGenerator.free() (AtomPairAtomInvariantsGenerator method) AtomPairAtomInvariantsGenerator.includeChirality (AtomPairAtomInvariantsGenerator attribute) AtomPairAtomInvariantsGenerator.infoString() (AtomPairAtomInvariantsGenerator method) AtomPairAtomInvariantsGenerator.toJson() (AtomPairAtomInvariantsGenerator method) AtomPairAtomInvariantsGenerator.topologicalTorsionCorrection (AtomPairAtomInvariantsGenerator attribute) AtomPairAtomInvariantsGeneratorOptions() (interface) AtomPairAtomInvariantsGeneratorOptions.includeChirality? (AtomPairAtomInvariantsGeneratorOptions attribute) AtomPairAtomInvariantsGeneratorOptions.topologicalTorsionCorrection? (AtomPairAtomInvariantsGeneratorOptions attribute) AtomPairFingerprintParams (class in cosmolkit) AtomPairFingerprintParams() (class) AtomPairFingerprintParams.[Symbol․dispose]() (AtomPairFingerprintParams method) AtomPairFingerprintParams.atomInvariantsGenerator (AtomPairFingerprintParams attribute) AtomPairFingerprintParams.conformerId (AtomPairFingerprintParams attribute) AtomPairFingerprintParams.customAtomInvariants (AtomPairFingerprintParams attribute) AtomPairFingerprintParams.customBondInvariants (AtomPairFingerprintParams attribute) AtomPairFingerprintParams.free() (AtomPairFingerprintParams method) AtomPairFingerprintParams.fromAtoms (AtomPairFingerprintParams attribute) AtomPairFingerprintParams.generator (AtomPairFingerprintParams attribute) AtomPairFingerprintParams.ignoreAtoms (AtomPairFingerprintParams attribute) AtomPairFingerprintParams.useLegacyStereoPerception (AtomPairFingerprintParams attribute) AtomPairFingerprintParamsOptions() (interface) AtomPairFingerprintParamsOptions.atomInvariantsGenerator? (AtomPairFingerprintParamsOptions attribute) AtomPairFingerprintParamsOptions.conformerId? (AtomPairFingerprintParamsOptions attribute) AtomPairFingerprintParamsOptions.customAtomInvariants? (AtomPairFingerprintParamsOptions attribute) AtomPairFingerprintParamsOptions.customBondInvariants? (AtomPairFingerprintParamsOptions attribute) AtomPairFingerprintParamsOptions.fromAtoms? (AtomPairFingerprintParamsOptions attribute) AtomPairFingerprintParamsOptions.generator? (AtomPairFingerprintParamsOptions attribute) AtomPairFingerprintParamsOptions.ignoreAtoms? (AtomPairFingerprintParamsOptions attribute) AtomPairFingerprintParamsOptions.useLegacyStereoPerception? (AtomPairFingerprintParamsOptions attribute) AtomPairParams (class in cosmolkit) AtomPairParams() (class) AtomPairParams.[Symbol․dispose]() (AtomPairParams method) AtomPairParams.bitsPerFeature (AtomPairParams attribute) AtomPairParams.countBounds (AtomPairParams attribute) AtomPairParams.countSimulation (AtomPairParams attribute) AtomPairParams.fpSize (AtomPairParams attribute) AtomPairParams.free() (AtomPairParams method) AtomPairParams.includeChirality (AtomPairParams attribute) AtomPairParams.infoString() (AtomPairParams method) AtomPairParams.maxDistance (AtomPairParams attribute) AtomPairParams.minDistance (AtomPairParams attribute) AtomPairParams.toJson() (AtomPairParams method) AtomPairParams.use2d (AtomPairParams attribute) AtomPairParams.withJson() (AtomPairParams method) AtomPairParamsOptions() (interface) AtomPairParamsOptions.bitsPerFeature? (AtomPairParamsOptions attribute) AtomPairParamsOptions.countBounds? (AtomPairParamsOptions attribute) AtomPairParamsOptions.countSimulation? (AtomPairParamsOptions attribute) AtomPairParamsOptions.fpSize? (AtomPairParamsOptions attribute) AtomPairParamsOptions.includeChirality? (AtomPairParamsOptions attribute) AtomPairParamsOptions.maxDistance? (AtomPairParamsOptions attribute) AtomPairParamsOptions.minDistance? (AtomPairParamsOptions attribute) AtomPairParamsOptions.use2d? (AtomPairParamsOptions attribute) AtomPairReadError AtomPairReadError() (class) AtomPairReadError.[Symbol․dispose]() (AtomPairReadError method) AtomPairReadError.cause (AtomPairReadError attribute) AtomPairReadError.domain (AtomPairReadError attribute) AtomPairReadError.free() (AtomPairReadError method) AtomPairReadError.kind (AtomPairReadError attribute) AtomPairReadError.message (AtomPairReadError attribute) AtomPairsParameters (class in cosmolkit) AtomPairsParameters() (class) AtomPairsParameters.[Symbol․dispose]() (AtomPairsParameters method) AtomPairsParameters.atomTypes() (AtomPairsParameters method) AtomPairsParameters.codeSize() (AtomPairsParameters method) AtomPairsParameters.free() (AtomPairsParameters method) AtomPairsParameters.maxPathLength() (AtomPairsParameters method) AtomPairsParameters.numAtomPairFingerprintBits() (AtomPairsParameters method) AtomPairsParameters.numBranchBits() (AtomPairsParameters method) AtomPairsParameters.numChiralBits() (AtomPairsParameters method) AtomPairsParameters.numPathBits() (AtomPairsParameters method) AtomPairsParameters.numPiBits() (AtomPairsParameters method) AtomPairsParameters.numTypeBits() (AtomPairsParameters method) AtomPairsParameters.version() (AtomPairsParameters method) AtomPositionParams (class in cosmolkit) AtomPositionParams() (class) AtomPositionParams.[Symbol․dispose]() (AtomPositionParams method) AtomPositionParams.conformerId (AtomPositionParams attribute) AtomPositionParams.free() (AtomPositionParams method) AtomPositionParamsOptions() (interface) AtomPositionParamsOptions.conformerId? (AtomPositionParamsOptions attribute) atoms (cosmolkit.BioMmcifWriteParams property) (cosmolkit.CipLabelOptions property) (cosmolkit.FragmentCxSmilesWriteParams property) (cosmolkit.FragmentSmilesWriteParams property) (cosmolkit.ProteinSelectionSummary attribute) (cosmolkit.TopologyBlock attribute) atoms() (cosmolkit.BioChainRow method) (cosmolkit.BioResidueRow method) (cosmolkit.BioStructure method) (cosmolkit.MmffProperties method) (cosmolkit.Molecule method) (cosmolkit.MoleculeBuilder method) (cosmolkit.Protein method) (cosmolkit.ProteinChainRef method) (cosmolkit.ProteinResidueRef method) (cosmolkit.StereoGroup method) (cosmolkit.TautomerMoleculeView method) atoms_per_bit() (cosmolkit.BatchFingerprintAdditionalOutput method) (cosmolkit.FingerprintAdditionalOutput method) AtomSites (cosmolkit.BioMmcifReadStage attribute) AtomSourceIds (class in cosmolkit) AtomSourceIds() (class) AtomSourceIds.[Symbol․dispose]() (AtomSourceIds method) AtomSourceIds.free() (AtomSourceIds method) AtomSourceIds.serial() (AtomSourceIds method) AtomSpec (class in cosmolkit) AtomSpec() (class) AtomSpec.[Symbol․dispose]() (AtomSpec method) AtomSpec.free() (AtomSpec method) AtomSpec.withAtomMap() (AtomSpec method) AtomSpec.withExplicitHydrogens() (AtomSpec method) AtomSpec.withFormalCharge() (AtomSpec method) AtomSpec.withIsotope() (AtomSpec method) AtomSpec.withNoImplicit() (AtomSpec method) ATP (cosmolkit.ResidueCode attribute) AU (cosmolkit.Element attribute) auth_all (cosmolkit.BioMmcifWriteParams property) auth_chain_id() (cosmolkit.ChainSourceIds method) author (cosmolkit.BioMmcifWriteParams property) author_determined (cosmolkit.BioAssembly attribute) authors (cosmolkit.BioMetadata attribute) auto() (cosmolkit.CxCoordinateSelection static method) (cosmolkit.MolCoordinateSelection static method) (cosmolkit.ReactionCoordinateSelection static method) auto_remap (cosmolkit.MoleculeOpSpec attribute) AvalonEngineError AvalonEngineError() (class) AvalonEngineError.[Symbol․dispose]() (AvalonEngineError method) AvalonEngineError.domain (AvalonEngineError attribute) AvalonEngineError.free() (AvalonEngineError method) AvalonEngineError.kind (AvalonEngineError attribute) AvalonEngineError.reason (AvalonEngineError attribute) AvalonFingerprintError AvalonFingerprintError() (class) AvalonFingerprintError.[Symbol․dispose]() (AvalonFingerprintError method) AvalonFingerprintError.cause (AvalonFingerprintError attribute) AvalonFingerprintError.domain (AvalonFingerprintError attribute) AvalonFingerprintError.free() (AvalonFingerprintError method) AvalonFingerprintError.kind (AvalonFingerprintError attribute) AvalonFingerprintError.message (AvalonFingerprintError attribute) AvalonFingerprintFlags (class in cosmolkit) AvalonFingerprintFlags() (class) AvalonFingerprintFlags.[Symbol․dispose]() (AvalonFingerprintFlags method) AvalonFingerprintFlags.bits() (AvalonFingerprintFlags method) AvalonFingerprintFlags.free() (AvalonFingerprintFlags method) AvalonFingerprintFlags.fromBitsRetain() (AvalonFingerprintFlags method) AvalonFingerprintFlags.toString() (AvalonFingerprintFlags method) AvalonFingerprintOptions() (interface) AvalonFingerprintOptions.bitFlags? (AvalonFingerprintOptions attribute) AvalonFingerprintOptions.isQuery? (AvalonFingerprintOptions attribute) AvalonFingerprintOptions.nBits? (AvalonFingerprintOptions attribute) AvalonFingerprintParams (class in cosmolkit) AvalonFingerprintParams() (class) AvalonFingerprintParams.[Symbol․dispose]() (AvalonFingerprintParams method) AvalonFingerprintParams.bitFlags (AvalonFingerprintParams attribute) AvalonFingerprintParams.free() (AvalonFingerprintParams method) AvalonFingerprintParams.isQuery (AvalonFingerprintParams attribute) AvalonFingerprintParams.nBits (AvalonFingerprintParams attribute) AvalonFingerprintParams.toString() (AvalonFingerprintParams method) AZI (cosmolkit.ResidueCode attribute) B b (cosmolkit.BioCrystalCell attribute) B (cosmolkit.Element attribute) B3E (cosmolkit.ResidueCode attribute) B3P (cosmolkit.ResidueCode attribute) B7G (cosmolkit.ResidueCode attribute) b_iso() (cosmolkit.BioAtomRow method) b_wilson (cosmolkit.BioExperimentInfo attribute) BA (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) basic (cosmolkit.BioRefinementInfo attribute) basin_thresh (cosmolkit.EmbedParams property) BATCH_ERROR_MODE_MAP (in module cosmolkit) BatchError (class in cosmolkit) BatchError() (class) BatchError.[Symbol․dispose]() (BatchError method) BatchError.asDict() (BatchError method) BatchError.cause() (BatchError method) BatchError.free() (BatchError method) BatchError.index() (BatchError method) BatchError.message() (BatchError method) BatchError.operation() (BatchError method) BatchErrorMode (class in cosmolkit) (None attribute) BatchErrorMode.KeepErrors (BatchErrorMode attribute) BatchErrorMode.Strict (BatchErrorMode attribute) batches() (cosmolkit.SdfDataset method) (cosmolkit.SdfReader method) (cosmolkit.SdfRecordStream method) BatchExportParams (class in cosmolkit) BatchExportParams() (class) BatchExportParams.[Symbol․dispose]() (BatchExportParams method) BatchExportParams.errors (BatchExportParams attribute) BatchExportParams.format (BatchExportParams attribute) BatchExportParams.free() (BatchExportParams method) BatchExportParams.nJobs (BatchExportParams attribute) BatchExportParams.progressBar (BatchExportParams attribute) BatchExportParamsOptions() (interface) BatchExportParamsOptions.errors? (BatchExportParamsOptions attribute) BatchExportParamsOptions.format? (BatchExportParamsOptions attribute) BatchExportParamsOptions.nJobs? (BatchExportParamsOptions attribute) BatchExportParamsOptions.progressBar? (BatchExportParamsOptions attribute) BatchExportReport (class in cosmolkit) BatchExportReport() (class) BatchExportReport.[Symbol․dispose]() (BatchExportReport method) BatchExportReport.errors() (BatchExportReport method) BatchExportReport.failed() (BatchExportReport method) BatchExportReport.free() (BatchExportReport method) BatchExportReport.success() (BatchExportReport method) BatchExportReport.total() (BatchExportReport method) BatchExportReport.writeReport() (BatchExportReport method) BatchExportReport.written (BatchExportReport attribute) BatchFingerprintAdditionalOutput (class in cosmolkit) BatchFingerprintAdditionalOutput() (class) BatchFingerprintAdditionalOutput.[Symbol․dispose]() (BatchFingerprintAdditionalOutput method) BatchFingerprintAdditionalOutput.atomCounts() (BatchFingerprintAdditionalOutput method) BatchFingerprintAdditionalOutput.atomsPerBit() (BatchFingerprintAdditionalOutput method) BatchFingerprintAdditionalOutput.atomToBits() (BatchFingerprintAdditionalOutput method) BatchFingerprintAdditionalOutput.bitInfoMap() (BatchFingerprintAdditionalOutput method) BatchFingerprintAdditionalOutput.bitPaths() (BatchFingerprintAdditionalOutput method) BatchFingerprintAdditionalOutput.free() (BatchFingerprintAdditionalOutput method) BatchFingerprintOutput (class in cosmolkit) BatchFingerprintOutput() (class) BatchFingerprintOutput.[Symbol․dispose]() (BatchFingerprintOutput method) BatchFingerprintOutput.additionalOutput() (BatchFingerprintOutput method) BatchFingerprintOutput.fingerprint() (BatchFingerprintOutput method) BatchFingerprintOutput.free() (BatchFingerprintOutput method) BatchFingerprintOutputError BatchFingerprintOutputError() (class) BatchFingerprintOutputError.[Symbol․dispose]() (BatchFingerprintOutputError method) BatchFingerprintOutputError.cause (BatchFingerprintOutputError attribute) BatchFingerprintOutputError.domain (BatchFingerprintOutputError attribute) BatchFingerprintOutputError.free() (BatchFingerprintOutputError method) BatchFingerprintOutputError.kind (BatchFingerprintOutputError attribute) BatchFingerprintOutputError.message (BatchFingerprintOutputError attribute) BatchImageError BatchImageError() (class) BatchImageError.[Symbol․dispose]() (BatchImageError method) BatchImageError.cause (BatchImageError attribute) BatchImageError.domain (BatchImageError attribute) BatchImageError.free() (BatchImageError method) BatchImageError.kind (BatchImageError attribute) BatchImageError.message (BatchImageError attribute) BatchImageParams (class in cosmolkit) BatchImageParams() (class) BatchImageParams.[Symbol․dispose]() (BatchImageParams method) BatchImageParams.execution (BatchImageParams attribute) BatchImageParams.filenames (BatchImageParams attribute) BatchImageParams.format (BatchImageParams attribute) BatchImageParams.free() (BatchImageParams method) BatchImageParams.height (BatchImageParams attribute) BatchImageParams.reportPath (BatchImageParams attribute) BatchImageParams.width (BatchImageParams attribute) BatchImageParamsOptions() (interface) BatchImageParamsOptions.execution? (BatchImageParamsOptions attribute) BatchImageParamsOptions.filenames? (BatchImageParamsOptions attribute) BatchImageParamsOptions.format? (BatchImageParamsOptions attribute) BatchImageParamsOptions.height? (BatchImageParamsOptions attribute) BatchImageParamsOptions.reportPath? (BatchImageParamsOptions attribute) BatchImageParamsOptions.width? (BatchImageParamsOptions attribute) BatchParams (class in cosmolkit) BatchParams() (class) BatchParams.[Symbol․dispose]() (BatchParams method) BatchParams.errors (BatchParams attribute) BatchParams.free() (BatchParams method) BatchParams.nJobs (BatchParams attribute) BatchParams.progressBar (BatchParams attribute) BatchParamsOptions() (interface) BatchParamsOptions.errors? (BatchParamsOptions attribute) BatchParamsOptions.nJobs? (BatchParamsOptions attribute) BatchParamsOptions.progressBar? (BatchParamsOptions attribute) BatchQueryParams (class in cosmolkit) BatchQueryParams() (class) BatchQueryParams.[Symbol․dispose]() (BatchQueryParams method) BatchQueryParams.free() (BatchQueryParams method) BatchQueryParams.nJobs (BatchQueryParams attribute) BatchQueryParams.progressBar (BatchQueryParams attribute) BatchQueryParams.progressCallback (BatchQueryParams attribute) BatchQueryParamsOptions() (interface) BatchQueryParamsOptions.nJobs? (BatchQueryParamsOptions attribute) BatchQueryParamsOptions.progressBar? (BatchQueryParamsOptions attribute) BatchQueryParamsOptions.progressCallback? (BatchQueryParamsOptions attribute) BatchRecord() (class) BatchRecord.[Symbol․dispose]() (BatchRecord method) BatchRecord.error() (BatchRecord method) BatchRecord.errorValue() (BatchRecord method) BatchRecord.free() (BatchRecord method) BatchRecord.molecule() (BatchRecord method) BatchRecord.moleculeValue() (BatchRecord method) BatchValidationError BatchValidationError() (class) BatchValidationError.[Symbol․dispose]() (BatchValidationError method) BatchValidationError.cause (BatchValidationError attribute) BatchValidationError.domain (BatchValidationError attribute) BatchValidationError.errors (BatchValidationError attribute) BatchValidationError.free() (BatchValidationError method) BatchValidationError.kind (BatchValidationError attribute) BatchValidationError.message (BatchValidationError attribute) BatchValidationError.reason (BatchValidationError attribute) BatchValidationError.recordErrors (BatchValidationError attribute) BCN (cosmolkit.ResidueCode attribute) BE (cosmolkit.Element attribute) BE7 (cosmolkit.ResidueCode attribute) beamline (cosmolkit.BioDiffractionInfo attribute) begin() (cosmolkit.Bond method) BEGINDASH (cosmolkit.BondDirection attribute) BEGINWEDGE (cosmolkit.BondDirection attribute) BEQ (cosmolkit.ResidueCode attribute) best_alignment_to() (cosmolkit.Molecule method) best_alignment_to_with_params() (cosmolkit.Molecule method) best_rmsd_to() (cosmolkit.Molecule method) best_rmsd_to_with_params() (cosmolkit.Molecule method) BestAlignmentParameters (class in cosmolkit) BestAlignmentParameters() (class) BestAlignmentParameters.[Symbol․dispose]() (BestAlignmentParameters method) BestAlignmentParameters.atomMaps (BestAlignmentParameters attribute) BestAlignmentParameters.free() (BestAlignmentParameters method) BestAlignmentParameters.ignoreHydrogens (BestAlignmentParameters attribute) BestAlignmentParameters.maxIterations (BestAlignmentParameters attribute) BestAlignmentParameters.maxMatches (BestAlignmentParameters attribute) BestAlignmentParameters.new() (BestAlignmentParameters method) BestAlignmentParameters.numThreads (BestAlignmentParameters attribute) BestAlignmentParameters.probeConformerId (BestAlignmentParameters attribute) BestAlignmentParameters.referenceConformerId (BestAlignmentParameters attribute) BestAlignmentParameters.reflect (BestAlignmentParameters attribute) BestAlignmentParameters.symmetrizeConjugatedTerminalGroups (BestAlignmentParameters attribute) BestAlignmentParameters.weights (BestAlignmentParameters attribute) BestAlignmentParametersOptions() (interface) BestAlignmentParametersOptions.atomMaps? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.ignoreHydrogens? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.maxIterations? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.maxMatches? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.numThreads? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.probeConformerId? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.referenceConformerId? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.reflect? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.symmetrizeConjugatedTerminalGroups? (BestAlignmentParametersOptions attribute) BestAlignmentParametersOptions.weights? (BestAlignmentParametersOptions attribute) beta (cosmolkit.BioCrystalCell attribute) BFD (cosmolkit.ResidueCode attribute) BGC (cosmolkit.ResidueCode attribute) BH (cosmolkit.Element attribute) BI (cosmolkit.Element attribute) bin_count (cosmolkit.BioRefinementInfo attribute) bins (cosmolkit.BioRefinementInfo attribute) bio_from_mmcif() (in module cosmolkit) bio_from_pdb() (in module cosmolkit) BioAltLocGroupId() (class) BioAltLocGroupId.[Symbol․dispose]() (BioAltLocGroupId method) BioAltLocGroupId.free() (BioAltLocGroupId method) BioAltLocGroupId.index() (BioAltLocGroupId method) BioAltLocGroupId.value() (BioAltLocGroupId method) BioAssembly (class in cosmolkit) BioAssembly() (class) BioAssembly.[Symbol․dispose]() (BioAssembly method) BioAssembly.authorDetermined (BioAssembly attribute) BioAssembly.buriedSurfaceArea (BioAssembly attribute) BioAssembly.free() (BioAssembly method) BioAssembly.generators (BioAssembly attribute) BioAssembly.name (BioAssembly attribute) BioAssembly.oligomericCount (BioAssembly attribute) BioAssembly.oligomericDetails (BioAssembly attribute) BioAssembly.softwareDetermined (BioAssembly attribute) BioAssembly.softwareName (BioAssembly attribute) BioAssembly.solventFreeEnergyChange (BioAssembly attribute) BioAssembly.specialKind (BioAssembly attribute) BioAssembly.surfaceArea (BioAssembly attribute) BioAssemblyGenerator (class in cosmolkit) BioAssemblyGenerator() (class) BioAssemblyGenerator.[Symbol․dispose]() (BioAssemblyGenerator method) BioAssemblyGenerator.chains (BioAssemblyGenerator attribute) BioAssemblyGenerator.free() (BioAssemblyGenerator method) BioAssemblyGenerator.operators (BioAssemblyGenerator attribute) BioAssemblyGenerator.subchains (BioAssemblyGenerator attribute) BioAssemblyId() (class) BioAssemblyId.[Symbol․dispose]() (BioAssemblyId method) BioAssemblyId.free() (BioAssemblyId method) BioAssemblyId.index() (BioAssemblyId method) BioAssemblyId.value() (BioAssemblyId method) BioAssemblyOperator (class in cosmolkit) BioAssemblyOperator() (class) BioAssemblyOperator.[Symbol․dispose]() (BioAssemblyOperator method) BioAssemblyOperator.free() (BioAssemblyOperator method) BioAssemblyOperator.name (BioAssemblyOperator attribute) BioAssemblyOperator.operatorType (BioAssemblyOperator attribute) BioAssemblyOperator.transform (BioAssemblyOperator attribute) BioAssemblySpecialKind (class in cosmolkit) (None attribute) BioAssemblySpecialKind.CompleteIcosahedral (BioAssemblySpecialKind attribute) BioAssemblySpecialKind.CompletePoint (BioAssemblySpecialKind attribute) BioAssemblySpecialKind.NotApplicable (BioAssemblySpecialKind attribute) BioAssemblySpecialKind.RepresentativeHelical (BioAssemblySpecialKind attribute) BioAsu (class in cosmolkit) (None attribute) BioAsu.Any (BioAsu attribute) BioAsu.Different (BioAsu attribute) BioAsu.Same (BioAsu attribute) BioAtomId() (class) BioAtomId.[Symbol․dispose]() (BioAtomId method) BioAtomId.free() (BioAtomId method) BioAtomId.index() (BioAtomId method) BioAtomId.value() (BioAtomId method) BioAtomRow (class in cosmolkit) BioAtomRow() (class) BioAtomRow.[Symbol․dispose]() (BioAtomRow method) BioAtomRow.altloc() (BioAtomRow method) BioAtomRow.bIso() (BioAtomRow method) BioAtomRow.element() (BioAtomRow method) BioAtomRow.elementSymbol() (BioAtomRow method) BioAtomRow.formalCharge() (BioAtomRow method) BioAtomRow.free() (BioAtomRow method) BioAtomRow.id() (BioAtomRow method) BioAtomRow.name() (BioAtomRow method) BioAtomRow.occupancy() (BioAtomRow method) BioAtomRow.position() (BioAtomRow method) BioAtomRow.residueId() (BioAtomRow method) BioAtomRow.source() (BioAtomRow method) BioBasicRefinementInfo (class in cosmolkit) BioBasicRefinementInfo() (class) BioBasicRefinementInfo.[Symbol․dispose]() (BioBasicRefinementInfo method) BioBasicRefinementInfo.ccFoFcFree (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.ccFoFcWork (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.ccIntensityFree (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.ccIntensityWork (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.completeness (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.free() (BioBasicRefinementInfo method) BioBasicRefinementInfo.fscFree (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.fscWork (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.rAll (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.reflectionCount (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.resolutionHigh (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.resolutionLow (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.rFree (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.rfreeSetCount (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.rWork (BioBasicRefinementInfo attribute) BioBasicRefinementInfo.workSetCount (BioBasicRefinementInfo attribute) BioCalcFlag (class in cosmolkit) (None attribute) BioCalcFlag.Calculated (BioCalcFlag attribute) BioCalcFlag.Determined (BioCalcFlag attribute) BioCalcFlag.Dummy (BioCalcFlag attribute) BioCalcFlag.NoHydrogen (BioCalcFlag attribute) BioCalcFlag.NotSet (BioCalcFlag attribute) BioChainId() (class) BioChainId.[Symbol․dispose]() (BioChainId method) BioChainId.free() (BioChainId method) BioChainId.index() (BioChainId method) BioChainId.value() (BioChainId method) BioChainRow (class in cosmolkit) BioChainRow() (class) BioChainRow.[Symbol․dispose]() (BioChainRow method) BioChainRow.atoms() (BioChainRow method) BioChainRow.entityId() (BioChainRow method) BioChainRow.free() (BioChainRow method) BioChainRow.id() (BioChainRow method) BioChainRow.kind() (BioChainRow method) BioChainRow.len() (BioChainRow method) BioChainRow.modelId() (BioChainRow method) BioChainRow.residues() (BioChainRow method) BioChainRow.source() (BioChainRow method) BioCisPep (class in cosmolkit) BioCisPep() (class) BioCisPep.[Symbol․dispose]() (BioCisPep method) BioCisPep.free() (BioCisPep method) BioCisPep.modelNum (BioCisPep attribute) BioCisPep.onlyAltloc (BioCisPep attribute) BioCisPep.partnerC (BioCisPep attribute) BioCisPep.partnerN (BioCisPep attribute) BioCisPep.reportedAngle (BioCisPep attribute) BioConnection (class in cosmolkit) BioConnection() (class) BioConnection.[Symbol․dispose]() (BioConnection method) BioConnection.asu (BioConnection attribute) BioConnection.free() (BioConnection method) BioConnection.kind (BioConnection attribute) BioConnection.linkId (BioConnection attribute) BioConnection.name (BioConnection attribute) BioConnection.partner1 (BioConnection attribute) BioConnection.partner2 (BioConnection attribute) BioConnection.reportedDistance (BioConnection attribute) BioConnection.reportedSym (BioConnection attribute) BioConnectionKind (class in cosmolkit) (None attribute) BioConnectionKind.Covale (BioConnectionKind attribute) BioConnectionKind.Disulf (BioConnectionKind attribute) BioConnectionKind.Hydrog (BioConnectionKind attribute) BioConnectionKind.MetalC (BioConnectionKind attribute) BioConnectionKind.Unknown (BioConnectionKind attribute) BioCoordinateBlock (class in cosmolkit) BioCoordinateBlock() (class) BioCoordinateBlock.[Symbol․dispose]() (BioCoordinateBlock method) BioCoordinateBlock.free() (BioCoordinateBlock method) BioCoordinateBlock.isEmpty() (BioCoordinateBlock method) BioCoordinateBlock.len() (BioCoordinateBlock method) BioCoordinateBlock.positions (BioCoordinateBlock attribute) BioCoordinateFormat (class in cosmolkit) (None attribute) BioCoordinateFormat.ChemComp (BioCoordinateFormat attribute) BioCoordinateFormat.Detect (BioCoordinateFormat attribute) BioCoordinateFormat.Mmcif (BioCoordinateFormat attribute) BioCoordinateFormat.Mmjson (BioCoordinateFormat attribute) BioCoordinateFormat.Pdb (BioCoordinateFormat attribute) BioCoordinateFormat.Unknown (BioCoordinateFormat attribute) BioCrystalCell (class in cosmolkit) BioCrystalCell() (class) BioCrystalCell.[Symbol․dispose]() (BioCrystalCell method) BioCrystalCell.a (BioCrystalCell attribute) BioCrystalCell.alpha (BioCrystalCell attribute) BioCrystalCell.b (BioCrystalCell attribute) BioCrystalCell.beta (BioCrystalCell attribute) BioCrystalCell.c (BioCrystalCell attribute) BioCrystalCell.free() (BioCrystalCell method) BioCrystalCell.gamma (BioCrystalCell attribute) BioCrystalInfo (class in cosmolkit) BioCrystalInfo() (class) BioCrystalInfo.[Symbol․dispose]() (BioCrystalInfo method) BioCrystalInfo.cell (BioCrystalInfo attribute) BioCrystalInfo.csCount (BioCrystalInfo attribute) BioCrystalInfo.explicitMatrices (BioCrystalInfo attribute) BioCrystalInfo.fractional (BioCrystalInfo attribute) BioCrystalInfo.free() (BioCrystalInfo method) BioCrystalInfo.isCrystal() (BioCrystalInfo method) BioCrystalInfo.orthogonal (BioCrystalInfo attribute) BioCrystalInfo.reciprocalCosines (BioCrystalInfo attribute) BioCrystalInfo.reciprocalLengths (BioCrystalInfo attribute) BioCrystalInfo.spaceGroupHm (BioCrystalInfo attribute) BioCrystalInfo.spaceGroupNumber() (BioCrystalInfo method) BioCrystalInfo.symmetryImages (BioCrystalInfo attribute) BioCrystalInfo.volume (BioCrystalInfo attribute) BioCrystalInfo.zPdb (BioCrystalInfo attribute) BioDiffractionInfo (class in cosmolkit) BioDiffractionInfo() (class) BioDiffractionInfo.[Symbol․dispose]() (BioDiffractionInfo method) BioDiffractionInfo.beamline (BioDiffractionInfo attribute) BioDiffractionInfo.collectionDate (BioDiffractionInfo attribute) BioDiffractionInfo.detector (BioDiffractionInfo attribute) BioDiffractionInfo.detectorMake (BioDiffractionInfo attribute) BioDiffractionInfo.free() (BioDiffractionInfo method) BioDiffractionInfo.id (BioDiffractionInfo attribute) BioDiffractionInfo.monochromator (BioDiffractionInfo attribute) BioDiffractionInfo.monoOrLaue (BioDiffractionInfo attribute) BioDiffractionInfo.optics (BioDiffractionInfo attribute) BioDiffractionInfo.scatteringType (BioDiffractionInfo attribute) BioDiffractionInfo.source (BioDiffractionInfo attribute) BioDiffractionInfo.sourceType (BioDiffractionInfo attribute) BioDiffractionInfo.synchrotron (BioDiffractionInfo attribute) BioDiffractionInfo.temperature (BioDiffractionInfo attribute) BioDiffractionInfo.wavelengths (BioDiffractionInfo attribute) BioEntityDbRef (class in cosmolkit) BioEntityDbRef() (class) BioEntityDbRef.[Symbol․dispose]() (BioEntityDbRef method) BioEntityDbRef.accessionCode (BioEntityDbRef attribute) BioEntityDbRef.dbBegin (BioEntityDbRef attribute) BioEntityDbRef.dbEnd (BioEntityDbRef attribute) BioEntityDbRef.dbName (BioEntityDbRef attribute) BioEntityDbRef.free() (BioEntityDbRef method) BioEntityDbRef.idCode (BioEntityDbRef attribute) BioEntityDbRef.isoform (BioEntityDbRef attribute) BioEntityDbRef.labelSeqBegin (BioEntityDbRef attribute) BioEntityDbRef.labelSeqEnd (BioEntityDbRef attribute) BioEntityDbRef.seqBegin (BioEntityDbRef attribute) BioEntityDbRef.seqEnd (BioEntityDbRef attribute) BioEntityId() (class) BioEntityId.[Symbol․dispose]() (BioEntityId method) BioEntityId.free() (BioEntityId method) BioEntityId.index() (BioEntityId method) BioEntityId.value() (BioEntityId method) BioEntityRow (class in cosmolkit) BioEntityRow() (class) BioEntityRow.[Symbol․dispose]() (BioEntityRow method) BioEntityRow.dbrefs() (BioEntityRow method) BioEntityRow.free() (BioEntityRow method) BioEntityRow.fullSequence() (BioEntityRow method) BioEntityRow.id() (BioEntityRow method) BioEntityRow.kind() (BioEntityRow method) BioEntityRow.len() (BioEntityRow method) BioEntityRow.polymerKind() (BioEntityRow method) BioEntityRow.reflectsMicrohetero() (BioEntityRow method) BioEntityRow.siftsUnpAccessions() (BioEntityRow method) BioEntityRow.source() (BioEntityRow method) BioEntityRow.subchains() (BioEntityRow method) BioExperimentalCrystalInfo (class in cosmolkit) BioExperimentalCrystalInfo() (class) BioExperimentalCrystalInfo.[Symbol․dispose]() (BioExperimentalCrystalInfo method) BioExperimentalCrystalInfo.description (BioExperimentalCrystalInfo attribute) BioExperimentalCrystalInfo.diffractions (BioExperimentalCrystalInfo attribute) BioExperimentalCrystalInfo.free() (BioExperimentalCrystalInfo method) BioExperimentalCrystalInfo.id (BioExperimentalCrystalInfo attribute) BioExperimentalCrystalInfo.ph (BioExperimentalCrystalInfo attribute) BioExperimentalCrystalInfo.phRange (BioExperimentalCrystalInfo attribute) BioExperimentInfo (class in cosmolkit) BioExperimentInfo() (class) BioExperimentInfo.[Symbol․dispose]() (BioExperimentInfo method) BioExperimentInfo.bWilson (BioExperimentInfo attribute) BioExperimentInfo.diffractionIds (BioExperimentInfo attribute) BioExperimentInfo.free() (BioExperimentInfo method) BioExperimentInfo.method (BioExperimentInfo attribute) BioExperimentInfo.numberOfCrystals (BioExperimentInfo attribute) BioExperimentInfo.reflections (BioExperimentInfo attribute) BioExperimentInfo.shells (BioExperimentInfo attribute) BioExperimentInfo.uniqueReflections (BioExperimentInfo attribute) BioHelix (class in cosmolkit) BioHelix() (class) BioHelix.[Symbol․dispose]() (BioHelix method) BioHelix.end (BioHelix attribute) BioHelix.free() (BioHelix method) BioHelix.length (BioHelix attribute) BioHelix.pdbHelixClass (BioHelix attribute) BioHelix.start (BioHelix attribute) BioHelixClass (class in cosmolkit) (None attribute) BioHelixClass.Helix27 (BioHelixClass attribute) BioHelixClass.HelixPolyProlineNone (BioHelixClass attribute) BioHelixClass.LAlpha (BioHelixClass attribute) BioHelixClass.LGamma (BioHelixClass attribute) BioHelixClass.LOmega (BioHelixClass attribute) BioHelixClass.R310 (BioHelixClass attribute) BioHelixClass.RAlpha (BioHelixClass attribute) BioHelixClass.RGamma (BioHelixClass attribute) BioHelixClass.ROmega (BioHelixClass attribute) BioHelixClass.RPi (BioHelixClass attribute) BioHelixClass.UnknownHelix (BioHelixClass attribute) BioMetadata (class in cosmolkit) BioMetadata() (class) BioMetadata.[Symbol․dispose]() (BioMetadata method) BioMetadata.authors (BioMetadata attribute) BioMetadata.crystals (BioMetadata attribute) BioMetadata.experiments (BioMetadata attribute) BioMetadata.free() (BioMetadata method) BioMetadata.refinement (BioMetadata attribute) BioMetadata.remark_300Detail (BioMetadata attribute) BioMetadata.software (BioMetadata attribute) BioMetadata.solvedBy (BioMetadata attribute) BioMetadata.startingModel (BioMetadata attribute) BioMmcifReadError BioMmcifReadError() (class) BioMmcifReadError.[Symbol․dispose]() (BioMmcifReadError method) BioMmcifReadError.cause (BioMmcifReadError attribute) BioMmcifReadError.domain (BioMmcifReadError attribute) BioMmcifReadError.free() (BioMmcifReadError method) BioMmcifReadError.kind (BioMmcifReadError attribute) BioMmcifReadError.message (BioMmcifReadError attribute) BioMmcifReadError.stage() (BioMmcifReadError method) BioMmcifReadStage (class in cosmolkit) (None attribute) BioMmcifReadStage.AnisotropicU (BioMmcifReadStage attribute) BioMmcifReadStage.Assemblies (BioMmcifReadStage attribute) BioMmcifReadStage.AtomSites (BioMmcifReadStage attribute) BioMmcifReadStage.CcdRestoration (BioMmcifReadStage attribute) BioMmcifReadStage.CifDocument (BioMmcifReadStage attribute) BioMmcifReadStage.CisPeptides (BioMmcifReadStage attribute) BioMmcifReadStage.Connections (BioMmcifReadStage attribute) BioMmcifReadStage.CoordinateBlock (BioMmcifReadStage attribute) BioMmcifReadStage.CrystalCell (BioMmcifReadStage attribute) BioMmcifReadStage.EntitySequence (BioMmcifReadStage attribute) BioMmcifReadStage.Experimental (BioMmcifReadStage attribute) BioMmcifReadStage.FractionalTransform (BioMmcifReadStage attribute) BioMmcifReadStage.Helices (BioMmcifReadStage attribute) BioMmcifReadStage.Materialization (BioMmcifReadStage attribute) BioMmcifReadStage.ModifiedResidues (BioMmcifReadStage attribute) BioMmcifReadStage.Ncs (BioMmcifReadStage attribute) BioMmcifReadStage.Origx (BioMmcifReadStage attribute) BioMmcifReadStage.Refinement (BioMmcifReadStage attribute) BioMmcifReadStage.Reflections (BioMmcifReadStage attribute) BioMmcifReadStage.Sheets (BioMmcifReadStage attribute) BioMmcifReadStage.SiftsUnp (BioMmcifReadStage attribute) BioMmcifReadStage.Software (BioMmcifReadStage attribute) BioMmcifReadStage.StructureValidation (BioMmcifReadStage attribute) BioMmcifReadStage.Tls (BioMmcifReadStage attribute) BioMmcifWriteError BioMmcifWriteError() (class) BioMmcifWriteError.[Symbol․dispose]() (BioMmcifWriteError method) BioMmcifWriteError.cause (BioMmcifWriteError attribute) BioMmcifWriteError.domain (BioMmcifWriteError attribute) BioMmcifWriteError.field (BioMmcifWriteError attribute) BioMmcifWriteError.free() (BioMmcifWriteError method) BioMmcifWriteError.kind (BioMmcifWriteError attribute) BioMmcifWriteError.message (BioMmcifWriteError attribute) BioMmcifWriteError.path (BioMmcifWriteError attribute) BioMmcifWriteParams (class in cosmolkit) BioMmcifWriteParams() (class) BioMmcifWriteParams.[Symbol․dispose]() (BioMmcifWriteParams method) BioMmcifWriteParams.alignLoops (BioMmcifWriteParams attribute) BioMmcifWriteParams.alignPairs (BioMmcifWriteParams attribute) BioMmcifWriteParams.allGroups (BioMmcifWriteParams attribute) BioMmcifWriteParams.assembly (BioMmcifWriteParams attribute) BioMmcifWriteParams.atoms (BioMmcifWriteParams attribute) BioMmcifWriteParams.atomType (BioMmcifWriteParams attribute) BioMmcifWriteParams.authAll (BioMmcifWriteParams attribute) BioMmcifWriteParams.author (BioMmcifWriteParams attribute) BioMmcifWriteParams.blockName (BioMmcifWriteParams attribute) BioMmcifWriteParams.cell (BioMmcifWriteParams attribute) BioMmcifWriteParams.chemComp (BioMmcifWriteParams attribute) BioMmcifWriteParams.cis (BioMmcifWriteParams attribute) BioMmcifWriteParams.compact (BioMmcifWriteParams attribute) BioMmcifWriteParams.conn (BioMmcifWriteParams attribute) BioMmcifWriteParams.databaseStatus (BioMmcifWriteParams attribute) BioMmcifWriteParams.diffrn (BioMmcifWriteParams attribute) BioMmcifWriteParams.entity (BioMmcifWriteParams attribute) BioMmcifWriteParams.entityPoly (BioMmcifWriteParams attribute) BioMmcifWriteParams.entityPolySeq (BioMmcifWriteParams attribute) BioMmcifWriteParams.entry (BioMmcifWriteParams attribute) BioMmcifWriteParams.exptl (BioMmcifWriteParams attribute) BioMmcifWriteParams.free() (BioMmcifWriteParams method) BioMmcifWriteParams.groupPdb (BioMmcifWriteParams attribute) BioMmcifWriteParams.misuseHash (BioMmcifWriteParams attribute) BioMmcifWriteParams.modres (BioMmcifWriteParams attribute) BioMmcifWriteParams.ncs (BioMmcifWriteParams attribute) BioMmcifWriteParams.origx (BioMmcifWriteParams attribute) BioMmcifWriteParams.preferPairs (BioMmcifWriteParams attribute) BioMmcifWriteParams.refine (BioMmcifWriteParams attribute) BioMmcifWriteParams.reflns (BioMmcifWriteParams attribute) BioMmcifWriteParams.scale (BioMmcifWriteParams attribute) BioMmcifWriteParams.software (BioMmcifWriteParams attribute) BioMmcifWriteParams.structAsym (BioMmcifWriteParams attribute) BioMmcifWriteParams.structBiol (BioMmcifWriteParams attribute) BioMmcifWriteParams.structConf (BioMmcifWriteParams attribute) BioMmcifWriteParams.structRef (BioMmcifWriteParams attribute) BioMmcifWriteParams.structSheet (BioMmcifWriteParams attribute) BioMmcifWriteParams.symmetry (BioMmcifWriteParams attribute) BioMmcifWriteParams.titleKeywords (BioMmcifWriteParams attribute) BioMmcifWriteParams.tls (BioMmcifWriteParams attribute) BioMmcifWriteParamsOptions() (interface) BioMmcifWriteParamsOptions.alignLoops? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.alignPairs? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.allGroups? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.assembly? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.atoms? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.atomType? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.authAll? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.author? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.blockName? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.cell? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.chemComp? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.cis? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.compact? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.conn? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.databaseStatus? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.diffrn? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.entity? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.entityPoly? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.entityPolySeq? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.entry? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.exptl? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.groupPdb? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.misuseHash? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.modres? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.ncs? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.origx? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.preferPairs? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.refine? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.reflns? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.scale? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.software? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.structAsym? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.structBiol? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.structConf? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.structRef? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.structSheet? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.symmetry? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.titleKeywords? (BioMmcifWriteParamsOptions attribute) BioMmcifWriteParamsOptions.tls? (BioMmcifWriteParamsOptions attribute) BioModelId() (class) BioModelId.[Symbol․dispose]() (BioModelId method) BioModelId.free() (BioModelId method) BioModelId.index() (BioModelId method) BioModelId.value() (BioModelId method) BioModelRow (class in cosmolkit) BioModelRow() (class) BioModelRow.[Symbol․dispose]() (BioModelRow method) BioModelRow.chains() (BioModelRow method) BioModelRow.free() (BioModelRow method) BioModelRow.id() (BioModelRow method) BioModelRow.len() (BioModelRow method) BioModelRow.sourceModelNumber() (BioModelRow method) BioModRes (class in cosmolkit) BioModRes() (class) BioModRes.[Symbol․dispose]() (BioModRes method) BioModRes.chainName (BioModRes attribute) BioModRes.details (BioModRes attribute) BioModRes.free() (BioModRes method) BioModRes.modId (BioModRes attribute) BioModRes.parentCompId (BioModRes attribute) BioModRes.resId (BioModRes attribute) BioMoleculeConversionError BioMoleculeConversionError() (class) BioMoleculeConversionError.[Symbol․dispose]() (BioMoleculeConversionError method) BioMoleculeConversionError.cause (BioMoleculeConversionError attribute) BioMoleculeConversionError.domain (BioMoleculeConversionError attribute) BioMoleculeConversionError.free() (BioMoleculeConversionError method) BioMoleculeConversionError.kind (BioMoleculeConversionError attribute) BioMoleculeConversionError.message (BioMoleculeConversionError attribute) BioMoleculeError BioMoleculeError() (class) BioMoleculeError.[Symbol․dispose]() (BioMoleculeError method) BioMoleculeError.cause (BioMoleculeError attribute) BioMoleculeError.domain (BioMoleculeError attribute) BioMoleculeError.free() (BioMoleculeError method) BioMoleculeError.kind (BioMoleculeError attribute) BioMoleculeError.message (BioMoleculeError attribute) BioMoleculeParams (class in cosmolkit) BioMoleculeParams() (class) BioMoleculeParams.[Symbol․dispose]() (BioMoleculeParams method) BioMoleculeParams.flavor (BioMoleculeParams attribute) BioMoleculeParams.free() (BioMoleculeParams method) BioMoleculeParams.proximityBonding (BioMoleculeParams attribute) BioMoleculeParams.removeHs (BioMoleculeParams attribute) BioMoleculeParams.sanitize (BioMoleculeParams attribute) BioMoleculeParamsOptions() (interface) BioMoleculeParamsOptions.flavor? (BioMoleculeParamsOptions attribute) BioMoleculeParamsOptions.proximityBonding? (BioMoleculeParamsOptions attribute) BioMoleculeParamsOptions.removeHs? (BioMoleculeParamsOptions attribute) BioMoleculeParamsOptions.sanitize? (BioMoleculeParamsOptions attribute) BioNcsOperator (class in cosmolkit) BioNcsOperator() (class) BioNcsOperator.[Symbol․dispose]() (BioNcsOperator method) BioNcsOperator.free() (BioNcsOperator method) BioNcsOperator.given (BioNcsOperator attribute) BioNcsOperator.id (BioNcsOperator attribute) BioNcsOperator.transform (BioNcsOperator attribute) BioOperationError BioOperationError() (class) BioOperationError.[Symbol․dispose]() (BioOperationError method) BioOperationError.cause (BioOperationError attribute) BioOperationError.domain (BioOperationError attribute) BioOperationError.free() (BioOperationError method) BioOperationError.kind (BioOperationError attribute) BioOperationError.message (BioOperationError attribute) BioPdbReadError BioPdbReadError() (class) BioPdbReadError.[Symbol․dispose]() (BioPdbReadError method) BioPdbReadError.cause (BioPdbReadError attribute) BioPdbReadError.domain (BioPdbReadError attribute) BioPdbReadError.free() (BioPdbReadError method) BioPdbReadError.kind (BioPdbReadError attribute) BioPdbReadError.lineNumber() (BioPdbReadError method) BioPdbReadError.message (BioPdbReadError attribute) BioPdbReadError.recordTag() (BioPdbReadError method) BioPdbReadError.stage() (BioPdbReadError method) BioPdbReadParams (class in cosmolkit) BioPdbReadParams() (class) BioPdbReadParams.[Symbol․dispose]() (BioPdbReadParams method) BioPdbReadParams.checkNonAscii (BioPdbReadParams attribute) BioPdbReadParams.free() (BioPdbReadParams method) BioPdbReadParams.ignoreTer (BioPdbReadParams attribute) BioPdbReadParams.maxLineLength (BioPdbReadParams attribute) BioPdbReadParams.skipRemarks (BioPdbReadParams attribute) BioPdbReadParams.splitChainOnTer (BioPdbReadParams attribute) BioPdbReadParamsOptions() (interface) BioPdbReadParamsOptions.checkNonAscii? (BioPdbReadParamsOptions attribute) BioPdbReadParamsOptions.ignoreTer? (BioPdbReadParamsOptions attribute) BioPdbReadParamsOptions.maxLineLength? (BioPdbReadParamsOptions attribute) BioPdbReadParamsOptions.skipRemarks? (BioPdbReadParamsOptions attribute) BioPdbReadParamsOptions.splitChainOnTer? (BioPdbReadParamsOptions attribute) BioPdbReadStage (class in cosmolkit) (None attribute) BioPdbReadStage.Finalization (BioPdbReadStage attribute) BioPdbReadStage.Record (BioPdbReadStage attribute) BioPdbReadStage.Stream (BioPdbReadStage attribute) BioPdbWriteError BioPdbWriteError() (class) BioPdbWriteError.[Symbol․dispose]() (BioPdbWriteError method) BioPdbWriteError.cause (BioPdbWriteError attribute) BioPdbWriteError.chain (BioPdbWriteError attribute) BioPdbWriteError.detail (BioPdbWriteError attribute) BioPdbWriteError.domain (BioPdbWriteError attribute) BioPdbWriteError.field (BioPdbWriteError attribute) BioPdbWriteError.free() (BioPdbWriteError method) BioPdbWriteError.from (BioPdbWriteError attribute) BioPdbWriteError.kind (BioPdbWriteError attribute) BioPdbWriteError.length (BioPdbWriteError attribute) BioPdbWriteError.message (BioPdbWriteError attribute) BioPdbWriteError.path (BioPdbWriteError attribute) BioPdbWriteError.serial (BioPdbWriteError attribute) BioPdbWriteError.value (BioPdbWriteError attribute) BioPdbWriteParams (class in cosmolkit) BioPdbWriteParams() (class) BioPdbWriteParams.[Symbol․dispose]() (BioPdbWriteParams method) BioPdbWriteParams.endRecord (BioPdbWriteParams attribute) BioPdbWriteParams.free() (BioPdbWriteParams method) BioPdbWriteParams.numberedTer (BioPdbWriteParams attribute) BioPdbWriteParams.preserveSerial (BioPdbWriteParams attribute) BioPdbWriteParams.terIgnoresType (BioPdbWriteParams attribute) BioPdbWriteParams.terRecords (BioPdbWriteParams attribute) BioPdbWriteParamsOptions() (interface) BioPdbWriteParamsOptions.endRecord? (BioPdbWriteParamsOptions attribute) BioPdbWriteParamsOptions.numberedTer? (BioPdbWriteParamsOptions attribute) BioPdbWriteParamsOptions.preserveSerial? (BioPdbWriteParamsOptions attribute) BioPdbWriteParamsOptions.terIgnoresType? (BioPdbWriteParamsOptions attribute) BioPdbWriteParamsOptions.terRecords? (BioPdbWriteParamsOptions attribute) BioReadError BioReadError() (class) BioReadError.[Symbol․dispose]() (BioReadError method) BioReadError.cause (BioReadError attribute) BioReadError.domain (BioReadError attribute) BioReadError.free() (BioReadError method) BioReadError.kind (BioReadError attribute) BioReadError.message (BioReadError attribute) BioReadParams (class in cosmolkit) BioReadParams() (class) BioReadParams.[Symbol․dispose]() (BioReadParams method) BioReadParams.format (BioReadParams attribute) BioReadParams.free() (BioReadParams method) BioReadParams.sourceName (BioReadParams attribute) BioReadParamsOptions() (interface) BioReadParamsOptions.format? (BioReadParamsOptions attribute) BioReadParamsOptions.sourceName? (BioReadParamsOptions attribute) BioRefinementInfo (class in cosmolkit) BioRefinementInfo() (class) BioRefinementInfo.[Symbol․dispose]() (BioRefinementInfo method) BioRefinementInfo.anisoB (BioRefinementInfo attribute) BioRefinementInfo.basic (BioRefinementInfo attribute) BioRefinementInfo.binCount (BioRefinementInfo attribute) BioRefinementInfo.bins (BioRefinementInfo attribute) BioRefinementInfo.crossValidationMethod (BioRefinementInfo attribute) BioRefinementInfo.dpiBlowR (BioRefinementInfo attribute) BioRefinementInfo.dpiBlowRfree (BioRefinementInfo attribute) BioRefinementInfo.dpiCruickshankR (BioRefinementInfo attribute) BioRefinementInfo.dpiCruickshankRfree (BioRefinementInfo attribute) BioRefinementInfo.free() (BioRefinementInfo method) BioRefinementInfo.id (BioRefinementInfo attribute) BioRefinementInfo.luzzatiError (BioRefinementInfo attribute) BioRefinementInfo.meanB (BioRefinementInfo attribute) BioRefinementInfo.remarks (BioRefinementInfo attribute) BioRefinementInfo.restrStats (BioRefinementInfo attribute) BioRefinementInfo.rfreeSelectionMethod (BioRefinementInfo attribute) BioRefinementInfo.tlsGroups (BioRefinementInfo attribute) BioRefinementRestraint (class in cosmolkit) BioRefinementRestraint() (class) BioRefinementRestraint.[Symbol․dispose]() (BioRefinementRestraint method) BioRefinementRestraint.count (BioRefinementRestraint attribute) BioRefinementRestraint.devIdeal (BioRefinementRestraint attribute) BioRefinementRestraint.free() (BioRefinementRestraint method) BioRefinementRestraint.function (BioRefinementRestraint attribute) BioRefinementRestraint.name (BioRefinementRestraint attribute) BioRefinementRestraint.weight (BioRefinementRestraint attribute) BioReflectionsInfo (class in cosmolkit) BioReflectionsInfo() (class) BioReflectionsInfo.[Symbol․dispose]() (BioReflectionsInfo method) BioReflectionsInfo.completeness (BioReflectionsInfo attribute) BioReflectionsInfo.free() (BioReflectionsInfo method) BioReflectionsInfo.meanIOverSigma (BioReflectionsInfo attribute) BioReflectionsInfo.redundancy (BioReflectionsInfo attribute) BioReflectionsInfo.resolutionHigh (BioReflectionsInfo attribute) BioReflectionsInfo.resolutionLow (BioReflectionsInfo attribute) BioReflectionsInfo.rMerge (BioReflectionsInfo attribute) BioReflectionsInfo.rSym (BioReflectionsInfo attribute) BioResidueId() (class) BioResidueId.[Symbol․dispose]() (BioResidueId method) BioResidueId.free() (BioResidueId method) BioResidueId.index() (BioResidueId method) BioResidueId.value() (BioResidueId method) BioResidueRow (class in cosmolkit) BioResidueRow() (class) BioResidueRow.[Symbol․dispose]() (BioResidueRow method) BioResidueRow.atoms() (BioResidueRow method) BioResidueRow.chainId() (BioResidueRow method) BioResidueRow.code() (BioResidueRow method) BioResidueRow.entityKind() (BioResidueRow method) BioResidueRow.free() (BioResidueRow method) BioResidueRow.id() (BioResidueRow method) BioResidueRow.info() (BioResidueRow method) BioResidueRow.kind() (BioResidueRow method) BioResidueRow.len() (BioResidueRow method) BioResidueRow.name() (BioResidueRow method) BioResidueRow.siftsUnp() (BioResidueRow method) BioResidueRow.source() (BioResidueRow method) BioRowChainError BioRowChainError() (class) BioRowChainError.[Symbol․dispose]() (BioRowChainError method) BioRowChainError.cause (BioRowChainError attribute) BioRowChainError.domain (BioRowChainError attribute) BioRowChainError.free() (BioRowChainError method) BioRowChainError.kind (BioRowChainError attribute) BioRowChainError.message (BioRowChainError attribute) BioRowModelError BioRowModelError() (class) BioRowModelError.[Symbol․dispose]() (BioRowModelError method) BioRowModelError.cause (BioRowModelError attribute) BioRowModelError.domain (BioRowModelError attribute) BioRowModelError.free() (BioRowModelError method) BioRowModelError.kind (BioRowModelError attribute) BioRowModelError.message (BioRowModelError attribute) BioRowSpan (class in cosmolkit) BioRowSpan() (class) BioRowSpan.[Symbol․dispose]() (BioRowSpan method) BioRowSpan.end() (BioRowSpan method) BioRowSpan.free() (BioRowSpan method) BioRowSpan.isEmpty() (BioRowSpan method) BioRowSpan.len() (BioRowSpan method) BioRowSpan.start() (BioRowSpan method) BioRowTraverseError BioRowTraverseError() (class) BioRowTraverseError.[Symbol․dispose]() (BioRowTraverseError method) BioRowTraverseError.cause (BioRowTraverseError attribute) BioRowTraverseError.domain (BioRowTraverseError attribute) BioRowTraverseError.free() (BioRowTraverseError method) BioRowTraverseError.kind (BioRowTraverseError attribute) BioRowTraverseError.message (BioRowTraverseError attribute) BioSelection (class in cosmolkit) BioSelection() (class) BioSelection.[Symbol․dispose]() (BioSelection method) BioSelection.free() (BioSelection method) BioSelection.fromCid() (BioSelection method) BioSelection.toCid() (BioSelection method) BioSelectionCopyCause BioSelectionCopyCause() (class) BioSelectionCopyCause.[Symbol․dispose]() (BioSelectionCopyCause method) BioSelectionCopyCause.cause (BioSelectionCopyCause attribute) BioSelectionCopyCause.domain (BioSelectionCopyCause attribute) BioSelectionCopyCause.free() (BioSelectionCopyCause method) BioSelectionCopyCause.kind (BioSelectionCopyCause attribute) BioSelectionCopyCause.message (BioSelectionCopyCause attribute) BioSelectionCopyError BioSelectionCopyError() (class) BioSelectionCopyError.[Symbol․dispose]() (BioSelectionCopyError method) BioSelectionCopyError.cause() (BioSelectionCopyError method) BioSelectionCopyError.domain (BioSelectionCopyError attribute) BioSelectionCopyError.free() (BioSelectionCopyError method) BioSelectionCopyError.kind (BioSelectionCopyError attribute) BioSelectionCopyError.message (BioSelectionCopyError attribute) BioSelectionMatchError BioSelectionMatchError() (class) BioSelectionMatchError.[Symbol․dispose]() (BioSelectionMatchError method) BioSelectionMatchError.cause (BioSelectionMatchError attribute) BioSelectionMatchError.domain (BioSelectionMatchError attribute) BioSelectionMatchError.free() (BioSelectionMatchError method) BioSelectionMatchError.kind (BioSelectionMatchError attribute) BioSelectionMatchError.message (BioSelectionMatchError attribute) BioSelectionParseError BioSelectionParseError() (class) BioSelectionParseError.[Symbol․dispose]() (BioSelectionParseError method) BioSelectionParseError.cause (BioSelectionParseError attribute) BioSelectionParseError.cid (BioSelectionParseError attribute) BioSelectionParseError.domain (BioSelectionParseError attribute) BioSelectionParseError.free() (BioSelectionParseError method) BioSelectionParseError.info (BioSelectionParseError attribute) BioSelectionParseError.kind (BioSelectionParseError attribute) BioSelectionParseError.message (BioSelectionParseError attribute) BioSelectionParseError.pos (BioSelectionParseError attribute) BioSelectionParseError.variant (BioSelectionParseError attribute) BioSheet (class in cosmolkit) BioSheet() (class) BioSheet.[Symbol․dispose]() (BioSheet method) BioSheet.free() (BioSheet method) BioSheet.name (BioSheet attribute) BioSheet.strands (BioSheet attribute) BioSiftsUnpResidue (class in cosmolkit) BioSiftsUnpResidue() (class) BioSiftsUnpResidue.[Symbol․dispose]() (BioSiftsUnpResidue method) BioSiftsUnpResidue.accessionIndex() (BioSiftsUnpResidue method) BioSiftsUnpResidue.free() (BioSiftsUnpResidue method) BioSiftsUnpResidue.number() (BioSiftsUnpResidue method) BioSiftsUnpResidue.residue() (BioSiftsUnpResidue method) BioSoftwareClassification (class in cosmolkit) (None attribute) BioSoftwareClassification.DataCollection (BioSoftwareClassification attribute) BioSoftwareClassification.DataExtraction (BioSoftwareClassification attribute) BioSoftwareClassification.DataProcessing (BioSoftwareClassification attribute) BioSoftwareClassification.DataReduction (BioSoftwareClassification attribute) BioSoftwareClassification.DataScaling (BioSoftwareClassification attribute) BioSoftwareClassification.ModelBuilding (BioSoftwareClassification attribute) BioSoftwareClassification.Phasing (BioSoftwareClassification attribute) BioSoftwareClassification.Refinement (BioSoftwareClassification attribute) BioSoftwareClassification.Unspecified (BioSoftwareClassification attribute) BioSoftwareItem (class in cosmolkit) BioSoftwareItem() (class) BioSoftwareItem.[Symbol․dispose]() (BioSoftwareItem method) BioSoftwareItem.classification (BioSoftwareItem attribute) BioSoftwareItem.contactAuthor (BioSoftwareItem attribute) BioSoftwareItem.contactAuthorEmail (BioSoftwareItem attribute) BioSoftwareItem.date (BioSoftwareItem attribute) BioSoftwareItem.description (BioSoftwareItem attribute) BioSoftwareItem.free() (BioSoftwareItem method) BioSoftwareItem.name (BioSoftwareItem attribute) BioSoftwareItem.version (BioSoftwareItem attribute) BioStrand (class in cosmolkit) BioStrand() (class) BioStrand.[Symbol․dispose]() (BioStrand method) BioStrand.end (BioStrand attribute) BioStrand.free() (BioStrand method) BioStrand.hbondAtom1 (BioStrand attribute) BioStrand.hbondAtom2 (BioStrand attribute) BioStrand.name (BioStrand attribute) BioStrand.sense (BioStrand attribute) BioStrand.start (BioStrand attribute) BioStructure (class in cosmolkit) BioStructure() (class) BioStructure.[Symbol․dispose]() (BioStructure method) BioStructure.assemblies() (BioStructure method) BioStructure.atomByAltloc() (BioStructure method) BioStructure.atomPosition() (BioStructure method) BioStructure.atoms() (BioStructure method) BioStructure.chains() (BioStructure method) BioStructure.cispeps() (BioStructure method) BioStructure.connections() (BioStructure method) BioStructure.coordinates() (BioStructure method) BioStructure.crystal() (BioStructure method) BioStructure.entities() (BioStructure method) BioStructure.findAtom() (BioStructure method) BioStructure.findEntity() (BioStructure method) BioStructure.findEntityOfSubchain() (BioStructure method) BioStructure.free() (BioStructure method) BioStructure.fromMmcif() (BioStructure method) BioStructure.fromParts() (BioStructure method) BioStructure.fromPdb() (BioStructure method) BioStructure.fromPdbWithParams() (BioStructure method) BioStructure.fromText() (BioStructure method) BioStructure.fromTextWithParams() (BioStructure method) BioStructure.hasOrigx() (BioStructure method) BioStructure.helices() (BioStructure method) BioStructure.inputFormat() (BioStructure method) BioStructure.intoParts() (BioStructure method) BioStructure.metadata() (BioStructure method) BioStructure.models() (BioStructure method) BioStructure.modResidues() (BioStructure method) BioStructure.name() (BioStructure method) BioStructure.ncsOperators() (BioStructure method) BioStructure.ncsOperIdentityId() (BioStructure method) BioStructure.numAtoms() (BioStructure method) BioStructure.numChains() (BioStructure method) BioStructure.numEntities() (BioStructure method) BioStructure.numModels() (BioStructure method) BioStructure.numResidues() (BioStructure method) BioStructure.origx() (BioStructure method) BioStructure.protein() (BioStructure method) BioStructure.read() (BioStructure method) BioStructure.readWithFormat() (BioStructure method) BioStructure.residueAtoms() (BioStructure method) BioStructure.residues() (BioStructure method) BioStructure.resolution() (BioStructure method) BioStructure.retainSelection() (BioStructure method) BioStructure.selectedAtomIds() (BioStructure method) BioStructure.sheets() (BioStructure method) BioStructure.sourceState() (BioStructure method) BioStructure.terStatus() (BioStructure method) BioStructure.toMmcif() (BioStructure method) BioStructure.toMmcifWithParams() (BioStructure method) BioStructure.toMolecule() (BioStructure method) BioStructure.toMoleculeWithParams() (BioStructure method) BioStructure.toPdb() (BioStructure method) BioStructure.toPdbWithParams() (BioStructure method) BioStructure.translate() (BioStructure method) BioStructure.validate() (BioStructure method) BioStructure.validateParts() (BioStructure method) BioStructure.withSelection() (BioStructure method) BioStructure.withTranslatedCoordinates() (BioStructure method) BioStructure.writeMmcif() (BioStructure method) BioStructure.writeMmcifWithParams() (BioStructure method) BioStructure.writePdb() (BioStructure method) BioStructure.writePdbWithParams() (BioStructure method) BioStructureError BioStructureError() (class) BioStructureError.[Symbol․dispose]() (BioStructureError method) BioStructureError.actualStart (BioStructureError attribute) BioStructureError.atomCount (BioStructureError attribute) BioStructureError.cause (BioStructureError attribute) BioStructureError.coordinateCount (BioStructureError attribute) BioStructureError.covered (BioStructureError attribute) BioStructureError.domain (BioStructureError attribute) BioStructureError.entityId (BioStructureError attribute) BioStructureError.expectedStart (BioStructureError attribute) BioStructureError.free() (BioStructureError method) BioStructureError.index (BioStructureError attribute) BioStructureError.kind (BioStructureError attribute) BioStructureError.len (BioStructureError attribute) BioStructureError.message (BioStructureError attribute) BioStructureError.operation (BioStructureError attribute) BioStructureError.start (BioStructureError attribute) BioStructureError.subchain (BioStructureError attribute) BioStructureError.table (BioStructureError attribute) BioStructureError.tableLen (BioStructureError attribute) BioStructureError.value (BioStructureError attribute) BioStructureParts (class in cosmolkit) BioStructureParts() (class) BioStructureParts.[Symbol․dispose]() (BioStructureParts method) BioStructureParts.free() (BioStructureParts method) BioStructureParts.inputFormat (BioStructureParts attribute) BioStructureSourceState (class in cosmolkit) BioStructureSourceState() (class) BioStructureSourceState.[Symbol․dispose]() (BioStructureSourceState method) BioStructureSourceState.conectMap (BioStructureSourceState attribute) BioStructureSourceState.free() (BioStructureSourceState method) BioStructureSourceState.hasDFraction (BioStructureSourceState attribute) BioStructureSourceState.hasOrigx (BioStructureSourceState attribute) BioStructureSourceState.info (BioStructureSourceState attribute) BioStructureSourceState.name (BioStructureSourceState attribute) BioStructureSourceState.nonAsciiLine (BioStructureSourceState attribute) BioStructureSourceState.origx (BioStructureSourceState attribute) BioStructureSourceState.rawRemarks (BioStructureSourceState attribute) BioStructureSourceState.resolution (BioStructureSourceState attribute) BioStructureSourceState.terStatus (BioStructureSourceState attribute) BioTlsGroup (class in cosmolkit) BioTlsGroup() (class) BioTlsGroup.[Symbol․dispose]() (BioTlsGroup method) BioTlsGroup.free() (BioTlsGroup method) BioTlsGroup.id (BioTlsGroup attribute) BioTlsGroup.l (BioTlsGroup attribute) BioTlsGroup.numId (BioTlsGroup attribute) BioTlsGroup.origin (BioTlsGroup attribute) BioTlsGroup.s (BioTlsGroup attribute) BioTlsGroup.selections (BioTlsGroup attribute) BioTlsGroup.t (BioTlsGroup attribute) BioTlsSelection (class in cosmolkit) BioTlsSelection() (class) BioTlsSelection.[Symbol․dispose]() (BioTlsSelection method) BioTlsSelection.chain (BioTlsSelection attribute) BioTlsSelection.details (BioTlsSelection attribute) BioTlsSelection.free() (BioTlsSelection method) BioTlsSelection.resBegin (BioTlsSelection attribute) BioTlsSelection.resEnd (BioTlsSelection attribute) BioTransform (class in cosmolkit) BioTransform() (class) BioTransform.[Symbol․dispose]() (BioTransform method) BioTransform.approx() (BioTransform method) BioTransform.free() (BioTransform method) BioTransform.matrix (BioTransform attribute) BioTransform.translation (BioTransform attribute) bit_flags (cosmolkit.AvalonFingerprintParams property) bit_info (cosmolkit.TopologicalFingerprintOutput attribute) (cosmolkit.TopologicalFingerprintOutputRequest property) bit_info() (cosmolkit.TopologicalFingerprintResult method) bit_info_map() (cosmolkit.BatchFingerprintAdditionalOutput method) (cosmolkit.FingerprintAdditionalOutput method) bit_paths() (cosmolkit.BatchFingerprintAdditionalOutput method) (cosmolkit.FingerprintAdditionalOutput method) bits() (cosmolkit.AvalonFingerprintFlags method) (cosmolkit.CxSmilesFields method) (cosmolkit.LayeredFingerprintLayers method) (cosmolkit.SanitizeOperations method) bits_per_entry (cosmolkit.LegacyTopologicalTorsionParams property) bits_per_feature (cosmolkit.AtomPairParams property) (cosmolkit.MorganParams property) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalTorsionParams property) (cosmolkit.TopologicalTorsionSettings attribute) BK (cosmolkit.Element attribute) block_name (cosmolkit.BioMmcifWriteParams property) BMA (cosmolkit.ResidueCode attribute) BME (cosmolkit.ResidueCode attribute) BMT (cosmolkit.ResidueCode attribute) BNG (cosmolkit.ResidueCode attribute) BOG (cosmolkit.ResidueCode attribute) Bond (class in cosmolkit) (cosmolkit.SdfPropertyListTarget attribute) Bond() (class) bond() (cosmolkit.Molecule method) (cosmolkit.SGroupCState method) (cosmolkit.TautomerMoleculeView method) Bond.[Symbol․dispose]() (Bond method) Bond.begin() (Bond method) Bond.cipDescriptor() (Bond method) Bond.cipNeighborOrder() (Bond method) Bond.direction() (Bond method) Bond.directionCode() (Bond method) Bond.directionName() (Bond method) Bond.end() (Bond method) Bond.free() (Bond method) Bond.id() (Bond method) Bond.isAromatic() (Bond method) Bond.order() (Bond method) Bond.orderCode() (Bond method) Bond.orderName() (Bond method) Bond.stereo() (Bond method) Bond.stereoAtoms() (Bond method) Bond.stereoCode() (Bond method) Bond.stereoName() (Bond method) BOND_ATROP_CCW (cosmolkit.PotentialStereoDescriptor attribute) BOND_ATROP_CW (cosmolkit.PotentialStereoDescriptor attribute) BOND_ATROPISOMER (cosmolkit.CxSmilesFields attribute) (cosmolkit.PotentialStereoType attribute) bond_between_atoms() (cosmolkit.MoleculeBuilder method) BOND_CFG (cosmolkit.CxSmilesFields attribute) BOND_CIS (cosmolkit.PotentialStereoDescriptor attribute) bond_comparator (cosmolkit.McsParameters property) bond_compare_parameters (cosmolkit.McsParameters property) bond_count (cosmolkit.McsResult attribute) BOND_CUMULENE_EVEN (cosmolkit.PotentialStereoType attribute) BOND_DOUBLE (cosmolkit.PotentialStereoType attribute) bond_mapping() (cosmolkit.MatchResult method) bond_match (cosmolkit.SubstructMatchParams property) bond_properties (cosmolkit.SubstructMatchParams property) bond_property_string() (cosmolkit.Molecule method) bond_symbols (cosmolkit.FragmentCxSmilesWriteParams property) (cosmolkit.FragmentSmilesWriteParams property) BOND_TRANS (cosmolkit.PotentialStereoDescriptor attribute) BondDirection (class in cosmolkit) (None attribute) BondDirection.BeginDash (BondDirection attribute) BondDirection.BeginWedge (BondDirection attribute) BondDirection.EitherDouble (BondDirection attribute) BondDirection.EndDownRight (BondDirection attribute) BondDirection.EndUpRight (BondDirection attribute) BondDirection.None (BondDirection attribute) BondDirection.Unknown (BondDirection attribute) BondOrder (class in cosmolkit) (None attribute) BondOrder.Aromatic (BondOrder attribute) BondOrder.Dative (BondOrder attribute) BondOrder.DativeLeft (BondOrder attribute) BondOrder.DativeOne (BondOrder attribute) BondOrder.DativeRight (BondOrder attribute) BondOrder.Double (BondOrder attribute) BondOrder.FiveAndHalf (BondOrder attribute) BondOrder.FourAndHalf (BondOrder attribute) BondOrder.Hextuple (BondOrder attribute) BondOrder.Hydrogen (BondOrder attribute) BondOrder.Ionic (BondOrder attribute) BondOrder.OneAndHalf (BondOrder attribute) BondOrder.Other (BondOrder attribute) BondOrder.Quadruple (BondOrder attribute) BondOrder.Quintuple (BondOrder attribute) BondOrder.Single (BondOrder attribute) BondOrder.ThreeAndHalf (BondOrder attribute) BondOrder.ThreeCenter (BondOrder attribute) BondOrder.Triple (BondOrder attribute) BondOrder.TwoAndHalf (BondOrder attribute) BondOrder.Unspecified (BondOrder attribute) BondOrder.Zero (BondOrder attribute) bonds (cosmolkit.CipLabelOptions property) (cosmolkit.FragmentCxSmilesWriteParams property) (cosmolkit.FragmentSmilesWriteParams property) (cosmolkit.TopologyBlock attribute) bonds() (cosmolkit.Molecule method) (cosmolkit.MoleculeBuilder method) (cosmolkit.StereoGroup method) (cosmolkit.TautomerMoleculeView method) BondSpec (class in cosmolkit) BondSpec() (class) BondSpec.[Symbol․dispose]() (BondSpec method) BondSpec.free() (BondSpec method) BondStereo (class in cosmolkit) (None attribute) BondStereo.Any (BondStereo attribute) BondStereo.AtropCcw (BondStereo attribute) BondStereo.AtropCw (BondStereo attribute) BondStereo.Cis (BondStereo attribute) BondStereo.E (BondStereo attribute) BondStereo.None (BondStereo attribute) BondStereo.Trans (BondStereo attribute) BondStereo.Z (BondStereo attribute) Bool (cosmolkit.PropertyValueKind attribute) bounds_mat_force_scaling (cosmolkit.EmbedParams property) box_size_mult (cosmolkit.EmbedParams property) BR (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) brackets() (cosmolkit.SGroupDisplay method) branch_count() (cosmolkit.AtomCodeExplanation method) Branched (cosmolkit.EntityKind attribute) branched_paths (cosmolkit.LayeredFingerprintParams property) (cosmolkit.TopologicalFingerprintParams property) BRO (cosmolkit.ResidueCode attribute) BRU (cosmolkit.ResidueCode attribute) BTB (cosmolkit.ResidueCode attribute) BU1 (cosmolkit.ResidueCode attribute) BU2 (cosmolkit.ResidueCode attribute) BU3 (cosmolkit.ResidueCode attribute) BUF (cosmolkit.ResidueInfoKind attribute) Buffer (cosmolkit.ResidueKind attribute) build() (cosmolkit.MoleculeBuilder method) buried_surface_area (cosmolkit.BioAssembly attribute) byte_len() (cosmolkit.SdfRecordMetadata method) byte_offset() (cosmolkit.SdfRecordMetadata method) byte_range() (cosmolkit.SdfRecordMetadata method) bytes_consumed() (cosmolkit.SdfRecordStream method) C c (cosmolkit.BioCrystalCell attribute) C (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) C10 (cosmolkit.ResidueCode attribute) C15 (cosmolkit.ResidueCode attribute) C8E (cosmolkit.ResidueCode attribute) CA (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CAC (cosmolkit.ResidueCode attribute) CAF (cosmolkit.ResidueCode attribute) calc_flag() (cosmolkit.BioAtomRow method) Calculated (cosmolkit.BioCalcFlag attribute) callback (cosmolkit.TautomerParams property) Canceled (cosmolkit.TautomerEnumerationStatus attribute) canonical (cosmolkit.KekulizeParams property) (cosmolkit.ReactionWriteParams property) (cosmolkit.SmilesWriteParams property) canonical_one_letter_code() (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueInfo method) canonical_orientation (cosmolkit.Coordinate2DParams property) canonical_smiles() (cosmolkit.TautomerEnumeration method) canonical_tautomer() (cosmolkit.Molecule method) (cosmolkit.TautomerEnumeration method) canonical_tautomer_from_molecules() (in module cosmolkit) canonical_tautomer_from_molecules_with_params() (in module cosmolkit) canonical_tautomer_with_params() (cosmolkit.Molecule method) (cosmolkit.TautomerEnumeration method) canonicalTautomerFromMolecules() (built-in function) canonicalTautomerFromMoleculesWithParams() (built-in function) CAS (cosmolkit.ResidueCode attribute) category (cosmolkit.FeatureSpec attribute) CBM (cosmolkit.ResidueCode attribute) CBR (cosmolkit.ResidueCode attribute) CBX (cosmolkit.ResidueCode attribute) cc_fo_fc_free (cosmolkit.BioBasicRefinementInfo attribute) cc_fo_fc_work (cosmolkit.BioBasicRefinementInfo attribute) cc_intensity_free (cosmolkit.BioBasicRefinementInfo attribute) cc_intensity_work (cosmolkit.BioBasicRefinementInfo attribute) CCC (cosmolkit.ResidueCode attribute) CcdRestoration (cosmolkit.BioMmcifReadStage attribute) CCN (cosmolkit.ResidueCode attribute) CD (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CE (cosmolkit.Element attribute) CE1 (cosmolkit.ResidueCode attribute) cell (cosmolkit.BioMmcifWriteParams property) cell() (cosmolkit.BioCrystalInfo method) center (cosmolkit.TetrahedralStereo attribute) centered_on (cosmolkit.PotentialStereoInfo attribute) CF (cosmolkit.Element attribute) CGU (cosmolkit.ResidueCode attribute) chain (cosmolkit.BioTlsSelection attribute) chain() (cosmolkit.Protein method) (cosmolkit.ProteinResidueRef method) chain_id() (cosmolkit.BioResidueRow method) chain_name (cosmolkit.AtomAddress attribute) (cosmolkit.BioModRes attribute) ChainKind (class in cosmolkit) (None attribute) ChainKind.Dna (ChainKind attribute) ChainKind.LigandOnly (ChainKind attribute) ChainKind.Mixed (ChainKind attribute) ChainKind.Protein (ChainKind attribute) ChainKind.ProteinDnaComplex (ChainKind attribute) ChainKind.ProteinRnaComplex (ChainKind attribute) ChainKind.Rna (ChainKind attribute) ChainKind.Unknown (ChainKind attribute) ChainKind.WaterOnly (ChainKind attribute) chains (cosmolkit.BioAssemblyGenerator attribute) (cosmolkit.ProteinSelectionSummary attribute) chains() (cosmolkit.BioModelRow method) (cosmolkit.BioStructure method) (cosmolkit.Protein method) ChainSourceIds (class in cosmolkit) ChainSourceIds() (class) ChainSourceIds.[Symbol․dispose]() (ChainSourceIds method) ChainSourceIds.authChainId() (ChainSourceIds method) ChainSourceIds.free() (ChainSourceIds method) ChainSourceIds.labelAsymId() (ChainSourceIds method) changed (cosmolkit.ReactionApplyResult attribute) check_non_ascii (cosmolkit.BioPdbReadParams property) chem_comp (cosmolkit.BioMmcifWriteParams property) ChemComp (cosmolkit.BioCoordinateFormat attribute) ChemistryProblem (class in cosmolkit) ChemistryProblem() (class) ChemistryProblem.[Symbol․dispose]() (ChemistryProblem method) ChemistryProblem.error (ChemistryProblem attribute) ChemistryProblem.free() (ChemistryProblem method) ChemistryProblem.operation (ChemistryProblem attribute) ChemistryProblemError ChemistryProblemError() (class) ChemistryProblemError.[Symbol․dispose]() (ChemistryProblemError method) ChemistryProblemError.cause (ChemistryProblemError attribute) ChemistryProblemError.domain (ChemistryProblemError attribute) ChemistryProblemError.free() (ChemistryProblemError method) ChemistryProblemError.kind (ChemistryProblemError attribute) ChemistryProblemError.message (ChemistryProblemError attribute) ChemistryProblemReport (class in cosmolkit) ChemistryProblemReport() (class) ChemistryProblemReport.[Symbol․dispose]() (ChemistryProblemReport method) ChemistryProblemReport.free() (ChemistryProblemReport method) ChemistryProblemReport.problems (ChemistryProblemReport attribute) chi_0() (cosmolkit.Molecule method) chi_0_n() (cosmolkit.Molecule method) chi_0_n_with_params() (cosmolkit.Molecule method) chi_0_v() (cosmolkit.Molecule method) chi_0_v_with_params() (cosmolkit.Molecule method) chi_1() (cosmolkit.Molecule method) chi_1_n() (cosmolkit.Molecule method) chi_1_n_with_params() (cosmolkit.Molecule method) chi_1_v() (cosmolkit.Molecule method) chi_1_v_with_params() (cosmolkit.Molecule method) chi_2_n() (cosmolkit.Molecule method) chi_2_n_with_params() (cosmolkit.Molecule method) chi_2_v() (cosmolkit.Molecule method) chi_2_v_with_params() (cosmolkit.Molecule method) chi_3_n() (cosmolkit.Molecule method) chi_3_n_with_params() (cosmolkit.Molecule method) chi_3_v() (cosmolkit.Molecule method) chi_3_v_with_params() (cosmolkit.Molecule method) chi_4_n() (cosmolkit.Molecule method) chi_4_n_with_params() (cosmolkit.Molecule method) chi_4_v() (cosmolkit.Molecule method) chi_4_v_with_params() (cosmolkit.Molecule method) CHI_ALLENE (cosmolkit.ChiralTag attribute) chi_n_n() (cosmolkit.Molecule method) chi_n_n_with_params() (cosmolkit.Molecule method) chi_n_v() (cosmolkit.Molecule method) chi_n_v_with_params() (cosmolkit.Molecule method) CHI_OCTAHEDRAL (cosmolkit.ChiralTag attribute) CHI_OTHER (cosmolkit.ChiralTag attribute) CHI_SQUAREPLANAR (cosmolkit.ChiralTag attribute) CHI_TETRAHEDRAL (cosmolkit.ChiralTag attribute) CHI_TETRAHEDRAL_CCW (cosmolkit.ChiralTag attribute) CHI_TETRAHEDRAL_CW (cosmolkit.ChiralTag attribute) CHI_TRIGONALBIPYRAMIDAL (cosmolkit.ChiralTag attribute) CHI_UNSPECIFIED (cosmolkit.ChiralTag attribute) chiral_tag() (cosmolkit.Atom method) chiral_tag_code() (cosmolkit.Atom method) chiral_tag_name() (cosmolkit.Atom method) chirality() (cosmolkit.AtomCodeExplanation method) ChiralTag (class in cosmolkit) (None attribute) ChiralTag.Allene (ChiralTag attribute) ChiralTag.Octahedral (ChiralTag attribute) ChiralTag.Other (ChiralTag attribute) ChiralTag.SquarePlanar (ChiralTag attribute) ChiralTag.Tetrahedral (ChiralTag attribute) ChiralTag.TetrahedralCcw (ChiralTag attribute) ChiralTag.TetrahedralCw (ChiralTag attribute) ChiralTag.TrigonalBipyramidal (ChiralTag attribute) ChiralTag.Unspecified (ChiralTag attribute) CifDocument (cosmolkit.BioMmcifReadStage attribute) cip_computed() (cosmolkit.Molecule method) cip_descriptor() (cosmolkit.Atom method) (cosmolkit.Bond method) cip_neighbor_order() (cosmolkit.Atom method) (cosmolkit.Bond method) cip_rank() (cosmolkit.Atom method) cip_state (cosmolkit.MoleculeOpSpec attribute) CipDescriptor (class in cosmolkit) (None attribute) CipDescriptor.E (CipDescriptor attribute) CipDescriptor.LowerE (CipDescriptor attribute) CipDescriptor.LowerM (CipDescriptor attribute) CipDescriptor.LowerP (CipDescriptor attribute) CipDescriptor.LowerR (CipDescriptor attribute) CipDescriptor.LowerS (CipDescriptor attribute) CipDescriptor.LowerZ (CipDescriptor attribute) CipDescriptor.M (CipDescriptor attribute) CipDescriptor.P (CipDescriptor attribute) CipDescriptor.R (CipDescriptor attribute) CipDescriptor.S (CipDescriptor attribute) CipDescriptor.Z (CipDescriptor attribute) CipDescriptorError CipDescriptorError() (class) CipDescriptorError.[Symbol․dispose]() (CipDescriptorError method) CipDescriptorError.cause (CipDescriptorError attribute) CipDescriptorError.free() (CipDescriptorError method) CipDescriptorError.kind (CipDescriptorError attribute) CipDescriptorError.message (CipDescriptorError attribute) CipDescriptorError.value (CipDescriptorError attribute) CipLabelerError CipLabelerError() (class) CipLabelerError.[Symbol․dispose]() (CipLabelerError method) CipLabelerError.cause (CipLabelerError attribute) CipLabelerError.domain (CipLabelerError attribute) CipLabelerError.free() (CipLabelerError method) CipLabelerError.kind (CipLabelerError attribute) CipLabelerError.message (CipLabelerError attribute) CipLabelOptions (class in cosmolkit) CipLabelOptions() (class) CipLabelOptions.[Symbol․dispose]() (CipLabelOptions method) CipLabelOptions.atoms (CipLabelOptions attribute) CipLabelOptions.bonds (CipLabelOptions attribute) CipLabelOptions.free() (CipLabelOptions method) CipLabelOptions.maxRecursiveIterations (CipLabelOptions attribute) CipLabelOptionsOptions() (interface) CipLabelOptionsOptions.atoms? (CipLabelOptionsOptions attribute) CipLabelOptionsOptions.bonds? (CipLabelOptionsOptions attribute) CipLabelOptionsOptions.maxRecursiveIterations? (CipLabelOptionsOptions attribute) CipRankError CipRankError() (class) CipRankError.[Symbol․dispose]() (CipRankError method) CipRankError.actual (CipRankError attribute) CipRankError.atom (CipRankError attribute) CipRankError.atomCount (CipRankError attribute) CipRankError.bond (CipRankError attribute) CipRankError.cause (CipRankError attribute) CipRankError.degree (CipRankError attribute) CipRankError.domain (CipRankError attribute) CipRankError.field (CipRankError attribute) CipRankError.free() (CipRankError method) CipRankError.kind (CipRankError attribute) CipRankError.mapNumber (CipRankError attribute) CipRankError.maximumSupported (CipRankError attribute) CipRankError.message (CipRankError attribute) CipRankError.order (CipRankError attribute) CipRankError.value (CipRankError attribute) CIR (cosmolkit.ResidueCode attribute) cis (cosmolkit.BioMmcifWriteParams property) cispeps() (cosmolkit.BioStructure method) CisPeptides (cosmolkit.BioMmcifReadStage attribute) CIT (cosmolkit.ResidueCode attribute) CL (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) classification (cosmolkit.BioSoftwareItem attribute) clean (cosmolkit.PotentialStereoParams property) clean_stereo (cosmolkit.SmilesWriteParams property) cleaned_molecule (cosmolkit.PotentialStereoResult attribute) CLEANUP (cosmolkit.SanitizeOperations attribute) Cleanup (cosmolkit.SanitizeStage attribute) CLEANUP_ATROPISOMERS (cosmolkit.SanitizeOperations attribute) CLEANUP_CHIRALITY (cosmolkit.SanitizeOperations attribute) CLEANUP_ORGANOMETALLICS (cosmolkit.SanitizeOperations attribute) cleanup_substructures (cosmolkit.Mol2ReadParams property) CleanupAtropisomers (cosmolkit.SanitizeStage attribute) CleanupChirality (cosmolkit.SanitizeStage attribute) CleanupOrganometallics (cosmolkit.SanitizeStage attribute) clear_3d_conformers_() (cosmolkit.Molecule method) clear_conformers (cosmolkit.EmbedParams property) clear_existing_2d (cosmolkit.Coordinate2DParams property) CLO (cosmolkit.ResidueCode attribute) CM (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CM5 (cosmolkit.ResidueCode attribute) CME (cosmolkit.ResidueCode attribute) CN (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CO (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) code (cosmolkit.AtomPairAtomCodeResult attribute) code() (cosmolkit.BioResidueRow method) (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueIdentity method) (cosmolkit.ResidueInfo method) code_size() (cosmolkit.AtomPairsParameters static method) collection_date (cosmolkit.BioDiffractionInfo attribute) compact (cosmolkit.BioMmcifWriteParams property) compile_query() (in module cosmolkit) CompiledQuery (class in cosmolkit) CompiledQuery() (class) CompiledQuery.[Symbol․dispose]() (CompiledQuery method) CompiledQuery.atomOrder() (CompiledQuery method) CompiledQuery.free() (CompiledQuery method) CompiledQuery.numAtoms() (CompiledQuery method) CompiledQuery.numBonds() (CompiledQuery method) CompiledQuery.query() (CompiledQuery method) compileQuery() (built-in function) complete_rings_only (cosmolkit.McsAtomCompareParameters property) (cosmolkit.McsBondCompareParameters property) completed (cosmolkit.McsResult attribute) Completed (cosmolkit.TautomerEnumerationStatus attribute) CompleteIcosahedral (cosmolkit.BioAssemblySpecialKind attribute) completeness (cosmolkit.BioBasicRefinementInfo attribute) (cosmolkit.BioReflectionsInfo attribute) CompletePoint (cosmolkit.BioAssemblySpecialKind attribute) component (cosmolkit.ForceFieldError property) (cosmolkit.MmffForceFieldError property) compute_2d_coordinates_() (cosmolkit.Molecule method) compute_2d_coordinates_with_params_() (cosmolkit.Molecule method) computed_prop_names() (cosmolkit.MoleculeProperties method) conect_map (cosmolkit.BioStructureSourceState attribute) conf_id() (cosmolkit.EmbedMoleculeResult method) conf_ids() (cosmolkit.EmbedMultipleConfsResult method) Conformer2D (class in cosmolkit) Conformer2D() (class) Conformer2D.[Symbol․dispose]() (Conformer2D method) Conformer2D.coordinates() (Conformer2D method) Conformer2D.free() (Conformer2D method) Conformer2D.id() (Conformer2D method) Conformer2D.props() (Conformer2D method) Conformer3D (class in cosmolkit) Conformer3D() (class) Conformer3D.[Symbol․dispose]() (Conformer3D method) Conformer3D.coordinates() (Conformer3D method) Conformer3D.free() (Conformer3D method) Conformer3D.id() (Conformer3D method) Conformer3D.is3d() (Conformer3D method) Conformer3D.props() (Conformer3D method) conformer_id (cosmolkit.AtomPairFingerprintParams property) (cosmolkit.AtomPositionParams property) (cosmolkit.DistanceMatrix3dParams property) (cosmolkit.MmffEvaluationParams property) (cosmolkit.MmffForceFieldParams property) (cosmolkit.MmffOptimizationParams property) (cosmolkit.MolCoordinateSelection attribute) (cosmolkit.MorganCallParams property) (cosmolkit.MorganFingerprintParams property) (cosmolkit.Replace3DCoordinatesParams property) (cosmolkit.StructureTagParams property) (cosmolkit.TopologicalTorsionCallParams property) (cosmolkit.TopologicalTorsionFingerprintParams property) (cosmolkit.UffEvaluationParams property) (cosmolkit.UffForceFieldParams property) (cosmolkit.UffOptimizationParams property) (cosmolkit.XyzWriteParams property) conformer_id() (cosmolkit.UffConformerResult method) conformer_ids (cosmolkit.ConformerAlignmentParameters property) conformer_results() (cosmolkit.MmffOptimizeMoleculeConfsResult method) (cosmolkit.UffConformerOptimizationResult method) ConformerAlignmentParameters (class in cosmolkit) ConformerAlignmentParameters() (class) ConformerAlignmentParameters.[Symbol․dispose]() (ConformerAlignmentParameters method) ConformerAlignmentParameters.atomIndices (ConformerAlignmentParameters attribute) ConformerAlignmentParameters.conformerIds (ConformerAlignmentParameters attribute) ConformerAlignmentParameters.free() (ConformerAlignmentParameters method) ConformerAlignmentParameters.maxIterations (ConformerAlignmentParameters attribute) ConformerAlignmentParameters.new() (ConformerAlignmentParameters method) ConformerAlignmentParameters.reflect (ConformerAlignmentParameters attribute) ConformerAlignmentParameters.weights (ConformerAlignmentParameters attribute) ConformerAlignmentParametersOptions() (interface) ConformerAlignmentParametersOptions.atomIndices? (ConformerAlignmentParametersOptions attribute) ConformerAlignmentParametersOptions.conformerIds? (ConformerAlignmentParametersOptions attribute) ConformerAlignmentParametersOptions.maxIterations? (ConformerAlignmentParametersOptions attribute) ConformerAlignmentParametersOptions.reflect? (ConformerAlignmentParametersOptions attribute) ConformerAlignmentParametersOptions.weights? (ConformerAlignmentParametersOptions attribute) ConformerAlignmentReport (class in cosmolkit) ConformerAlignmentReport() (class) ConformerAlignmentReport.[Symbol․dispose]() (ConformerAlignmentReport method) ConformerAlignmentReport.free() (ConformerAlignmentReport method) ConformerAlignmentReport.rmsds() (ConformerAlignmentReport method) ConformerError() (class) ConformerError.[Symbol․dispose]() (ConformerError method) ConformerError.detail (ConformerError attribute) ConformerError.domain (ConformerError attribute) ConformerError.free() (ConformerError method) ConformerError.kind (ConformerError attribute) ConformerError.message (ConformerError attribute) ConformerRmsd (class in cosmolkit) ConformerRmsd() (class) ConformerRmsd.[Symbol․dispose]() (ConformerRmsd method) ConformerRmsd.free() (ConformerRmsd method) ConformerRmsd.probeConformerId() (ConformerRmsd method) ConformerRmsd.referenceConformerId() (ConformerRmsd method) ConformerRmsd.rmsd() (ConformerRmsd method) ConformerRunError() (class) ConformerRunError.[Symbol․dispose]() (ConformerRunError method) ConformerRunError.cause (ConformerRunError attribute) ConformerRunError.domain (ConformerRunError attribute) ConformerRunError.free() (ConformerRunError method) ConformerRunError.message (ConformerRunError attribute) conformers_2d (cosmolkit.CoordinateBlock attribute) conformers_3d (cosmolkit.CoordinateBlock attribute) conformers_3d() (cosmolkit.Molecule method) conn (cosmolkit.BioMmcifWriteParams property) Connections (cosmolkit.BioMmcifReadStage attribute) connections() (cosmolkit.BioStructure method) connectivity() (cosmolkit.MorganAtomInvariantsGenerator static method) (cosmolkit.MorganInvariants static method) Construction (cosmolkit.MolecularForceFieldErrorKind attribute) contact_author (cosmolkit.BioSoftwareItem attribute) contact_author_email (cosmolkit.BioSoftwareItem attribute) contains() (cosmolkit.CxSmilesFields method) (cosmolkit.SanitizeOperations method) controlling_atoms (cosmolkit.PotentialStereoInfo attribute) converged (cosmolkit.ForceFieldMinimizeOutcome attribute) coord_map (cosmolkit.EmbedParams property) Coordinate2DError Coordinate2DError() (class) Coordinate2DError.[Symbol․dispose]() (Coordinate2DError method) Coordinate2DError.cause (Coordinate2DError attribute) Coordinate2DError.domain (Coordinate2DError attribute) Coordinate2DError.free() (Coordinate2DError method) Coordinate2DError.kind (Coordinate2DError attribute) Coordinate2DError.message (Coordinate2DError attribute) Coordinate2DInputParams (class in cosmolkit) Coordinate2DInputParams() (class) Coordinate2DInputParams.[Symbol․dispose]() (Coordinate2DInputParams method) Coordinate2DInputParams.free() (Coordinate2DInputParams method) Coordinate2DInputParams.zPolicy (Coordinate2DInputParams attribute) Coordinate2DInputParamsOptions() (interface) Coordinate2DInputParamsOptions.zPolicy? (Coordinate2DInputParamsOptions attribute) Coordinate2DLayoutError Coordinate2DLayoutError() (class) Coordinate2DLayoutError.[Symbol․dispose]() (Coordinate2DLayoutError method) Coordinate2DLayoutError.atom (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.atomCount (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.bond (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.cause (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.centre (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.count (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.domain (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.first (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.free() (Coordinate2DLayoutError method) Coordinate2DLayoutError.key (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.kind (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.message (Coordinate2DLayoutError attribute) Coordinate2DLayoutError.second (Coordinate2DLayoutError attribute) Coordinate2DParams (class in cosmolkit) Coordinate2DParams() (class) Coordinate2DParams.[Symbol․dispose]() (Coordinate2DParams method) Coordinate2DParams.canonicalOrientation (Coordinate2DParams attribute) Coordinate2DParams.clearExisting2d (Coordinate2DParams attribute) Coordinate2DParams.coordinateMap (Coordinate2DParams attribute) Coordinate2DParams.flipsPerSample (Coordinate2DParams attribute) Coordinate2DParams.forceRdkit (Coordinate2DParams attribute) Coordinate2DParams.free() (Coordinate2DParams method) Coordinate2DParams.permuteDegreeFour (Coordinate2DParams attribute) Coordinate2DParams.samples (Coordinate2DParams attribute) Coordinate2DParams.sampleSeed (Coordinate2DParams attribute) Coordinate2DParams.useRingTemplates (Coordinate2DParams attribute) Coordinate2DParamsOptions() (interface) Coordinate2DParamsOptions.canonicalOrientation? (Coordinate2DParamsOptions attribute) Coordinate2DParamsOptions.clearExisting2d? (Coordinate2DParamsOptions attribute) Coordinate2DParamsOptions.coordinateMap? (Coordinate2DParamsOptions attribute) Coordinate2DParamsOptions.flipsPerSample? (Coordinate2DParamsOptions attribute) Coordinate2DParamsOptions.forceRdkit? (Coordinate2DParamsOptions attribute) Coordinate2DParamsOptions.permuteDegreeFour? (Coordinate2DParamsOptions attribute) Coordinate2DParamsOptions.samples? (Coordinate2DParamsOptions attribute) Coordinate2DParamsOptions.sampleSeed? (Coordinate2DParamsOptions attribute) Coordinate2DParamsOptions.useRingTemplates? (Coordinate2DParamsOptions attribute) Coordinate2DTemplateError Coordinate2DTemplateError() (class) Coordinate2DTemplateError.[Symbol․dispose]() (Coordinate2DTemplateError method) Coordinate2DTemplateError.cause (Coordinate2DTemplateError attribute) Coordinate2DTemplateError.domain (Coordinate2DTemplateError attribute) Coordinate2DTemplateError.free() (Coordinate2DTemplateError method) Coordinate2DTemplateError.index (Coordinate2DTemplateError attribute) Coordinate2DTemplateError.kind (Coordinate2DTemplateError attribute) Coordinate2DTemplateError.line (Coordinate2DTemplateError attribute) Coordinate2DTemplateError.message (Coordinate2DTemplateError attribute) Coordinate2DTemplateError.path (Coordinate2DTemplateError attribute) Coordinate2DTemplateError.row (Coordinate2DTemplateError attribute) Coordinate3DInputParams (class in cosmolkit) Coordinate3DInputParams() (class) Coordinate3DInputParams.[Symbol․dispose]() (Coordinate3DInputParams method) Coordinate3DInputParams.free() (Coordinate3DInputParams method) Coordinate3DInputParams.is3d (Coordinate3DInputParams attribute) Coordinate3DInputParamsOptions() (interface) Coordinate3DInputParamsOptions.is3d? (Coordinate3DInputParamsOptions attribute) Coordinate3DReadError Coordinate3DReadError() (class) Coordinate3DReadError.[Symbol․dispose]() (Coordinate3DReadError method) Coordinate3DReadError.conformerId (Coordinate3DReadError attribute) Coordinate3DReadError.count (Coordinate3DReadError attribute) Coordinate3DReadError.domain (Coordinate3DReadError attribute) Coordinate3DReadError.free() (Coordinate3DReadError method) Coordinate3DReadError.kind (Coordinate3DReadError attribute) Coordinate3DReadError.message (Coordinate3DReadError attribute) COORDINATE_BONDS (cosmolkit.CxSmilesFields attribute) coordinate_map (cosmolkit.Coordinate2DParams property) coordinate_mode (cosmolkit.SdfReadParams property) coordinate_rmsd_to() (cosmolkit.Molecule method) coordinate_rmsd_to_with_params() (cosmolkit.Molecule method) coordinate_selection (cosmolkit.CxSmilesWriteParams property) (cosmolkit.MolBlockWriteParams property) (cosmolkit.ReactionSingleRunParams property) coordinate_selections (cosmolkit.ReactionRunParams property) (cosmolkit.ReactionWriteParams property) CoordinateBlock (class in cosmolkit) (cosmolkit.BioMmcifReadStage attribute) CoordinateBlock() (class) CoordinateBlock.[Symbol․dispose]() (CoordinateBlock method) CoordinateBlock.conformers2d (CoordinateBlock attribute) CoordinateBlock.conformers3d (CoordinateBlock attribute) CoordinateBlock.free() (CoordinateBlock method) CoordinateBlock.sourceConformerOrder (CoordinateBlock attribute) CoordinateBlock.sourceCoordinateDim (CoordinateBlock attribute) CoordinateCount (cosmolkit.MolecularForceFieldErrorKind attribute) CoordinateDimension (class in cosmolkit) (None attribute) CoordinateDimension.ThreeD (CoordinateDimension attribute) CoordinateDimension.TwoD (CoordinateDimension attribute) CoordinateInputError CoordinateInputError() (class) CoordinateInputError.[Symbol․dispose]() (CoordinateInputError method) CoordinateInputError.cause (CoordinateInputError attribute) CoordinateInputError.domain (CoordinateInputError attribute) CoordinateInputError.free() (CoordinateInputError method) CoordinateInputError.kind (CoordinateInputError attribute) CoordinateInputError.message (CoordinateInputError attribute) CoordinateRmsdParameters (class in cosmolkit) CoordinateRmsdParameters() (class) CoordinateRmsdParameters.[Symbol․dispose]() (CoordinateRmsdParameters method) CoordinateRmsdParameters.atomMaps (CoordinateRmsdParameters attribute) CoordinateRmsdParameters.free() (CoordinateRmsdParameters method) CoordinateRmsdParameters.maxMatches (CoordinateRmsdParameters attribute) CoordinateRmsdParameters.new() (CoordinateRmsdParameters method) CoordinateRmsdParameters.probeConformerId (CoordinateRmsdParameters attribute) CoordinateRmsdParameters.referenceConformerId (CoordinateRmsdParameters attribute) CoordinateRmsdParameters.symmetrizeConjugatedTerminalGroups (CoordinateRmsdParameters attribute) CoordinateRmsdParameters.weights (CoordinateRmsdParameters attribute) CoordinateRmsdParametersOptions() (interface) CoordinateRmsdParametersOptions.atomMaps? (CoordinateRmsdParametersOptions attribute) CoordinateRmsdParametersOptions.maxMatches? (CoordinateRmsdParametersOptions attribute) CoordinateRmsdParametersOptions.probeConformerId? (CoordinateRmsdParametersOptions attribute) CoordinateRmsdParametersOptions.referenceConformerId? (CoordinateRmsdParametersOptions attribute) CoordinateRmsdParametersOptions.symmetrizeConjugatedTerminalGroups? (CoordinateRmsdParametersOptions attribute) CoordinateRmsdParametersOptions.weights? (CoordinateRmsdParametersOptions attribute) coordinates() (cosmolkit.BioStructure method) (cosmolkit.Conformer2D method) (cosmolkit.Conformer3D method) (cosmolkit.MoleculeBuilder method) coordinates_2d() (cosmolkit.Molecule method) coordinates_3d() (cosmolkit.Molecule method) CoordinateShape (cosmolkit.MolecularForceFieldErrorKind attribute) CoordinateZPolicy (class in cosmolkit) CoordinateZPolicy() (class) CoordinateZPolicy.[Symbol․dispose]() (CoordinateZPolicy method) CoordinateZPolicy.Error (CoordinateZPolicy attribute) CoordinateZPolicy.free() (CoordinateZPolicy method) CoordinateZPolicy.fromName() (CoordinateZPolicy method) CoordinateZPolicy.Ignore (CoordinateZPolicy attribute) CoordinateZPolicy.RequireZero (CoordinateZPolicy attribute) COORDS (cosmolkit.CxSmilesFields attribute) Copolymer (cosmolkit.SubstanceGroupKind attribute) copy_atom_properties (cosmolkit.ReactionRunParams property) Corina (cosmolkit.Mol2Type attribute) cosmolkit module count (cosmolkit.BioRefinementRestraint attribute) count_bounds (cosmolkit.AtomPairParams property) (cosmolkit.MorganParams property) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalTorsionParams property) (cosmolkit.TopologicalTorsionSettings attribute) count_simulation (cosmolkit.AtomPairParams property) (cosmolkit.MorganParams property) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalTorsionParams property) (cosmolkit.TopologicalTorsionSettings attribute) counts() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) Covale (cosmolkit.BioConnectionKind attribute) cpci (cosmolkit.EmbedParams property) CPS (cosmolkit.ResidueCode attribute) CR (cosmolkit.Element attribute) CR2 (cosmolkit.ResidueCode attribute) CR8 (cosmolkit.ResidueCode attribute) CRF (cosmolkit.ResidueCode attribute) crippen_descriptors() (cosmolkit.Molecule method) crippen_descriptors_with_params() (cosmolkit.Molecule method) CrippenTotals (class in cosmolkit) CrippenTotals() (class) CrippenTotals.[Symbol․dispose]() (CrippenTotals method) CrippenTotals.free() (CrippenTotals method) CrippenTotals.logp (CrippenTotals attribute) CrippenTotals.molarRefractivity (CrippenTotals attribute) CRO (cosmolkit.ResidueCode attribute) cross_validation_method (cosmolkit.BioRefinementInfo attribute) crossing_bond_correspondence() (cosmolkit.SubstanceGroup method) Crosslink (cosmolkit.SubstanceGroupKind attribute) CRQ (cosmolkit.ResidueCode attribute) CRY (cosmolkit.ResidueCode attribute) crystal() (cosmolkit.BioStructure method) CrystalCell (cosmolkit.BioMmcifReadStage attribute) crystals (cosmolkit.BioMetadata attribute) CS (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CSD (cosmolkit.ResidueCode attribute) CSH (cosmolkit.ResidueCode attribute) CSO (cosmolkit.ResidueCode attribute) CSS (cosmolkit.ResidueCode attribute) cstates() (cosmolkit.SubstanceGroup method) CSX (cosmolkit.ResidueCode attribute) CU (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) CU1 (cosmolkit.ResidueCode attribute) Custom (cosmolkit.AromaticityModel attribute) custom_atom_invariants (cosmolkit.AtomPairFingerprintParams property) (cosmolkit.LegacyTopologicalTorsionParams property) (cosmolkit.MorganCallParams property) (cosmolkit.MorganFingerprintParams property) (cosmolkit.TopologicalTorsionCallParams property) (cosmolkit.TopologicalTorsionFingerprintParams property) custom_bond_invariants (cosmolkit.AtomPairFingerprintParams property) (cosmolkit.MorganCallParams property) (cosmolkit.MorganFingerprintParams property) (cosmolkit.TopologicalTorsionCallParams property) (cosmolkit.TopologicalTorsionFingerprintParams property) cx (cosmolkit.FragmentCxSmilesWriteParams property) cx_fields (cosmolkit.ReactionWriteParams property) CxCoordinateSelection (class in cosmolkit) CxCoordinateSelection() (class) CxCoordinateSelection.[Symbol․dispose]() (CxCoordinateSelection method) CxCoordinateSelection.auto() (CxCoordinateSelection method) CxCoordinateSelection.free() (CxCoordinateSelection method) CxCoordinateSelection.threeD() (CxCoordinateSelection method) CxCoordinateSelection.twoD() (CxCoordinateSelection method) CXE (cosmolkit.ResidueCode attribute) CXM (cosmolkit.ResidueCode attribute) CxSmilesFields (class in cosmolkit) CxSmilesFields() (class) CxSmilesFields.[Symbol․dispose]() (CxSmilesFields method) CxSmilesFields.ALL (CxSmilesFields attribute) CxSmilesFields.ALL_BUT_COORDS (CxSmilesFields attribute) CxSmilesFields.ATOM_LABELS (CxSmilesFields attribute) CxSmilesFields.ATOM_PROPS (CxSmilesFields attribute) CxSmilesFields.bits() (CxSmilesFields method) CxSmilesFields.BOND_ATROPISOMER (CxSmilesFields attribute) CxSmilesFields.BOND_CFG (CxSmilesFields attribute) CxSmilesFields.contains() (CxSmilesFields method) CxSmilesFields.COORDINATE_BONDS (CxSmilesFields attribute) CxSmilesFields.COORDS (CxSmilesFields attribute) CxSmilesFields.ENHANCED_STEREO (CxSmilesFields attribute) CxSmilesFields.free() (CxSmilesFields method) CxSmilesFields.HYDROGEN_BONDS (CxSmilesFields attribute) CxSmilesFields.LINKNODES (CxSmilesFields attribute) CxSmilesFields.MOLFILE_VALUES (CxSmilesFields attribute) CxSmilesFields.NONE (CxSmilesFields attribute) CxSmilesFields.or() (CxSmilesFields method) CxSmilesFields.POLYMER (CxSmilesFields attribute) CxSmilesFields.RADICALS (CxSmilesFields attribute) CxSmilesFields.SGROUPS (CxSmilesFields attribute) CxSmilesFields.ZERO_BONDS (CxSmilesFields attribute) CxSmilesWriteParams (class in cosmolkit) CxSmilesWriteParams() (class) CxSmilesWriteParams.[Symbol․dispose]() (CxSmilesWriteParams method) CxSmilesWriteParams.coordinateSelection (CxSmilesWriteParams attribute) CxSmilesWriteParams.fields (CxSmilesWriteParams attribute) CxSmilesWriteParams.free() (CxSmilesWriteParams method) CxSmilesWriteParams.smiles (CxSmilesWriteParams attribute) CxSmilesWriteParamsOptions() (interface) CxSmilesWriteParamsOptions.coordinateSelection? (CxSmilesWriteParamsOptions attribute) CxSmilesWriteParamsOptions.fields? (CxSmilesWriteParamsOptions attribute) CxSmilesWriteParamsOptions.smiles? (CxSmilesWriteParamsOptions attribute) CyclicPseudoPeptide (cosmolkit.PolymerKind attribute) CYN (cosmolkit.ResidueCode attribute) CYS (cosmolkit.ResidueCode attribute) D DA (cosmolkit.ResidueCode attribute) DAB (cosmolkit.ResidueCode attribute) DAL (cosmolkit.ResidueCode attribute) DAR (cosmolkit.ResidueCode attribute) DAS (cosmolkit.ResidueCode attribute) Data (cosmolkit.SubstanceGroupKind attribute) data_field() (cosmolkit.SdfRecord method) data_fields() (cosmolkit.SdfRecord method) database_status (cosmolkit.BioMmcifWriteParams property) DataCollection (cosmolkit.BioSoftwareClassification attribute) DataExtraction (cosmolkit.BioSoftwareClassification attribute) DataProcessing (cosmolkit.BioSoftwareClassification attribute) DataReduction (cosmolkit.BioSoftwareClassification attribute) DataScaling (cosmolkit.BioSoftwareClassification attribute) date (cosmolkit.BioSoftwareItem attribute) DATIVE (cosmolkit.BondOrder attribute) DATIVEL (cosmolkit.BondOrder attribute) DATIVEONE (cosmolkit.BondOrder attribute) DATIVER (cosmolkit.BondOrder attribute) DB (cosmolkit.Element attribute) db_begin (cosmolkit.BioEntityDbRef attribute) db_end (cosmolkit.BioEntityDbRef attribute) db_name (cosmolkit.BioEntityDbRef attribute) dbrefs() (cosmolkit.BioEntityRow method) DC (cosmolkit.ResidueCode attribute) DCY (cosmolkit.ResidueCode attribute) DDQ (cosmolkit.ResidueCode attribute) debug_parse (cosmolkit.SmartsParseParams property) (cosmolkit.SmilesParseParams property) Default (cosmolkit.RotatableBondsOptions attribute) default() (built-in function) (cosmolkit.FingerprintAdditionalOutput static method) (cosmolkit.StereoisomerOptions static method) default_tautomer_score_terms() (in module cosmolkit) defaultTautomerScoreTerms() (built-in function) degenerate (cosmolkit.McsResult attribute) degree() (cosmolkit.Atom method) (cosmolkit.AtomMetadata method) (cosmolkit.MoleculeBuilder method) (cosmolkit.QueryAtom method) DenseMatrix (class in cosmolkit) DenseMatrix() (class) DenseMatrix.[Symbol․dispose]() (DenseMatrix method) DenseMatrix.dimension() (DenseMatrix method) DenseMatrix.free() (DenseMatrix method) DenseMatrix.get() (DenseMatrix method) DenseMatrix.values() (DenseMatrix method) derived_effects (cosmolkit.MoleculeOpSpec attribute) description (cosmolkit.BioExperimentalCrystalInfo attribute) (cosmolkit.BioSoftwareItem attribute) descriptor (cosmolkit.PotentialStereoInfo attribute) DescriptorError DescriptorError() (class) DescriptorError.[Symbol․dispose]() (DescriptorError method) DescriptorError.actual (DescriptorError attribute) DescriptorError.actualRows (DescriptorError attribute) DescriptorError.binPropLen (DescriptorError attribute) DescriptorError.binsLen (DescriptorError attribute) DescriptorError.cause (DescriptorError attribute) DescriptorError.cell (DescriptorError attribute) DescriptorError.contribsLen (DescriptorError attribute) DescriptorError.detail (DescriptorError attribute) DescriptorError.domain (DescriptorError attribute) DescriptorError.expected (DescriptorError attribute) DescriptorError.expectedRows (DescriptorError attribute) DescriptorError.field (DescriptorError attribute) DescriptorError.free() (DescriptorError method) DescriptorError.function (DescriptorError attribute) DescriptorError.includeSulfurPhosphorus (DescriptorError attribute) DescriptorError.kind (DescriptorError attribute) DescriptorError.message (DescriptorError attribute) DescriptorError.minimum (DescriptorError attribute) DescriptorError.row (DescriptorError attribute) DescriptorReadError DescriptorReadError() (class) DescriptorReadError.[Symbol․dispose]() (DescriptorReadError method) DescriptorReadError.cause (DescriptorReadError attribute) DescriptorReadError.domain (DescriptorReadError attribute) DescriptorReadError.free() (DescriptorReadError method) DescriptorReadError.kind (DescriptorReadError attribute) DescriptorReadError.message (DescriptorReadError attribute) detail (cosmolkit.ReactionValidationIssue attribute) details (cosmolkit.BioModRes attribute) (cosmolkit.BioTlsSelection attribute) Detect (cosmolkit.BioCoordinateFormat attribute) detect_chemistry_problems() (cosmolkit.Molecule method) detect_chemistry_problems_with_params() (cosmolkit.Molecule method) detector (cosmolkit.BioDiffractionInfo attribute) detector_make (cosmolkit.BioDiffractionInfo attribute) Determined (cosmolkit.BioCalcFlag attribute) dev_ideal (cosmolkit.BioRefinementRestraint attribute) DG (cosmolkit.ResidueCode attribute) dg() (cosmolkit.EmbedParams static method) dg_bounds_matrix() (cosmolkit.Molecule method) dg_bounds_matrix_list() (cosmolkit.MoleculeBatch method) dg_bounds_matrix_list_with_params() (cosmolkit.MoleculeBatch method) DGL (cosmolkit.ResidueCode attribute) DGN (cosmolkit.ResidueCode attribute) DHA (cosmolkit.ResidueCode attribute) DHD (cosmolkit.ResidueCode attribute) DHI (cosmolkit.ResidueCode attribute) DI (cosmolkit.ResidueCode attribute) DIA (cosmolkit.ResidueCode attribute) Different (cosmolkit.BioAsu attribute) diffraction_ids (cosmolkit.BioExperimentInfo attribute) diffractions (cosmolkit.BioExperimentalCrystalInfo attribute) diffrn (cosmolkit.BioMmcifWriteParams property) DIL (cosmolkit.ResidueCode attribute) dimension (cosmolkit.MolCoordinateSelection attribute) dimension() (cosmolkit.DenseMatrix method) DIO (cosmolkit.ResidueCode attribute) direction() (cosmolkit.Bond method) direction_code() (cosmolkit.Bond method) direction_name() (cosmolkit.Bond method) display() (cosmolkit.SubstanceGroup method) distance_matrix() (cosmolkit.Molecule method) distance_matrix_3d() (cosmolkit.Molecule method) distance_matrix_3d_with_params() (cosmolkit.Molecule method) distance_matrix_with_params() (cosmolkit.Molecule method) DistanceMatrix3dParams (class in cosmolkit) DistanceMatrix3dParams() (class) DistanceMatrix3dParams.[Symbol․dispose]() (DistanceMatrix3dParams method) DistanceMatrix3dParams.conformerId (DistanceMatrix3dParams attribute) DistanceMatrix3dParams.free() (DistanceMatrix3dParams method) DistanceMatrix3dParams.useAtomWeights (DistanceMatrix3dParams attribute) DistanceMatrix3dParamsOptions() (interface) DistanceMatrix3dParamsOptions.conformerId? (DistanceMatrix3dParamsOptions attribute) DistanceMatrix3dParamsOptions.useAtomWeights? (DistanceMatrix3dParamsOptions attribute) DistanceMatrixParams (class in cosmolkit) DistanceMatrixParams() (class) DistanceMatrixParams.[Symbol․dispose]() (DistanceMatrixParams method) DistanceMatrixParams.free() (DistanceMatrixParams method) DistanceMatrixParams.useAtomWeights (DistanceMatrixParams attribute) DistanceMatrixParams.useBondOrder (DistanceMatrixParams attribute) DistanceMatrixParamsOptions() (interface) DistanceMatrixParamsOptions.useAtomWeights? (DistanceMatrixParamsOptions attribute) DistanceMatrixParamsOptions.useBondOrder? (DistanceMatrixParamsOptions attribute) Disulf (cosmolkit.BioConnectionKind attribute) DLE (cosmolkit.ResidueCode attribute) DLY (cosmolkit.ResidueCode attribute) DMF (cosmolkit.ResidueCode attribute) DMS (cosmolkit.ResidueCode attribute) DMU (cosmolkit.ResidueCode attribute) DMX (cosmolkit.ResidueCode attribute) DN (cosmolkit.ResidueCode attribute) Dna (cosmolkit.ChainKind attribute) (cosmolkit.PolymerKind attribute) DNA (cosmolkit.ResidueInfoKind attribute) Dna (cosmolkit.ResidueKind attribute) DnaRnaHybrid (cosmolkit.PolymerKind attribute) DOC (cosmolkit.ResidueCode attribute) docs (cosmolkit.FeatureSpec attribute) DOD (cosmolkit.ResidueCode attribute) domain (cosmolkit.MoleculeOpSpec attribute) DOUBLE (cosmolkit.BondOrder attribute) Double (cosmolkit.PropertyValueKind attribute) DOX (cosmolkit.ResidueCode attribute) dpi_blow_r (cosmolkit.BioRefinementInfo attribute) dpi_blow_rfree (cosmolkit.BioRefinementInfo attribute) dpi_cruickshank_r (cosmolkit.BioRefinementInfo attribute) dpi_cruickshank_rfree (cosmolkit.BioRefinementInfo attribute) DPN (cosmolkit.ResidueCode attribute) DPR (cosmolkit.ResidueCode attribute) DR6 (cosmolkit.ResidueCode attribute) DrawingError DrawingError() (class) DrawingError.[Symbol․dispose]() (DrawingError method) DrawingError.cause (DrawingError attribute) DrawingError.domain (DrawingError attribute) DrawingError.free() (DrawingError method) DrawingError.kind (DrawingError attribute) DrawingError.message (DrawingError attribute) DrawingWriteError DrawingWriteError() (class) DrawingWriteError.[Symbol․dispose]() (DrawingWriteError method) DrawingWriteError.cause (DrawingWriteError attribute) DrawingWriteError.domain (DrawingWriteError attribute) DrawingWriteError.free() (DrawingWriteError method) DrawingWriteError.kind (DrawingWriteError attribute) DrawingWriteError.message (DrawingWriteError attribute) DS (cosmolkit.Element attribute) DSG (cosmolkit.ResidueCode attribute) DSN (cosmolkit.ResidueCode attribute) DT (cosmolkit.ResidueCode attribute) DTH (cosmolkit.ResidueCode attribute) DTR (cosmolkit.ResidueCode attribute) DTY (cosmolkit.ResidueCode attribute) DU (cosmolkit.ResidueCode attribute) Dummy (cosmolkit.BioCalcFlag attribute) DUMMY (cosmolkit.Element attribute) DuplicateProductMap (cosmolkit.ReactionValidationIssueKind attribute) DuplicateReactantMap (cosmolkit.ReactionValidationIssueKind attribute) DVA (cosmolkit.ResidueCode attribute) DXG (cosmolkit.ResidueCode attribute) DY (cosmolkit.Element attribute) E E (cosmolkit.CipDescriptor attribute) e (cosmolkit.CipDescriptor attribute) EDO (cosmolkit.ResidueCode attribute) EEE (cosmolkit.ResidueCode attribute) EGL (cosmolkit.ResidueCode attribute) EITHERDOUBLE (cosmolkit.BondDirection attribute) Element (class in cosmolkit) Element() (class) element() (cosmolkit.Atom method) (cosmolkit.BioAtomRow method) (cosmolkit.ElementInfo method) (cosmolkit.ProteinAtomRef method) Element.[Symbol․dispose]() (Element method) Element.atomicNumber() (Element method) Element.free() (Element method) Element.fromAtomicNumber() (Element method) Element.fromSymbol() (Element method) Element.symbol() (Element method) element_info() (in module cosmolkit) element_symbol() (cosmolkit.BioAtomRow method) (cosmolkit.ProteinAtomRef method) ElementInfo (class in cosmolkit) elementInfo() (built-in function) ElementInfo() (class) ElementInfo.[Symbol․dispose]() (ElementInfo method) ElementInfo.atomicNumber() (ElementInfo method) ElementInfo.atomicWeight() (ElementInfo method) ElementInfo.element() (ElementInfo method) ElementInfo.free() (ElementInfo method) ElementInfo.outerElectrons() (ElementInfo method) ElementInfo.period() (ElementInfo method) ElementInfo.rb0() (ElementInfo method) ElementInfo.symbol() (ElementInfo method) ElementInfo.valences() (ElementInfo method) Elements (cosmolkit.McsAtomComparator attribute) ELS (cosmolkit.ResidueInfoKind attribute) embed_3d_conformer_() (cosmolkit.Molecule method) embed_3d_conformer_result_() (cosmolkit.Molecule method) embed_3d_conformer_result_with_params_() (cosmolkit.Molecule method) embed_3d_conformer_with_params_() (cosmolkit.Molecule method) embed_3d_conformers_() (cosmolkit.Molecule method) embed_3d_conformers_result_() (cosmolkit.Molecule method) embed_3d_conformers_result_with_params_() (cosmolkit.Molecule method) embed_3d_conformers_with_params_() (cosmolkit.Molecule method) embed_fragments_separately (cosmolkit.EmbedParams property) EmbedMoleculeResult (class in cosmolkit) EmbedMoleculeResult() (class) EmbedMoleculeResult.[Symbol․dispose]() (EmbedMoleculeResult method) EmbedMoleculeResult.confId() (EmbedMoleculeResult method) EmbedMoleculeResult.free() (EmbedMoleculeResult method) EmbedMoleculeResult.molecule() (EmbedMoleculeResult method) EmbedMoleculeResult.ok() (EmbedMoleculeResult method) EmbedMoleculeResult.params() (EmbedMoleculeResult method) EmbedMultipleConfsResult (class in cosmolkit) EmbedMultipleConfsResult() (class) EmbedMultipleConfsResult.[Symbol․dispose]() (EmbedMultipleConfsResult method) EmbedMultipleConfsResult.confIds() (EmbedMultipleConfsResult method) EmbedMultipleConfsResult.free() (EmbedMultipleConfsResult method) EmbedMultipleConfsResult.generatedCount() (EmbedMultipleConfsResult method) EmbedMultipleConfsResult.molecule() (EmbedMultipleConfsResult method) EmbedMultipleConfsResult.params() (EmbedMultipleConfsResult method) EmbedMultipleConfsResult.requestedNumConfs() (EmbedMultipleConfsResult method) EmbedParams (class in cosmolkit) EmbedParams() (class) EmbedParams.[Symbol․dispose]() (EmbedParams method) EmbedParams.basinThresh (EmbedParams attribute) EmbedParams.boundsMatForceScaling (EmbedParams attribute) EmbedParams.boxSizeMult (EmbedParams attribute) EmbedParams.clearConformers (EmbedParams attribute) EmbedParams.coordMap (EmbedParams attribute) EmbedParams.cpci (EmbedParams attribute) EmbedParams.dg() (EmbedParams method) EmbedParams.embedFragmentsSeparately (EmbedParams attribute) EmbedParams.enableSequentialRandomSeeds (EmbedParams attribute) EmbedParams.enforceChirality (EmbedParams attribute) EmbedParams.etdg() (EmbedParams method) EmbedParams.etdgV2() (EmbedParams method) EmbedParams.etkdg() (EmbedParams method) EmbedParams.etkdgV2() (EmbedParams method) EmbedParams.etkdgV3() (EmbedParams method) EmbedParams.etVersion (EmbedParams attribute) EmbedParams.failures() (EmbedParams method) EmbedParams.forceTransAmides (EmbedParams attribute) EmbedParams.free() (EmbedParams method) EmbedParams.ignoreSmoothingFailures (EmbedParams attribute) EmbedParams.kdg() (EmbedParams method) EmbedParams.maxIterations (EmbedParams attribute) EmbedParams.new() (EmbedParams method) EmbedParams.numThreads (EmbedParams attribute) EmbedParams.numZeroFail (EmbedParams attribute) EmbedParams.onlyHeavyAtomsForRms (EmbedParams attribute) EmbedParams.optimizerForceTol (EmbedParams attribute) EmbedParams.pruneRmsThresh (EmbedParams attribute) EmbedParams.randNegEig (EmbedParams attribute) EmbedParams.randomSeed (EmbedParams attribute) EmbedParams.srEtkdgV3() (EmbedParams method) EmbedParams.symmetrizeConjugatedTerminalGroupsForPruning (EmbedParams attribute) EmbedParams.timeout (EmbedParams attribute) EmbedParams.toJson() (EmbedParams method) EmbedParams.trackFailures (EmbedParams attribute) EmbedParams.useBasicKnowledge (EmbedParams attribute) EmbedParams.useExpTorsionAnglePrefs (EmbedParams attribute) EmbedParams.useMacrocycle14config (EmbedParams attribute) EmbedParams.useMacrocycleTorsions (EmbedParams attribute) EmbedParams.useRandomCoords (EmbedParams attribute) EmbedParams.useSmallRingTorsions (EmbedParams attribute) EmbedParams.useSymmetryForPruning (EmbedParams attribute) EmbedParams.verbose (EmbedParams attribute) EmbedParams.withJson() (EmbedParams method) EmbedParamsOptions() (interface) EmbedParamsOptions.basinThresh? (EmbedParamsOptions attribute) EmbedParamsOptions.boundsMatForceScaling? (EmbedParamsOptions attribute) EmbedParamsOptions.boxSizeMult? (EmbedParamsOptions attribute) EmbedParamsOptions.clearConformers? (EmbedParamsOptions attribute) EmbedParamsOptions.coordMap? (EmbedParamsOptions attribute) EmbedParamsOptions.cpci? (EmbedParamsOptions attribute) EmbedParamsOptions.embedFragmentsSeparately? (EmbedParamsOptions attribute) EmbedParamsOptions.enableSequentialRandomSeeds? (EmbedParamsOptions attribute) EmbedParamsOptions.enforceChirality? (EmbedParamsOptions attribute) EmbedParamsOptions.etVersion? (EmbedParamsOptions attribute) EmbedParamsOptions.forceTransAmides? (EmbedParamsOptions attribute) EmbedParamsOptions.ignoreSmoothingFailures? (EmbedParamsOptions attribute) EmbedParamsOptions.maxIterations? (EmbedParamsOptions attribute) EmbedParamsOptions.numThreads? (EmbedParamsOptions attribute) EmbedParamsOptions.numZeroFail? (EmbedParamsOptions attribute) EmbedParamsOptions.onlyHeavyAtomsForRms? (EmbedParamsOptions attribute) EmbedParamsOptions.optimizerForceTol? (EmbedParamsOptions attribute) EmbedParamsOptions.pruneRmsThresh? (EmbedParamsOptions attribute) EmbedParamsOptions.randNegEig? (EmbedParamsOptions attribute) EmbedParamsOptions.randomSeed? (EmbedParamsOptions attribute) EmbedParamsOptions.symmetrizeConjugatedTerminalGroupsForPruning? (EmbedParamsOptions attribute) EmbedParamsOptions.timeout? (EmbedParamsOptions attribute) EmbedParamsOptions.trackFailures? (EmbedParamsOptions attribute) EmbedParamsOptions.useBasicKnowledge? (EmbedParamsOptions attribute) EmbedParamsOptions.useExpTorsionAnglePrefs? (EmbedParamsOptions attribute) EmbedParamsOptions.useMacrocycle14config? (EmbedParamsOptions attribute) EmbedParamsOptions.useMacrocycleTorsions? (EmbedParamsOptions attribute) EmbedParamsOptions.useRandomCoords? (EmbedParamsOptions attribute) EmbedParamsOptions.useSmallRingTorsions? (EmbedParamsOptions attribute) EmbedParamsOptions.useSymmetryForPruning? (EmbedParamsOptions attribute) EmbedParamsOptions.verbose? (EmbedParamsOptions attribute) enable_sequential_random_seeds (cosmolkit.EmbedParams property) end (cosmolkit.BioHelix attribute) (cosmolkit.BioStrand attribute) end() (cosmolkit.BioRowSpan method) (cosmolkit.Bond method) end_record (cosmolkit.BioPdbWriteParams property) ENDDOWNRIGHT (cosmolkit.BondDirection attribute) ENDUPRIGHT (cosmolkit.BondDirection attribute) energy (cosmolkit.ForceFieldEnergyGradient attribute) (cosmolkit.ForceFieldMinimizeOutcome attribute) energy() (cosmolkit.MmffEnergyGradient method) (cosmolkit.MmffOptimizeMoleculeConfResult method) (cosmolkit.MolecularForceField method) (cosmolkit.UffConformerResult method) (cosmolkit.UffEnergyGradient method) (cosmolkit.UffOptimizationResult method) energy_gradient() (cosmolkit.MolecularForceField method) energy_tolerance (cosmolkit.ForceFieldMinimizeParams property) enforce_chirality (cosmolkit.EmbedParams property) ENHANCED_STEREO (cosmolkit.CxSmilesFields attribute) entities() (cosmolkit.BioStructure method) entity (cosmolkit.BioMmcifWriteParams property) entity_id() (cosmolkit.BioChainRow method) entity_kind() (cosmolkit.BioResidueRow method) entity_poly (cosmolkit.BioMmcifWriteParams property) entity_poly_seq (cosmolkit.BioMmcifWriteParams property) EntityKind (class in cosmolkit) (None attribute) EntityKind.Branched (EntityKind attribute) EntityKind.NonPolymer (EntityKind attribute) EntityKind.Polymer (EntityKind attribute) EntityKind.Unknown (EntityKind attribute) EntityKind.Water (EntityKind attribute) EntitySequence (cosmolkit.BioMmcifReadStage attribute) EntitySourceIds (class in cosmolkit) EntitySourceIds() (class) EntitySourceIds.[Symbol․dispose]() (EntitySourceIds method) EntitySourceIds.free() (EntitySourceIds method) EntitySourceIds.sourceEntityId() (EntitySourceIds method) entries() (cosmolkit.TautomerEnumeration method) (cosmolkit.TautomerProgress method) (cosmolkit.TemplateAttachmentOrder method) entry (cosmolkit.BioMmcifWriteParams property) enumerate_stereoisomers() (cosmolkit.Molecule method) enumerate_stereoisomers_with_options() (cosmolkit.Molecule method) enumerate_stereoisomers_with_random_bits() (cosmolkit.Molecule method) enumerate_tautomers() (cosmolkit.Molecule method) enumerate_tautomers_with_params() (cosmolkit.Molecule method) EnumerationError EnumerationError() (class) EnumerationError.[Symbol․dispose]() (EnumerationError method) EnumerationError.cause (EnumerationError attribute) EnumerationError.domain (EnumerationError attribute) EnumerationError.free() (EnumerationError method) EnumerationError.kind (EnumerationError attribute) EnumerationError.message (EnumerationError attribute) EnumerationRunError EnumerationRunError() (class) EnumerationRunError.[Symbol․dispose]() (EnumerationRunError method) EnumerationRunError.cause (EnumerationRunError attribute) EnumerationRunError.domain (EnumerationRunError attribute) EnumerationRunError.free() (EnumerationRunError method) EnumerationRunError.kind (EnumerationRunError attribute) EnumerationRunError.message (EnumerationRunError attribute) EOH (cosmolkit.ResidueCode attribute) EPE (cosmolkit.ResidueCode attribute) ER (cosmolkit.Element attribute) error (cosmolkit.ChemistryProblem attribute) Error (cosmolkit.CoordinateZPolicy attribute) (cosmolkit.ReactionValidationSeverity attribute) error_mode() (cosmolkit.MoleculeBatch method) errors (cosmolkit.BatchExportParams property) (cosmolkit.BatchParams property) (cosmolkit.ReactionValidationReport attribute) errors() (cosmolkit.BatchExportReport method) (cosmolkit.BatchValidationError method) (cosmolkit.MoleculeBatch method) ES (cosmolkit.Element attribute) et_version (cosmolkit.EmbedParams property) etdg() (cosmolkit.EmbedParams static method) etdg_v2() (cosmolkit.EmbedParams static method) ETF (cosmolkit.ResidueCode attribute) etkdg() (cosmolkit.EmbedParams static method) etkdg_v2() (cosmolkit.EmbedParams static method) etkdg_v3() (cosmolkit.EmbedParams static method) EU (cosmolkit.Element attribute) Exact() (cosmolkit.AltLocRequest static method) exact_molecular_weight() (cosmolkit.Molecule method) exact_molecular_weight_with_params() (cosmolkit.Molecule method) execution (cosmolkit.BatchImageParams property) expand_attachment_points (cosmolkit.SdfReadParams property) expand_one_letter() (in module cosmolkit) expand_one_letter_sequence() (in module cosmolkit) expandOneLetter() (built-in function) expandOneLetterSequence() (built-in function) expected (cosmolkit.ForceFieldError property) (cosmolkit.MmffForceFieldError property) expected() (cosmolkit.PropertyValueError method) Experimental (cosmolkit.BioMmcifReadStage attribute) experiments (cosmolkit.BioMetadata attribute) explain_path_score() (in module cosmolkit) explainPathScore() (built-in function) explanation (cosmolkit.FunctionStatus attribute) explicit_hydrogens() (cosmolkit.Atom method) (cosmolkit.QueryAtom method) explicit_only (cosmolkit.AddHsParams property) explicit_valence() (cosmolkit.Atom method) (cosmolkit.AtomMetadata method) exptl (cosmolkit.BioMmcifWriteParams property) extra_atom_check (cosmolkit.SubstructMatchParams property) extra_atom_check_overrides_default_check (cosmolkit.SubstructMatchParams property) extra_bond_check (cosmolkit.SubstructMatchParams property) extra_bond_check_overrides_default_check (cosmolkit.SubstructMatchParams property) extra_final_check (cosmolkit.SubstructMatchParams property) F F (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) FAD (cosmolkit.ResidueCode attribute) failed() (cosmolkit.BatchExportReport method) failures (cosmolkit.EmbedParams attribute) fasta_code() (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueInfo method) FCY (cosmolkit.ResidueCode attribute) FE (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) FE2 (cosmolkit.ResidueCode attribute) feature (cosmolkit.ParityMatrixEntry attribute) (cosmolkit.SupportMatrixEntry attribute) feature_spec() (in module cosmolkit) feature_specs() (in module cosmolkit) features() (cosmolkit.MorganAtomInvariantsGenerator static method) (cosmolkit.MorganInvariants static method) FeatureSpec (class in cosmolkit) featureSpec() (built-in function) FeatureSpec() (class) FeatureSpec.[Symbol․dispose]() (FeatureSpec method) FeatureSpec.category (FeatureSpec attribute) FeatureSpec.docs (FeatureSpec attribute) FeatureSpec.free() (FeatureSpec method) FeatureSpec.name (FeatureSpec attribute) FeatureSpecIter (class in cosmolkit) FeatureSpecIter() (class) FeatureSpecIter.[Symbol․dispose]() (FeatureSpecIter method) FeatureSpecIter.free() (FeatureSpecIter method) FeatureSpecIter.next() (FeatureSpecIter method) featureSpecs() (built-in function) FGA (cosmolkit.ResidueCode attribute) fields (cosmolkit.CxSmilesWriteParams property) filenames (cosmolkit.BatchImageParams property) final_match (cosmolkit.SubstructMatchParams property) Finalization (cosmolkit.BioPdbReadStage attribute) find_atom() (cosmolkit.BioStructure method) find_chiral_centers() (cosmolkit.Molecule method) find_entity() (cosmolkit.BioStructure method) find_entity_of_subchain() (cosmolkit.BioStructure method) FIND_RADICALS (cosmolkit.SanitizeOperations attribute) find_residue_info() (in module cosmolkit) find_residue_info_index() (in module cosmolkit) FindRadicals (cosmolkit.SanitizeStage attribute) findResidueInfo() (built-in function) findResidueInfoIndex() (built-in function) Fingerprint (class in cosmolkit) Fingerprint() (class) fingerprint() (cosmolkit.BatchFingerprintOutput method) (cosmolkit.LayeredFingerprintResult method) (cosmolkit.TopologicalFingerprintResult method) Fingerprint.[Symbol․dispose]() (Fingerprint method) Fingerprint.free() (Fingerprint method) Fingerprint.fromOnBits() (Fingerprint method) Fingerprint.nBits() (Fingerprint method) Fingerprint.onBits() (Fingerprint method) Fingerprint.tanimoto() (Fingerprint method) fingerprint_atom_pair() (cosmolkit.Molecule method) fingerprint_atom_pair_count() (cosmolkit.Molecule method) fingerprint_atom_pair_count_list() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_count_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_count_with_params() (cosmolkit.Molecule method) fingerprint_atom_pair_list() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse() (cosmolkit.Molecule method) fingerprint_atom_pair_sparse_bits_list() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse_bits_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse_count() (cosmolkit.Molecule method) fingerprint_atom_pair_sparse_count_list() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse_count_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_sparse_count_with_params() (cosmolkit.Molecule method) fingerprint_atom_pair_sparse_with_params() (cosmolkit.Molecule method) fingerprint_atom_pair_with_output_list() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_with_output_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_atom_pair_with_params() (cosmolkit.Molecule method) fingerprint_avalon() (cosmolkit.Molecule method) fingerprint_avalon_with_params() (cosmolkit.Molecule method) fingerprint_layered() (cosmolkit.Molecule method) fingerprint_layered_list() (cosmolkit.MoleculeBatch method) fingerprint_layered_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_layered_query_with_output_with_params() (in module cosmolkit) fingerprint_layered_query_with_params() (in module cosmolkit) fingerprint_layered_with_output() (cosmolkit.Molecule method) fingerprint_layered_with_output_list() (cosmolkit.MoleculeBatch method) fingerprint_layered_with_output_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_layered_with_output_with_params() (cosmolkit.Molecule method) fingerprint_layered_with_params() (cosmolkit.Molecule method) fingerprint_maccs() (cosmolkit.Molecule method) fingerprint_maccs_raw() (cosmolkit.Molecule method) fingerprint_maccs_with_params() (cosmolkit.Molecule method) fingerprint_morgan() (cosmolkit.Molecule method) fingerprint_morgan_count() (cosmolkit.Molecule method) fingerprint_morgan_count_with_generator() (cosmolkit.Molecule method) fingerprint_morgan_count_with_params() (cosmolkit.Molecule method) fingerprint_morgan_list() (cosmolkit.MoleculeBatch method) fingerprint_morgan_list_with_generator_params() (cosmolkit.MoleculeBatch method) fingerprint_morgan_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_morgan_sparse() (cosmolkit.Molecule method) fingerprint_morgan_sparse_count() (cosmolkit.Molecule method) fingerprint_morgan_sparse_count_with_generator() (cosmolkit.Molecule method) fingerprint_morgan_sparse_count_with_params() (cosmolkit.Molecule method) fingerprint_morgan_sparse_with_generator() (cosmolkit.Molecule method) fingerprint_morgan_sparse_with_params() (cosmolkit.Molecule method) fingerprint_morgan_with_generator() (cosmolkit.Molecule method) fingerprint_morgan_with_output_list() (cosmolkit.MoleculeBatch method) fingerprint_morgan_with_output_list_with_generator_params() (cosmolkit.MoleculeBatch method) fingerprint_morgan_with_output_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_morgan_with_params() (cosmolkit.Molecule method) fingerprint_pattern() (cosmolkit.Molecule method) fingerprint_pattern_list() (cosmolkit.MoleculeBatch method) fingerprint_pattern_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_pattern_query() (in module cosmolkit) fingerprint_pattern_query_with_params() (in module cosmolkit) fingerprint_pattern_with_params() (cosmolkit.Molecule method) fingerprint_topological() (cosmolkit.Molecule method) fingerprint_topological_query_with_output_with_params() (in module cosmolkit) fingerprint_topological_query_with_params() (in module cosmolkit) fingerprint_topological_torsion() (cosmolkit.Molecule method) fingerprint_topological_torsion_count() (cosmolkit.Molecule method) fingerprint_topological_torsion_count_legacy() (cosmolkit.Molecule method) fingerprint_topological_torsion_count_legacy_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_count_with_generator() (cosmolkit.Molecule method) fingerprint_topological_torsion_count_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_legacy() (cosmolkit.Molecule method) fingerprint_topological_torsion_legacy_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_list() (cosmolkit.MoleculeBatch method) fingerprint_topological_torsion_list_with_params() (cosmolkit.MoleculeBatch method) fingerprint_topological_torsion_sparse() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count_legacy() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count_legacy_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count_with_generator() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_count_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_with_generator() (cosmolkit.Molecule method) fingerprint_topological_torsion_sparse_with_params() (cosmolkit.Molecule method) fingerprint_topological_torsion_with_generator() (cosmolkit.Molecule method) fingerprint_topological_torsion_with_params() (cosmolkit.Molecule method) fingerprint_topological_with_output() (cosmolkit.Molecule method) fingerprint_topological_with_output_with_params() (cosmolkit.Molecule method) fingerprint_topological_with_params() (cosmolkit.Molecule method) FingerprintAdditionalOutput (class in cosmolkit) FingerprintAdditionalOutput() (class) FingerprintAdditionalOutput.[Symbol․dispose]() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.allocateAtomCounts() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.allocateAtomsPerBit() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.allocateAtomToBits() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.allocateBitInfoMap() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.allocateBitPaths() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.atomCounts() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.atomsPerBit() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.atomToBits() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.bitInfoMap() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.bitPaths() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.default() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.free() (FingerprintAdditionalOutput method) FingerprintAdditionalOutput.new() (FingerprintAdditionalOutput method) FingerprintBatch (class in cosmolkit) FingerprintError FingerprintError() (class) FingerprintError.[Symbol․dispose]() (FingerprintError method) FingerprintError.cause (FingerprintError attribute) FingerprintError.domain (FingerprintError attribute) FingerprintError.free() (FingerprintError method) FingerprintError.kind (FingerprintError attribute) FingerprintError.message (FingerprintError attribute) FingerprintJsonError FingerprintJsonError() (class) FingerprintJsonError.[Symbol․dispose]() (FingerprintJsonError method) FingerprintJsonError.cause (FingerprintJsonError attribute) FingerprintJsonError.domain (FingerprintJsonError attribute) FingerprintJsonError.free() (FingerprintJsonError method) FingerprintJsonError.kind (FingerprintJsonError attribute) FingerprintJsonError.message (FingerprintJsonError attribute) fingerprintLayeredQueryWithOutputWithParams() (built-in function) fingerprintLayeredQueryWithParams() (built-in function) fingerprintPatternQuery() (built-in function) fingerprintPatternQueryWithParams() (built-in function) FingerprintPreparationError FingerprintPreparationError() (class) FingerprintPreparationError.[Symbol․dispose]() (FingerprintPreparationError method) FingerprintPreparationError.cause (FingerprintPreparationError attribute) FingerprintPreparationError.domain (FingerprintPreparationError attribute) FingerprintPreparationError.free() (FingerprintPreparationError method) FingerprintPreparationError.kind (FingerprintPreparationError attribute) FingerprintPreparationError.message (FingerprintPreparationError attribute) fingerprints() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) fingerprintTopologicalQueryWithOutputWithParams() (built-in function) fingerprintTopologicalQueryWithParams() (built-in function) FIVEANDAHALF (cosmolkit.BondOrder attribute) fixed_atoms() (cosmolkit.MolecularForceField method) FL (cosmolkit.Element attribute) flag_possible (cosmolkit.PotentialStereoParams property) flavor (cosmolkit.BioMoleculeParams property) flips_per_sample (cosmolkit.Coordinate2DParams property) FLO (cosmolkit.ResidueCode attribute) FM (cosmolkit.Element attribute) FME (cosmolkit.ResidueCode attribute) FMN (cosmolkit.ResidueCode attribute) FMT (cosmolkit.ResidueCode attribute) force_2d (cosmolkit.MolBlockWriteParams property) force_rdkit (cosmolkit.Coordinate2DParams property) force_tolerance (cosmolkit.ForceFieldMinimizeParams property) force_trans_amides (cosmolkit.EmbedParams property) ForceFieldEnergyGradient (class in cosmolkit) ForceFieldEnergyGradient() (class) ForceFieldEnergyGradient.[Symbol․dispose]() (ForceFieldEnergyGradient method) ForceFieldEnergyGradient.energy() (ForceFieldEnergyGradient method) ForceFieldEnergyGradient.free() (ForceFieldEnergyGradient method) ForceFieldEnergyGradient.gradient() (ForceFieldEnergyGradient method) ForceFieldError ForceFieldError() (class) ForceFieldError.[Symbol․dispose]() (ForceFieldError method) ForceFieldError.actual() (ForceFieldError method) ForceFieldError.atomIndex() (ForceFieldError method) ForceFieldError.cause (ForceFieldError attribute) ForceFieldError.component() (ForceFieldError method) ForceFieldError.expected() (ForceFieldError method) ForceFieldError.free() (ForceFieldError method) ForceFieldError.kind() (ForceFieldError method) ForceFieldError.message (ForceFieldError attribute) ForceFieldError.requested() (ForceFieldError method) ForceFieldMinimizeOutcome (class in cosmolkit) ForceFieldMinimizeOutcome() (class) ForceFieldMinimizeOutcome.[Symbol․dispose]() (ForceFieldMinimizeOutcome method) ForceFieldMinimizeOutcome.converged() (ForceFieldMinimizeOutcome method) ForceFieldMinimizeOutcome.energy() (ForceFieldMinimizeOutcome method) ForceFieldMinimizeOutcome.free() (ForceFieldMinimizeOutcome method) ForceFieldMinimizeOutcome.iterations() (ForceFieldMinimizeOutcome method) ForceFieldMinimizeParams (class in cosmolkit) ForceFieldMinimizeParams() (class) ForceFieldMinimizeParams.[Symbol․dispose]() (ForceFieldMinimizeParams method) ForceFieldMinimizeParams.energyTolerance (ForceFieldMinimizeParams attribute) ForceFieldMinimizeParams.forceTolerance (ForceFieldMinimizeParams attribute) ForceFieldMinimizeParams.free() (ForceFieldMinimizeParams method) ForceFieldMinimizeParams.maxIterations (ForceFieldMinimizeParams attribute) ForceFieldMinimizeParamsOptions() (interface) ForceFieldMinimizeParamsOptions.energyTolerance? (ForceFieldMinimizeParamsOptions attribute) ForceFieldMinimizeParamsOptions.forceTolerance? (ForceFieldMinimizeParamsOptions attribute) ForceFieldMinimizeParamsOptions.maxIterations? (ForceFieldMinimizeParamsOptions attribute) formal_charge() (cosmolkit.Atom method) (cosmolkit.BioAtomRow method) (cosmolkit.MmffAtomProperties method) (cosmolkit.MmffProperties method) (cosmolkit.QueryAtom method) format (cosmolkit.BatchExportParams property) (cosmolkit.BatchImageParams property) (cosmolkit.BioReadParams property) (cosmolkit.MolBlockWriteParams property) Formulation (cosmolkit.SubstanceGroupKind attribute) found() (cosmolkit.ResidueInfo method) FOURANDAHALF (cosmolkit.BondOrder attribute) fp_size (cosmolkit.AtomPairParams property) (cosmolkit.LayeredFingerprintParams property) (cosmolkit.LegacyTopologicalTorsionParams property) (cosmolkit.MorganParams property) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalFingerprintParams property) (cosmolkit.TopologicalTorsionParams property) (cosmolkit.TopologicalTorsionSettings attribute) FR (cosmolkit.Element attribute) fraction_csp3() (cosmolkit.Molecule method) FractionalTransform (cosmolkit.BioMmcifReadStage attribute) FragmentCxSmilesWriteParams (class in cosmolkit) FragmentCxSmilesWriteParams() (class) FragmentCxSmilesWriteParams.[Symbol․dispose]() (FragmentCxSmilesWriteParams method) FragmentCxSmilesWriteParams.atoms (FragmentCxSmilesWriteParams attribute) FragmentCxSmilesWriteParams.atomSymbols (FragmentCxSmilesWriteParams attribute) FragmentCxSmilesWriteParams.bonds (FragmentCxSmilesWriteParams attribute) FragmentCxSmilesWriteParams.bondSymbols (FragmentCxSmilesWriteParams attribute) FragmentCxSmilesWriteParams.cx (FragmentCxSmilesWriteParams attribute) FragmentCxSmilesWriteParams.free() (FragmentCxSmilesWriteParams method) FragmentCxSmilesWriteParamsOptions() (interface) FragmentCxSmilesWriteParamsOptions.atoms? (FragmentCxSmilesWriteParamsOptions attribute) FragmentCxSmilesWriteParamsOptions.atomSymbols? (FragmentCxSmilesWriteParamsOptions attribute) FragmentCxSmilesWriteParamsOptions.bonds? (FragmentCxSmilesWriteParamsOptions attribute) FragmentCxSmilesWriteParamsOptions.bondSymbols? (FragmentCxSmilesWriteParamsOptions attribute) FragmentCxSmilesWriteParamsOptions.cx? (FragmentCxSmilesWriteParamsOptions attribute) fragments() (cosmolkit.Molecule method) FragmentSmilesWriteParams (class in cosmolkit) FragmentSmilesWriteParams() (class) FragmentSmilesWriteParams.[Symbol․dispose]() (FragmentSmilesWriteParams method) FragmentSmilesWriteParams.atoms (FragmentSmilesWriteParams attribute) FragmentSmilesWriteParams.atomSymbols (FragmentSmilesWriteParams attribute) FragmentSmilesWriteParams.bonds (FragmentSmilesWriteParams attribute) FragmentSmilesWriteParams.bondSymbols (FragmentSmilesWriteParams attribute) FragmentSmilesWriteParams.free() (FragmentSmilesWriteParams method) FragmentSmilesWriteParams.smiles (FragmentSmilesWriteParams attribute) FragmentSmilesWriteParamsOptions() (interface) FragmentSmilesWriteParamsOptions.atoms? (FragmentSmilesWriteParamsOptions attribute) FragmentSmilesWriteParamsOptions.atomSymbols? (FragmentSmilesWriteParamsOptions attribute) FragmentSmilesWriteParamsOptions.bonds? (FragmentSmilesWriteParamsOptions attribute) FragmentSmilesWriteParamsOptions.bondSymbols? (FragmentSmilesWriteParamsOptions attribute) FragmentSmilesWriteParamsOptions.smiles? (FragmentSmilesWriteParamsOptions attribute) from_ascii() (cosmolkit.AtomName static method) from_atomic_number() (cosmolkit.Element static method) from_atoms (cosmolkit.AtomPairFingerprintParams property) (cosmolkit.LayeredFingerprintParams property) (cosmolkit.LegacyTopologicalTorsionParams property) (cosmolkit.MorganCallParams property) (cosmolkit.MorganFingerprintParams property) (cosmolkit.TopologicalFingerprintParams property) (cosmolkit.TopologicalTorsionCallParams property) (cosmolkit.TopologicalTorsionFingerprintParams property) from_binary() (cosmolkit.Molecule static method) from_bits() (cosmolkit.SanitizeOperations static method) from_bits_retain() (cosmolkit.AvalonFingerprintFlags static method) (cosmolkit.LayeredFingerprintLayers static method) from_cid() (cosmolkit.BioSelection static method) from_code() (cosmolkit.AtomCodeExplanation static method) from_dataset_indices() (cosmolkit.MoleculeBatch static method) from_inchi() (cosmolkit.Molecule static method) from_inchi_with_params() (cosmolkit.Molecule static method) from_integer_seed() (cosmolkit.StereoisomerRandomSource static method) from_json() (cosmolkit.MorganFingerprintGenerator static method) (cosmolkit.TopologicalTorsionFingerprintGenerator static method) from_mmcif() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) from_mol() (cosmolkit.Molecule static method) from_mol2() (cosmolkit.Molecule static method) from_mol2_with_params() (cosmolkit.Molecule static method) from_mol_with_params() (cosmolkit.Molecule static method) from_name() (cosmolkit.CoordinateZPolicy static method) from_on_bits() (cosmolkit.Fingerprint static method) from_parts() (cosmolkit.BioStructure static method) (cosmolkit.Molecule static method) (cosmolkit.MoleculeBuilder static method) from_pdb() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) from_pdb_with_params() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) from_query_graph() (cosmolkit.SdfRecord static method) from_random_bits() (cosmolkit.StereoisomerRandomSource static method) from_rdkit() (cosmolkit.Molecule class method) from_records() (cosmolkit.MoleculeBatch static method) from_sdf() (cosmolkit.Molecule static method) (cosmolkit.SdfRecord static method) from_sdf_records() (cosmolkit.MoleculeBatch static method) from_sdf_records_with_params() (cosmolkit.MoleculeBatch static method) from_sdf_with_params() (cosmolkit.Molecule static method) (cosmolkit.SdfRecord static method) from_smarts() (cosmolkit.QueryGraph static method) from_smarts_with_params() (cosmolkit.QueryGraph static method) from_smiles() (cosmolkit.Molecule static method) from_smiles_list() (cosmolkit.MoleculeBatch static method) from_smiles_list_with_params() (cosmolkit.MoleculeBatch static method) from_smiles_with_params() (cosmolkit.Molecule static method) from_smirks() (cosmolkit.Reaction static method) from_smirks_with_params() (cosmolkit.Reaction static method) from_symbol() (cosmolkit.Element static method) from_templates() (cosmolkit.Reaction static method) from_text() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) from_text_with_params() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) from_transform_data() (cosmolkit.TautomerParams static method) from_transform_file() (cosmolkit.TautomerParams static method) from_xyz_block() (cosmolkit.Molecule static method) FRU (cosmolkit.ResidueCode attribute) fsc_free (cosmolkit.BioBasicRefinementInfo attribute) fsc_work (cosmolkit.BioBasicRefinementInfo attribute) FUC (cosmolkit.ResidueCode attribute) full_sequence() (cosmolkit.BioEntityRow method) function (cosmolkit.BioRefinementRestraint attribute) FunctionStatus (class in cosmolkit) FunctionStatus() (class) FunctionStatus.[Symbol․dispose]() (FunctionStatus method) FunctionStatus.explanation (FunctionStatus attribute) FunctionStatus.free() (FunctionStatus method) FunctionStatus.kind (FunctionStatus attribute) FunctionStatus.reference (FunctionStatus attribute) fuzzy_and() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) fuzzy_or() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) FVA (cosmolkit.ResidueCode attribute) G G (cosmolkit.ResidueCode attribute) GA (cosmolkit.Element attribute) GAL (cosmolkit.ResidueCode attribute) gamma (cosmolkit.BioCrystalCell attribute) GBL (cosmolkit.ResidueCode attribute) GCD (cosmolkit.ResidueCode attribute) GD (cosmolkit.Element attribute) GDP (cosmolkit.ResidueCode attribute) GE (cosmolkit.Element attribute) generated_count() (cosmolkit.EmbedMultipleConfsResult method) generator (cosmolkit.AtomPairFingerprintParams property) (cosmolkit.MorganFingerprintParams property) (cosmolkit.TopologicalTorsionFingerprintParams property) generators (cosmolkit.BioAssembly attribute) Generic() (cosmolkit.SubstanceGroupKind static method) generic_value (cosmolkit.SubstanceGroupKind attribute) get() (cosmolkit.DenseMatrix method) (cosmolkit.MoleculeBatch method) (cosmolkit.TautomerEnumeration method) GHP (cosmolkit.ResidueCode attribute) given (cosmolkit.BioNcsOperator attribute) GL3 (cosmolkit.ResidueCode attribute) GLA (cosmolkit.ResidueCode attribute) GLC (cosmolkit.ResidueCode attribute) GLN (cosmolkit.ResidueCode attribute) GLO (cosmolkit.ResidueCode attribute) GLU (cosmolkit.ResidueCode attribute) GLX (cosmolkit.ResidueCode attribute) GLY (cosmolkit.ResidueCode attribute) GOL (cosmolkit.ResidueCode attribute) GPX (cosmolkit.ResidueCode attribute) gradient (cosmolkit.ForceFieldEnergyGradient attribute) gradient() (cosmolkit.MmffEnergyGradient method) (cosmolkit.MolecularForceField method) (cosmolkit.UffEnergyGradient method) gradient_unconstrained() (cosmolkit.MolecularForceField method) Graft (cosmolkit.SubstanceGroupKind attribute) graph() (cosmolkit.SdfRecord method) group_pdb (cosmolkit.BioMmcifWriteParams property) GYS (cosmolkit.ResidueCode attribute) H H (cosmolkit.Element attribute) H2U (cosmolkit.ResidueCode attribute) hall_kier_alpha() (cosmolkit.Molecule method) hall_kier_alpha_with_contributions() (cosmolkit.Molecule method) has_2d_coordinates() (cosmolkit.Molecule method) has_d_fraction (cosmolkit.BioStructureSourceState attribute) has_origx (cosmolkit.BioStructureSourceState attribute) has_origx() (cosmolkit.BioStructure method) has_substruct_match() (cosmolkit.Molecule method) has_substruct_match_with_params() (cosmolkit.Molecule method) has_valence_violation() (cosmolkit.Molecule method) hbond_atom1 (cosmolkit.BioStrand attribute) hbond_atom2 (cosmolkit.BioStrand attribute) HE (cosmolkit.Element attribute) head_crossing_bonds() (cosmolkit.SubstanceGroup method) height (cosmolkit.BatchImageParams property) Helices (cosmolkit.BioMmcifReadStage attribute) helices() (cosmolkit.BioStructure method) Helix27 (cosmolkit.BioHelixClass attribute) HelixPolyProlineNone (cosmolkit.BioHelixClass attribute) HEM (cosmolkit.ResidueCode attribute) hetero_hydrogen() (cosmolkit.TautomerScore method) HEXTUPLE (cosmolkit.BondOrder attribute) HEZ (cosmolkit.ResidueCode attribute) HF (cosmolkit.Element attribute) HG (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) HIC (cosmolkit.ResidueCode attribute) HIS (cosmolkit.ResidueCode attribute) HO (cosmolkit.Element attribute) HOH (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueInfoKind attribute) HS (cosmolkit.Element attribute) HTG (cosmolkit.ResidueCode attribute) HTO (cosmolkit.ResidueCode attribute) Hybridization (class in cosmolkit) (None attribute) hybridization() (cosmolkit.Atom method) Hybridization.Other (Hybridization attribute) Hybridization.S (Hybridization attribute) Hybridization.Sp (Hybridization attribute) Hybridization.Sp2 (Hybridization attribute) Hybridization.Sp2d (Hybridization attribute) Hybridization.Sp3 (Hybridization attribute) Hybridization.Sp3d (Hybridization attribute) Hybridization.Sp3d2 (Hybridization attribute) Hybridization.Unspecified (Hybridization attribute) Hydrog (cosmolkit.BioConnectionKind attribute) HYDROGEN (cosmolkit.BondOrder attribute) HYDROGEN_BONDS (cosmolkit.CxSmilesFields attribute) hydrogen_contribution (cosmolkit.LabuteAsaContributions attribute) hydrogen_count() (cosmolkit.ResidueInfo method) HydrogenError HydrogenError() (class) HydrogenError.[Symbol․dispose]() (HydrogenError method) HydrogenError.cause (HydrogenError attribute) HydrogenError.domain (HydrogenError attribute) HydrogenError.free() (HydrogenError method) HydrogenError.kind (HydrogenError attribute) HydrogenError.message (HydrogenError attribute) HYP (cosmolkit.ResidueCode attribute) I I (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) IAS (cosmolkit.ResidueCode attribute) ICI (cosmolkit.ResidueCode attribute) ICT (cosmolkit.ResidueCode attribute) id (cosmolkit.BioDiffractionInfo attribute) (cosmolkit.BioExperimentalCrystalInfo attribute) (cosmolkit.BioNcsOperator attribute) (cosmolkit.BioRefinementInfo attribute) (cosmolkit.BioTlsGroup attribute) (cosmolkit.ReactionCoordinateSelection attribute) id() (cosmolkit.Atom method) (cosmolkit.BioAtomRow method) (cosmolkit.BioChainRow method) (cosmolkit.BioEntityRow method) (cosmolkit.BioModelRow method) (cosmolkit.BioResidueRow method) (cosmolkit.Bond method) (cosmolkit.Conformer2D method) (cosmolkit.Conformer3D method) (cosmolkit.ProteinAtomRef method) (cosmolkit.ProteinChainRef method) (cosmolkit.ProteinResidueRef method) (cosmolkit.QueryAtom method) (cosmolkit.StereoGroup method) (cosmolkit.SubstanceGroup method) id_code (cosmolkit.BioEntityDbRef attribute) IDO (cosmolkit.ResidueCode attribute) Ignore (cosmolkit.CoordinateZPolicy attribute) ignore_atom_map_numbers (cosmolkit.SmilesWriteParams property) ignore_atoms (cosmolkit.AtomPairFingerprintParams property) (cosmolkit.LegacyTopologicalTorsionParams property) (cosmolkit.MorganCallParams property) (cosmolkit.MorganFingerprintParams property) (cosmolkit.TopologicalTorsionCallParams property) (cosmolkit.TopologicalTorsionFingerprintParams property) ignore_hydrogens (cosmolkit.AllConformerRmsdParameters property) (cosmolkit.BestAlignmentParameters property) ignore_interfragment_interactions (cosmolkit.MmffConformerOptimizationParams property) (cosmolkit.MmffEvaluationParams property) (cosmolkit.MmffForceFieldParams property) (cosmolkit.MmffOptimizationParams property) (cosmolkit.UffConformerOptimizationParams property) (cosmolkit.UffEvaluationParams property) (cosmolkit.UffForceFieldParams property) (cosmolkit.UffOptimizationParams property) ignore_smoothing_failures (cosmolkit.EmbedParams property) ignore_ter (cosmolkit.BioPdbReadParams property) ILE (cosmolkit.ResidueCode attribute) impl_fn (cosmolkit.MoleculeOpSpec attribute) implicit_hydrogens() (cosmolkit.Atom method) (cosmolkit.AtomMetadata method) implicit_properties() (cosmolkit.Reaction method) IN (cosmolkit.Element attribute) inchi_to_key() (in module cosmolkit) InchiError InchiError() (class) InchiError.[Symbol․dispose]() (InchiError method) InchiError.detail (InchiError attribute) InchiError.domain (InchiError attribute) InchiError.free() (InchiError method) InchiError.kind (InchiError attribute) InchiError.message (InchiError attribute) InchiError.operation (InchiError attribute) InchiErrorKind (class in cosmolkit) (None attribute) InchiErrorKind.AllocationFailed (InchiErrorKind attribute) InchiErrorKind.InvalidInput (InchiErrorKind attribute) InchiErrorKind.InvalidSourceOutput (InchiErrorKind attribute) InchiErrorKind.SanitizeFailed (InchiErrorKind attribute) InchiErrorKind.SourcePort (InchiErrorKind attribute) InchiErrorKind.Toolkit (InchiErrorKind attribute) InchiErrorKind.UnsupportedState (InchiErrorKind attribute) InchiReadParams (class in cosmolkit) InchiReadParams() (class) InchiReadParams.[Symbol․dispose]() (InchiReadParams method) InchiReadParams.free() (InchiReadParams method) InchiReadParams.removeHs (InchiReadParams attribute) InchiReadParams.sanitize (InchiReadParams attribute) InchiReadParams.setRemoveHs() (InchiReadParams method) InchiReadParams.setSanitize() (InchiReadParams method) InchiReadParamsOptions() (interface) InchiReadParamsOptions.removeHs? (InchiReadParamsOptions attribute) InchiReadParamsOptions.sanitize? (InchiReadParamsOptions attribute) inchiToKey() (built-in function) InchiWriteParams (class in cosmolkit) InchiWriteParams() (class) InchiWriteParams.[Symbol․dispose]() (InchiWriteParams method) InchiWriteParams.free() (InchiWriteParams method) InchiWriteParams.options (InchiWriteParams attribute) InchiWriteParams.setOptions() (InchiWriteParams method) InchiWriteParamsOptions() (interface) InchiWriteParamsOptions.options? (InchiWriteParamsOptions attribute) include_atom_maps (cosmolkit.SmartsWriteParams property) include_chirality (cosmolkit.AtomPairAtomInvariantsGenerator property) (cosmolkit.AtomPairParams property) (cosmolkit.LegacyTopologicalTorsionParams property) (cosmolkit.MorganBondInvariantsGenerator property) (cosmolkit.MorganParams property) (cosmolkit.MorganSettings attribute) (cosmolkit.TopologicalTorsionParams property) (cosmolkit.TopologicalTorsionSettings attribute) include_coordinates (cosmolkit.MolBlockWriteParams property) include_cx (cosmolkit.ReactionWriteParams property) include_dative_bonds (cosmolkit.ReactionWriteParams property) (cosmolkit.RingSearchParams property) (cosmolkit.SmartsWriteParams property) (cosmolkit.SmilesWriteParams property) include_hydrogen_bonds (cosmolkit.RingSearchParams property) include_redundant_environments (cosmolkit.MorganParams property) (cosmolkit.MorganSettings attribute) include_ring_membership (cosmolkit.MorganParams property) include_stereo (cosmolkit.MolBlockWriteParams property) index (cosmolkit.PotentialStereoCenter attribute) index() (cosmolkit.BatchError method) (cosmolkit.SdfRecord method) (cosmolkit.SdfRecordMetadata method) (cosmolkit.SubstanceGroupId method) info (cosmolkit.BioStructureSourceState attribute) info() (cosmolkit.BioResidueRow method) (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueIdentity method) info_string() (cosmolkit.AtomPairAtomInvariantsGenerator method) (cosmolkit.AtomPairParams method) (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.MorganParams method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) (cosmolkit.TopologicalTorsionParams method) initial_seed (cosmolkit.McsParameters property) Initialization (cosmolkit.MolecularForceFieldErrorKind attribute) InitOutput() (interface) InitOutput.__externref_drop_slice() (InitOutput method) InitOutput.__externref_table_alloc() (InitOutput method) InitOutput.__externref_table_dealloc() (InitOutput method) InitOutput.__wbg_addhsparams_free() (InitOutput method) InitOutput.__wbg_alignmentatommap_free() (InitOutput method) InitOutput.__wbg_alignmenterror_free() (InitOutput method) InitOutput.__wbg_alignmentparameters_free() (InitOutput method) InitOutput.__wbg_alignmentresult_free() (InitOutput method) InitOutput.__wbg_alignmenttransform_free() (InitOutput method) InitOutput.__wbg_allconformerrmsdparameters_free() (InitOutput method) InitOutput.__wbg_altloclabel_free() (InitOutput method) InitOutput.__wbg_altlocrequest_free() (InitOutput method) InitOutput.__wbg_aromaticityerror_free() (InitOutput method) InitOutput.__wbg_aromaticityparams_free() (InitOutput method) InitOutput.__wbg_atom_free() (InitOutput method) InitOutput.__wbg_atomaddress_free() (InitOutput method) InitOutput.__wbg_atomcodeexplanation_free() (InitOutput method) InitOutput.__wbg_atomcodeexplanationerror_free() (InitOutput method) InitOutput.__wbg_atommetadata_free() (InitOutput method) InitOutput.__wbg_atomname_free() (InitOutput method) InitOutput.__wbg_atompairatomcoderesult_free() (InitOutput method) InitOutput.__wbg_atompairatominvariantsgenerator_free() (InitOutput method) InitOutput.__wbg_atompairfingerprintparams_free() (InitOutput method) InitOutput.__wbg_atompairparams_free() (InitOutput method) InitOutput.__wbg_atompairreaderror_free() (InitOutput method) InitOutput.__wbg_atompairsparameters_free() (InitOutput method) InitOutput.__wbg_atompositionparams_free() (InitOutput method) InitOutput.__wbg_atomsourceids_free() (InitOutput method) InitOutput.__wbg_atomspec_free() (InitOutput method) InitOutput.__wbg_avalonengineerror_free() (InitOutput method) InitOutput.__wbg_avalonfingerprinterror_free() (InitOutput method) InitOutput.__wbg_avalonfingerprintflags_free() (InitOutput method) InitOutput.__wbg_avalonfingerprintparams_free() (InitOutput method) InitOutput.__wbg_batcherror_free() (InitOutput method) InitOutput.__wbg_batchexportparams_free() (InitOutput method) InitOutput.__wbg_batchexportreport_free() (InitOutput method) InitOutput.__wbg_batchfingerprintadditionaloutput_free() (InitOutput method) InitOutput.__wbg_batchfingerprintoutput_free() (InitOutput method) InitOutput.__wbg_batchfingerprintoutputerror_free() (InitOutput method) InitOutput.__wbg_batchimageerror_free() (InitOutput method) InitOutput.__wbg_batchimageparams_free() (InitOutput method) InitOutput.__wbg_batchparams_free() (InitOutput method) InitOutput.__wbg_batchqueryparams_free() (InitOutput method) InitOutput.__wbg_batchrecord_free() (InitOutput method) InitOutput.__wbg_batchvalidationerror_free() (InitOutput method) InitOutput.__wbg_bestalignmentparameters_free() (InitOutput method) InitOutput.__wbg_bioaltlocgroupid_free() (InitOutput method) InitOutput.__wbg_bioassembly_free() (InitOutput method) InitOutput.__wbg_bioassemblygenerator_free() (InitOutput method) InitOutput.__wbg_bioassemblyid_free() (InitOutput method) InitOutput.__wbg_bioassemblyoperator_free() (InitOutput method) InitOutput.__wbg_bioatomid_free() (InitOutput method) InitOutput.__wbg_bioatomrow_free() (InitOutput method) InitOutput.__wbg_biobasicrefinementinfo_free() (InitOutput method) InitOutput.__wbg_biochainid_free() (InitOutput method) InitOutput.__wbg_biochainrow_free() (InitOutput method) InitOutput.__wbg_biocispep_free() (InitOutput method) InitOutput.__wbg_bioconnection_free() (InitOutput method) InitOutput.__wbg_biocoordinateblock_free() (InitOutput method) InitOutput.__wbg_biocrystalcell_free() (InitOutput method) InitOutput.__wbg_biocrystalinfo_free() (InitOutput method) InitOutput.__wbg_biodiffractioninfo_free() (InitOutput method) InitOutput.__wbg_bioentitydbref_free() (InitOutput method) InitOutput.__wbg_bioentityid_free() (InitOutput method) InitOutput.__wbg_bioentityrow_free() (InitOutput method) InitOutput.__wbg_bioexperimentalcrystalinfo_free() (InitOutput method) InitOutput.__wbg_bioexperimentinfo_free() (InitOutput method) InitOutput.__wbg_biohelix_free() (InitOutput method) InitOutput.__wbg_biometadata_free() (InitOutput method) InitOutput.__wbg_biommcifreaderror_free() (InitOutput method) InitOutput.__wbg_biommcifwriteerror_free() (InitOutput method) InitOutput.__wbg_biommcifwriteparams_free() (InitOutput method) InitOutput.__wbg_biomodelid_free() (InitOutput method) InitOutput.__wbg_biomodelrow_free() (InitOutput method) InitOutput.__wbg_biomodres_free() (InitOutput method) InitOutput.__wbg_biomoleculeconversionerror_free() (InitOutput method) InitOutput.__wbg_biomoleculeerror_free() (InitOutput method) InitOutput.__wbg_biomoleculeparams_free() (InitOutput method) InitOutput.__wbg_bioncsoperator_free() (InitOutput method) InitOutput.__wbg_biooperationerror_free() (InitOutput method) InitOutput.__wbg_biopdbreaderror_free() (InitOutput method) InitOutput.__wbg_biopdbreadparams_free() (InitOutput method) InitOutput.__wbg_biopdbwriteerror_free() (InitOutput method) InitOutput.__wbg_biopdbwriteparams_free() (InitOutput method) InitOutput.__wbg_bioreaderror_free() (InitOutput method) InitOutput.__wbg_bioreadparams_free() (InitOutput method) InitOutput.__wbg_biorefinementinfo_free() (InitOutput method) InitOutput.__wbg_biorefinementrestraint_free() (InitOutput method) InitOutput.__wbg_bioreflectionsinfo_free() (InitOutput method) InitOutput.__wbg_bioresidueid_free() (InitOutput method) InitOutput.__wbg_bioresiduerow_free() (InitOutput method) InitOutput.__wbg_biorowchainerror_free() (InitOutput method) InitOutput.__wbg_biorowmodelerror_free() (InitOutput method) InitOutput.__wbg_biorowspan_free() (InitOutput method) InitOutput.__wbg_biorowtraverseerror_free() (InitOutput method) InitOutput.__wbg_bioselection_free() (InitOutput method) InitOutput.__wbg_bioselectioncopycause_free() (InitOutput method) InitOutput.__wbg_bioselectioncopyerror_free() (InitOutput method) InitOutput.__wbg_bioselectionmatcherror_free() (InitOutput method) InitOutput.__wbg_bioselectionparseerror_free() (InitOutput method) InitOutput.__wbg_biosheet_free() (InitOutput method) InitOutput.__wbg_biosiftsunpresidue_free() (InitOutput method) InitOutput.__wbg_biosoftwareitem_free() (InitOutput method) InitOutput.__wbg_biostrand_free() (InitOutput method) InitOutput.__wbg_biostructure_free() (InitOutput method) InitOutput.__wbg_biostructureerror_free() (InitOutput method) InitOutput.__wbg_biostructureparts_free() (InitOutput method) InitOutput.__wbg_biostructuresourcestate_free() (InitOutput method) InitOutput.__wbg_biotlsgroup_free() (InitOutput method) InitOutput.__wbg_biotlsselection_free() (InitOutput method) InitOutput.__wbg_biotransform_free() (InitOutput method) InitOutput.__wbg_bond_free() (InitOutput method) InitOutput.__wbg_bondspec_free() (InitOutput method) InitOutput.__wbg_chainsourceids_free() (InitOutput method) InitOutput.__wbg_chemistryproblem_free() (InitOutput method) InitOutput.__wbg_chemistryproblemerror_free() (InitOutput method) InitOutput.__wbg_chemistryproblemreport_free() (InitOutput method) InitOutput.__wbg_cipdescriptorerror_free() (InitOutput method) InitOutput.__wbg_ciplabelererror_free() (InitOutput method) InitOutput.__wbg_ciplabeloptions_free() (InitOutput method) InitOutput.__wbg_ciprankerror_free() (InitOutput method) InitOutput.__wbg_compiledquery_free() (InitOutput method) InitOutput.__wbg_conformer2d_free() (InitOutput method) InitOutput.__wbg_conformer3d_free() (InitOutput method) InitOutput.__wbg_conformeralignmentparameters_free() (InitOutput method) InitOutput.__wbg_conformeralignmentreport_free() (InitOutput method) InitOutput.__wbg_conformererror_free() (InitOutput method) InitOutput.__wbg_conformerrmsd_free() (InitOutput method) InitOutput.__wbg_conformerrunerror_free() (InitOutput method) InitOutput.__wbg_coordinate2derror_free() (InitOutput method) InitOutput.__wbg_coordinate2dinputparams_free() (InitOutput method) InitOutput.__wbg_coordinate2dlayouterror_free() (InitOutput method) InitOutput.__wbg_coordinate2dparams_free() (InitOutput method) InitOutput.__wbg_coordinate2dtemplateerror_free() (InitOutput method) InitOutput.__wbg_coordinate3dinputparams_free() (InitOutput method) InitOutput.__wbg_coordinate3dreaderror_free() (InitOutput method) InitOutput.__wbg_coordinateblock_free() (InitOutput method) InitOutput.__wbg_coordinateinputerror_free() (InitOutput method) InitOutput.__wbg_coordinatermsdparameters_free() (InitOutput method) InitOutput.__wbg_coordinatezpolicy_free() (InitOutput method) InitOutput.__wbg_crippentotals_free() (InitOutput method) InitOutput.__wbg_cxcoordinateselection_free() (InitOutput method) InitOutput.__wbg_cxsmilesfields_free() (InitOutput method) InitOutput.__wbg_cxsmileswriteparams_free() (InitOutput method) InitOutput.__wbg_densematrix_free() (InitOutput method) InitOutput.__wbg_descriptorerror_free() (InitOutput method) InitOutput.__wbg_descriptorreaderror_free() (InitOutput method) InitOutput.__wbg_distancematrix3dparams_free() (InitOutput method) InitOutput.__wbg_distancematrixparams_free() (InitOutput method) InitOutput.__wbg_drawingerror_free() (InitOutput method) InitOutput.__wbg_drawingwriteerror_free() (InitOutput method) InitOutput.__wbg_element_free() (InitOutput method) InitOutput.__wbg_elementinfo_free() (InitOutput method) InitOutput.__wbg_embedmoleculeresult_free() (InitOutput method) InitOutput.__wbg_embedmultipleconfsresult_free() (InitOutput method) InitOutput.__wbg_embedparams_free() (InitOutput method) InitOutput.__wbg_entitysourceids_free() (InitOutput method) InitOutput.__wbg_enumerationerror_free() (InitOutput method) InitOutput.__wbg_enumerationrunerror_free() (InitOutput method) InitOutput.__wbg_featurespec_free() (InitOutput method) InitOutput.__wbg_featurespeciter_free() (InitOutput method) InitOutput.__wbg_fingerprint_free() (InitOutput method) InitOutput.__wbg_fingerprintadditionaloutput_free() (InitOutput method) InitOutput.__wbg_fingerprinterror_free() (InitOutput method) InitOutput.__wbg_fingerprintjsonerror_free() (InitOutput method) InitOutput.__wbg_fingerprintpreparationerror_free() (InitOutput method) InitOutput.__wbg_forcefieldenergygradient_free() (InitOutput method) InitOutput.__wbg_forcefielderror_free() (InitOutput method) InitOutput.__wbg_forcefieldminimizeoutcome_free() (InitOutput method) InitOutput.__wbg_forcefieldminimizeparams_free() (InitOutput method) InitOutput.__wbg_fragmentcxsmileswriteparams_free() (InitOutput method) InitOutput.__wbg_fragmentsmileswriteparams_free() (InitOutput method) InitOutput.__wbg_functionstatus_free() (InitOutput method) InitOutput.__wbg_hydrogenerror_free() (InitOutput method) InitOutput.__wbg_inchierror_free() (InitOutput method) InitOutput.__wbg_inchireadparams_free() (InitOutput method) InitOutput.__wbg_inchiwriteparams_free() (InitOutput method) InitOutput.__wbg_kekulizeerror_free() (InitOutput method) InitOutput.__wbg_kekulizeparams_free() (InitOutput method) InitOutput.__wbg_labuteasacontributions_free() (InitOutput method) InitOutput.__wbg_layeredfingerprinterror_free() (InitOutput method) InitOutput.__wbg_layeredfingerprintlayers_free() (InitOutput method) InitOutput.__wbg_layeredfingerprintparams_free() (InitOutput method) InitOutput.__wbg_layeredfingerprintresult_free() (InitOutput method) InitOutput.__wbg_legacytopologicaltorsionparams_free() (InitOutput method) InitOutput.__wbg_ligandref_free() (InitOutput method) InitOutput.__wbg_maccsfingerprinterror_free() (InitOutput method) InitOutput.__wbg_maccsfingerprintparams_free() (InitOutput method) InitOutput.__wbg_matcherror_free() (InitOutput method) InitOutput.__wbg_matchresult_free() (InitOutput method) InitOutput.__wbg_matrixerror_free() (InitOutput method) InitOutput.__wbg_mcsatomcompareparameters_free() (InitOutput method) InitOutput.__wbg_mcsbondcompareparameters_free() (InitOutput method) InitOutput.__wbg_mcserror_free() (InitOutput method) InitOutput.__wbg_mcsparameters_free() (InitOutput method) InitOutput.__wbg_mcsresult_free() (InitOutput method) InitOutput.__wbg_mmffatomproperties_free() (InitOutput method) InitOutput.__wbg_mmffconformeroptimizationparams_free() (InitOutput method) InitOutput.__wbg_mmffenergygradient_free() (InitOutput method) InitOutput.__wbg_mmffevaluationparams_free() (InitOutput method) InitOutput.__wbg_mmffforcefielderror_free() (InitOutput method) InitOutput.__wbg_mmffforcefieldparams_free() (InitOutput method) InitOutput.__wbg_mmffmolpropertieserror_free() (InitOutput method) InitOutput.__wbg_mmffoptimizationerror_free() (InitOutput method) InitOutput.__wbg_mmffoptimizationparams_free() (InitOutput method) InitOutput.__wbg_mmffoptimizemoleculeconfresult_free() (InitOutput method) InitOutput.__wbg_mmffoptimizemoleculeconfsresult_free() (InitOutput method) InitOutput.__wbg_mmffoptimizemoleculeresult_free() (InitOutput method) InitOutput.__wbg_mmffproperties_free() (InitOutput method) InitOutput.__wbg_mmffpropertiesparams_free() (InitOutput method) InitOutput.__wbg_mol2posterror_free() (InitOutput method) InitOutput.__wbg_mol2readerror_free() (InitOutput method) InitOutput.__wbg_mol2readparams_free() (InitOutput method) InitOutput.__wbg_molblockwriteparams_free() (InitOutput method) InitOutput.__wbg_molcoordinateselection_free() (InitOutput method) InitOutput.__wbg_molecularforcefield_free() (InitOutput method) InitOutput.__wbg_molecularioerror_free() (InitOutput method) InitOutput.__wbg_molecule_free() (InitOutput method) InitOutput.__wbg_moleculebatch_free() (InitOutput method) InitOutput.__wbg_moleculebuilder_free() (InitOutput method) InitOutput.__wbg_moleculehasherror_free() (InitOutput method) InitOutput.__wbg_moleculeopspec_free() (InitOutput method) InitOutput.__wbg_moleculeproperties_free() (InitOutput method) InitOutput.__wbg_molwriteerror_free() (InitOutput method) InitOutput.__wbg_morganatominvariantsgenerator_free() (InitOutput method) InitOutput.__wbg_morganbondinvariantsgenerator_free() (InitOutput method) InitOutput.__wbg_morgancallparams_free() (InitOutput method) InitOutput.__wbg_morganfingerprintgenerator_free() (InitOutput method) InitOutput.__wbg_morganfingerprintparams_free() (InitOutput method) InitOutput.__wbg_morganinvariants_free() (InitOutput method) InitOutput.__wbg_morganparams_free() (InitOutput method) InitOutput.__wbg_morganreaderror_free() (InitOutput method) InitOutput.__wbg_morgansettings_free() (InitOutput method) InitOutput.__wbg_operationerror_free() (InitOutput method) InitOutput.__wbg_operationinvariantentry_free() (InitOutput method) InitOutput.__wbg_paritymatrixentry_free() (InitOutput method) InitOutput.__wbg_patternfingerprinterror_free() (InitOutput method) InitOutput.__wbg_patternfingerprintparams_free() (InitOutput method) InitOutput.__wbg_pdbatomserial_free() (InitOutput method) InitOutput.__wbg_pdbchainid_free() (InitOutput method) InitOutput.__wbg_pdbseqid_free() (InitOutput method) InitOutput.__wbg_potentialstereocenter_free() (InitOutput method) InitOutput.__wbg_potentialstereoerror_free() (InitOutput method) InitOutput.__wbg_potentialstereoinfo_free() (InitOutput method) InitOutput.__wbg_potentialstereoparams_free() (InitOutput method) InitOutput.__wbg_potentialstereoresult_free() (InitOutput method) InitOutput.__wbg_propertystringerror_free() (InitOutput method) InitOutput.__wbg_propertyvalue_free() (InitOutput method) InitOutput.__wbg_propertyvalueerror_free() (InitOutput method) InitOutput.__wbg_protein_free() (InitOutput method) InitOutput.__wbg_proteinatomiter_free() (InitOutput method) InitOutput.__wbg_proteinatomref_free() (InitOutput method) InitOutput.__wbg_proteinchainiter_free() (InitOutput method) InitOutput.__wbg_proteinchainref_free() (InitOutput method) InitOutput.__wbg_proteinprojectionerror_free() (InitOutput method) InitOutput.__wbg_proteinreaderror_free() (InitOutput method) InitOutput.__wbg_proteinresidueiter_free() (InitOutput method) InitOutput.__wbg_proteinresidueref_free() (InitOutput method) InitOutput.__wbg_proteinselectionsummary_free() (InitOutput method) InitOutput.__wbg_queryatom_free() (InitOutput method) InitOutput.__wbg_querycompileerror_free() (InitOutput method) InitOutput.__wbg_querygraph_free() (InitOutput method) InitOutput.__wbg_randomsmileswriteparams_free() (InitOutput method) InitOutput.__wbg_reaction_free() (InitOutput method) InitOutput.__wbg_reactionapplyerror_free() (InitOutput method) InitOutput.__wbg_reactionapplyparams_free() (InitOutput method) InitOutput.__wbg_reactionapplyresult_free() (InitOutput method) InitOutput.__wbg_reactioncoordinateselection_free() (InitOutput method) InitOutput.__wbg_reactioninitializationerror_free() (InitOutput method) InitOutput.__wbg_reactionmodelerror_free() (InitOutput method) InitOutput.__wbg_reactionparseerror_free() (InitOutput method) InitOutput.__wbg_reactionparseparams_free() (InitOutput method) InitOutput.__wbg_reactionproducterror_free() (InitOutput method) InitOutput.__wbg_reactionrunerror_free() (InitOutput method) InitOutput.__wbg_reactionrunparams_free() (InitOutput method) InitOutput.__wbg_reactionsinglerunparams_free() (InitOutput method) InitOutput.__wbg_reactiontemplateremoval_free() (InitOutput method) InitOutput.__wbg_reactiontemplateremovalparams_free() (InitOutput method) InitOutput.__wbg_reactionvalidationerror_free() (InitOutput method) InitOutput.__wbg_reactionvalidationissue_free() (InitOutput method) InitOutput.__wbg_reactionvalidationparams_free() (InitOutput method) InitOutput.__wbg_reactionvalidationreport_free() (InitOutput method) InitOutput.__wbg_reactionwriteerror_free() (InitOutput method) InitOutput.__wbg_reactionwriteparams_free() (InitOutput method) InitOutput.__wbg_removehsparams_free() (InitOutput method) InitOutput.__wbg_replace3dcoordinatesparams_free() (InitOutput method) InitOutput.__wbg_residueaddress_free() (InitOutput method) InitOutput.__wbg_residuecodeparseerror_free() (InitOutput method) InitOutput.__wbg_residueidentity_free() (InitOutput method) InitOutput.__wbg_residueinfo_free() (InitOutput method) InitOutput.__wbg_residueinfokind_free() (InitOutput method) InitOutput.__wbg_residuename_free() (InitOutput method) InitOutput.__wbg_residuesequenceerror_free() (InitOutput method) InitOutput.__wbg_residuesourceids_free() (InitOutput method) InitOutput.__wbg_ringsearchparams_free() (InitOutput method) InitOutput.__wbg_ringstereorelation_free() (InitOutput method) InitOutput.__wbg_sanitizeerror_free() (InitOutput method) InitOutput.__wbg_sanitizeoperations_free() (InitOutput method) InitOutput.__wbg_sanitizeparams_free() (InitOutput method) InitOutput.__wbg_sdfbatchiterator_free() (InitOutput method) InitOutput.__wbg_sdfdataset_free() (InitOutput method) InitOutput.__wbg_sdfdatasetiterator_free() (InitOutput method) InitOutput.__wbg_sdferror_free() (InitOutput method) InitOutput.__wbg_sdfgraph_free() (InitOutput method) InitOutput.__wbg_sdfpropertylist_free() (InitOutput method) InitOutput.__wbg_sdfreader_free() (InitOutput method) InitOutput.__wbg_sdfreaderbatchiterator_free() (InitOutput method) InitOutput.__wbg_sdfreaderror_free() (InitOutput method) InitOutput.__wbg_sdfreadparams_free() (InitOutput method) InitOutput.__wbg_sdfrecord_free() (InitOutput method) InitOutput.__wbg_sdfrecordmetadata_free() (InitOutput method) InitOutput.__wbg_sdfrecordstream_free() (InitOutput method) InitOutput.__wbg_sgroupbracket_free() (InitOutput method) InitOutput.__wbg_sgroupcstate_free() (InitOutput method) InitOutput.__wbg_sgroupdisplay_free() (InitOutput method) InitOutput.__wbg_smartsparseerror_free() (InitOutput method) InitOutput.__wbg_smartsparseparams_free() (InitOutput method) InitOutput.__wbg_smartswriteerror_free() (InitOutput method) InitOutput.__wbg_smartswriteparams_free() (InitOutput method) InitOutput.__wbg_smileserror_free() (InitOutput method) InitOutput.__wbg_smilesparseparams_free() (InitOutput method) InitOutput.__wbg_smilesstereoerror_free() (InitOutput method) InitOutput.__wbg_smileswriteerror_free() (InitOutput method) InitOutput.__wbg_smileswriteparams_free() (InitOutput method) InitOutput.__wbg_sparsebitfingerprint_free() (InitOutput method) InitOutput.__wbg_sparsecountfingerprint32_free() (InitOutput method) InitOutput.__wbg_sparsecountfingerprint_free() (InitOutput method) InitOutput.__wbg_stereoerror_free() (InitOutput method) InitOutput.__wbg_stereogroup_free() (InitOutput method) InitOutput.__wbg_stereoisomeriterator_free() (InitOutput method) InitOutput.__wbg_stereoisomeroptions_free() (InitOutput method) InitOutput.__wbg_stereoisomerrandomsource_free() (InitOutput method) InitOutput.__wbg_stereoreaderror_free() (InitOutput method) InitOutput.__wbg_structuretagparams_free() (InitOutput method) InitOutput.__wbg_substancegroup_free() (InitOutput method) InitOutput.__wbg_substancegroupid_free() (InitOutput method) InitOutput.__wbg_substancegroupkind_free() (InitOutput method) InitOutput.__wbg_substructmatcherror_free() (InitOutput method) InitOutput.__wbg_substructmatchparams_free() (InitOutput method) InitOutput.__wbg_supportmatrixentry_free() (InitOutput method) InitOutput.__wbg_tautomercatalogerror_free() (InitOutput method) InitOutput.__wbg_tautomerenumeration_free() (InitOutput method) InitOutput.__wbg_tautomermoleculeview_free() (InitOutput method) InitOutput.__wbg_tautomerparams_free() (InitOutput method) InitOutput.__wbg_tautomerprogress_free() (InitOutput method) InitOutput.__wbg_tautomerrunerror_free() (InitOutput method) InitOutput.__wbg_tautomerscore_free() (InitOutput method) InitOutput.__wbg_tautomerscoreparams_free() (InitOutput method) InitOutput.__wbg_tautomerscoreterm_free() (InitOutput method) InitOutput.__wbg_templateattachment_free() (InitOutput method) InitOutput.__wbg_templateattachmentorder_free() (InitOutput method) InitOutput.__wbg_templateattachmentordererror_free() (InitOutput method) InitOutput.__wbg_tetrahedralstereo_free() (InitOutput method) InitOutput.__wbg_topologicalfingerprinterror_free() (InitOutput method) InitOutput.__wbg_topologicalfingerprintoutput_free() (InitOutput method) InitOutput.__wbg_topologicalfingerprintoutputrequest_free() (InitOutput method) InitOutput.__wbg_topologicalfingerprintparams_free() (InitOutput method) InitOutput.__wbg_topologicalfingerprintresult_free() (InitOutput method) InitOutput.__wbg_topologicaltorsioncallparams_free() (InitOutput method) InitOutput.__wbg_topologicaltorsionfingerprintgenerator_free() (InitOutput method) InitOutput.__wbg_topologicaltorsionfingerprintparams_free() (InitOutput method) InitOutput.__wbg_topologicaltorsionparams_free() (InitOutput method) InitOutput.__wbg_topologicaltorsionpathscoreerror_free() (InitOutput method) InitOutput.__wbg_topologicaltorsionreaderror_free() (InitOutput method) InitOutput.__wbg_topologicaltorsionsettings_free() (InitOutput method) InitOutput.__wbg_topologyblock_free() (InitOutput method) InitOutput.__wbg_transformerror_free() (InitOutput method) InitOutput.__wbg_uffconformeroptimizationparams_free() (InitOutput method) InitOutput.__wbg_uffconformeroptimizationresult_free() (InitOutput method) InitOutput.__wbg_uffconformerresult_free() (InitOutput method) InitOutput.__wbg_uffenergygradient_free() (InitOutput method) InitOutput.__wbg_uffevaluationparams_free() (InitOutput method) InitOutput.__wbg_uffforcefielderror_free() (InitOutput method) InitOutput.__wbg_uffforcefieldparams_free() (InitOutput method) InitOutput.__wbg_uffoptimizationerror_free() (InitOutput method) InitOutput.__wbg_uffoptimizationerrorkind_free() (InitOutput method) InitOutput.__wbg_uffoptimizationparams_free() (InitOutput method) InitOutput.__wbg_uffoptimizationresult_free() (InitOutput method) InitOutput.__wbg_uffparametererror_free() (InitOutput method) InitOutput.__wbg_uffparameterqueryerror_free() (InitOutput method) InitOutput.__wbg_valenceerror_free() (InitOutput method) InitOutput.__wbg_valenceparams_free() (InitOutput method) InitOutput.__wbg_xyzreaderror_free() (InitOutput method) InitOutput.__wbg_xyzwriteerror_free() (InitOutput method) InitOutput.__wbg_xyzwriteparams_free() (InitOutput method) InitOutput.__wbindgen_exn_store() (InitOutput method) InitOutput.__wbindgen_externrefs (InitOutput attribute) InitOutput.__wbindgen_free() (InitOutput method) InitOutput.__wbindgen_malloc() (InitOutput method) InitOutput.__wbindgen_realloc() (InitOutput method) InitOutput.__wbindgen_start() (InitOutput method) InitOutput.addhsparams_addCoords() (InitOutput method) InitOutput.addhsparams_addResidueInfo() (InitOutput method) InitOutput.addhsparams_explicitOnly() (InitOutput method) InitOutput.addhsparams_new() (InitOutput method) InitOutput.addhsparams_onlyOnAtoms() (InitOutput method) InitOutput.addhsparams_set_addCoords() (InitOutput method) InitOutput.addhsparams_set_addResidueInfo() (InitOutput method) InitOutput.addhsparams_set_explicitOnly() (InitOutput method) InitOutput.addhsparams_set_onlyOnAtoms() (InitOutput method) InitOutput.addhsparams_set_skipQueries() (InitOutput method) InitOutput.addhsparams_skipQueries() (InitOutput method) InitOutput.alignmentatommap_constructor() (InitOutput method) InitOutput.alignmentatommap_new() (InitOutput method) InitOutput.alignmentatommap_probeAtom() (InitOutput method) InitOutput.alignmentatommap_referenceAtom() (InitOutput method) InitOutput.alignmentatommap_set_probeAtom() (InitOutput method) InitOutput.alignmentatommap_set_referenceAtom() (InitOutput method) InitOutput.alignmenterror_cause() (InitOutput method) InitOutput.alignmenterror_domain() (InitOutput method) InitOutput.alignmenterror_kind() (InitOutput method) InitOutput.alignmenterror_message() (InitOutput method) InitOutput.alignmentparameters_atomMap() (InitOutput method) InitOutput.alignmentparameters_constructor() (InitOutput method) InitOutput.alignmentparameters_maxIterations() (InitOutput method) InitOutput.alignmentparameters_new() (InitOutput method) InitOutput.alignmentparameters_probeConformerId() (InitOutput method) InitOutput.alignmentparameters_referenceConformerId() (InitOutput method) InitOutput.alignmentparameters_reflect() (InitOutput method) InitOutput.alignmentparameters_set_atomMap() (InitOutput method) InitOutput.alignmentparameters_set_maxIterations() (InitOutput method) InitOutput.alignmentparameters_set_probeConformerId() (InitOutput method) InitOutput.alignmentparameters_set_referenceConformerId() (InitOutput method) InitOutput.alignmentparameters_set_reflect() (InitOutput method) InitOutput.alignmentparameters_set_weights() (InitOutput method) InitOutput.alignmentparameters_weights() (InitOutput method) InitOutput.alignmentresult_atomMap() (InitOutput method) InitOutput.alignmentresult_rmsd() (InitOutput method) InitOutput.alignmentresult_transform() (InitOutput method) InitOutput.alignmenttransform_matrix() (InitOutput method) InitOutput.allconformerrmsdparameters_atomMaps() (InitOutput method) InitOutput.allconformerrmsdparameters_constructor() (InitOutput method) InitOutput.allconformerrmsdparameters_ignoreHydrogens() (InitOutput method) InitOutput.allconformerrmsdparameters_maxMatches() (InitOutput method) InitOutput.allconformerrmsdparameters_new() (InitOutput method) InitOutput.allconformerrmsdparameters_numThreads() (InitOutput method) InitOutput.allconformerrmsdparameters_set_atomMaps() (InitOutput method) InitOutput.allconformerrmsdparameters_set_ignoreHydrogens() (InitOutput method) InitOutput.allconformerrmsdparameters_set_maxMatches() (InitOutput method) InitOutput.allconformerrmsdparameters_set_numThreads() (InitOutput method) InitOutput.allconformerrmsdparameters_set_symmetrizeConjugatedTerminalGroups() (InitOutput method) InitOutput.allconformerrmsdparameters_set_weights() (InitOutput method) InitOutput.allconformerrmsdparameters_symmetrizeConjugatedTerminalGroups() (InitOutput method) InitOutput.allconformerrmsdparameters_weights() (InitOutput method) InitOutput.altloclabel_new() (InitOutput method) InitOutput.altloclabel_value() (InitOutput method) InitOutput.altlocrequest_Any() (InitOutput method) InitOutput.altlocrequest_Exact() (InitOutput method) InitOutput.aromaticityerror_cause() (InitOutput method) InitOutput.aromaticityerror_domain() (InitOutput method) InitOutput.aromaticityerror_kind() (InitOutput method) InitOutput.aromaticityerror_message() (InitOutput method) InitOutput.aromaticityparams_model() (InitOutput method) InitOutput.aromaticityparams_new() (InitOutput method) InitOutput.aromaticityparams_set_model() (InitOutput method) InitOutput.atom_atomicNumber() (InitOutput method) InitOutput.atom_atomMap() (InitOutput method) InitOutput.atom_chiralTag() (InitOutput method) InitOutput.atom_chiralTagCode() (InitOutput method) InitOutput.atom_chiralTagName() (InitOutput method) InitOutput.atom_cipDescriptor() (InitOutput method) InitOutput.atom_cipNeighborOrder() (InitOutput method) InitOutput.atom_cipRank() (InitOutput method) InitOutput.atom_element() (InitOutput method) InitOutput.atom_explicitHydrogens() (InitOutput method) InitOutput.atom_formalCharge() (InitOutput method) InitOutput.atom_hybridization() (InitOutput method) InitOutput.atom_id() (InitOutput method) InitOutput.atom_isAromatic() (InitOutput method) InitOutput.atom_isotope() (InitOutput method) InitOutput.atom_noImplicit() (InitOutput method) InitOutput.atom_radicalElectrons() (InitOutput method) InitOutput.atom_templateAttachmentOrder() (InitOutput method) InitOutput.atomaddress_altloc() (InitOutput method) InitOutput.atomaddress_chainName() (InitOutput method) InitOutput.atomaddress_logicalAtomName() (InitOutput method) InitOutput.atomaddress_residue() (InitOutput method) InitOutput.atomcodeexplanation_branchCount() (InitOutput method) InitOutput.atomcodeexplanation_chirality() (InitOutput method) InitOutput.atomcodeexplanation_fromCode() (InitOutput method) InitOutput.atomcodeexplanation_piElectrons() (InitOutput method) InitOutput.atomcodeexplanation_symbol() (InitOutput method) InitOutput.atomcodeexplanationerror_cause() (InitOutput method) InitOutput.atomcodeexplanationerror_code() (InitOutput method) InitOutput.atomcodeexplanationerror_domain() (InitOutput method) InitOutput.atomcodeexplanationerror_kind() (InitOutput method) InitOutput.atomcodeexplanationerror_message() (InitOutput method) InitOutput.atommetadata_degree() (InitOutput method) InitOutput.atommetadata_explicitValence() (InitOutput method) InitOutput.atommetadata_implicitHydrogens() (InitOutput method) InitOutput.atommetadata_totalHydrogens() (InitOutput method) InitOutput.atommetadata_totalValence() (InitOutput method) InitOutput.atomname_asBytes() (InitOutput method) InitOutput.atomname_asStr() (InitOutput method) InitOutput.atomname_fromAscii() (InitOutput method) InitOutput.atompairatomcoderesult_code() (InitOutput method) InitOutput.atompairatomcoderesult_molecule() (InitOutput method) InitOutput.atompairatominvariantsgenerator_includeChirality() (InitOutput method) InitOutput.atompairatominvariantsgenerator_infoString() (InitOutput method) InitOutput.atompairatominvariantsgenerator_new() (InitOutput method) InitOutput.atompairatominvariantsgenerator_set_includeChirality() (InitOutput method) InitOutput.atompairatominvariantsgenerator_set_topologicalTorsionCorrection() (InitOutput method) InitOutput.atompairatominvariantsgenerator_toJson() (InitOutput method) InitOutput.atompairatominvariantsgenerator_topologicalTorsionCorrection() (InitOutput method) InitOutput.atompairfingerprintparams_atomInvariantsGenerator() (InitOutput method) InitOutput.atompairfingerprintparams_conformerId() (InitOutput method) InitOutput.atompairfingerprintparams_customAtomInvariants() (InitOutput method) InitOutput.atompairfingerprintparams_customBondInvariants() (InitOutput method) InitOutput.atompairfingerprintparams_fromAtoms() (InitOutput method) InitOutput.atompairfingerprintparams_generator() (InitOutput method) InitOutput.atompairfingerprintparams_ignoreAtoms() (InitOutput method) InitOutput.atompairfingerprintparams_new() (InitOutput method) InitOutput.atompairfingerprintparams_set_atomInvariantsGenerator() (InitOutput method) InitOutput.atompairfingerprintparams_set_conformerId() (InitOutput method) InitOutput.atompairfingerprintparams_set_customAtomInvariants() (InitOutput method) InitOutput.atompairfingerprintparams_set_customBondInvariants() (InitOutput method) InitOutput.atompairfingerprintparams_set_fromAtoms() (InitOutput method) InitOutput.atompairfingerprintparams_set_generator() (InitOutput method) InitOutput.atompairfingerprintparams_set_ignoreAtoms() (InitOutput method) InitOutput.atompairfingerprintparams_set_useLegacyStereoPerception() (InitOutput method) InitOutput.atompairfingerprintparams_useLegacyStereoPerception() (InitOutput method) InitOutput.atompairparams_bitsPerFeature() (InitOutput method) InitOutput.atompairparams_countBounds() (InitOutput method) InitOutput.atompairparams_countSimulation() (InitOutput method) InitOutput.atompairparams_fpSize() (InitOutput method) InitOutput.atompairparams_includeChirality() (InitOutput method) InitOutput.atompairparams_infoString() (InitOutput method) InitOutput.atompairparams_maxDistance() (InitOutput method) InitOutput.atompairparams_minDistance() (InitOutput method) InitOutput.atompairparams_new() (InitOutput method) InitOutput.atompairparams_set_bitsPerFeature() (InitOutput method) InitOutput.atompairparams_set_countBounds() (InitOutput method) InitOutput.atompairparams_set_countSimulation() (InitOutput method) InitOutput.atompairparams_set_fpSize() (InitOutput method) InitOutput.atompairparams_set_includeChirality() (InitOutput method) InitOutput.atompairparams_set_maxDistance() (InitOutput method) InitOutput.atompairparams_set_minDistance() (InitOutput method) InitOutput.atompairparams_set_use2d() (InitOutput method) InitOutput.atompairparams_toJson() (InitOutput method) InitOutput.atompairparams_use2d() (InitOutput method) InitOutput.atompairparams_withJson() (InitOutput method) InitOutput.atompairreaderror_cause() (InitOutput method) InitOutput.atompairreaderror_domain() (InitOutput method) InitOutput.atompairreaderror_kind() (InitOutput method) InitOutput.atompairreaderror_message() (InitOutput method) InitOutput.atompairsparameters_atomTypes() (InitOutput method) InitOutput.atompairsparameters_codeSize() (InitOutput method) InitOutput.atompairsparameters_maxPathLength() (InitOutput method) InitOutput.atompairsparameters_numAtomPairFingerprintBits() (InitOutput method) InitOutput.atompairsparameters_numBranchBits() (InitOutput method) InitOutput.atompairsparameters_numChiralBits() (InitOutput method) InitOutput.atompairsparameters_numPathBits() (InitOutput method) InitOutput.atompairsparameters_numPiBits() (InitOutput method) InitOutput.atompairsparameters_numTypeBits() (InitOutput method) InitOutput.atompairsparameters_version() (InitOutput method) InitOutput.atompositionparams_conformerId() (InitOutput method) InitOutput.atompositionparams_new() (InitOutput method) InitOutput.atompositionparams_set_conformerId() (InitOutput method) InitOutput.atomsourceids_serial() (InitOutput method) InitOutput.atomspec_new() (InitOutput method) InitOutput.atomspec_withAtomMap() (InitOutput method) InitOutput.atomspec_withExplicitHydrogens() (InitOutput method) InitOutput.atomspec_withFormalCharge() (InitOutput method) InitOutput.atomspec_withIsotope() (InitOutput method) InitOutput.atomspec_withNoImplicit() (InitOutput method) InitOutput.avalonengineerror_domain() (InitOutput method) InitOutput.avalonengineerror_kind() (InitOutput method) InitOutput.avalonengineerror_reason() (InitOutput method) InitOutput.avalonfingerprinterror_cause() (InitOutput method) InitOutput.avalonfingerprinterror_domain() (InitOutput method) InitOutput.avalonfingerprinterror_kind() (InitOutput method) InitOutput.avalonfingerprinterror_message() (InitOutput method) InitOutput.avalonfingerprintflags_bits() (InitOutput method) InitOutput.avalonfingerprintflags_fromBitsRetain() (InitOutput method) InitOutput.avalonfingerprintflags_toString() (InitOutput method) InitOutput.avalonfingerprintparams_bitFlags() (InitOutput method) InitOutput.avalonfingerprintparams_isQuery() (InitOutput method) InitOutput.avalonfingerprintparams_nBits() (InitOutput method) InitOutput.avalonfingerprintparams_new() (InitOutput method) InitOutput.avalonfingerprintparams_set_bitFlags() (InitOutput method) InitOutput.avalonfingerprintparams_set_isQuery() (InitOutput method) InitOutput.avalonfingerprintparams_set_nBits() (InitOutput method) InitOutput.avalonfingerprintparams_toString() (InitOutput method) InitOutput.batcherror_asDict() (InitOutput method) InitOutput.batcherror_cause() (InitOutput method) InitOutput.batcherror_index() (InitOutput method) InitOutput.batcherror_message() (InitOutput method) InitOutput.batcherror_operation() (InitOutput method) InitOutput.batchexportparams_errors() (InitOutput method) InitOutput.batchexportparams_format() (InitOutput method) InitOutput.batchexportparams_new() (InitOutput method) InitOutput.batchexportparams_nJobs() (InitOutput method) InitOutput.batchexportparams_progressBar() (InitOutput method) InitOutput.batchexportparams_set_errors() (InitOutput method) InitOutput.batchexportparams_set_format() (InitOutput method) InitOutput.batchexportparams_set_nJobs() (InitOutput method) InitOutput.batchexportparams_set_progressBar() (InitOutput method) InitOutput.batchexportreport_errors() (InitOutput method) InitOutput.batchexportreport_failed() (InitOutput method) InitOutput.batchexportreport_success() (InitOutput method) InitOutput.batchexportreport_total() (InitOutput method) InitOutput.batchexportreport_writeReport() (InitOutput method) InitOutput.batchexportreport_written() (InitOutput method) InitOutput.batchfingerprintadditionaloutput_atomCounts() (InitOutput method) InitOutput.batchfingerprintadditionaloutput_atomsPerBit() (InitOutput method) InitOutput.batchfingerprintadditionaloutput_atomToBits() (InitOutput method) InitOutput.batchfingerprintadditionaloutput_bitInfoMap() (InitOutput method) InitOutput.batchfingerprintadditionaloutput_bitPaths() (InitOutput method) InitOutput.batchfingerprintoutput_additionalOutput() (InitOutput method) InitOutput.batchfingerprintoutput_fingerprint() (InitOutput method) InitOutput.batchfingerprintoutputerror_cause() (InitOutput method) InitOutput.batchfingerprintoutputerror_domain() (InitOutput method) InitOutput.batchfingerprintoutputerror_kind() (InitOutput method) InitOutput.batchfingerprintoutputerror_message() (InitOutput method) InitOutput.batchimageerror_cause() (InitOutput method) InitOutput.batchimageerror_domain() (InitOutput method) InitOutput.batchimageerror_kind() (InitOutput method) InitOutput.batchimageerror_message() (InitOutput method) InitOutput.batchimageparams_execution() (InitOutput method) InitOutput.batchimageparams_filenames() (InitOutput method) InitOutput.batchimageparams_format() (InitOutput method) InitOutput.batchimageparams_height() (InitOutput method) InitOutput.batchimageparams_new() (InitOutput method) InitOutput.batchimageparams_reportPath() (InitOutput method) InitOutput.batchimageparams_set_execution() (InitOutput method) InitOutput.batchimageparams_set_filenames() (InitOutput method) InitOutput.batchimageparams_set_format() (InitOutput method) InitOutput.batchimageparams_set_height() (InitOutput method) InitOutput.batchimageparams_set_reportPath() (InitOutput method) InitOutput.batchimageparams_set_width() (InitOutput method) InitOutput.batchimageparams_width() (InitOutput method) InitOutput.batchparams_errors() (InitOutput method) InitOutput.batchparams_new() (InitOutput method) InitOutput.batchparams_nJobs() (InitOutput method) InitOutput.batchparams_progressBar() (InitOutput method) InitOutput.batchparams_set_errors() (InitOutput method) InitOutput.batchparams_set_nJobs() (InitOutput method) InitOutput.batchparams_set_progressBar() (InitOutput method) InitOutput.batchqueryparams_new() (InitOutput method) InitOutput.batchqueryparams_nJobs() (InitOutput method) InitOutput.batchqueryparams_progressBar() (InitOutput method) InitOutput.batchqueryparams_progressCallback() (InitOutput method) InitOutput.batchqueryparams_set_nJobs() (InitOutput method) InitOutput.batchqueryparams_set_progressBar() (InitOutput method) InitOutput.batchqueryparams_set_progressCallback() (InitOutput method) InitOutput.batchrecord_error() (InitOutput method) InitOutput.batchrecord_errorValue() (InitOutput method) InitOutput.batchrecord_molecule() (InitOutput method) InitOutput.batchrecord_moleculeValue() (InitOutput method) InitOutput.batchvalidationerror_cause() (InitOutput method) InitOutput.batchvalidationerror_domain() (InitOutput method) InitOutput.batchvalidationerror_errors() (InitOutput method) InitOutput.batchvalidationerror_kind() (InitOutput method) InitOutput.batchvalidationerror_message() (InitOutput method) InitOutput.batchvalidationerror_reason() (InitOutput method) InitOutput.batchvalidationerror_recordErrors() (InitOutput method) InitOutput.bestalignmentparameters_atomMaps() (InitOutput method) InitOutput.bestalignmentparameters_constructor() (InitOutput method) InitOutput.bestalignmentparameters_ignoreHydrogens() (InitOutput method) InitOutput.bestalignmentparameters_maxIterations() (InitOutput method) InitOutput.bestalignmentparameters_maxMatches() (InitOutput method) InitOutput.bestalignmentparameters_new() (InitOutput method) InitOutput.bestalignmentparameters_numThreads() (InitOutput method) InitOutput.bestalignmentparameters_probeConformerId() (InitOutput method) InitOutput.bestalignmentparameters_referenceConformerId() (InitOutput method) InitOutput.bestalignmentparameters_reflect() (InitOutput method) InitOutput.bestalignmentparameters_set_atomMaps() (InitOutput method) InitOutput.bestalignmentparameters_set_ignoreHydrogens() (InitOutput method) InitOutput.bestalignmentparameters_set_maxIterations() (InitOutput method) InitOutput.bestalignmentparameters_set_maxMatches() (InitOutput method) InitOutput.bestalignmentparameters_set_numThreads() (InitOutput method) InitOutput.bestalignmentparameters_set_probeConformerId() (InitOutput method) InitOutput.bestalignmentparameters_set_referenceConformerId() (InitOutput method) InitOutput.bestalignmentparameters_set_reflect() (InitOutput method) InitOutput.bestalignmentparameters_set_symmetrizeConjugatedTerminalGroups() (InitOutput method) InitOutput.bestalignmentparameters_set_weights() (InitOutput method) InitOutput.bestalignmentparameters_symmetrizeConjugatedTerminalGroups() (InitOutput method) InitOutput.bestalignmentparameters_weights() (InitOutput method) InitOutput.bioaltlocgroupid_index() (InitOutput method) InitOutput.bioaltlocgroupid_new() (InitOutput method) InitOutput.bioaltlocgroupid_value() (InitOutput method) InitOutput.bioassembly_authorDetermined() (InitOutput method) InitOutput.bioassembly_buriedSurfaceArea() (InitOutput method) InitOutput.bioassembly_generators() (InitOutput method) InitOutput.bioassembly_name() (InitOutput method) InitOutput.bioassembly_oligomericCount() (InitOutput method) InitOutput.bioassembly_oligomericDetails() (InitOutput method) InitOutput.bioassembly_softwareDetermined() (InitOutput method) InitOutput.bioassembly_softwareName() (InitOutput method) InitOutput.bioassembly_solventFreeEnergyChange() (InitOutput method) InitOutput.bioassembly_specialKind() (InitOutput method) InitOutput.bioassembly_surfaceArea() (InitOutput method) InitOutput.bioassemblygenerator_chains() (InitOutput method) InitOutput.bioassemblygenerator_operators() (InitOutput method) InitOutput.bioassemblygenerator_subchains() (InitOutput method) InitOutput.bioassemblyid_index() (InitOutput method) InitOutput.bioassemblyid_new() (InitOutput method) InitOutput.bioassemblyid_value() (InitOutput method) InitOutput.bioassemblyoperator_name() (InitOutput method) InitOutput.bioassemblyoperator_operatorType() (InitOutput method) InitOutput.bioassemblyoperator_transform() (InitOutput method) InitOutput.bioatomid_index() (InitOutput method) InitOutput.bioatomid_new() (InitOutput method) InitOutput.bioatomid_value() (InitOutput method) InitOutput.bioatomrow_altloc() (InitOutput method) InitOutput.bioatomrow_bIso() (InitOutput method) InitOutput.bioatomrow_element() (InitOutput method) InitOutput.bioatomrow_elementSymbol() (InitOutput method) InitOutput.bioatomrow_formalCharge() (InitOutput method) InitOutput.bioatomrow_id() (InitOutput method) InitOutput.bioatomrow_name() (InitOutput method) InitOutput.bioatomrow_occupancy() (InitOutput method) InitOutput.bioatomrow_position() (InitOutput method) InitOutput.bioatomrow_residueId() (InitOutput method) InitOutput.bioatomrow_source() (InitOutput method) InitOutput.biobasicrefinementinfo_ccFoFcFree() (InitOutput method) InitOutput.biobasicrefinementinfo_ccFoFcWork() (InitOutput method) InitOutput.biobasicrefinementinfo_ccIntensityFree() (InitOutput method) InitOutput.biobasicrefinementinfo_ccIntensityWork() (InitOutput method) InitOutput.biobasicrefinementinfo_completeness() (InitOutput method) InitOutput.biobasicrefinementinfo_fscFree() (InitOutput method) InitOutput.biobasicrefinementinfo_fscWork() (InitOutput method) InitOutput.biobasicrefinementinfo_rAll() (InitOutput method) InitOutput.biobasicrefinementinfo_reflectionCount() (InitOutput method) InitOutput.biobasicrefinementinfo_resolutionHigh() (InitOutput method) InitOutput.biobasicrefinementinfo_resolutionLow() (InitOutput method) InitOutput.biobasicrefinementinfo_rFree() (InitOutput method) InitOutput.biobasicrefinementinfo_rfreeSetCount() (InitOutput method) InitOutput.biobasicrefinementinfo_rWork() (InitOutput method) InitOutput.biobasicrefinementinfo_workSetCount() (InitOutput method) InitOutput.biochainid_index() (InitOutput method) InitOutput.biochainid_new() (InitOutput method) InitOutput.biochainid_value() (InitOutput method) InitOutput.biochainrow_atoms() (InitOutput method) InitOutput.biochainrow_entityId() (InitOutput method) InitOutput.biochainrow_id() (InitOutput method) InitOutput.biochainrow_kind() (InitOutput method) InitOutput.biochainrow_len() (InitOutput method) InitOutput.biochainrow_modelId() (InitOutput method) InitOutput.biochainrow_residues() (InitOutput method) InitOutput.biochainrow_source() (InitOutput method) InitOutput.biocispep_modelNum() (InitOutput method) InitOutput.biocispep_onlyAltloc() (InitOutput method) InitOutput.biocispep_partnerC() (InitOutput method) InitOutput.biocispep_partnerN() (InitOutput method) InitOutput.biocispep_reportedAngle() (InitOutput method) InitOutput.bioconnection_asu() (InitOutput method) InitOutput.bioconnection_kind() (InitOutput method) InitOutput.bioconnection_linkId() (InitOutput method) InitOutput.bioconnection_name() (InitOutput method) InitOutput.bioconnection_partner1() (InitOutput method) InitOutput.bioconnection_partner2() (InitOutput method) InitOutput.bioconnection_reportedDistance() (InitOutput method) InitOutput.bioconnection_reportedSym() (InitOutput method) InitOutput.biocoordinateblock_isEmpty() (InitOutput method) InitOutput.biocoordinateblock_len() (InitOutput method) InitOutput.biocoordinateblock_positions() (InitOutput method) InitOutput.biocrystalcell_a() (InitOutput method) InitOutput.biocrystalcell_alpha() (InitOutput method) InitOutput.biocrystalcell_b() (InitOutput method) InitOutput.biocrystalcell_beta() (InitOutput method) InitOutput.biocrystalcell_c() (InitOutput method) InitOutput.biocrystalcell_gamma() (InitOutput method) InitOutput.biocrystalinfo_cell() (InitOutput method) InitOutput.biocrystalinfo_csCount() (InitOutput method) InitOutput.biocrystalinfo_explicitMatrices() (InitOutput method) InitOutput.biocrystalinfo_fractional() (InitOutput method) InitOutput.biocrystalinfo_isCrystal() (InitOutput method) InitOutput.biocrystalinfo_orthogonal() (InitOutput method) InitOutput.biocrystalinfo_reciprocalCosines() (InitOutput method) InitOutput.biocrystalinfo_reciprocalLengths() (InitOutput method) InitOutput.biocrystalinfo_spaceGroupHm() (InitOutput method) InitOutput.biocrystalinfo_spaceGroupNumber() (InitOutput method) InitOutput.biocrystalinfo_symmetryImages() (InitOutput method) InitOutput.biocrystalinfo_volume() (InitOutput method) InitOutput.biocrystalinfo_zPdb() (InitOutput method) InitOutput.biodiffractioninfo_beamline() (InitOutput method) InitOutput.biodiffractioninfo_collectionDate() (InitOutput method) InitOutput.biodiffractioninfo_detector() (InitOutput method) InitOutput.biodiffractioninfo_detectorMake() (InitOutput method) InitOutput.biodiffractioninfo_id() (InitOutput method) InitOutput.biodiffractioninfo_monochromator() (InitOutput method) InitOutput.biodiffractioninfo_monoOrLaue() (InitOutput method) InitOutput.biodiffractioninfo_optics() (InitOutput method) InitOutput.biodiffractioninfo_scatteringType() (InitOutput method) InitOutput.biodiffractioninfo_source() (InitOutput method) InitOutput.biodiffractioninfo_sourceType() (InitOutput method) InitOutput.biodiffractioninfo_synchrotron() (InitOutput method) InitOutput.biodiffractioninfo_temperature() (InitOutput method) InitOutput.biodiffractioninfo_wavelengths() (InitOutput method) InitOutput.bioentitydbref_accessionCode() (InitOutput method) InitOutput.bioentitydbref_dbBegin() (InitOutput method) InitOutput.bioentitydbref_dbEnd() (InitOutput method) InitOutput.bioentitydbref_dbName() (InitOutput method) InitOutput.bioentitydbref_idCode() (InitOutput method) InitOutput.bioentitydbref_isoform() (InitOutput method) InitOutput.bioentitydbref_labelSeqBegin() (InitOutput method) InitOutput.bioentitydbref_labelSeqEnd() (InitOutput method) InitOutput.bioentitydbref_seqBegin() (InitOutput method) InitOutput.bioentitydbref_seqEnd() (InitOutput method) InitOutput.bioentityid_index() (InitOutput method) InitOutput.bioentityid_new() (InitOutput method) InitOutput.bioentityid_value() (InitOutput method) InitOutput.bioentityrow_dbrefs() (InitOutput method) InitOutput.bioentityrow_fullSequence() (InitOutput method) InitOutput.bioentityrow_id() (InitOutput method) InitOutput.bioentityrow_kind() (InitOutput method) InitOutput.bioentityrow_len() (InitOutput method) InitOutput.bioentityrow_polymerKind() (InitOutput method) InitOutput.bioentityrow_reflectsMicrohetero() (InitOutput method) InitOutput.bioentityrow_siftsUnpAccessions() (InitOutput method) InitOutput.bioentityrow_source() (InitOutput method) InitOutput.bioentityrow_subchains() (InitOutput method) InitOutput.bioexperimentalcrystalinfo_description() (InitOutput method) InitOutput.bioexperimentalcrystalinfo_diffractions() (InitOutput method) InitOutput.bioexperimentalcrystalinfo_id() (InitOutput method) InitOutput.bioexperimentalcrystalinfo_ph() (InitOutput method) InitOutput.bioexperimentalcrystalinfo_phRange() (InitOutput method) InitOutput.bioexperimentinfo_bWilson() (InitOutput method) InitOutput.bioexperimentinfo_diffractionIds() (InitOutput method) InitOutput.bioexperimentinfo_method() (InitOutput method) InitOutput.bioexperimentinfo_numberOfCrystals() (InitOutput method) InitOutput.bioexperimentinfo_reflections() (InitOutput method) InitOutput.bioexperimentinfo_shells() (InitOutput method) InitOutput.bioexperimentinfo_uniqueReflections() (InitOutput method) InitOutput.biohelix_end() (InitOutput method) InitOutput.biohelix_length() (InitOutput method) InitOutput.biohelix_pdbHelixClass() (InitOutput method) InitOutput.biohelix_start() (InitOutput method) InitOutput.biometadata_authors() (InitOutput method) InitOutput.biometadata_crystals() (InitOutput method) InitOutput.biometadata_experiments() (InitOutput method) InitOutput.biometadata_refinement() (InitOutput method) InitOutput.biometadata_remark_300Detail() (InitOutput method) InitOutput.biometadata_software() (InitOutput method) InitOutput.biometadata_solvedBy() (InitOutput method) InitOutput.biometadata_startingModel() (InitOutput method) InitOutput.biommcifreaderror_cause() (InitOutput method) InitOutput.biommcifreaderror_domain() (InitOutput method) InitOutput.biommcifreaderror_kind() (InitOutput method) InitOutput.biommcifreaderror_message() (InitOutput method) InitOutput.biommcifreaderror_stage() (InitOutput method) InitOutput.biommcifwriteerror_cause() (InitOutput method) InitOutput.biommcifwriteerror_domain() (InitOutput method) InitOutput.biommcifwriteerror_field() (InitOutput method) InitOutput.biommcifwriteerror_kind() (InitOutput method) InitOutput.biommcifwriteerror_message() (InitOutput method) InitOutput.biommcifwriteerror_path() (InitOutput method) InitOutput.biommcifwriteparams_alignLoops() (InitOutput method) InitOutput.biommcifwriteparams_alignPairs() (InitOutput method) InitOutput.biommcifwriteparams_allGroups() (InitOutput method) InitOutput.biommcifwriteparams_assembly() (InitOutput method) InitOutput.biommcifwriteparams_atoms() (InitOutput method) InitOutput.biommcifwriteparams_atomType() (InitOutput method) InitOutput.biommcifwriteparams_authAll() (InitOutput method) InitOutput.biommcifwriteparams_author() (InitOutput method) InitOutput.biommcifwriteparams_blockName() (InitOutput method) InitOutput.biommcifwriteparams_cell() (InitOutput method) InitOutput.biommcifwriteparams_chemComp() (InitOutput method) InitOutput.biommcifwriteparams_cis() (InitOutput method) InitOutput.biommcifwriteparams_compact() (InitOutput method) InitOutput.biommcifwriteparams_conn() (InitOutput method) InitOutput.biommcifwriteparams_databaseStatus() (InitOutput method) InitOutput.biommcifwriteparams_diffrn() (InitOutput method) InitOutput.biommcifwriteparams_entity() (InitOutput method) InitOutput.biommcifwriteparams_entityPoly() (InitOutput method) InitOutput.biommcifwriteparams_entityPolySeq() (InitOutput method) InitOutput.biommcifwriteparams_entry() (InitOutput method) InitOutput.biommcifwriteparams_exptl() (InitOutput method) InitOutput.biommcifwriteparams_groupPdb() (InitOutput method) InitOutput.biommcifwriteparams_misuseHash() (InitOutput method) InitOutput.biommcifwriteparams_modres() (InitOutput method) InitOutput.biommcifwriteparams_ncs() (InitOutput method) InitOutput.biommcifwriteparams_new() (InitOutput method) InitOutput.biommcifwriteparams_origx() (InitOutput method) InitOutput.biommcifwriteparams_preferPairs() (InitOutput method) InitOutput.biommcifwriteparams_refine() (InitOutput method) InitOutput.biommcifwriteparams_reflns() (InitOutput method) InitOutput.biommcifwriteparams_scale() (InitOutput method) InitOutput.biommcifwriteparams_set_alignLoops() (InitOutput method) InitOutput.biommcifwriteparams_set_alignPairs() (InitOutput method) InitOutput.biommcifwriteparams_set_allGroups() (InitOutput method) InitOutput.biommcifwriteparams_set_assembly() (InitOutput method) InitOutput.biommcifwriteparams_set_atoms() (InitOutput method) InitOutput.biommcifwriteparams_set_atomType() (InitOutput method) InitOutput.biommcifwriteparams_set_authAll() (InitOutput method) InitOutput.biommcifwriteparams_set_author() (InitOutput method) InitOutput.biommcifwriteparams_set_blockName() (InitOutput method) InitOutput.biommcifwriteparams_set_cell() (InitOutput method) InitOutput.biommcifwriteparams_set_chemComp() (InitOutput method) InitOutput.biommcifwriteparams_set_cis() (InitOutput method) InitOutput.biommcifwriteparams_set_compact() (InitOutput method) InitOutput.biommcifwriteparams_set_conn() (InitOutput method) InitOutput.biommcifwriteparams_set_databaseStatus() (InitOutput method) InitOutput.biommcifwriteparams_set_diffrn() (InitOutput method) InitOutput.biommcifwriteparams_set_entity() (InitOutput method) InitOutput.biommcifwriteparams_set_entityPoly() (InitOutput method) InitOutput.biommcifwriteparams_set_entityPolySeq() (InitOutput method) InitOutput.biommcifwriteparams_set_entry() (InitOutput method) InitOutput.biommcifwriteparams_set_exptl() (InitOutput method) InitOutput.biommcifwriteparams_set_groupPdb() (InitOutput method) InitOutput.biommcifwriteparams_set_misuseHash() (InitOutput method) InitOutput.biommcifwriteparams_set_modres() (InitOutput method) InitOutput.biommcifwriteparams_set_ncs() (InitOutput method) InitOutput.biommcifwriteparams_set_origx() (InitOutput method) InitOutput.biommcifwriteparams_set_preferPairs() (InitOutput method) InitOutput.biommcifwriteparams_set_refine() (InitOutput method) InitOutput.biommcifwriteparams_set_reflns() (InitOutput method) InitOutput.biommcifwriteparams_set_scale() (InitOutput method) InitOutput.biommcifwriteparams_set_software() (InitOutput method) InitOutput.biommcifwriteparams_set_structAsym() (InitOutput method) InitOutput.biommcifwriteparams_set_structBiol() (InitOutput method) InitOutput.biommcifwriteparams_set_structConf() (InitOutput method) InitOutput.biommcifwriteparams_set_structRef() (InitOutput method) InitOutput.biommcifwriteparams_set_structSheet() (InitOutput method) InitOutput.biommcifwriteparams_set_symmetry() (InitOutput method) InitOutput.biommcifwriteparams_set_titleKeywords() (InitOutput method) InitOutput.biommcifwriteparams_set_tls() (InitOutput method) InitOutput.biommcifwriteparams_software() (InitOutput method) InitOutput.biommcifwriteparams_structAsym() (InitOutput method) InitOutput.biommcifwriteparams_structBiol() (InitOutput method) InitOutput.biommcifwriteparams_structConf() (InitOutput method) InitOutput.biommcifwriteparams_structRef() (InitOutput method) InitOutput.biommcifwriteparams_structSheet() (InitOutput method) InitOutput.biommcifwriteparams_symmetry() (InitOutput method) InitOutput.biommcifwriteparams_titleKeywords() (InitOutput method) InitOutput.biommcifwriteparams_tls() (InitOutput method) InitOutput.biomodelid_index() (InitOutput method) InitOutput.biomodelid_new() (InitOutput method) InitOutput.biomodelid_value() (InitOutput method) InitOutput.biomodelrow_chains() (InitOutput method) InitOutput.biomodelrow_id() (InitOutput method) InitOutput.biomodelrow_len() (InitOutput method) InitOutput.biomodelrow_sourceModelNumber() (InitOutput method) InitOutput.biomodres_chainName() (InitOutput method) InitOutput.biomodres_details() (InitOutput method) InitOutput.biomodres_modId() (InitOutput method) InitOutput.biomodres_parentCompId() (InitOutput method) InitOutput.biomodres_resId() (InitOutput method) InitOutput.biomoleculeconversionerror_cause() (InitOutput method) InitOutput.biomoleculeconversionerror_domain() (InitOutput method) InitOutput.biomoleculeconversionerror_kind() (InitOutput method) InitOutput.biomoleculeconversionerror_message() (InitOutput method) InitOutput.biomoleculeerror_cause() (InitOutput method) InitOutput.biomoleculeerror_domain() (InitOutput method) InitOutput.biomoleculeerror_kind() (InitOutput method) InitOutput.biomoleculeerror_message() (InitOutput method) InitOutput.biomoleculeparams_flavor() (InitOutput method) InitOutput.biomoleculeparams_new() (InitOutput method) InitOutput.biomoleculeparams_proximityBonding() (InitOutput method) InitOutput.biomoleculeparams_removeHs() (InitOutput method) InitOutput.biomoleculeparams_sanitize() (InitOutput method) InitOutput.biomoleculeparams_set_flavor() (InitOutput method) InitOutput.biomoleculeparams_set_proximityBonding() (InitOutput method) InitOutput.biomoleculeparams_set_removeHs() (InitOutput method) InitOutput.biomoleculeparams_set_sanitize() (InitOutput method) InitOutput.bioncsoperator_given() (InitOutput method) InitOutput.bioncsoperator_id() (InitOutput method) InitOutput.bioncsoperator_transform() (InitOutput method) InitOutput.biooperationerror_cause() (InitOutput method) InitOutput.biooperationerror_domain() (InitOutput method) InitOutput.biooperationerror_kind() (InitOutput method) InitOutput.biooperationerror_message() (InitOutput method) InitOutput.biopdbreaderror_cause() (InitOutput method) InitOutput.biopdbreaderror_domain() (InitOutput method) InitOutput.biopdbreaderror_kind() (InitOutput method) InitOutput.biopdbreaderror_lineNumber() (InitOutput method) InitOutput.biopdbreaderror_message() (InitOutput method) InitOutput.biopdbreaderror_recordTag() (InitOutput method) InitOutput.biopdbreaderror_stage() (InitOutput method) InitOutput.biopdbreadparams_checkNonAscii() (InitOutput method) InitOutput.biopdbreadparams_ignoreTer() (InitOutput method) InitOutput.biopdbreadparams_maxLineLength() (InitOutput method) InitOutput.biopdbreadparams_new() (InitOutput method) InitOutput.biopdbreadparams_set_checkNonAscii() (InitOutput method) InitOutput.biopdbreadparams_set_ignoreTer() (InitOutput method) InitOutput.biopdbreadparams_set_maxLineLength() (InitOutput method) InitOutput.biopdbreadparams_set_skipRemarks() (InitOutput method) InitOutput.biopdbreadparams_set_splitChainOnTer() (InitOutput method) InitOutput.biopdbreadparams_skipRemarks() (InitOutput method) InitOutput.biopdbreadparams_splitChainOnTer() (InitOutput method) InitOutput.biopdbwriteerror_cause() (InitOutput method) InitOutput.biopdbwriteerror_chain() (InitOutput method) InitOutput.biopdbwriteerror_detail() (InitOutput method) InitOutput.biopdbwriteerror_domain() (InitOutput method) InitOutput.biopdbwriteerror_field() (InitOutput method) InitOutput.biopdbwriteerror_from() (InitOutput method) InitOutput.biopdbwriteerror_kind() (InitOutput method) InitOutput.biopdbwriteerror_length() (InitOutput method) InitOutput.biopdbwriteerror_message() (InitOutput method) InitOutput.biopdbwriteerror_path() (InitOutput method) InitOutput.biopdbwriteerror_serial() (InitOutput method) InitOutput.biopdbwriteerror_value() (InitOutput method) InitOutput.biopdbwriteparams_endRecord() (InitOutput method) InitOutput.biopdbwriteparams_new() (InitOutput method) InitOutput.biopdbwriteparams_numberedTer() (InitOutput method) InitOutput.biopdbwriteparams_preserveSerial() (InitOutput method) InitOutput.biopdbwriteparams_set_endRecord() (InitOutput method) InitOutput.biopdbwriteparams_set_numberedTer() (InitOutput method) InitOutput.biopdbwriteparams_set_preserveSerial() (InitOutput method) InitOutput.biopdbwriteparams_set_terIgnoresType() (InitOutput method) InitOutput.biopdbwriteparams_set_terRecords() (InitOutput method) InitOutput.biopdbwriteparams_terIgnoresType() (InitOutput method) InitOutput.biopdbwriteparams_terRecords() (InitOutput method) InitOutput.bioreaderror_cause() (InitOutput method) InitOutput.bioreaderror_domain() (InitOutput method) InitOutput.bioreaderror_kind() (InitOutput method) InitOutput.bioreaderror_message() (InitOutput method) InitOutput.bioreadparams_format() (InitOutput method) InitOutput.bioreadparams_new() (InitOutput method) InitOutput.bioreadparams_set_format() (InitOutput method) InitOutput.bioreadparams_set_sourceName() (InitOutput method) InitOutput.bioreadparams_sourceName() (InitOutput method) InitOutput.biorefinementinfo_anisoB() (InitOutput method) InitOutput.biorefinementinfo_basic() (InitOutput method) InitOutput.biorefinementinfo_binCount() (InitOutput method) InitOutput.biorefinementinfo_bins() (InitOutput method) InitOutput.biorefinementinfo_crossValidationMethod() (InitOutput method) InitOutput.biorefinementinfo_dpiBlowR() (InitOutput method) InitOutput.biorefinementinfo_dpiBlowRfree() (InitOutput method) InitOutput.biorefinementinfo_dpiCruickshankR() (InitOutput method) InitOutput.biorefinementinfo_dpiCruickshankRfree() (InitOutput method) InitOutput.biorefinementinfo_id() (InitOutput method) InitOutput.biorefinementinfo_luzzatiError() (InitOutput method) InitOutput.biorefinementinfo_meanB() (InitOutput method) InitOutput.biorefinementinfo_remarks() (InitOutput method) InitOutput.biorefinementinfo_restrStats() (InitOutput method) InitOutput.biorefinementinfo_rfreeSelectionMethod() (InitOutput method) InitOutput.biorefinementinfo_tlsGroups() (InitOutput method) InitOutput.biorefinementrestraint_count() (InitOutput method) InitOutput.biorefinementrestraint_devIdeal() (InitOutput method) InitOutput.biorefinementrestraint_function() (InitOutput method) InitOutput.biorefinementrestraint_name() (InitOutput method) InitOutput.biorefinementrestraint_weight() (InitOutput method) InitOutput.bioreflectionsinfo_completeness() (InitOutput method) InitOutput.bioreflectionsinfo_meanIOverSigma() (InitOutput method) InitOutput.bioreflectionsinfo_redundancy() (InitOutput method) InitOutput.bioreflectionsinfo_resolutionHigh() (InitOutput method) InitOutput.bioreflectionsinfo_resolutionLow() (InitOutput method) InitOutput.bioreflectionsinfo_rMerge() (InitOutput method) InitOutput.bioreflectionsinfo_rSym() (InitOutput method) InitOutput.bioresidueid_index() (InitOutput method) InitOutput.bioresidueid_new() (InitOutput method) InitOutput.bioresidueid_value() (InitOutput method) InitOutput.bioresiduerow_atoms() (InitOutput method) InitOutput.bioresiduerow_chainId() (InitOutput method) InitOutput.bioresiduerow_code() (InitOutput method) InitOutput.bioresiduerow_entityKind() (InitOutput method) InitOutput.bioresiduerow_id() (InitOutput method) InitOutput.bioresiduerow_info() (InitOutput method) InitOutput.bioresiduerow_kind() (InitOutput method) InitOutput.bioresiduerow_len() (InitOutput method) InitOutput.bioresiduerow_name() (InitOutput method) InitOutput.bioresiduerow_siftsUnp() (InitOutput method) InitOutput.bioresiduerow_source() (InitOutput method) InitOutput.biorowchainerror_cause() (InitOutput method) InitOutput.biorowchainerror_domain() (InitOutput method) InitOutput.biorowchainerror_kind() (InitOutput method) InitOutput.biorowchainerror_message() (InitOutput method) InitOutput.biorowmodelerror_cause() (InitOutput method) InitOutput.biorowmodelerror_domain() (InitOutput method) InitOutput.biorowmodelerror_kind() (InitOutput method) InitOutput.biorowmodelerror_message() (InitOutput method) InitOutput.biorowspan_end() (InitOutput method) InitOutput.biorowspan_isEmpty() (InitOutput method) InitOutput.biorowspan_len() (InitOutput method) InitOutput.biorowspan_new() (InitOutput method) InitOutput.biorowspan_start() (InitOutput method) InitOutput.biorowtraverseerror_cause() (InitOutput method) InitOutput.biorowtraverseerror_domain() (InitOutput method) InitOutput.biorowtraverseerror_kind() (InitOutput method) InitOutput.biorowtraverseerror_message() (InitOutput method) InitOutput.bioselection_fromCid() (InitOutput method) InitOutput.bioselection_toCid() (InitOutput method) InitOutput.bioselectioncopycause_cause() (InitOutput method) InitOutput.bioselectioncopycause_domain() (InitOutput method) InitOutput.bioselectioncopycause_kind() (InitOutput method) InitOutput.bioselectioncopycause_message() (InitOutput method) InitOutput.bioselectioncopyerror_cause() (InitOutput method) InitOutput.bioselectioncopyerror_domain() (InitOutput method) InitOutput.bioselectioncopyerror_kind() (InitOutput method) InitOutput.bioselectioncopyerror_message() (InitOutput method) InitOutput.bioselectionmatcherror_cause() (InitOutput method) InitOutput.bioselectionmatcherror_domain() (InitOutput method) InitOutput.bioselectionmatcherror_kind() (InitOutput method) InitOutput.bioselectionmatcherror_message() (InitOutput method) InitOutput.bioselectionparseerror_cause() (InitOutput method) InitOutput.bioselectionparseerror_cid() (InitOutput method) InitOutput.bioselectionparseerror_domain() (InitOutput method) InitOutput.bioselectionparseerror_info() (InitOutput method) InitOutput.bioselectionparseerror_kind() (InitOutput method) InitOutput.bioselectionparseerror_message() (InitOutput method) InitOutput.bioselectionparseerror_pos() (InitOutput method) InitOutput.bioselectionparseerror_variant() (InitOutput method) InitOutput.biosheet_name() (InitOutput method) InitOutput.biosheet_strands() (InitOutput method) InitOutput.biosiftsunpresidue_accessionIndex() (InitOutput method) InitOutput.biosiftsunpresidue_number() (InitOutput method) InitOutput.biosiftsunpresidue_residue() (InitOutput method) InitOutput.biosoftwareitem_classification() (InitOutput method) InitOutput.biosoftwareitem_contactAuthor() (InitOutput method) InitOutput.biosoftwareitem_contactAuthorEmail() (InitOutput method) InitOutput.biosoftwareitem_date() (InitOutput method) InitOutput.biosoftwareitem_description() (InitOutput method) InitOutput.biosoftwareitem_name() (InitOutput method) InitOutput.biosoftwareitem_version() (InitOutput method) InitOutput.biostrand_end() (InitOutput method) InitOutput.biostrand_hbondAtom1() (InitOutput method) InitOutput.biostrand_hbondAtom2() (InitOutput method) InitOutput.biostrand_name() (InitOutput method) InitOutput.biostrand_sense() (InitOutput method) InitOutput.biostrand_start() (InitOutput method) InitOutput.biostructure_assemblies() (InitOutput method) InitOutput.biostructure_atomByAltloc() (InitOutput method) InitOutput.biostructure_atomPosition() (InitOutput method) InitOutput.biostructure_atoms() (InitOutput method) InitOutput.biostructure_chains() (InitOutput method) InitOutput.biostructure_cispeps() (InitOutput method) InitOutput.biostructure_connections() (InitOutput method) InitOutput.biostructure_coordinates() (InitOutput method) InitOutput.biostructure_crystal() (InitOutput method) InitOutput.biostructure_entities() (InitOutput method) InitOutput.biostructure_findAtom() (InitOutput method) InitOutput.biostructure_findEntity() (InitOutput method) InitOutput.biostructure_findEntityOfSubchain() (InitOutput method) InitOutput.biostructure_fromMmcif() (InitOutput method) InitOutput.biostructure_fromParts() (InitOutput method) InitOutput.biostructure_fromPdb() (InitOutput method) InitOutput.biostructure_fromPdbWithParams() (InitOutput method) InitOutput.biostructure_fromText() (InitOutput method) InitOutput.biostructure_fromTextWithParams() (InitOutput method) InitOutput.biostructure_hasOrigx() (InitOutput method) InitOutput.biostructure_helices() (InitOutput method) InitOutput.biostructure_inputFormat() (InitOutput method) InitOutput.biostructure_intoParts() (InitOutput method) InitOutput.biostructure_metadata() (InitOutput method) InitOutput.biostructure_models() (InitOutput method) InitOutput.biostructure_modResidues() (InitOutput method) InitOutput.biostructure_name() (InitOutput method) InitOutput.biostructure_ncsOperators() (InitOutput method) InitOutput.biostructure_ncsOperIdentityId() (InitOutput method) InitOutput.biostructure_numAtoms() (InitOutput method) InitOutput.biostructure_numChains() (InitOutput method) InitOutput.biostructure_numEntities() (InitOutput method) InitOutput.biostructure_numModels() (InitOutput method) InitOutput.biostructure_numResidues() (InitOutput method) InitOutput.biostructure_origx() (InitOutput method) InitOutput.biostructure_protein() (InitOutput method) InitOutput.biostructure_read() (InitOutput method) InitOutput.biostructure_readWithFormat() (InitOutput method) InitOutput.biostructure_residueAtoms() (InitOutput method) InitOutput.biostructure_residues() (InitOutput method) InitOutput.biostructure_resolution() (InitOutput method) InitOutput.biostructure_retainSelection() (InitOutput method) InitOutput.biostructure_selectedAtomIds() (InitOutput method) InitOutput.biostructure_sheets() (InitOutput method) InitOutput.biostructure_sourceState() (InitOutput method) InitOutput.biostructure_terStatus() (InitOutput method) InitOutput.biostructure_toMmcif() (InitOutput method) InitOutput.biostructure_toMmcifWithParams() (InitOutput method) InitOutput.biostructure_toMolecule() (InitOutput method) InitOutput.biostructure_toMoleculeWithParams() (InitOutput method) InitOutput.biostructure_toPdb() (InitOutput method) InitOutput.biostructure_toPdbWithParams() (InitOutput method) InitOutput.biostructure_translate() (InitOutput method) InitOutput.biostructure_validate() (InitOutput method) InitOutput.biostructure_validateParts() (InitOutput method) InitOutput.biostructure_withSelection() (InitOutput method) InitOutput.biostructure_withTranslatedCoordinates() (InitOutput method) InitOutput.biostructure_writeMmcif() (InitOutput method) InitOutput.biostructure_writeMmcifWithParams() (InitOutput method) InitOutput.biostructure_writePdb() (InitOutput method) InitOutput.biostructure_writePdbWithParams() (InitOutput method) InitOutput.biostructureerror_actualStart() (InitOutput method) InitOutput.biostructureerror_atomCount() (InitOutput method) InitOutput.biostructureerror_cause() (InitOutput method) InitOutput.biostructureerror_coordinateCount() (InitOutput method) InitOutput.biostructureerror_covered() (InitOutput method) InitOutput.biostructureerror_domain() (InitOutput method) InitOutput.biostructureerror_entityId() (InitOutput method) InitOutput.biostructureerror_expectedStart() (InitOutput method) InitOutput.biostructureerror_index() (InitOutput method) InitOutput.biostructureerror_kind() (InitOutput method) InitOutput.biostructureerror_len() (InitOutput method) InitOutput.biostructureerror_message() (InitOutput method) InitOutput.biostructureerror_operation() (InitOutput method) InitOutput.biostructureerror_start() (InitOutput method) InitOutput.biostructureerror_subchain() (InitOutput method) InitOutput.biostructureerror_table() (InitOutput method) InitOutput.biostructureerror_tableLen() (InitOutput method) InitOutput.biostructureerror_value() (InitOutput method) InitOutput.biostructureparts_inputFormat() (InitOutput method) InitOutput.biostructuresourcestate_conectMap() (InitOutput method) InitOutput.biostructuresourcestate_hasDFraction() (InitOutput method) InitOutput.biostructuresourcestate_hasOrigx() (InitOutput method) InitOutput.biostructuresourcestate_info() (InitOutput method) InitOutput.biostructuresourcestate_name() (InitOutput method) InitOutput.biostructuresourcestate_nonAsciiLine() (InitOutput method) InitOutput.biostructuresourcestate_origx() (InitOutput method) InitOutput.biostructuresourcestate_rawRemarks() (InitOutput method) InitOutput.biostructuresourcestate_resolution() (InitOutput method) InitOutput.biostructuresourcestate_terStatus() (InitOutput method) InitOutput.biotlsgroup_id() (InitOutput method) InitOutput.biotlsgroup_l() (InitOutput method) InitOutput.biotlsgroup_numId() (InitOutput method) InitOutput.biotlsgroup_origin() (InitOutput method) InitOutput.biotlsgroup_s() (InitOutput method) InitOutput.biotlsgroup_selections() (InitOutput method) InitOutput.biotlsgroup_t() (InitOutput method) InitOutput.biotlsselection_chain() (InitOutput method) InitOutput.biotlsselection_details() (InitOutput method) InitOutput.biotlsselection_resBegin() (InitOutput method) InitOutput.biotlsselection_resEnd() (InitOutput method) InitOutput.biotransform_approx() (InitOutput method) InitOutput.biotransform_matrix() (InitOutput method) InitOutput.biotransform_translation() (InitOutput method) InitOutput.bond_begin() (InitOutput method) InitOutput.bond_cipDescriptor() (InitOutput method) InitOutput.bond_cipNeighborOrder() (InitOutput method) InitOutput.bond_direction() (InitOutput method) InitOutput.bond_directionCode() (InitOutput method) InitOutput.bond_directionName() (InitOutput method) InitOutput.bond_end() (InitOutput method) InitOutput.bond_id() (InitOutput method) InitOutput.bond_isAromatic() (InitOutput method) InitOutput.bond_order() (InitOutput method) InitOutput.bond_orderCode() (InitOutput method) InitOutput.bond_orderName() (InitOutput method) InitOutput.bond_stereo() (InitOutput method) InitOutput.bond_stereoAtoms() (InitOutput method) InitOutput.bond_stereoCode() (InitOutput method) InitOutput.bond_stereoName() (InitOutput method) InitOutput.bondspec_new() (InitOutput method) InitOutput.canonicalTautomerFromMolecules() (InitOutput method) InitOutput.canonicalTautomerFromMoleculesWithParams() (InitOutput method) InitOutput.chainsourceids_authChainId() (InitOutput method) InitOutput.chainsourceids_labelAsymId() (InitOutput method) InitOutput.chemistryproblem_error() (InitOutput method) InitOutput.chemistryproblem_operation() (InitOutput method) InitOutput.chemistryproblemerror_cause() (InitOutput method) InitOutput.chemistryproblemerror_domain() (InitOutput method) InitOutput.chemistryproblemerror_kind() (InitOutput method) InitOutput.chemistryproblemerror_message() (InitOutput method) InitOutput.chemistryproblemreport_problems() (InitOutput method) InitOutput.cipdescriptorerror_cause() (InitOutput method) InitOutput.cipdescriptorerror_kind() (InitOutput method) InitOutput.cipdescriptorerror_message() (InitOutput method) InitOutput.cipdescriptorerror_value() (InitOutput method) InitOutput.ciplabelererror_cause() (InitOutput method) InitOutput.ciplabelererror_domain() (InitOutput method) InitOutput.ciplabelererror_kind() (InitOutput method) InitOutput.ciplabelererror_message() (InitOutput method) InitOutput.ciplabeloptions_atoms() (InitOutput method) InitOutput.ciplabeloptions_bonds() (InitOutput method) InitOutput.ciplabeloptions_maxRecursiveIterations() (InitOutput method) InitOutput.ciplabeloptions_new() (InitOutput method) InitOutput.ciplabeloptions_set_atoms() (InitOutput method) InitOutput.ciplabeloptions_set_bonds() (InitOutput method) InitOutput.ciplabeloptions_set_maxRecursiveIterations() (InitOutput method) InitOutput.ciprankerror_actual() (InitOutput method) InitOutput.ciprankerror_atom() (InitOutput method) InitOutput.ciprankerror_atomCount() (InitOutput method) InitOutput.ciprankerror_bond() (InitOutput method) InitOutput.ciprankerror_cause() (InitOutput method) InitOutput.ciprankerror_degree() (InitOutput method) InitOutput.ciprankerror_domain() (InitOutput method) InitOutput.ciprankerror_field() (InitOutput method) InitOutput.ciprankerror_kind() (InitOutput method) InitOutput.ciprankerror_mapNumber() (InitOutput method) InitOutput.ciprankerror_maximumSupported() (InitOutput method) InitOutput.ciprankerror_message() (InitOutput method) InitOutput.ciprankerror_order() (InitOutput method) InitOutput.ciprankerror_value() (InitOutput method) InitOutput.compiledquery_atomOrder() (InitOutput method) InitOutput.compiledquery_numAtoms() (InitOutput method) InitOutput.compiledquery_numBonds() (InitOutput method) InitOutput.compiledquery_query() (InitOutput method) InitOutput.compileQuery() (InitOutput method) InitOutput.conformer2d_coordinates() (InitOutput method) InitOutput.conformer2d_id() (InitOutput method) InitOutput.conformer2d_props() (InitOutput method) InitOutput.conformer3d_coordinates() (InitOutput method) InitOutput.conformer3d_id() (InitOutput method) InitOutput.conformer3d_is3d() (InitOutput method) InitOutput.conformer3d_props() (InitOutput method) InitOutput.conformeralignmentparameters_atomIndices() (InitOutput method) InitOutput.conformeralignmentparameters_conformerIds() (InitOutput method) InitOutput.conformeralignmentparameters_constructor() (InitOutput method) InitOutput.conformeralignmentparameters_maxIterations() (InitOutput method) InitOutput.conformeralignmentparameters_new() (InitOutput method) InitOutput.conformeralignmentparameters_reflect() (InitOutput method) InitOutput.conformeralignmentparameters_set_atomIndices() (InitOutput method) InitOutput.conformeralignmentparameters_set_conformerIds() (InitOutput method) InitOutput.conformeralignmentparameters_set_maxIterations() (InitOutput method) InitOutput.conformeralignmentparameters_set_reflect() (InitOutput method) InitOutput.conformeralignmentparameters_set_weights() (InitOutput method) InitOutput.conformeralignmentparameters_weights() (InitOutput method) InitOutput.conformeralignmentreport_rmsds() (InitOutput method) InitOutput.conformererror_detail() (InitOutput method) InitOutput.conformererror_domain() (InitOutput method) InitOutput.conformererror_kind() (InitOutput method) InitOutput.conformererror_message() (InitOutput method) InitOutput.conformerrmsd_probeConformerId() (InitOutput method) InitOutput.conformerrmsd_referenceConformerId() (InitOutput method) InitOutput.conformerrmsd_rmsd() (InitOutput method) InitOutput.conformerrunerror_cause() (InitOutput method) InitOutput.conformerrunerror_domain() (InitOutput method) InitOutput.conformerrunerror_message() (InitOutput method) InitOutput.coordinate2derror_cause() (InitOutput method) InitOutput.coordinate2derror_domain() (InitOutput method) InitOutput.coordinate2derror_kind() (InitOutput method) InitOutput.coordinate2derror_message() (InitOutput method) InitOutput.coordinate2dinputparams_new() (InitOutput method) InitOutput.coordinate2dinputparams_set_zPolicy() (InitOutput method) InitOutput.coordinate2dinputparams_zPolicy() (InitOutput method) InitOutput.coordinate2dlayouterror_atom() (InitOutput method) InitOutput.coordinate2dlayouterror_atomCount() (InitOutput method) InitOutput.coordinate2dlayouterror_bond() (InitOutput method) InitOutput.coordinate2dlayouterror_cause() (InitOutput method) InitOutput.coordinate2dlayouterror_centre() (InitOutput method) InitOutput.coordinate2dlayouterror_count() (InitOutput method) InitOutput.coordinate2dlayouterror_domain() (InitOutput method) InitOutput.coordinate2dlayouterror_first() (InitOutput method) InitOutput.coordinate2dlayouterror_key() (InitOutput method) InitOutput.coordinate2dlayouterror_kind() (InitOutput method) InitOutput.coordinate2dlayouterror_message() (InitOutput method) InitOutput.coordinate2dlayouterror_second() (InitOutput method) InitOutput.coordinate2dparams_canonicalOrientation() (InitOutput method) InitOutput.coordinate2dparams_clearExisting2d() (InitOutput method) InitOutput.coordinate2dparams_coordinateMap() (InitOutput method) InitOutput.coordinate2dparams_flipsPerSample() (InitOutput method) InitOutput.coordinate2dparams_forceRdkit() (InitOutput method) InitOutput.coordinate2dparams_new() (InitOutput method) InitOutput.coordinate2dparams_permuteDegreeFour() (InitOutput method) InitOutput.coordinate2dparams_samples() (InitOutput method) InitOutput.coordinate2dparams_sampleSeed() (InitOutput method) InitOutput.coordinate2dparams_set_canonicalOrientation() (InitOutput method) InitOutput.coordinate2dparams_set_clearExisting2d() (InitOutput method) InitOutput.coordinate2dparams_set_coordinateMap() (InitOutput method) InitOutput.coordinate2dparams_set_flipsPerSample() (InitOutput method) InitOutput.coordinate2dparams_set_forceRdkit() (InitOutput method) InitOutput.coordinate2dparams_set_permuteDegreeFour() (InitOutput method) InitOutput.coordinate2dparams_set_samples() (InitOutput method) InitOutput.coordinate2dparams_set_sampleSeed() (InitOutput method) InitOutput.coordinate2dparams_set_useRingTemplates() (InitOutput method) InitOutput.coordinate2dparams_useRingTemplates() (InitOutput method) InitOutput.coordinate2dtemplateerror_cause() (InitOutput method) InitOutput.coordinate2dtemplateerror_domain() (InitOutput method) InitOutput.coordinate2dtemplateerror_index() (InitOutput method) InitOutput.coordinate2dtemplateerror_kind() (InitOutput method) InitOutput.coordinate2dtemplateerror_line() (InitOutput method) InitOutput.coordinate2dtemplateerror_message() (InitOutput method) InitOutput.coordinate2dtemplateerror_path() (InitOutput method) InitOutput.coordinate2dtemplateerror_row() (InitOutput method) InitOutput.coordinate3dinputparams_is3d() (InitOutput method) InitOutput.coordinate3dinputparams_new() (InitOutput method) InitOutput.coordinate3dinputparams_set_is3d() (InitOutput method) InitOutput.coordinate3dreaderror_conformerId() (InitOutput method) InitOutput.coordinate3dreaderror_count() (InitOutput method) InitOutput.coordinate3dreaderror_domain() (InitOutput method) InitOutput.coordinate3dreaderror_kind() (InitOutput method) InitOutput.coordinate3dreaderror_message() (InitOutput method) InitOutput.coordinateblock_conformers2d() (InitOutput method) InitOutput.coordinateblock_conformers3d() (InitOutput method) InitOutput.coordinateblock_sourceConformerOrder() (InitOutput method) InitOutput.coordinateblock_sourceCoordinateDim() (InitOutput method) InitOutput.coordinateinputerror_cause() (InitOutput method) InitOutput.coordinateinputerror_domain() (InitOutput method) InitOutput.coordinateinputerror_kind() (InitOutput method) InitOutput.coordinateinputerror_message() (InitOutput method) InitOutput.coordinatermsdparameters_atomMaps() (InitOutput method) InitOutput.coordinatermsdparameters_constructor() (InitOutput method) InitOutput.coordinatermsdparameters_maxMatches() (InitOutput method) InitOutput.coordinatermsdparameters_new() (InitOutput method) InitOutput.coordinatermsdparameters_probeConformerId() (InitOutput method) InitOutput.coordinatermsdparameters_referenceConformerId() (InitOutput method) InitOutput.coordinatermsdparameters_set_atomMaps() (InitOutput method) InitOutput.coordinatermsdparameters_set_maxMatches() (InitOutput method) InitOutput.coordinatermsdparameters_set_probeConformerId() (InitOutput method) InitOutput.coordinatermsdparameters_set_referenceConformerId() (InitOutput method) InitOutput.coordinatermsdparameters_set_symmetrizeConjugatedTerminalGroups() (InitOutput method) InitOutput.coordinatermsdparameters_set_weights() (InitOutput method) InitOutput.coordinatermsdparameters_symmetrizeConjugatedTerminalGroups() (InitOutput method) InitOutput.coordinatermsdparameters_weights() (InitOutput method) InitOutput.coordinatezpolicy_Error() (InitOutput method) InitOutput.coordinatezpolicy_fromName() (InitOutput method) InitOutput.coordinatezpolicy_Ignore() (InitOutput method) InitOutput.coordinatezpolicy_RequireZero() (InitOutput method) InitOutput.crippentotals_logp() (InitOutput method) InitOutput.crippentotals_molarRefractivity() (InitOutput method) InitOutput.cxcoordinateselection_auto() (InitOutput method) InitOutput.cxcoordinateselection_threeD() (InitOutput method) InitOutput.cxcoordinateselection_twoD() (InitOutput method) InitOutput.cxsmilesfields_ALL() (InitOutput method) InitOutput.cxsmilesfields_ALL_BUT_COORDS() (InitOutput method) InitOutput.cxsmilesfields_ATOM_LABELS() (InitOutput method) InitOutput.cxsmilesfields_ATOM_PROPS() (InitOutput method) InitOutput.cxsmilesfields_bits() (InitOutput method) InitOutput.cxsmilesfields_BOND_ATROPISOMER() (InitOutput method) InitOutput.cxsmilesfields_BOND_CFG() (InitOutput method) InitOutput.cxsmilesfields_contains() (InitOutput method) InitOutput.cxsmilesfields_COORDINATE_BONDS() (InitOutput method) InitOutput.cxsmilesfields_COORDS() (InitOutput method) InitOutput.cxsmilesfields_ENHANCED_STEREO() (InitOutput method) InitOutput.cxsmilesfields_HYDROGEN_BONDS() (InitOutput method) InitOutput.cxsmilesfields_LINKNODES() (InitOutput method) InitOutput.cxsmilesfields_MOLFILE_VALUES() (InitOutput method) InitOutput.cxsmilesfields_NONE() (InitOutput method) InitOutput.cxsmilesfields_or() (InitOutput method) InitOutput.cxsmilesfields_POLYMER() (InitOutput method) InitOutput.cxsmilesfields_RADICALS() (InitOutput method) InitOutput.cxsmilesfields_SGROUPS() (InitOutput method) InitOutput.cxsmilesfields_ZERO_BONDS() (InitOutput method) InitOutput.cxsmileswriteparams_coordinateSelection() (InitOutput method) InitOutput.cxsmileswriteparams_fields() (InitOutput method) InitOutput.cxsmileswriteparams_new() (InitOutput method) InitOutput.cxsmileswriteparams_set_coordinateSelection() (InitOutput method) InitOutput.cxsmileswriteparams_set_fields() (InitOutput method) InitOutput.cxsmileswriteparams_set_smiles() (InitOutput method) InitOutput.cxsmileswriteparams_smiles() (InitOutput method) InitOutput.defaultTautomerScoreTerms() (InitOutput method) InitOutput.densematrix_dimension() (InitOutput method) InitOutput.densematrix_get() (InitOutput method) InitOutput.densematrix_values() (InitOutput method) InitOutput.descriptorerror_actual() (InitOutput method) InitOutput.descriptorerror_actualRows() (InitOutput method) InitOutput.descriptorerror_binPropLen() (InitOutput method) InitOutput.descriptorerror_binsLen() (InitOutput method) InitOutput.descriptorerror_cause() (InitOutput method) InitOutput.descriptorerror_cell() (InitOutput method) InitOutput.descriptorerror_contribsLen() (InitOutput method) InitOutput.descriptorerror_detail() (InitOutput method) InitOutput.descriptorerror_domain() (InitOutput method) InitOutput.descriptorerror_expected() (InitOutput method) InitOutput.descriptorerror_expectedRows() (InitOutput method) InitOutput.descriptorerror_field() (InitOutput method) InitOutput.descriptorerror_function() (InitOutput method) InitOutput.descriptorerror_includeSulfurPhosphorus() (InitOutput method) InitOutput.descriptorerror_kind() (InitOutput method) InitOutput.descriptorerror_message() (InitOutput method) InitOutput.descriptorerror_minimum() (InitOutput method) InitOutput.descriptorerror_row() (InitOutput method) InitOutput.descriptorreaderror_cause() (InitOutput method) InitOutput.descriptorreaderror_domain() (InitOutput method) InitOutput.descriptorreaderror_kind() (InitOutput method) InitOutput.descriptorreaderror_message() (InitOutput method) InitOutput.distancematrix3dparams_conformerId() (InitOutput method) InitOutput.distancematrix3dparams_new() (InitOutput method) InitOutput.distancematrix3dparams_set_conformerId() (InitOutput method) InitOutput.distancematrix3dparams_set_useAtomWeights() (InitOutput method) InitOutput.distancematrix3dparams_useAtomWeights() (InitOutput method) InitOutput.distancematrixparams_new() (InitOutput method) InitOutput.distancematrixparams_set_useAtomWeights() (InitOutput method) InitOutput.distancematrixparams_set_useBondOrder() (InitOutput method) InitOutput.distancematrixparams_useAtomWeights() (InitOutput method) InitOutput.distancematrixparams_useBondOrder() (InitOutput method) InitOutput.drawingerror_cause() (InitOutput method) InitOutput.drawingerror_domain() (InitOutput method) InitOutput.drawingerror_kind() (InitOutput method) InitOutput.drawingerror_message() (InitOutput method) InitOutput.drawingwriteerror_cause() (InitOutput method) InitOutput.drawingwriteerror_domain() (InitOutput method) InitOutput.drawingwriteerror_kind() (InitOutput method) InitOutput.drawingwriteerror_message() (InitOutput method) InitOutput.element_atomicNumber() (InitOutput method) InitOutput.element_fromAtomicNumber() (InitOutput method) InitOutput.element_fromSymbol() (InitOutput method) InitOutput.element_symbol() (InitOutput method) InitOutput.elementInfo() (InitOutput method) InitOutput.elementinfo_atomicNumber() (InitOutput method) InitOutput.elementinfo_atomicWeight() (InitOutput method) InitOutput.elementinfo_element() (InitOutput method) InitOutput.elementinfo_outerElectrons() (InitOutput method) InitOutput.elementinfo_period() (InitOutput method) InitOutput.elementinfo_rb0() (InitOutput method) InitOutput.elementinfo_symbol() (InitOutput method) InitOutput.elementinfo_valences() (InitOutput method) InitOutput.embedmoleculeresult_confId() (InitOutput method) InitOutput.embedmoleculeresult_molecule() (InitOutput method) InitOutput.embedmoleculeresult_ok() (InitOutput method) InitOutput.embedmoleculeresult_params() (InitOutput method) InitOutput.embedmultipleconfsresult_confIds() (InitOutput method) InitOutput.embedmultipleconfsresult_generatedCount() (InitOutput method) InitOutput.embedmultipleconfsresult_molecule() (InitOutput method) InitOutput.embedmultipleconfsresult_params() (InitOutput method) InitOutput.embedmultipleconfsresult_requestedNumConfs() (InitOutput method) InitOutput.embedparams_basinThresh() (InitOutput method) InitOutput.embedparams_boundsMatForceScaling() (InitOutput method) InitOutput.embedparams_boxSizeMult() (InitOutput method) InitOutput.embedparams_clearConformers() (InitOutput method) InitOutput.embedparams_construct() (InitOutput method) InitOutput.embedparams_coordMap() (InitOutput method) InitOutput.embedparams_cpci() (InitOutput method) InitOutput.embedparams_dg() (InitOutput method) InitOutput.embedparams_embedFragmentsSeparately() (InitOutput method) InitOutput.embedparams_enableSequentialRandomSeeds() (InitOutput method) InitOutput.embedparams_enforceChirality() (InitOutput method) InitOutput.embedparams_etdg() (InitOutput method) InitOutput.embedparams_etdgV2() (InitOutput method) InitOutput.embedparams_etkdg() (InitOutput method) InitOutput.embedparams_etkdgV2() (InitOutput method) InitOutput.embedparams_etkdgV3() (InitOutput method) InitOutput.embedparams_etVersion() (InitOutput method) InitOutput.embedparams_failures() (InitOutput method) InitOutput.embedparams_forceTransAmides() (InitOutput method) InitOutput.embedparams_ignoreSmoothingFailures() (InitOutput method) InitOutput.embedparams_kdg() (InitOutput method) InitOutput.embedparams_maxIterations() (InitOutput method) InitOutput.embedparams_new() (InitOutput method) InitOutput.embedparams_numThreads() (InitOutput method) InitOutput.embedparams_numZeroFail() (InitOutput method) InitOutput.embedparams_onlyHeavyAtomsForRms() (InitOutput method) InitOutput.embedparams_optimizerForceTol() (InitOutput method) InitOutput.embedparams_pruneRmsThresh() (InitOutput method) InitOutput.embedparams_randNegEig() (InitOutput method) InitOutput.embedparams_randomSeed() (InitOutput method) InitOutput.embedparams_set_basinThresh() (InitOutput method) InitOutput.embedparams_set_boundsMatForceScaling() (InitOutput method) InitOutput.embedparams_set_boxSizeMult() (InitOutput method) InitOutput.embedparams_set_clearConformers() (InitOutput method) InitOutput.embedparams_set_coordMap() (InitOutput method) InitOutput.embedparams_set_cpci() (InitOutput method) InitOutput.embedparams_set_embedFragmentsSeparately() (InitOutput method) InitOutput.embedparams_set_enableSequentialRandomSeeds() (InitOutput method) InitOutput.embedparams_set_enforceChirality() (InitOutput method) InitOutput.embedparams_set_etVersion() (InitOutput method) InitOutput.embedparams_set_forceTransAmides() (InitOutput method) InitOutput.embedparams_set_ignoreSmoothingFailures() (InitOutput method) InitOutput.embedparams_set_maxIterations() (InitOutput method) InitOutput.embedparams_set_numThreads() (InitOutput method) InitOutput.embedparams_set_numZeroFail() (InitOutput method) InitOutput.embedparams_set_onlyHeavyAtomsForRms() (InitOutput method) InitOutput.embedparams_set_optimizerForceTol() (InitOutput method) InitOutput.embedparams_set_pruneRmsThresh() (InitOutput method) InitOutput.embedparams_set_randNegEig() (InitOutput method) InitOutput.embedparams_set_randomSeed() (InitOutput method) InitOutput.embedparams_set_symmetrizeConjugatedTerminalGroupsForPruning() (InitOutput method) InitOutput.embedparams_set_timeout() (InitOutput method) InitOutput.embedparams_set_trackFailures() (InitOutput method) InitOutput.embedparams_set_useBasicKnowledge() (InitOutput method) InitOutput.embedparams_set_useExpTorsionAnglePrefs() (InitOutput method) InitOutput.embedparams_set_useMacrocycle14config() (InitOutput method) InitOutput.embedparams_set_useMacrocycleTorsions() (InitOutput method) InitOutput.embedparams_set_useRandomCoords() (InitOutput method) InitOutput.embedparams_set_useSmallRingTorsions() (InitOutput method) InitOutput.embedparams_set_useSymmetryForPruning() (InitOutput method) InitOutput.embedparams_set_verbose() (InitOutput method) InitOutput.embedparams_srEtkdgV3() (InitOutput method) InitOutput.embedparams_symmetrizeConjugatedTerminalGroupsForPruning() (InitOutput method) InitOutput.embedparams_timeout() (InitOutput method) InitOutput.embedparams_toJson() (InitOutput method) InitOutput.embedparams_trackFailures() (InitOutput method) InitOutput.embedparams_useBasicKnowledge() (InitOutput method) InitOutput.embedparams_useExpTorsionAnglePrefs() (InitOutput method) InitOutput.embedparams_useMacrocycle14config() (InitOutput method) InitOutput.embedparams_useMacrocycleTorsions() (InitOutput method) InitOutput.embedparams_useRandomCoords() (InitOutput method) InitOutput.embedparams_useSmallRingTorsions() (InitOutput method) InitOutput.embedparams_useSymmetryForPruning() (InitOutput method) InitOutput.embedparams_verbose() (InitOutput method) InitOutput.embedparams_withJson() (InitOutput method) InitOutput.entitysourceids_sourceEntityId() (InitOutput method) InitOutput.enumerationerror_cause() (InitOutput method) InitOutput.enumerationerror_domain() (InitOutput method) InitOutput.enumerationerror_kind() (InitOutput method) InitOutput.enumerationerror_message() (InitOutput method) InitOutput.enumerationrunerror_cause() (InitOutput method) InitOutput.enumerationrunerror_domain() (InitOutput method) InitOutput.enumerationrunerror_kind() (InitOutput method) InitOutput.enumerationrunerror_message() (InitOutput method) InitOutput.expandOneLetter() (InitOutput method) InitOutput.expandOneLetterSequence() (InitOutput method) InitOutput.explainPathScore() (InitOutput method) InitOutput.featureSpec() (InitOutput method) InitOutput.featurespec_category() (InitOutput method) InitOutput.featurespec_docs() (InitOutput method) InitOutput.featurespec_name() (InitOutput method) InitOutput.featurespeciter_next() (InitOutput method) InitOutput.featureSpecs() (InitOutput method) InitOutput.findResidueInfo() (InitOutput method) InitOutput.findResidueInfoIndex() (InitOutput method) InitOutput.fingerprint_fromOnBits() (InitOutput method) InitOutput.fingerprint_nBits() (InitOutput method) InitOutput.fingerprint_onBits() (InitOutput method) InitOutput.fingerprint_tanimoto() (InitOutput method) InitOutput.fingerprintadditionaloutput_allocateAtomCounts() (InitOutput method) InitOutput.fingerprintadditionaloutput_allocateAtomsPerBit() (InitOutput method) InitOutput.fingerprintadditionaloutput_allocateAtomToBits() (InitOutput method) InitOutput.fingerprintadditionaloutput_allocateBitInfoMap() (InitOutput method) InitOutput.fingerprintadditionaloutput_allocateBitPaths() (InitOutput method) InitOutput.fingerprintadditionaloutput_atomCounts() (InitOutput method) InitOutput.fingerprintadditionaloutput_atomsPerBit() (InitOutput method) InitOutput.fingerprintadditionaloutput_atomToBits() (InitOutput method) InitOutput.fingerprintadditionaloutput_bitInfoMap() (InitOutput method) InitOutput.fingerprintadditionaloutput_bitPaths() (InitOutput method) InitOutput.fingerprintadditionaloutput_constructor() (InitOutput method) InitOutput.fingerprintadditionaloutput_default() (InitOutput method) InitOutput.fingerprintadditionaloutput_new() (InitOutput method) InitOutput.fingerprinterror_cause() (InitOutput method) InitOutput.fingerprinterror_domain() (InitOutput method) InitOutput.fingerprinterror_kind() (InitOutput method) InitOutput.fingerprinterror_message() (InitOutput method) InitOutput.fingerprintjsonerror_cause() (InitOutput method) InitOutput.fingerprintjsonerror_domain() (InitOutput method) InitOutput.fingerprintjsonerror_kind() (InitOutput method) InitOutput.fingerprintjsonerror_message() (InitOutput method) InitOutput.fingerprintLayeredQueryWithOutputWithParams() (InitOutput method) InitOutput.fingerprintLayeredQueryWithParams() (InitOutput method) InitOutput.fingerprintPatternQuery() (InitOutput method) InitOutput.fingerprintPatternQueryWithParams() (InitOutput method) InitOutput.fingerprintpreparationerror_cause() (InitOutput method) InitOutput.fingerprintpreparationerror_domain() (InitOutput method) InitOutput.fingerprintpreparationerror_kind() (InitOutput method) InitOutput.fingerprintpreparationerror_message() (InitOutput method) InitOutput.fingerprintTopologicalQueryWithOutputWithParams() (InitOutput method) InitOutput.fingerprintTopologicalQueryWithParams() (InitOutput method) InitOutput.forcefieldenergygradient_energy() (InitOutput method) InitOutput.forcefieldenergygradient_gradient() (InitOutput method) InitOutput.forcefielderror_actual() (InitOutput method) InitOutput.forcefielderror_atomIndex() (InitOutput method) InitOutput.forcefielderror_cause() (InitOutput method) InitOutput.forcefielderror_component() (InitOutput method) InitOutput.forcefielderror_expected() (InitOutput method) InitOutput.forcefielderror_kind() (InitOutput method) InitOutput.forcefielderror_message() (InitOutput method) InitOutput.forcefielderror_requested() (InitOutput method) InitOutput.forcefieldminimizeoutcome_converged() (InitOutput method) InitOutput.forcefieldminimizeoutcome_energy() (InitOutput method) InitOutput.forcefieldminimizeoutcome_iterations() (InitOutput method) InitOutput.forcefieldminimizeparams_energyTolerance() (InitOutput method) InitOutput.forcefieldminimizeparams_forceTolerance() (InitOutput method) InitOutput.forcefieldminimizeparams_maxIterations() (InitOutput method) InitOutput.forcefieldminimizeparams_new() (InitOutput method) InitOutput.forcefieldminimizeparams_set_energyTolerance() (InitOutput method) InitOutput.forcefieldminimizeparams_set_forceTolerance() (InitOutput method) InitOutput.forcefieldminimizeparams_set_maxIterations() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_atoms() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_atomSymbols() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_bonds() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_bondSymbols() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_cx() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_new() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_set_atoms() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_set_atomSymbols() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_set_bonds() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_set_bondSymbols() (InitOutput method) InitOutput.fragmentcxsmileswriteparams_set_cx() (InitOutput method) InitOutput.fragmentsmileswriteparams_atoms() (InitOutput method) InitOutput.fragmentsmileswriteparams_atomSymbols() (InitOutput method) InitOutput.fragmentsmileswriteparams_bonds() (InitOutput method) InitOutput.fragmentsmileswriteparams_bondSymbols() (InitOutput method) InitOutput.fragmentsmileswriteparams_new() (InitOutput method) InitOutput.fragmentsmileswriteparams_set_atoms() (InitOutput method) InitOutput.fragmentsmileswriteparams_set_atomSymbols() (InitOutput method) InitOutput.fragmentsmileswriteparams_set_bonds() (InitOutput method) InitOutput.fragmentsmileswriteparams_set_bondSymbols() (InitOutput method) InitOutput.fragmentsmileswriteparams_set_smiles() (InitOutput method) InitOutput.fragmentsmileswriteparams_smiles() (InitOutput method) InitOutput.functionstatus_explanation() (InitOutput method) InitOutput.functionstatus_kind() (InitOutput method) InitOutput.functionstatus_reference() (InitOutput method) InitOutput.hydrogenerror_cause() (InitOutput method) InitOutput.hydrogenerror_domain() (InitOutput method) InitOutput.hydrogenerror_kind() (InitOutput method) InitOutput.hydrogenerror_message() (InitOutput method) InitOutput.inchierror_detail() (InitOutput method) InitOutput.inchierror_domain() (InitOutput method) InitOutput.inchierror_kind() (InitOutput method) InitOutput.inchierror_message() (InitOutput method) InitOutput.inchierror_operation() (InitOutput method) InitOutput.inchireadparams_new() (InitOutput method) InitOutput.inchireadparams_removeHs() (InitOutput method) InitOutput.inchireadparams_sanitize() (InitOutput method) InitOutput.inchireadparams_set_removeHs() (InitOutput method) InitOutput.inchireadparams_set_sanitize() (InitOutput method) InitOutput.inchireadparams_setRemoveHs() (InitOutput method) InitOutput.inchireadparams_setSanitize() (InitOutput method) InitOutput.inchiToKey() (InitOutput method) InitOutput.inchiwriteparams_new() (InitOutput method) InitOutput.inchiwriteparams_options() (InitOutput method) InitOutput.inchiwriteparams_set_options() (InitOutput method) InitOutput.inchiwriteparams_setOptions() (InitOutput method) InitOutput.kekulizeerror_actual() (InitOutput method) InitOutput.kekulizeerror_after() (InitOutput method) InitOutput.kekulizeerror_atom() (InitOutput method) InitOutput.kekulizeerror_atomCount() (InitOutput method) InitOutput.kekulizeerror_before() (InitOutput method) InitOutput.kekulizeerror_begin() (InitOutput method) InitOutput.kekulizeerror_bitWidth() (InitOutput method) InitOutput.kekulizeerror_bond() (InitOutput method) InitOutput.kekulizeerror_cause() (InitOutput method) InitOutput.kekulizeerror_domain() (InitOutput method) InitOutput.kekulizeerror_end() (InitOutput method) InitOutput.kekulizeerror_expected() (InitOutput method) InitOutput.kekulizeerror_field() (InitOutput method) InitOutput.kekulizeerror_kind() (InitOutput method) InitOutput.kekulizeerror_message() (InitOutput method) InitOutput.kekulizeerror_problemAtoms() (InitOutput method) InitOutput.kekulizeerror_questions() (InitOutput method) InitOutput.kekulizeerror_reason() (InitOutput method) InitOutput.kekulizeparams_canonical() (InitOutput method) InitOutput.kekulizeparams_markAtomsBonds() (InitOutput method) InitOutput.kekulizeparams_maxBacktracks() (InitOutput method) InitOutput.kekulizeparams_new() (InitOutput method) InitOutput.kekulizeparams_set_canonical() (InitOutput method) InitOutput.kekulizeparams_set_markAtomsBonds() (InitOutput method) InitOutput.kekulizeparams_set_maxBacktracks() (InitOutput method) InitOutput.labuteasacontributions_asa() (InitOutput method) InitOutput.labuteasacontributions_atomContributions() (InitOutput method) InitOutput.labuteasacontributions_hydrogenContribution() (InitOutput method) InitOutput.layeredfingerprinterror_cause() (InitOutput method) InitOutput.layeredfingerprinterror_domain() (InitOutput method) InitOutput.layeredfingerprinterror_kind() (InitOutput method) InitOutput.layeredfingerprinterror_message() (InitOutput method) InitOutput.layeredfingerprintlayers_bits() (InitOutput method) InitOutput.layeredfingerprintlayers_fromBitsRetain() (InitOutput method) InitOutput.layeredfingerprintparams_atomCounts() (InitOutput method) InitOutput.layeredfingerprintparams_branchedPaths() (InitOutput method) InitOutput.layeredfingerprintparams_fpSize() (InitOutput method) InitOutput.layeredfingerprintparams_fromAtoms() (InitOutput method) InitOutput.layeredfingerprintparams_layers() (InitOutput method) InitOutput.layeredfingerprintparams_maxPath() (InitOutput method) InitOutput.layeredfingerprintparams_minPath() (InitOutput method) InitOutput.layeredfingerprintparams_new() (InitOutput method) InitOutput.layeredfingerprintparams_set_atomCounts() (InitOutput method) InitOutput.layeredfingerprintparams_set_branchedPaths() (InitOutput method) InitOutput.layeredfingerprintparams_set_fpSize() (InitOutput method) InitOutput.layeredfingerprintparams_set_fromAtoms() (InitOutput method) InitOutput.layeredfingerprintparams_set_layers() (InitOutput method) InitOutput.layeredfingerprintparams_set_maxPath() (InitOutput method) InitOutput.layeredfingerprintparams_set_minPath() (InitOutput method) InitOutput.layeredfingerprintparams_set_setOnlyBits() (InitOutput method) InitOutput.layeredfingerprintparams_setOnlyBits() (InitOutput method) InitOutput.layeredfingerprintresult_atomCounts() (InitOutput method) InitOutput.layeredfingerprintresult_fingerprint() (InitOutput method) InitOutput.legacytopologicaltorsionparams_bitsPerEntry() (InitOutput method) InitOutput.legacytopologicaltorsionparams_construct() (InitOutput method) InitOutput.legacytopologicaltorsionparams_customAtomInvariants() (InitOutput method) InitOutput.legacytopologicaltorsionparams_fpSize() (InitOutput method) InitOutput.legacytopologicaltorsionparams_fromAtoms() (InitOutput method) InitOutput.legacytopologicaltorsionparams_ignoreAtoms() (InitOutput method) InitOutput.legacytopologicaltorsionparams_includeChirality() (InitOutput method) InitOutput.legacytopologicaltorsionparams_new() (InitOutput method) InitOutput.legacytopologicaltorsionparams_set_bitsPerEntry() (InitOutput method) InitOutput.legacytopologicaltorsionparams_set_customAtomInvariants() (InitOutput method) InitOutput.legacytopologicaltorsionparams_set_fpSize() (InitOutput method) InitOutput.legacytopologicaltorsionparams_set_fromAtoms() (InitOutput method) InitOutput.legacytopologicaltorsionparams_set_ignoreAtoms() (InitOutput method) InitOutput.legacytopologicaltorsionparams_set_includeChirality() (InitOutput method) InitOutput.legacytopologicaltorsionparams_set_torsionAtomCount() (InitOutput method) InitOutput.legacytopologicaltorsionparams_torsionAtomCount() (InitOutput method) InitOutput.ligandref_atom() (InitOutput method) InitOutput.ligandref_isImplicitHydrogen() (InitOutput method) InitOutput.ligandref_new() (InitOutput method) InitOutput.maccsfingerprinterror_bit() (InitOutput method) InitOutput.maccsfingerprinterror_cause() (InitOutput method) InitOutput.maccsfingerprinterror_domain() (InitOutput method) InitOutput.maccsfingerprinterror_kind() (InitOutput method) InitOutput.maccsfingerprinterror_message() (InitOutput method) InitOutput.maccsfingerprinterror_option() (InitOutput method) InitOutput.maccsfingerprinterror_reason() (InitOutput method) InitOutput.maccsfingerprintparams_nBits() (InitOutput method) InitOutput.maccsfingerprintparams_new() (InitOutput method) InitOutput.maccsfingerprintparams_set_nBits() (InitOutput method) InitOutput.matcherror_cause() (InitOutput method) InitOutput.matcherror_domain() (InitOutput method) InitOutput.matcherror_kind() (InitOutput method) InitOutput.matcherror_message() (InitOutput method) InitOutput.matchresult_atomMapping() (InitOutput method) InitOutput.matchresult_atomPairs() (InitOutput method) InitOutput.matchresult_bondMapping() (InitOutput method) InitOutput.matrixerror_atom() (InitOutput method) InitOutput.matrixerror_atomCount() (InitOutput method) InitOutput.matrixerror_bond() (InitOutput method) InitOutput.matrixerror_bondCount() (InitOutput method) InitOutput.matrixerror_cause() (InitOutput method) InitOutput.matrixerror_conformerId() (InitOutput method) InitOutput.matrixerror_dimension() (InitOutput method) InitOutput.matrixerror_domain() (InitOutput method) InitOutput.matrixerror_endpoint() (InitOutput method) InitOutput.matrixerror_firstPosition() (InitOutput method) InitOutput.matrixerror_kind() (InitOutput method) InitOutput.matrixerror_message() (InitOutput method) InitOutput.matrixerror_order() (InitOutput method) InitOutput.matrixerror_position() (InitOutput method) InitOutput.matrixerror_secondPosition() (InitOutput method) InitOutput.maximumCommonSubstructure() (InitOutput method) InitOutput.maximumCommonSubstructureWithParams() (InitOutput method) InitOutput.mcsatomcompareparameters_completeRingsOnly() (InitOutput method) InitOutput.mcsatomcompareparameters_matchChiralTag() (InitOutput method) InitOutput.mcsatomcompareparameters_matchFormalCharge() (InitOutput method) InitOutput.mcsatomcompareparameters_matchIsotope() (InitOutput method) InitOutput.mcsatomcompareparameters_matchValences() (InitOutput method) InitOutput.mcsatomcompareparameters_maxDistance() (InitOutput method) InitOutput.mcsatomcompareparameters_new() (InitOutput method) InitOutput.mcsatomcompareparameters_ringMatchesRingOnly() (InitOutput method) InitOutput.mcsatomcompareparameters_set_completeRingsOnly() (InitOutput method) InitOutput.mcsatomcompareparameters_set_matchChiralTag() (InitOutput method) InitOutput.mcsatomcompareparameters_set_matchFormalCharge() (InitOutput method) InitOutput.mcsatomcompareparameters_set_matchIsotope() (InitOutput method) InitOutput.mcsatomcompareparameters_set_matchValences() (InitOutput method) InitOutput.mcsatomcompareparameters_set_maxDistance() (InitOutput method) InitOutput.mcsatomcompareparameters_set_ringMatchesRingOnly() (InitOutput method) InitOutput.mcsbondcompareparameters_completeRingsOnly() (InitOutput method) InitOutput.mcsbondcompareparameters_matchFusedRings() (InitOutput method) InitOutput.mcsbondcompareparameters_matchFusedRingsStrict() (InitOutput method) InitOutput.mcsbondcompareparameters_matchStereo() (InitOutput method) InitOutput.mcsbondcompareparameters_new() (InitOutput method) InitOutput.mcsbondcompareparameters_ringMatchesRingOnly() (InitOutput method) InitOutput.mcsbondcompareparameters_set_completeRingsOnly() (InitOutput method) InitOutput.mcsbondcompareparameters_set_matchFusedRings() (InitOutput method) InitOutput.mcsbondcompareparameters_set_matchFusedRingsStrict() (InitOutput method) InitOutput.mcsbondcompareparameters_set_matchStereo() (InitOutput method) InitOutput.mcsbondcompareparameters_set_ringMatchesRingOnly() (InitOutput method) InitOutput.mcserror_domain() (InitOutput method) InitOutput.mcserror_kind() (InitOutput method) InitOutput.mcserror_message() (InitOutput method) InitOutput.mcsparameters_atomComparator() (InitOutput method) InitOutput.mcsparameters_atomCompareParameters() (InitOutput method) InitOutput.mcsparameters_bondComparator() (InitOutput method) InitOutput.mcsparameters_bondCompareParameters() (InitOutput method) InitOutput.mcsparameters_initialSeed() (InitOutput method) InitOutput.mcsparameters_maximizeBonds() (InitOutput method) InitOutput.mcsparameters_new() (InitOutput method) InitOutput.mcsparameters_set_atomComparator() (InitOutput method) InitOutput.mcsparameters_set_atomCompareParameters() (InitOutput method) InitOutput.mcsparameters_set_bondComparator() (InitOutput method) InitOutput.mcsparameters_set_bondCompareParameters() (InitOutput method) InitOutput.mcsparameters_set_initialSeed() (InitOutput method) InitOutput.mcsparameters_set_maximizeBonds() (InitOutput method) InitOutput.mcsparameters_set_storeAll() (InitOutput method) InitOutput.mcsparameters_set_threshold() (InitOutput method) InitOutput.mcsparameters_set_timeout() (InitOutput method) InitOutput.mcsparameters_set_verbose() (InitOutput method) InitOutput.mcsparameters_storeAll() (InitOutput method) InitOutput.mcsparameters_threshold() (InitOutput method) InitOutput.mcsparameters_timeout() (InitOutput method) InitOutput.mcsparameters_verbose() (InitOutput method) InitOutput.mcsresult_atomCount() (InitOutput method) InitOutput.mcsresult_bondCount() (InitOutput method) InitOutput.mcsresult_completed() (InitOutput method) InitOutput.mcsresult_degenerate() (InitOutput method) InitOutput.mcsresult_query() (InitOutput method) InitOutput.mcsresult_smarts() (InitOutput method) InitOutput.memory (InitOutput attribute) InitOutput.mmffatomproperties_atomType() (InitOutput method) InitOutput.mmffatomproperties_formalCharge() (InitOutput method) InitOutput.mmffatomproperties_partialCharge() (InitOutput method) InitOutput.mmffconformeroptimizationparams_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.mmffconformeroptimizationparams_maxIterations() (InitOutput method) InitOutput.mmffconformeroptimizationparams_mmffVariant() (InitOutput method) InitOutput.mmffconformeroptimizationparams_new() (InitOutput method) InitOutput.mmffconformeroptimizationparams_nonBondedThreshold() (InitOutput method) InitOutput.mmffconformeroptimizationparams_numThreads() (InitOutput method) InitOutput.mmffconformeroptimizationparams_set_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.mmffconformeroptimizationparams_set_maxIterations() (InitOutput method) InitOutput.mmffconformeroptimizationparams_set_mmffVariant() (InitOutput method) InitOutput.mmffconformeroptimizationparams_set_nonBondedThreshold() (InitOutput method) InitOutput.mmffconformeroptimizationparams_set_numThreads() (InitOutput method) InitOutput.mmffenergygradient_energy() (InitOutput method) InitOutput.mmffenergygradient_gradient() (InitOutput method) InitOutput.mmffevaluationparams_conformerId() (InitOutput method) InitOutput.mmffevaluationparams_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.mmffevaluationparams_mmffVariant() (InitOutput method) InitOutput.mmffevaluationparams_new() (InitOutput method) InitOutput.mmffevaluationparams_nonBondedThreshold() (InitOutput method) InitOutput.mmffevaluationparams_set_conformerId() (InitOutput method) InitOutput.mmffevaluationparams_set_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.mmffevaluationparams_set_mmffVariant() (InitOutput method) InitOutput.mmffevaluationparams_set_nonBondedThreshold() (InitOutput method) InitOutput.mmffforcefielderror_actual() (InitOutput method) InitOutput.mmffforcefielderror_atomIndex() (InitOutput method) InitOutput.mmffforcefielderror_cause() (InitOutput method) InitOutput.mmffforcefielderror_component() (InitOutput method) InitOutput.mmffforcefielderror_expected() (InitOutput method) InitOutput.mmffforcefielderror_kind() (InitOutput method) InitOutput.mmffforcefielderror_message() (InitOutput method) InitOutput.mmffforcefielderror_requested() (InitOutput method) InitOutput.mmffforcefieldparams_conformerId() (InitOutput method) InitOutput.mmffforcefieldparams_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.mmffforcefieldparams_mmffVariant() (InitOutput method) InitOutput.mmffforcefieldparams_new() (InitOutput method) InitOutput.mmffforcefieldparams_nonBondedThreshold() (InitOutput method) InitOutput.mmffforcefieldparams_set_conformerId() (InitOutput method) InitOutput.mmffforcefieldparams_set_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.mmffforcefieldparams_set_mmffVariant() (InitOutput method) InitOutput.mmffforcefieldparams_set_nonBondedThreshold() (InitOutput method) InitOutput.mmffmolpropertieserror_cause() (InitOutput method) InitOutput.mmffmolpropertieserror_domain() (InitOutput method) InitOutput.mmffmolpropertieserror_kind() (InitOutput method) InitOutput.mmffmolpropertieserror_message() (InitOutput method) InitOutput.mmffoptimizationerror_cause() (InitOutput method) InitOutput.mmffoptimizationerror_message() (InitOutput method) InitOutput.mmffoptimizationparams_conformerId() (InitOutput method) InitOutput.mmffoptimizationparams_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.mmffoptimizationparams_maxIterations() (InitOutput method) InitOutput.mmffoptimizationparams_mmffVariant() (InitOutput method) InitOutput.mmffoptimizationparams_new() (InitOutput method) InitOutput.mmffoptimizationparams_nonBondedThreshold() (InitOutput method) InitOutput.mmffoptimizationparams_set_conformerId() (InitOutput method) InitOutput.mmffoptimizationparams_set_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.mmffoptimizationparams_set_maxIterations() (InitOutput method) InitOutput.mmffoptimizationparams_set_mmffVariant() (InitOutput method) InitOutput.mmffoptimizationparams_set_nonBondedThreshold() (InitOutput method) InitOutput.mmffoptimizemoleculeconfresult_energy() (InitOutput method) InitOutput.mmffoptimizemoleculeconfresult_needsMore() (InitOutput method) InitOutput.mmffoptimizemoleculeconfresult_statusCode() (InitOutput method) InitOutput.mmffoptimizemoleculeconfsresult_conformerResults() (InitOutput method) InitOutput.mmffoptimizemoleculeconfsresult_molecule() (InitOutput method) InitOutput.mmffoptimizemoleculeresult_molecule() (InitOutput method) InitOutput.mmffoptimizemoleculeresult_needsMore() (InitOutput method) InitOutput.mmffoptimizemoleculeresult_statusCode() (InitOutput method) InitOutput.mmffproperties_atoms() (InitOutput method) InitOutput.mmffproperties_atomType() (InitOutput method) InitOutput.mmffproperties_formalCharge() (InitOutput method) InitOutput.mmffproperties_isValid() (InitOutput method) InitOutput.mmffproperties_partialCharge() (InitOutput method) InitOutput.mmffproperties_variant() (InitOutput method) InitOutput.mmffpropertiesparams_mmffVariant() (InitOutput method) InitOutput.mmffpropertiesparams_new() (InitOutput method) InitOutput.mmffpropertiesparams_set_mmffVariant() (InitOutput method) InitOutput.mol2posterror_cause() (InitOutput method) InitOutput.mol2posterror_domain() (InitOutput method) InitOutput.mol2posterror_kind() (InitOutput method) InitOutput.mol2posterror_message() (InitOutput method) InitOutput.mol2posterror_stage() (InitOutput method) InitOutput.mol2readerror_cause() (InitOutput method) InitOutput.mol2readerror_domain() (InitOutput method) InitOutput.mol2readerror_feature() (InitOutput method) InitOutput.mol2readerror_kind() (InitOutput method) InitOutput.mol2readerror_message() (InitOutput method) InitOutput.mol2readerror_parseDetail() (InitOutput method) InitOutput.mol2readparams_cleanupSubstructures() (InitOutput method) InitOutput.mol2readparams_new() (InitOutput method) InitOutput.mol2readparams_removeHs() (InitOutput method) InitOutput.mol2readparams_sanitize() (InitOutput method) InitOutput.mol2readparams_set_cleanupSubstructures() (InitOutput method) InitOutput.mol2readparams_set_removeHs() (InitOutput method) InitOutput.mol2readparams_set_sanitize() (InitOutput method) InitOutput.mol2readparams_set_variant() (InitOutput method) InitOutput.mol2readparams_variant() (InitOutput method) InitOutput.molblockwriteparams_coordinateSelection() (InitOutput method) InitOutput.molblockwriteparams_force2d() (InitOutput method) InitOutput.molblockwriteparams_format() (InitOutput method) InitOutput.molblockwriteparams_includeCoordinates() (InitOutput method) InitOutput.molblockwriteparams_includeStereo() (InitOutput method) InitOutput.molblockwriteparams_kekulize() (InitOutput method) InitOutput.molblockwriteparams_new() (InitOutput method) InitOutput.molblockwriteparams_precision() (InitOutput method) InitOutput.molblockwriteparams_set_coordinateSelection() (InitOutput method) InitOutput.molblockwriteparams_set_force2d() (InitOutput method) InitOutput.molblockwriteparams_set_format() (InitOutput method) InitOutput.molblockwriteparams_set_includeCoordinates() (InitOutput method) InitOutput.molblockwriteparams_set_includeStereo() (InitOutput method) InitOutput.molblockwriteparams_set_kekulize() (InitOutput method) InitOutput.molblockwriteparams_set_precision() (InitOutput method) InitOutput.molcoordinateselection_Auto() (InitOutput method) InitOutput.molcoordinateselection_id() (InitOutput method) InitOutput.molcoordinateselection_kind() (InitOutput method) InitOutput.molcoordinateselection_ThreeD() (InitOutput method) InitOutput.molcoordinateselection_TwoD() (InitOutput method) InitOutput.molecularforcefield_energy() (InitOutput method) InitOutput.molecularforcefield_energyGradient() (InitOutput method) InitOutput.molecularforcefield_fixedAtoms() (InitOutput method) InitOutput.molecularforcefield_gradient() (InitOutput method) InitOutput.molecularforcefield_gradientUnconstrained() (InitOutput method) InitOutput.molecularforcefield_minimize() (InitOutput method) InitOutput.molecularforcefield_minimizeWithParams() (InitOutput method) InitOutput.molecularforcefield_position() (InitOutput method) InitOutput.molecularforcefield_positions() (InitOutput method) InitOutput.molecularforcefield_setFixedAtoms() (InitOutput method) InitOutput.molecularforcefield_setPosition() (InitOutput method) InitOutput.molecularforcefield_setPositions() (InitOutput method) InitOutput.molecularioerror_cause() (InitOutput method) InitOutput.molecularioerror_coordinateId() (InitOutput method) InitOutput.molecularioerror_coordinateKind() (InitOutput method) InitOutput.molecularioerror_dimension() (InitOutput method) InitOutput.molecularioerror_domain() (InitOutput method) InitOutput.molecularioerror_errno() (InitOutput method) InitOutput.molecularioerror_filename() (InitOutput method) InitOutput.molecularioerror_format() (InitOutput method) InitOutput.molecularioerror_ioKind() (InitOutput method) InitOutput.molecularioerror_kind() (InitOutput method) InitOutput.molecularioerror_message() (InitOutput method) InitOutput.molecularioerror_parameterDetail() (InitOutput method) InitOutput.molecularioerror_parameterName() (InitOutput method) InitOutput.molecularioerror_stage() (InitOutput method) InitOutput.molecularioerror_threeD() (InitOutput method) InitOutput.molecularioerror_twoD() (InitOutput method) InitOutput.molecule_add3dConformer() (InitOutput method) InitOutput.molecule_add3dConformerWithParams() (InitOutput method) InitOutput.molecule_addHydrogens() (InitOutput method) InitOutput.molecule_addHydrogensWithParams() (InitOutput method) InitOutput.molecule_alignConformers() (InitOutput method) InitOutput.molecule_alignConformersWithParams() (InitOutput method) InitOutput.molecule_alignmentTransformTo() (InitOutput method) InitOutput.molecule_alignmentTransformToWithParams() (InitOutput method) InitOutput.molecule_alignTo() (InitOutput method) InitOutput.molecule_alignToWithParams() (InitOutput method) InitOutput.molecule_allConformerBestRmsds() (InitOutput method) InitOutput.molecule_allConformerBestRmsdsWithParams() (InitOutput method) InitOutput.molecule_applyReaction() (InitOutput method) InitOutput.molecule_applyReaction_() (InitOutput method) InitOutput.molecule_applyReactionWithParams() (InitOutput method) InitOutput.molecule_applyReactionWithParams_() (InitOutput method) InitOutput.molecule_assignAromaticity() (InitOutput method) InitOutput.molecule_assignAromaticityWithParams() (InitOutput method) InitOutput.molecule_assignChiralTagsFromStructure() (InitOutput method) InitOutput.molecule_assignChiralTagsFromStructureWithParams() (InitOutput method) InitOutput.molecule_assignCipLabels() (InitOutput method) InitOutput.molecule_assignCipLabelsWithOptions() (InitOutput method) InitOutput.molecule_assignRadicals() (InitOutput method) InitOutput.molecule_assignRingFamilies() (InitOutput method) InitOutput.molecule_assignRingFamiliesWithParams() (InitOutput method) InitOutput.molecule_assignRings() (InitOutput method) InitOutput.molecule_assignValence() (InitOutput method) InitOutput.molecule_assignValenceWithParams() (InitOutput method) InitOutput.molecule_atom() (InitOutput method) InitOutput.molecule_atomicNumbers() (InitOutput method) InitOutput.molecule_atomMetadata() (InitOutput method) InitOutput.molecule_atomProperty() (InitOutput method) InitOutput.molecule_atomPropertyString() (InitOutput method) InitOutput.molecule_atoms() (InitOutput method) InitOutput.molecule_bestAlignmentTo() (InitOutput method) InitOutput.molecule_bestAlignmentToWithParams() (InitOutput method) InitOutput.molecule_bestRmsdTo() (InitOutput method) InitOutput.molecule_bestRmsdToWithParams() (InitOutput method) InitOutput.molecule_bond() (InitOutput method) InitOutput.molecule_bondPropertyString() (InitOutput method) InitOutput.molecule_bonds() (InitOutput method) InitOutput.molecule_canonicalTautomer() (InitOutput method) InitOutput.molecule_canonicalTautomerWithParams() (InitOutput method) InitOutput.molecule_chi0() (InitOutput method) InitOutput.molecule_chi0N() (InitOutput method) InitOutput.molecule_chi0NWithParams() (InitOutput method) InitOutput.molecule_chi0V() (InitOutput method) InitOutput.molecule_chi0VWithParams() (InitOutput method) InitOutput.molecule_chi1() (InitOutput method) InitOutput.molecule_chi1N() (InitOutput method) InitOutput.molecule_chi1NWithParams() (InitOutput method) InitOutput.molecule_chi1V() (InitOutput method) InitOutput.molecule_chi1VWithParams() (InitOutput method) InitOutput.molecule_chi2N() (InitOutput method) InitOutput.molecule_chi2NWithParams() (InitOutput method) InitOutput.molecule_chi2V() (InitOutput method) InitOutput.molecule_chi2VWithParams() (InitOutput method) InitOutput.molecule_chi3N() (InitOutput method) InitOutput.molecule_chi3NWithParams() (InitOutput method) InitOutput.molecule_chi3V() (InitOutput method) InitOutput.molecule_chi3VWithParams() (InitOutput method) InitOutput.molecule_chi4N() (InitOutput method) InitOutput.molecule_chi4NWithParams() (InitOutput method) InitOutput.molecule_chi4V() (InitOutput method) InitOutput.molecule_chi4VWithParams() (InitOutput method) InitOutput.molecule_chiNN() (InitOutput method) InitOutput.molecule_chiNNWithParams() (InitOutput method) InitOutput.molecule_chiNV() (InitOutput method) InitOutput.molecule_chiNVWithParams() (InitOutput method) InitOutput.molecule_cipComputed() (InitOutput method) InitOutput.molecule_clear3dConformers() (InitOutput method) InitOutput.molecule_compute2dCoordinates() (InitOutput method) InitOutput.molecule_compute2dCoordinatesWithParams() (InitOutput method) InitOutput.molecule_conformers3d() (InitOutput method) InitOutput.molecule_coordinateRmsdTo() (InitOutput method) InitOutput.molecule_coordinateRmsdToWithParams() (InitOutput method) InitOutput.molecule_coordinates2d() (InitOutput method) InitOutput.molecule_coordinates3d() (InitOutput method) InitOutput.molecule_crippenDescriptors() (InitOutput method) InitOutput.molecule_crippenDescriptorsWithParams() (InitOutput method) InitOutput.molecule_detectChemistryProblems() (InitOutput method) InitOutput.molecule_detectChemistryProblemsWithParams() (InitOutput method) InitOutput.molecule_dgBoundsMatrix() (InitOutput method) InitOutput.molecule_distanceMatrix() (InitOutput method) InitOutput.molecule_distanceMatrix3d() (InitOutput method) InitOutput.molecule_distanceMatrix3dWithParams() (InitOutput method) InitOutput.molecule_distanceMatrixWithParams() (InitOutput method) InitOutput.molecule_embed3dConformer() (InitOutput method) InitOutput.molecule_embed3dConformerResult() (InitOutput method) InitOutput.molecule_embed3dConformerResultWithParams() (InitOutput method) InitOutput.molecule_embed3dConformers() (InitOutput method) InitOutput.molecule_embed3dConformersResult() (InitOutput method) InitOutput.molecule_embed3dConformersResultWithParams() (InitOutput method) InitOutput.molecule_embed3dConformersWithParams() (InitOutput method) InitOutput.molecule_embed3dConformerWithParams() (InitOutput method) InitOutput.molecule_enumerateStereoisomers() (InitOutput method) InitOutput.molecule_enumerateStereoisomersWithOptions() (InitOutput method) InitOutput.molecule_enumerateStereoisomersWithRandomBits() (InitOutput method) InitOutput.molecule_enumerateTautomers() (InitOutput method) InitOutput.molecule_enumerateTautomersWithParams() (InitOutput method) InitOutput.molecule_exactMolecularWeight() (InitOutput method) InitOutput.molecule_exactMolecularWeightWithParams() (InitOutput method) InitOutput.molecule_findChiralCenters() (InitOutput method) InitOutput.molecule_fingerprintAtomPair() (InitOutput method) InitOutput.molecule_fingerprintAtomPairCount() (InitOutput method) InitOutput.molecule_fingerprintAtomPairCountWithParams() (InitOutput method) InitOutput.molecule_fingerprintAtomPairSparse() (InitOutput method) InitOutput.molecule_fingerprintAtomPairSparseCount() (InitOutput method) InitOutput.molecule_fingerprintAtomPairSparseCountWithParams() (InitOutput method) InitOutput.molecule_fingerprintAtomPairSparseWithParams() (InitOutput method) InitOutput.molecule_fingerprintAtomPairWithParams() (InitOutput method) InitOutput.molecule_fingerprintAvalon() (InitOutput method) InitOutput.molecule_fingerprintAvalonWithParams() (InitOutput method) InitOutput.molecule_fingerprintLayered() (InitOutput method) InitOutput.molecule_fingerprintLayeredWithOutput() (InitOutput method) InitOutput.molecule_fingerprintLayeredWithOutputWithParams() (InitOutput method) InitOutput.molecule_fingerprintLayeredWithParams() (InitOutput method) InitOutput.molecule_fingerprintMaccs() (InitOutput method) InitOutput.molecule_fingerprintMaccsRaw() (InitOutput method) InitOutput.molecule_fingerprintMaccsWithParams() (InitOutput method) InitOutput.molecule_fingerprintMorgan() (InitOutput method) InitOutput.molecule_fingerprintMorganCount() (InitOutput method) InitOutput.molecule_fingerprintMorganCountWithGenerator() (InitOutput method) InitOutput.molecule_fingerprintMorganCountWithParams() (InitOutput method) InitOutput.molecule_fingerprintMorganSparse() (InitOutput method) InitOutput.molecule_fingerprintMorganSparseCount() (InitOutput method) InitOutput.molecule_fingerprintMorganSparseCountWithGenerator() (InitOutput method) InitOutput.molecule_fingerprintMorganSparseCountWithParams() (InitOutput method) InitOutput.molecule_fingerprintMorganSparseWithGenerator() (InitOutput method) InitOutput.molecule_fingerprintMorganSparseWithParams() (InitOutput method) InitOutput.molecule_fingerprintMorganWithGenerator() (InitOutput method) InitOutput.molecule_fingerprintMorganWithParams() (InitOutput method) InitOutput.molecule_fingerprintPattern() (InitOutput method) InitOutput.molecule_fingerprintPatternWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopological() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsion() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionCount() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionCountLegacy() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionCountLegacyWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionCountWithGenerator() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionCountWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionLegacy() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionLegacyWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionSparse() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionSparseCount() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionSparseCountLegacy() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionSparseCountLegacyWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionSparseCountWithGenerator() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionSparseCountWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionSparseWithGenerator() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionSparseWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionWithGenerator() (InitOutput method) InitOutput.molecule_fingerprintTopologicalTorsionWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopologicalWithOutput() (InitOutput method) InitOutput.molecule_fingerprintTopologicalWithOutputWithParams() (InitOutput method) InitOutput.molecule_fingerprintTopologicalWithParams() (InitOutput method) InitOutput.molecule_fractionCsp3() (InitOutput method) InitOutput.molecule_fragments() (InitOutput method) InitOutput.molecule_fromInchi() (InitOutput method) InitOutput.molecule_fromInchiWithParams() (InitOutput method) InitOutput.molecule_fromMol() (InitOutput method) InitOutput.molecule_fromMol2() (InitOutput method) InitOutput.molecule_fromMol2WithParams() (InitOutput method) InitOutput.molecule_fromMolWithParams() (InitOutput method) InitOutput.molecule_fromParts() (InitOutput method) InitOutput.molecule_fromSdf() (InitOutput method) InitOutput.molecule_fromSdfWithParams() (InitOutput method) InitOutput.molecule_fromSmiles() (InitOutput method) InitOutput.molecule_fromSmilesWithParams() (InitOutput method) InitOutput.molecule_fromSmilesWithSanitize() (InitOutput method) InitOutput.molecule_fromXyzBlock() (InitOutput method) InitOutput.molecule_hallKierAlpha() (InitOutput method) InitOutput.molecule_hallKierAlphaWithContributions() (InitOutput method) InitOutput.molecule_has2dCoordinates() (InitOutput method) InitOutput.molecule_hasSubstructMatch() (InitOutput method) InitOutput.molecule_hasSubstructMatchWithParams() (InitOutput method) InitOutput.molecule_hasValenceViolation() (InitOutput method) InitOutput.molecule_kappa1() (InitOutput method) InitOutput.molecule_kappa2() (InitOutput method) InitOutput.molecule_kappa3() (InitOutput method) InitOutput.molecule_kekulizeBonds() (InitOutput method) InitOutput.molecule_kekulizeBondsWithParams() (InitOutput method) InitOutput.molecule_labuteAsa() (InitOutput method) InitOutput.molecule_labuteAsaContributions() (InitOutput method) InitOutput.molecule_labuteAsaContributionsWithParams() (InitOutput method) InitOutput.molecule_labuteAsaWithParams() (InitOutput method) InitOutput.molecule_largestFragment() (InitOutput method) InitOutput.molecule_lipinskiHba() (InitOutput method) InitOutput.molecule_lipinskiHbd() (InitOutput method) InitOutput.molecule_mmffEnergyGradient() (InitOutput method) InitOutput.molecule_mmffEnergyGradientWithParams() (InitOutput method) InitOutput.molecule_mmffForceField() (InitOutput method) InitOutput.molecule_mmffForceFieldWithParams() (InitOutput method) InitOutput.molecule_mmffHasAllMoleculeParams() (InitOutput method) InitOutput.molecule_mmffProperties() (InitOutput method) InitOutput.molecule_mmffPropertiesWithParams() (InitOutput method) InitOutput.molecule_molecularFormula() (InitOutput method) InitOutput.molecule_molecularFormulaWithParams() (InitOutput method) InitOutput.molecule_molecularHash() (InitOutput method) InitOutput.molecule_molecularHashWithRanks() (InitOutput method) InitOutput.molecule_molecularWeight() (InitOutput method) InitOutput.molecule_molecularWeightWithParams() (InitOutput method) InitOutput.molecule_mqns() (InitOutput method) InitOutput.molecule_murckoDecompose() (InitOutput method) InitOutput.molecule_murckoScaffold() (InitOutput method) InitOutput.molecule_nameOrEmpty() (InitOutput method) InitOutput.molecule_netScaffold() (InitOutput method) InitOutput.molecule_new() (InitOutput method) InitOutput.molecule_num3dConformers() (InitOutput method) InitOutput.molecule_numAliphaticCarbocycles() (InitOutput method) InitOutput.molecule_numAliphaticHeterocycles() (InitOutput method) InitOutput.molecule_numAliphaticRings() (InitOutput method) InitOutput.molecule_numAmideBonds() (InitOutput method) InitOutput.molecule_numAromaticCarbocycles() (InitOutput method) InitOutput.molecule_numAromaticHeterocycles() (InitOutput method) InitOutput.molecule_numAromaticRings() (InitOutput method) InitOutput.molecule_numAtoms() (InitOutput method) InitOutput.molecule_numAtomStereoCenters() (InitOutput method) InitOutput.molecule_numBonds() (InitOutput method) InitOutput.molecule_numBridgeheadAtoms() (InitOutput method) InitOutput.molecule_numConformers3d() (InitOutput method) InitOutput.molecule_numHba() (InitOutput method) InitOutput.molecule_numHbd() (InitOutput method) InitOutput.molecule_numHeavyAtoms() (InitOutput method) InitOutput.molecule_numHeteroatoms() (InitOutput method) InitOutput.molecule_numHeterocycles() (InitOutput method) InitOutput.molecule_numRings() (InitOutput method) InitOutput.molecule_numRotatableBonds() (InitOutput method) InitOutput.molecule_numRotatableBondsWithParams() (InitOutput method) InitOutput.molecule_numSaturatedCarbocycles() (InitOutput method) InitOutput.molecule_numSaturatedHeterocycles() (InitOutput method) InitOutput.molecule_numSaturatedRings() (InitOutput method) InitOutput.molecule_numSpiroAtoms() (InitOutput method) InitOutput.molecule_numUnspecifiedAtomStereoCenters() (InitOutput method) InitOutput.molecule_perceiveStereochemistry() (InitOutput method) InitOutput.molecule_phi() (InitOutput method) InitOutput.molecule_potentialStereo() (InitOutput method) InitOutput.molecule_potentialStereoWithParams() (InitOutput method) InitOutput.molecule_properties() (InitOutput method) InitOutput.molecule_property() (InitOutput method) InitOutput.molecule_propertyKeys() (InitOutput method) InitOutput.molecule_propertyOrEmpty() (InitOutput method) InitOutput.molecule_qed() (InitOutput method) InitOutput.molecule_reactionProducts() (InitOutput method) InitOutput.molecule_reactionProductsFromInputs() (InitOutput method) InitOutput.molecule_reactionProductsWithParams() (InitOutput method) InitOutput.molecule_readMol() (InitOutput method) InitOutput.molecule_readMol2() (InitOutput method) InitOutput.molecule_readMol2WithParams() (InitOutput method) InitOutput.molecule_readMolWithParams() (InitOutput method) InitOutput.molecule_readSdf() (InitOutput method) InitOutput.molecule_readSdfWithParams() (InitOutput method) InitOutput.molecule_readXyz() (InitOutput method) InitOutput.molecule_removeHydrogens() (InitOutput method) InitOutput.molecule_removeHydrogensWithParams() (InitOutput method) InitOutput.molecule_sanitize() (InitOutput method) InitOutput.molecule_sanitize_() (InitOutput method) InitOutput.molecule_sanitizeWithParams() (InitOutput method) InitOutput.molecule_sanitizeWithParams_() (InitOutput method) InitOutput.molecule_sdfDataFieldNames() (InitOutput method) InitOutput.molecule_sdfDataFieldOrEmpty() (InitOutput method) InitOutput.molecule_set2dCoordinates() (InitOutput method) InitOutput.molecule_set2dCoordinatesWithParams() (InitOutput method) InitOutput.molecule_set3dCoordinates() (InitOutput method) InitOutput.molecule_set3dCoordinatesWithParams() (InitOutput method) InitOutput.molecule_setAtomPosition() (InitOutput method) InitOutput.molecule_setAtomPositionWithParams() (InitOutput method) InitOutput.molecule_setAtomProperty() (InitOutput method) InitOutput.molecule_setOnly3dConformer() (InitOutput method) InitOutput.molecule_setOnly3dConformerWithParams() (InitOutput method) InitOutput.molecule_slogpVsa() (InitOutput method) InitOutput.molecule_slogpVsa1() (InitOutput method) InitOutput.molecule_slogpVsa10() (InitOutput method) InitOutput.molecule_slogpVsa11() (InitOutput method) InitOutput.molecule_slogpVsa12() (InitOutput method) InitOutput.molecule_slogpVsa2() (InitOutput method) InitOutput.molecule_slogpVsa3() (InitOutput method) InitOutput.molecule_slogpVsa4() (InitOutput method) InitOutput.molecule_slogpVsa5() (InitOutput method) InitOutput.molecule_slogpVsa6() (InitOutput method) InitOutput.molecule_slogpVsa7() (InitOutput method) InitOutput.molecule_slogpVsa8() (InitOutput method) InitOutput.molecule_slogpVsa9() (InitOutput method) InitOutput.molecule_slogpVsaWithParams() (InitOutput method) InitOutput.molecule_smrVsa() (InitOutput method) InitOutput.molecule_smrVsa1() (InitOutput method) InitOutput.molecule_smrVsa10() (InitOutput method) InitOutput.molecule_smrVsa2() (InitOutput method) InitOutput.molecule_smrVsa3() (InitOutput method) InitOutput.molecule_smrVsa4() (InitOutput method) InitOutput.molecule_smrVsa5() (InitOutput method) InitOutput.molecule_smrVsa6() (InitOutput method) InitOutput.molecule_smrVsa7() (InitOutput method) InitOutput.molecule_smrVsa8() (InitOutput method) InitOutput.molecule_smrVsa9() (InitOutput method) InitOutput.molecule_smrVsaWithParams() (InitOutput method) InitOutput.molecule_stereoisomerCount() (InitOutput method) InitOutput.molecule_stereoisomerCountWithOptions() (InitOutput method) InitOutput.molecule_substructMatch() (InitOutput method) InitOutput.molecule_substructMatches() (InitOutput method) InitOutput.molecule_substructMatchesCompiled() (InitOutput method) InitOutput.molecule_substructMatchesWithParams() (InitOutput method) InitOutput.molecule_substructMatchWithParams() (InitOutput method) InitOutput.molecule_tautomerScore() (InitOutput method) InitOutput.molecule_tautomerScoreWithParams() (InitOutput method) InitOutput.molecule_tetrahedralStereo() (InitOutput method) InitOutput.molecule_toBuilder() (InitOutput method) InitOutput.molecule_toCxSmarts() (InitOutput method) InitOutput.molecule_toCxSmartsWithParams() (InitOutput method) InitOutput.molecule_toCxSmiles() (InitOutput method) InitOutput.molecule_toCxSmilesWithParams() (InitOutput method) InitOutput.molecule_toFragmentCxSmiles() (InitOutput method) InitOutput.molecule_toFragmentCxSmilesWithParams() (InitOutput method) InitOutput.molecule_toFragmentSmiles() (InitOutput method) InitOutput.molecule_toFragmentSmilesWithParams() (InitOutput method) InitOutput.molecule_toInchi() (InitOutput method) InitOutput.molecule_toInchiKey() (InitOutput method) InitOutput.molecule_toInchiKeyWithParams() (InitOutput method) InitOutput.molecule_toInchiWithParams() (InitOutput method) InitOutput.molecule_toMol() (InitOutput method) InitOutput.molecule_toMolWithParams() (InitOutput method) InitOutput.molecule_toPng() (InitOutput method) InitOutput.molecule_topologicalTorsionIds() (InitOutput method) InitOutput.molecule_topologicalTorsionIdsWithParams() (InitOutput method) InitOutput.molecule_topologicalTorsionPathScore() (InitOutput method) InitOutput.molecule_topology() (InitOutput method) InitOutput.molecule_toRandomSmiles() (InitOutput method) InitOutput.molecule_toRandomSmilesWithParams() (InitOutput method) InitOutput.molecule_toSdf() (InitOutput method) InitOutput.molecule_toSdf2d() (InitOutput method) InitOutput.molecule_toSdf2dWithParams() (InitOutput method) InitOutput.molecule_toSdf3d() (InitOutput method) InitOutput.molecule_toSdf3dWithParams() (InitOutput method) InitOutput.molecule_toSdfWithParams() (InitOutput method) InitOutput.molecule_toSmarts() (InitOutput method) InitOutput.molecule_toSmartsWithParams() (InitOutput method) InitOutput.molecule_toSmiles() (InitOutput method) InitOutput.molecule_toSmilesWithParams() (InitOutput method) InitOutput.molecule_toSvg() (InitOutput method) InitOutput.molecule_totalAtomCount() (InitOutput method) InitOutput.molecule_toXyz() (InitOutput method) InitOutput.molecule_toXyzWithParams() (InitOutput method) InitOutput.molecule_tpsa() (InitOutput method) InitOutput.molecule_tpsaWithParams() (InitOutput method) InitOutput.molecule_uffEnergyGradient() (InitOutput method) InitOutput.molecule_uffEnergyGradientWithParams() (InitOutput method) InitOutput.molecule_uffForceField() (InitOutput method) InitOutput.molecule_uffForceFieldWithParams() (InitOutput method) InitOutput.molecule_uffHasAllMoleculeParams() (InitOutput method) InitOutput.molecule_with2dCoordinateBlock() (InitOutput method) InitOutput.molecule_with2dCoordinateBlockWithParams() (InitOutput method) InitOutput.molecule_with2dCoordinates() (InitOutput method) InitOutput.molecule_with2dCoordinatesWithParams() (InitOutput method) InitOutput.molecule_with3dConformer() (InitOutput method) InitOutput.molecule_with3dConformerResult() (InitOutput method) InitOutput.molecule_with3dConformerResultWithParams() (InitOutput method) InitOutput.molecule_with3dConformers() (InitOutput method) InitOutput.molecule_with3dConformersResult() (InitOutput method) InitOutput.molecule_with3dConformersResultWithParams() (InitOutput method) InitOutput.molecule_with3dConformersWithParams() (InitOutput method) InitOutput.molecule_with3dConformerWithParams() (InitOutput method) InitOutput.molecule_with3dCoordinates() (InitOutput method) InitOutput.molecule_with3dCoordinatesWithParams() (InitOutput method) InitOutput.molecule_withAdded3dConformer() (InitOutput method) InitOutput.molecule_withAdded3dConformerWithParams() (InitOutput method) InitOutput.molecule_withAlignedConformers() (InitOutput method) InitOutput.molecule_withAlignedConformersWithParams() (InitOutput method) InitOutput.molecule_withAlignmentTo() (InitOutput method) InitOutput.molecule_withAlignmentToWithParams() (InitOutput method) InitOutput.molecule_withAssignedAromaticity() (InitOutput method) InitOutput.molecule_withAssignedAromaticityWithParams() (InitOutput method) InitOutput.molecule_withAssignedRadicals() (InitOutput method) InitOutput.molecule_withAssignedRingFamilies() (InitOutput method) InitOutput.molecule_withAssignedRingFamiliesWithParams() (InitOutput method) InitOutput.molecule_withAssignedRings() (InitOutput method) InitOutput.molecule_withAssignedValence() (InitOutput method) InitOutput.molecule_withAssignedValenceWithParams() (InitOutput method) InitOutput.molecule_withAtomPairAtomCode() (InitOutput method) InitOutput.molecule_withAtomPosition() (InitOutput method) InitOutput.molecule_withAtomPositionWithParams() (InitOutput method) InitOutput.molecule_withAtomProperty() (InitOutput method) InitOutput.molecule_withChiralTagsFromStructure() (InitOutput method) InitOutput.molecule_withChiralTagsFromStructureWithParams() (InitOutput method) InitOutput.molecule_withCipLabels() (InitOutput method) InitOutput.molecule_withCipLabelsWithOptions() (InitOutput method) InitOutput.molecule_withCleared3dConformers() (InitOutput method) InitOutput.molecule_withHydrogens() (InitOutput method) InitOutput.molecule_withHydrogensWithParams() (InitOutput method) InitOutput.molecule_withKekulizedBonds() (InitOutput method) InitOutput.molecule_withKekulizedBondsWithParams() (InitOutput method) InitOutput.molecule_withMmffOptimized() (InitOutput method) InitOutput.molecule_withMmffOptimizedConformers() (InitOutput method) InitOutput.molecule_withMmffOptimizedConformersWithParams() (InitOutput method) InitOutput.molecule_withMmffOptimizedWithParams() (InitOutput method) InitOutput.molecule_withName() (InitOutput method) InitOutput.molecule_withOnly3dConformer() (InitOutput method) InitOutput.molecule_withOnly3dConformerWithParams() (InitOutput method) InitOutput.molecule_withoutHydrogens() (InitOutput method) InitOutput.molecule_withoutHydrogensWithParams() (InitOutput method) InitOutput.molecule_withProperty() (InitOutput method) InitOutput.molecule_withSdfDataField() (InitOutput method) InitOutput.molecule_withUffOptimized() (InitOutput method) InitOutput.molecule_withUffOptimizedConformers() (InitOutput method) InitOutput.molecule_withUffOptimizedConformersWithParams() (InitOutput method) InitOutput.molecule_withUffOptimizedWithParams() (InitOutput method) InitOutput.molecule_writeMol() (InitOutput method) InitOutput.molecule_writeMolWithParams() (InitOutput method) InitOutput.molecule_writePng() (InitOutput method) InitOutput.molecule_writeSdf() (InitOutput method) InitOutput.molecule_writeSdfFiles() (InitOutput method) InitOutput.molecule_writeSdfFilesWithParams() (InitOutput method) InitOutput.molecule_writeSdfWithParams() (InitOutput method) InitOutput.molecule_writeSvg() (InitOutput method) InitOutput.molecule_writeXyz() (InitOutput method) InitOutput.molecule_writeXyzWithParams() (InitOutput method) InitOutput.moleculebatch_dgBoundsMatrixList() (InitOutput method) InitOutput.moleculebatch_dgBoundsMatrixListWithParams() (InitOutput method) InitOutput.moleculebatch_errorMode() (InitOutput method) InitOutput.moleculebatch_errors() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairCountList() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairCountListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairList() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairSparseBitsList() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairSparseBitsListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairSparseCountList() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairSparseCountListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairWithOutputList() (InitOutput method) InitOutput.moleculebatch_fingerprintAtomPairWithOutputListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintLayeredList() (InitOutput method) InitOutput.moleculebatch_fingerprintLayeredListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintLayeredWithOutputList() (InitOutput method) InitOutput.moleculebatch_fingerprintLayeredWithOutputListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintMorganList() (InitOutput method) InitOutput.moleculebatch_fingerprintMorganListWithGeneratorParams() (InitOutput method) InitOutput.moleculebatch_fingerprintMorganListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintMorganWithOutputList() (InitOutput method) InitOutput.moleculebatch_fingerprintMorganWithOutputListWithGeneratorParams() (InitOutput method) InitOutput.moleculebatch_fingerprintMorganWithOutputListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintPatternList() (InitOutput method) InitOutput.moleculebatch_fingerprintPatternListWithParams() (InitOutput method) InitOutput.moleculebatch_fingerprintTopologicalTorsionList() (InitOutput method) InitOutput.moleculebatch_fingerprintTopologicalTorsionListWithParams() (InitOutput method) InitOutput.moleculebatch_fromDatasetIndices() (InitOutput method) InitOutput.moleculebatch_fromRecords() (InitOutput method) InitOutput.moleculebatch_fromSdfRecords() (InitOutput method) InitOutput.moleculebatch_fromSdfRecordsWithParams() (InitOutput method) InitOutput.moleculebatch_fromSmilesList() (InitOutput method) InitOutput.moleculebatch_fromSmilesListWithParams() (InitOutput method) InitOutput.moleculebatch_get() (InitOutput method) InitOutput.moleculebatch_invalidCount() (InitOutput method) InitOutput.moleculebatch_invalidMask() (InitOutput method) InitOutput.moleculebatch_isEmpty() (InitOutput method) InitOutput.moleculebatch_len() (InitOutput method) InitOutput.moleculebatch_parallelJobs() (InitOutput method) InitOutput.moleculebatch_progressBar() (InitOutput method) InitOutput.moleculebatch_readSdf() (InitOutput method) InitOutput.moleculebatch_readSdfWithParams() (InitOutput method) InitOutput.moleculebatch_records() (InitOutput method) InitOutput.moleculebatch_sanitize() (InitOutput method) InitOutput.moleculebatch_sanitizeWithParams() (InitOutput method) InitOutput.moleculebatch_toList() (InitOutput method) InitOutput.moleculebatch_toSmilesList() (InitOutput method) InitOutput.moleculebatch_toSmilesListWithParams() (InitOutput method) InitOutput.moleculebatch_toSvgList() (InitOutput method) InitOutput.moleculebatch_toSvgListWithParams() (InitOutput method) InitOutput.moleculebatch_validCount() (InitOutput method) InitOutput.moleculebatch_validMask() (InitOutput method) InitOutput.moleculebatch_with2dCoordinates() (InitOutput method) InitOutput.moleculebatch_with2dCoordinatesWithParams() (InitOutput method) InitOutput.moleculebatch_withHydrogens() (InitOutput method) InitOutput.moleculebatch_withHydrogensWithParams() (InitOutput method) InitOutput.moleculebatch_withKekulizedBonds() (InitOutput method) InitOutput.moleculebatch_withKekulizedBondsWithParams() (InitOutput method) InitOutput.moleculebatch_withoutHydrogens() (InitOutput method) InitOutput.moleculebatch_withoutHydrogensWithParams() (InitOutput method) InitOutput.moleculebatch_withParallelJobs() (InitOutput method) InitOutput.moleculebatch_withProgressBar() (InitOutput method) InitOutput.moleculebatch_withValidRecords() (InitOutput method) InitOutput.moleculebatch_writeImages() (InitOutput method) InitOutput.moleculebatch_writeImagesWithParams() (InitOutput method) InitOutput.moleculebatch_writeSdf() (InitOutput method) InitOutput.moleculebatch_writeSdfFiles() (InitOutput method) InitOutput.moleculebatch_writeSdfFilesWithParams() (InitOutput method) InitOutput.moleculebatch_writeSdfWithParams() (InitOutput method) InitOutput.moleculebuilder_add2dConformer() (InitOutput method) InitOutput.moleculebuilder_add3dConformer() (InitOutput method) InitOutput.moleculebuilder_addAtom() (InitOutput method) InitOutput.moleculebuilder_addBond() (InitOutput method) InitOutput.moleculebuilder_addStereoGroup() (InitOutput method) InitOutput.moleculebuilder_addSubstanceGroup() (InitOutput method) InitOutput.moleculebuilder_atoms() (InitOutput method) InitOutput.moleculebuilder_bondBetweenAtoms() (InitOutput method) InitOutput.moleculebuilder_bonds() (InitOutput method) InitOutput.moleculebuilder_build() (InitOutput method) InitOutput.moleculebuilder_coordinates() (InitOutput method) InitOutput.moleculebuilder_degree() (InitOutput method) InitOutput.moleculebuilder_fromParts() (InitOutput method) InitOutput.moleculebuilder_neighborBonds() (InitOutput method) InitOutput.moleculebuilder_new() (InitOutput method) InitOutput.moleculebuilder_properties() (InitOutput method) InitOutput.moleculebuilder_removeBondBetweenAtoms() (InitOutput method) InitOutput.moleculebuilder_set2dCoordinates() (InitOutput method) InitOutput.moleculebuilder_setAtomFormalCharge() (InitOutput method) InitOutput.moleculebuilder_setBondOrder() (InitOutput method) InitOutput.moleculebuilder_stereoGroups() (InitOutput method) InitOutput.moleculebuilder_substanceGroups() (InitOutput method) InitOutput.moleculebuilder_withName() (InitOutput method) InitOutput.moleculebuilder_withProperties() (InitOutput method) InitOutput.moleculebuilder_withProperty() (InitOutput method) InitOutput.moleculebuilder_withSdfDataField() (InitOutput method) InitOutput.moleculehasherror_actual() (InitOutput method) InitOutput.moleculehasherror_atomCount() (InitOutput method) InitOutput.moleculehasherror_cause() (InitOutput method) InitOutput.moleculehasherror_domain() (InitOutput method) InitOutput.moleculehasherror_kind() (InitOutput method) InitOutput.moleculehasherror_message() (InitOutput method) InitOutput.moleculeopspec_access() (InitOutput method) InitOutput.moleculeopspec_autoRemap() (InitOutput method) InitOutput.moleculeopspec_cipState() (InitOutput method) InitOutput.moleculeopspec_derivedEffects() (InitOutput method) InitOutput.moleculeopspec_domain() (InitOutput method) InitOutput.moleculeopspec_implFn() (InitOutput method) InitOutput.moleculeopspec_ioRoundtrip() (InitOutput method) InitOutput.moleculeopspec_kind() (InitOutput method) InitOutput.moleculeopspec_mayMutate() (InitOutput method) InitOutput.moleculeopspec_method() (InitOutput method) InitOutput.moleculeopspec_output() (InitOutput method) InitOutput.moleculeopspec_parity() (InitOutput method) InitOutput.moleculeopspec_requiresMapping() (InitOutput method) InitOutput.moleculeopspec_resultType() (InitOutput method) InitOutput.moleculeopspec_semanticPreconditions() (InitOutput method) InitOutput.moleculeopspec_status() (InitOutput method) InitOutput.moleculeopspec_topologyEdit() (InitOutput method) InitOutput.moleculeproperties_computedPropNames() (InitOutput method) InitOutput.moleculeproperties_isPropComputed() (InitOutput method) InitOutput.moleculeproperties_name() (InitOutput method) InitOutput.moleculeproperties_prop() (InitOutput method) InitOutput.moleculeproperties_props() (InitOutput method) InitOutput.moleculeproperties_sdfDataFields() (InitOutput method) InitOutput.moleculeproperties_sdfPropertyLists() (InitOutput method) InitOutput.molwriteerror_capability() (InitOutput method) InitOutput.molwriteerror_cause() (InitOutput method) InitOutput.molwriteerror_dimension() (InitOutput method) InitOutput.molwriteerror_domain() (InitOutput method) InitOutput.molwriteerror_id() (InitOutput method) InitOutput.molwriteerror_kind() (InitOutput method) InitOutput.molwriteerror_message() (InitOutput method) InitOutput.molwriteerror_subset() (InitOutput method) InitOutput.molwriteerror_threeD() (InitOutput method) InitOutput.molwriteerror_twoD() (InitOutput method) InitOutput.molwriteerror_valueDetail() (InitOutput method) InitOutput.morganatominvariantsgenerator_atomPair() (InitOutput method) InitOutput.morganatominvariantsgenerator_connectivity() (InitOutput method) InitOutput.morganatominvariantsgenerator_features() (InitOutput method) InitOutput.morganbondinvariantsgenerator_construct() (InitOutput method) InitOutput.morganbondinvariantsgenerator_includeChirality() (InitOutput method) InitOutput.morganbondinvariantsgenerator_new() (InitOutput method) InitOutput.morganbondinvariantsgenerator_set_includeChirality() (InitOutput method) InitOutput.morganbondinvariantsgenerator_set_useBondTypes() (InitOutput method) InitOutput.morganbondinvariantsgenerator_useBondTypes() (InitOutput method) InitOutput.morgancallparams_conformerId() (InitOutput method) InitOutput.morgancallparams_construct() (InitOutput method) InitOutput.morgancallparams_customAtomInvariants() (InitOutput method) InitOutput.morgancallparams_customBondInvariants() (InitOutput method) InitOutput.morgancallparams_fromAtoms() (InitOutput method) InitOutput.morgancallparams_ignoreAtoms() (InitOutput method) InitOutput.morgancallparams_new() (InitOutput method) InitOutput.morgancallparams_set_conformerId() (InitOutput method) InitOutput.morgancallparams_set_customAtomInvariants() (InitOutput method) InitOutput.morgancallparams_set_customBondInvariants() (InitOutput method) InitOutput.morgancallparams_set_fromAtoms() (InitOutput method) InitOutput.morgancallparams_set_ignoreAtoms() (InitOutput method) InitOutput.morganfingerprintgenerator_construct() (InitOutput method) InitOutput.morganfingerprintgenerator_counts() (InitOutput method) InitOutput.morganfingerprintgenerator_fingerprints() (InitOutput method) InitOutput.morganfingerprintgenerator_fromJson() (InitOutput method) InitOutput.morganfingerprintgenerator_infoString() (InitOutput method) InitOutput.morganfingerprintgenerator_new() (InitOutput method) InitOutput.morganfingerprintgenerator_settings() (InitOutput method) InitOutput.morganfingerprintgenerator_sparseCounts() (InitOutput method) InitOutput.morganfingerprintgenerator_sparseFingerprints() (InitOutput method) InitOutput.morganfingerprintgenerator_toJson() (InitOutput method) InitOutput.morganfingerprintparams_conformerId() (InitOutput method) InitOutput.morganfingerprintparams_customAtomInvariants() (InitOutput method) InitOutput.morganfingerprintparams_customBondInvariants() (InitOutput method) InitOutput.morganfingerprintparams_fromAtoms() (InitOutput method) InitOutput.morganfingerprintparams_generator() (InitOutput method) InitOutput.morganfingerprintparams_ignoreAtoms() (InitOutput method) InitOutput.morganfingerprintparams_invariants() (InitOutput method) InitOutput.morganfingerprintparams_new() (InitOutput method) InitOutput.morganfingerprintparams_set_conformerId() (InitOutput method) InitOutput.morganfingerprintparams_set_customAtomInvariants() (InitOutput method) InitOutput.morganfingerprintparams_set_customBondInvariants() (InitOutput method) InitOutput.morganfingerprintparams_set_fromAtoms() (InitOutput method) InitOutput.morganfingerprintparams_set_generator() (InitOutput method) InitOutput.morganfingerprintparams_set_ignoreAtoms() (InitOutput method) InitOutput.morganfingerprintparams_set_invariants() (InitOutput method) InitOutput.morganinvariants_connectivity() (InitOutput method) InitOutput.morganinvariants_features() (InitOutput method) InitOutput.morganparams_bitsPerFeature() (InitOutput method) InitOutput.morganparams_countBounds() (InitOutput method) InitOutput.morganparams_countSimulation() (InitOutput method) InitOutput.morganparams_fpSize() (InitOutput method) InitOutput.morganparams_includeChirality() (InitOutput method) InitOutput.morganparams_includeRedundantEnvironments() (InitOutput method) InitOutput.morganparams_includeRingMembership() (InitOutput method) InitOutput.morganparams_infoString() (InitOutput method) InitOutput.morganparams_new() (InitOutput method) InitOutput.morganparams_onlyNonzeroInvariants() (InitOutput method) InitOutput.morganparams_radius() (InitOutput method) InitOutput.morganparams_set_bitsPerFeature() (InitOutput method) InitOutput.morganparams_set_countBounds() (InitOutput method) InitOutput.morganparams_set_countSimulation() (InitOutput method) InitOutput.morganparams_set_fpSize() (InitOutput method) InitOutput.morganparams_set_includeChirality() (InitOutput method) InitOutput.morganparams_set_includeRedundantEnvironments() (InitOutput method) InitOutput.morganparams_set_includeRingMembership() (InitOutput method) InitOutput.morganparams_set_onlyNonzeroInvariants() (InitOutput method) InitOutput.morganparams_set_radius() (InitOutput method) InitOutput.morganparams_set_useBondTypes() (InitOutput method) InitOutput.morganparams_toJson() (InitOutput method) InitOutput.morganparams_useBondTypes() (InitOutput method) InitOutput.morganparams_withJson() (InitOutput method) InitOutput.morganreaderror_cause() (InitOutput method) InitOutput.morganreaderror_domain() (InitOutput method) InitOutput.morganreaderror_kind() (InitOutput method) InitOutput.morganreaderror_message() (InitOutput method) InitOutput.morgansettings_bitsPerFeature() (InitOutput method) InitOutput.morgansettings_countBounds() (InitOutput method) InitOutput.morgansettings_countSimulation() (InitOutput method) InitOutput.morgansettings_fpSize() (InitOutput method) InitOutput.morgansettings_includeChirality() (InitOutput method) InitOutput.morgansettings_includeRedundantEnvironments() (InitOutput method) InitOutput.morgansettings_onlyNonzeroInvariants() (InitOutput method) InitOutput.morgansettings_params() (InitOutput method) InitOutput.morgansettings_radius() (InitOutput method) InitOutput.morgansettings_set_bitsPerFeature() (InitOutput method) InitOutput.morgansettings_set_countBounds() (InitOutput method) InitOutput.morgansettings_set_countSimulation() (InitOutput method) InitOutput.morgansettings_set_fpSize() (InitOutput method) InitOutput.morgansettings_set_includeChirality() (InitOutput method) InitOutput.morgansettings_set_includeRedundantEnvironments() (InitOutput method) InitOutput.morgansettings_set_onlyNonzeroInvariants() (InitOutput method) InitOutput.morgansettings_set_radius() (InitOutput method) InitOutput.morgansettings_setBitsPerFeature() (InitOutput method) InitOutput.morgansettings_setCountBounds() (InitOutput method) InitOutput.morgansettings_setCountSimulation() (InitOutput method) InitOutput.morgansettings_setFpSize() (InitOutput method) InitOutput.morgansettings_setIncludeChirality() (InitOutput method) InitOutput.morgansettings_setIncludeRedundantEnvironments() (InitOutput method) InitOutput.morgansettings_setOnlyNonzeroInvariants() (InitOutput method) InitOutput.morgansettings_setRadius() (InitOutput method) InitOutput.operationerror_cause() (InitOutput method) InitOutput.operationerror_domain() (InitOutput method) InitOutput.operationerror_kind() (InitOutput method) InitOutput.operationerror_message() (InitOutput method) InitOutput.operationInvariant() (InitOutput method) InitOutput.operationinvariantentry_operation() (InitOutput method) InitOutput.operationinvariantentry_profile() (InitOutput method) InitOutput.operationInvariantMatrix() (InitOutput method) InitOutput.operationParity() (InitOutput method) InitOutput.operationSpec() (InitOutput method) InitOutput.operationSpecs() (InitOutput method) InitOutput.parityMatrix() (InitOutput method) InitOutput.paritymatrixentry_feature() (InitOutput method) InitOutput.paritymatrixentry_operation() (InitOutput method) InitOutput.paritymatrixentry_profile() (InitOutput method) InitOutput.paritymatrixentry_rdkitVersion() (InitOutput method) InitOutput.parseSmarts() (InitOutput method) InitOutput.parseSmartsWithParams() (InitOutput method) InitOutput.parseSmirks() (InitOutput method) InitOutput.parseSmirksWithParams() (InitOutput method) InitOutput.patternfingerprinterror_cause() (InitOutput method) InitOutput.patternfingerprinterror_domain() (InitOutput method) InitOutput.patternfingerprinterror_kind() (InitOutput method) InitOutput.patternfingerprinterror_message() (InitOutput method) InitOutput.patternfingerprintparams_nBits() (InitOutput method) InitOutput.patternfingerprintparams_new() (InitOutput method) InitOutput.patternfingerprintparams_set_nBits() (InitOutput method) InitOutput.patternfingerprintparams_set_tautomeric() (InitOutput method) InitOutput.patternfingerprintparams_tautomeric() (InitOutput method) InitOutput.pdbatomserial_new() (InitOutput method) InitOutput.pdbatomserial_value() (InitOutput method) InitOutput.pdbchainid_asBytes() (InitOutput method) InitOutput.pdbchainid_asStr() (InitOutput method) InitOutput.pdbchainid_fromAscii() (InitOutput method) InitOutput.pdbseqid_insCode() (InitOutput method) InitOutput.pdbseqid_seqNum() (InitOutput method) InitOutput.potentialstereocenter_index() (InitOutput method) InitOutput.potentialstereocenter_kind() (InitOutput method) InitOutput.potentialstereoerror_cause() (InitOutput method) InitOutput.potentialstereoerror_domain() (InitOutput method) InitOutput.potentialstereoerror_kind() (InitOutput method) InitOutput.potentialstereoerror_message() (InitOutput method) InitOutput.potentialstereoinfo_centeredOn() (InitOutput method) InitOutput.potentialstereoinfo_controllingAtoms() (InitOutput method) InitOutput.potentialstereoinfo_descriptor() (InitOutput method) InitOutput.potentialstereoinfo_permutation() (InitOutput method) InitOutput.potentialstereoinfo_specified() (InitOutput method) InitOutput.potentialstereoinfo_stereoType() (InitOutput method) InitOutput.potentialstereoparams_allowNontetrahedral() (InitOutput method) InitOutput.potentialstereoparams_clean() (InitOutput method) InitOutput.potentialstereoparams_flagPossible() (InitOutput method) InitOutput.potentialstereoparams_new() (InitOutput method) InitOutput.potentialstereoparams_set_allowNontetrahedral() (InitOutput method) InitOutput.potentialstereoparams_set_clean() (InitOutput method) InitOutput.potentialstereoparams_set_flagPossible() (InitOutput method) InitOutput.potentialstereoresult_atomRanks() (InitOutput method) InitOutput.potentialstereoresult_cleanedMolecule() (InitOutput method) InitOutput.potentialstereoresult_ringRelations() (InitOutput method) InitOutput.potentialstereoresult_stereo() (InitOutput method) InitOutput.propertystringerror_cause() (InitOutput method) InitOutput.propertystringerror_domain() (InitOutput method) InitOutput.propertystringerror_kind() (InitOutput method) InitOutput.propertystringerror_message() (InitOutput method) InitOutput.propertyvalue_asBool() (InitOutput method) InitOutput.propertyvalue_asDouble() (InitOutput method) InitOutput.propertyvalue_asInt() (InitOutput method) InitOutput.propertyvalue_asIntVector() (InitOutput method) InitOutput.propertyvalue_asString() (InitOutput method) InitOutput.propertyvalue_asStringVector() (InitOutput method) InitOutput.propertyvalue_asUint() (InitOutput method) InitOutput.propertyvalue_kind() (InitOutput method) InitOutput.propertyvalueerror_actual() (InitOutput method) InitOutput.propertyvalueerror_cause() (InitOutput method) InitOutput.propertyvalueerror_domain() (InitOutput method) InitOutput.propertyvalueerror_expected() (InitOutput method) InitOutput.propertyvalueerror_kind() (InitOutput method) InitOutput.propertyvalueerror_message() (InitOutput method) InitOutput.propertyValueToText() (InitOutput method) InitOutput.protein_asBioStructure() (InitOutput method) InitOutput.protein_atoms() (InitOutput method) InitOutput.protein_chain() (InitOutput method) InitOutput.protein_chains() (InitOutput method) InitOutput.protein_fromMmcif() (InitOutput method) InitOutput.protein_fromPdb() (InitOutput method) InitOutput.protein_fromPdbWithParams() (InitOutput method) InitOutput.protein_fromText() (InitOutput method) InitOutput.protein_fromTextWithParams() (InitOutput method) InitOutput.protein_inputFormat() (InitOutput method) InitOutput.protein_intoBioStructure() (InitOutput method) InitOutput.protein_len() (InitOutput method) InitOutput.protein_numAtoms() (InitOutput method) InitOutput.protein_numChains() (InitOutput method) InitOutput.protein_numModels() (InitOutput method) InitOutput.protein_numResidues() (InitOutput method) InitOutput.protein_read() (InitOutput method) InitOutput.protein_readWithFormat() (InitOutput method) InitOutput.protein_residues() (InitOutput method) InitOutput.protein_retainSelection() (InitOutput method) InitOutput.protein_selectedAtomIds() (InitOutput method) InitOutput.protein_selectionSummary() (InitOutput method) InitOutput.protein_toMolecule() (InitOutput method) InitOutput.protein_toMoleculeWithParams() (InitOutput method) InitOutput.protein_translate() (InitOutput method) InitOutput.protein_withSelection() (InitOutput method) InitOutput.protein_withTranslatedCoordinates() (InitOutput method) InitOutput.proteinatomiter_len() (InitOutput method) InitOutput.proteinatomiter_next() (InitOutput method) InitOutput.proteinatomref_altloc() (InitOutput method) InitOutput.proteinatomref_atomicNumber() (InitOutput method) InitOutput.proteinatomref_element() (InitOutput method) InitOutput.proteinatomref_elementSymbol() (InitOutput method) InitOutput.proteinatomref_id() (InitOutput method) InitOutput.proteinatomref_name() (InitOutput method) InitOutput.proteinatomref_position() (InitOutput method) InitOutput.proteinatomref_residue() (InitOutput method) InitOutput.proteinatomref_row() (InitOutput method) InitOutput.proteinchainiter_len() (InitOutput method) InitOutput.proteinchainiter_next() (InitOutput method) InitOutput.proteinchainref_atoms() (InitOutput method) InitOutput.proteinchainref_id() (InitOutput method) InitOutput.proteinchainref_kind() (InitOutput method) InitOutput.proteinchainref_len() (InitOutput method) InitOutput.proteinchainref_residues() (InitOutput method) InitOutput.proteinchainref_row() (InitOutput method) InitOutput.proteinchainref_source() (InitOutput method) InitOutput.proteinprojectionerror_cause() (InitOutput method) InitOutput.proteinprojectionerror_domain() (InitOutput method) InitOutput.proteinprojectionerror_index() (InitOutput method) InitOutput.proteinprojectionerror_kind() (InitOutput method) InitOutput.proteinprojectionerror_message() (InitOutput method) InitOutput.proteinprojectionerror_source() (InitOutput method) InitOutput.proteinreaderror_cause() (InitOutput method) InitOutput.proteinreaderror_domain() (InitOutput method) InitOutput.proteinreaderror_kind() (InitOutput method) InitOutput.proteinreaderror_message() (InitOutput method) InitOutput.proteinresidueiter_len() (InitOutput method) InitOutput.proteinresidueiter_next() (InitOutput method) InitOutput.proteinresidueref_atoms() (InitOutput method) InitOutput.proteinresidueref_canonicalOneLetterCode() (InitOutput method) InitOutput.proteinresidueref_chain() (InitOutput method) InitOutput.proteinresidueref_code() (InitOutput method) InitOutput.proteinresidueref_fastaCode() (InitOutput method) InitOutput.proteinresidueref_id() (InitOutput method) InitOutput.proteinresidueref_info() (InitOutput method) InitOutput.proteinresidueref_isModifiedAminoAcid() (InitOutput method) InitOutput.proteinresidueref_isStandard() (InitOutput method) InitOutput.proteinresidueref_kind() (InitOutput method) InitOutput.proteinresidueref_len() (InitOutput method) InitOutput.proteinresidueref_name() (InitOutput method) InitOutput.proteinresidueref_oneLetterCode() (InitOutput method) InitOutput.proteinresidueref_parentStandardCode() (InitOutput method) InitOutput.proteinresidueref_row() (InitOutput method) InitOutput.proteinselectionsummary_atoms() (InitOutput method) InitOutput.proteinselectionsummary_chains() (InitOutput method) InitOutput.proteinselectionsummary_residues() (InitOutput method) InitOutput.queryatom_atomicNumber() (InitOutput method) InitOutput.queryatom_atomMap() (InitOutput method) InitOutput.queryatom_explicitHydrogens() (InitOutput method) InitOutput.queryatom_formalCharge() (InitOutput method) InitOutput.queryatom_id() (InitOutput method) InitOutput.queryatom_isAromatic() (InitOutput method) InitOutput.queryatom_isotope() (InitOutput method) InitOutput.queryatom_noImplicit() (InitOutput method) InitOutput.queryatom_radicalElectrons() (InitOutput method) InitOutput.querycompileerror_cause() (InitOutput method) InitOutput.querycompileerror_domain() (InitOutput method) InitOutput.querycompileerror_kind() (InitOutput method) InitOutput.querycompileerror_message() (InitOutput method) InitOutput.querygraph_fromSmarts() (InitOutput method) InitOutput.querygraph_fromSmartsWithParams() (InitOutput method) InitOutput.querygraph_name() (InitOutput method) InitOutput.querygraph_numAtoms() (InitOutput method) InitOutput.querygraph_numBonds() (InitOutput method) InitOutput.randomsmileswriteparams_allBondsExplicit() (InitOutput method) InitOutput.randomsmileswriteparams_allHydrogensExplicit() (InitOutput method) InitOutput.randomsmileswriteparams_isomericSmiles() (InitOutput method) InitOutput.randomsmileswriteparams_kekule() (InitOutput method) InitOutput.randomsmileswriteparams_new() (InitOutput method) InitOutput.randomsmileswriteparams_set_allBondsExplicit() (InitOutput method) InitOutput.randomsmileswriteparams_set_allHydrogensExplicit() (InitOutput method) InitOutput.randomsmileswriteparams_set_isomericSmiles() (InitOutput method) InitOutput.randomsmileswriteparams_set_kekule() (InitOutput method) InitOutput.reaction_agentTemplate() (InitOutput method) InitOutput.reaction_agentTemplates() (InitOutput method) InitOutput.reaction_fromSmirks() (InitOutput method) InitOutput.reaction_fromSmirksWithParams() (InitOutput method) InitOutput.reaction_fromTemplates() (InitOutput method) InitOutput.reaction_implicitProperties() (InitOutput method) InitOutput.reaction_isInitialized() (InitOutput method) InitOutput.reaction_matchParams() (InitOutput method) InitOutput.reaction_new() (InitOutput method) InitOutput.reaction_numAgentTemplates() (InitOutput method) InitOutput.reaction_numProductTemplates() (InitOutput method) InitOutput.reaction_numReactantTemplates() (InitOutput method) InitOutput.reaction_productTemplate() (InitOutput method) InitOutput.reaction_productTemplates() (InitOutput method) InitOutput.reaction_reactantTemplate() (InitOutput method) InitOutput.reaction_reactantTemplates() (InitOutput method) InitOutput.reaction_run() (InitOutput method) InitOutput.reaction_toCxSmirks() (InitOutput method) InitOutput.reaction_toCxSmirksWithParams() (InitOutput method) InitOutput.reaction_toSmirks() (InitOutput method) InitOutput.reaction_toSmirksWithParams() (InitOutput method) InitOutput.reaction_validate() (InitOutput method) InitOutput.reaction_validateWithParams() (InitOutput method) InitOutput.reaction_withAgentTemplate() (InitOutput method) InitOutput.reaction_withImplicitProperties() (InitOutput method) InitOutput.reaction_withInitialized() (InitOutput method) InitOutput.reaction_withInitializedWithParams() (InitOutput method) InitOutput.reaction_withMatchParams() (InitOutput method) InitOutput.reaction_withoutAgents() (InitOutput method) InitOutput.reaction_withoutUnmappedProducts() (InitOutput method) InitOutput.reaction_withoutUnmappedProductsWithParams() (InitOutput method) InitOutput.reaction_withoutUnmappedReactants() (InitOutput method) InitOutput.reaction_withoutUnmappedReactantsWithParams() (InitOutput method) InitOutput.reaction_withProductTemplate() (InitOutput method) InitOutput.reaction_withReactantTemplate() (InitOutput method) InitOutput.reactionapplyerror_atom() (InitOutput method) InitOutput.reactionapplyerror_cause() (InitOutput method) InitOutput.reactionapplyerror_kind() (InitOutput method) InitOutput.reactionapplyerror_message() (InitOutput method) InitOutput.reactionapplyerror_products() (InitOutput method) InitOutput.reactionapplyerror_reactants() (InitOutput method) InitOutput.reactionapplyparams_new() (InitOutput method) InitOutput.reactionapplyparams_removeUnmatchedAtoms() (InitOutput method) InitOutput.reactionapplyparams_set_removeUnmatchedAtoms() (InitOutput method) InitOutput.reactionapplyresult_changed() (InitOutput method) InitOutput.reactionapplyresult_molecule() (InitOutput method) InitOutput.reactioncoordinateselection_auto() (InitOutput method) InitOutput.reactioncoordinateselection_id() (InitOutput method) InitOutput.reactioncoordinateselection_is2d() (InitOutput method) InitOutput.reactioncoordinateselection_is3d() (InitOutput method) InitOutput.reactioncoordinateselection_isAuto() (InitOutput method) InitOutput.reactioncoordinateselection_threeD() (InitOutput method) InitOutput.reactioncoordinateselection_twoD() (InitOutput method) InitOutput.reactioninitializationerror_cause() (InitOutput method) InitOutput.reactioninitializationerror_kind() (InitOutput method) InitOutput.reactioninitializationerror_message() (InitOutput method) InitOutput.reactioninitializationerror_report() (InitOutput method) InitOutput.reactionmodelerror_cause() (InitOutput method) InitOutput.reactionmodelerror_count() (InitOutput method) InitOutput.reactionmodelerror_index() (InitOutput method) InitOutput.reactionmodelerror_kind() (InitOutput method) InitOutput.reactionmodelerror_message() (InitOutput method) InitOutput.reactionmodelerror_role() (InitOutput method) InitOutput.reactionmodelerror_template() (InitOutput method) InitOutput.reactionparseerror_atom() (InitOutput method) InitOutput.reactionparseerror_atomCount() (InitOutput method) InitOutput.reactionparseerror_cause() (InitOutput method) InitOutput.reactionparseerror_count() (InitOutput method) InitOutput.reactionparseerror_end() (InitOutput method) InitOutput.reactionparseerror_flag() (InitOutput method) InitOutput.reactionparseerror_kind() (InitOutput method) InitOutput.reactionparseerror_message() (InitOutput method) InitOutput.reactionparseerror_product() (InitOutput method) InitOutput.reactionparseerror_reactant() (InitOutput method) InitOutput.reactionparseerror_role() (InitOutput method) InitOutput.reactionparseerror_start() (InitOutput method) InitOutput.reactionparseerror_startAtom() (InitOutput method) InitOutput.reactionparseerror_startBond() (InitOutput method) InitOutput.reactionparseerror_template() (InitOutput method) InitOutput.reactionparseerror_text() (InitOutput method) InitOutput.reactionparseparams_allowCxsmiles() (InitOutput method) InitOutput.reactionparseparams_new() (InitOutput method) InitOutput.reactionparseparams_replacements() (InitOutput method) InitOutput.reactionparseparams_sanitize() (InitOutput method) InitOutput.reactionparseparams_set_allowCxsmiles() (InitOutput method) InitOutput.reactionparseparams_set_replacements() (InitOutput method) InitOutput.reactionparseparams_set_sanitize() (InitOutput method) InitOutput.reactionparseparams_set_strictCxsmiles() (InitOutput method) InitOutput.reactionparseparams_set_useSmiles() (InitOutput method) InitOutput.reactionparseparams_strictCxsmiles() (InitOutput method) InitOutput.reactionparseparams_useSmiles() (InitOutput method) InitOutput.reactionproducterror_atom() (InitOutput method) InitOutput.reactionproducterror_bond() (InitOutput method) InitOutput.reactionproducterror_cause() (InitOutput method) InitOutput.reactionproducterror_detail() (InitOutput method) InitOutput.reactionproducterror_index() (InitOutput method) InitOutput.reactionproducterror_key() (InitOutput method) InitOutput.reactionproducterror_kind() (InitOutput method) InitOutput.reactionproducterror_message() (InitOutput method) InitOutput.reactionproducterror_productAtom() (InitOutput method) InitOutput.reactionproducterror_reactantAtom() (InitOutput method) InitOutput.reactionproducterror_rowKind() (InitOutput method) InitOutput.reactionproducterror_stage() (InitOutput method) InitOutput.reactionrunerror_actual() (InitOutput method) InitOutput.reactionrunerror_atom() (InitOutput method) InitOutput.reactionrunerror_atomCount() (InitOutput method) InitOutput.reactionrunerror_cause() (InitOutput method) InitOutput.reactionrunerror_count() (InitOutput method) InitOutput.reactionrunerror_expected() (InitOutput method) InitOutput.reactionrunerror_index() (InitOutput method) InitOutput.reactionrunerror_kind() (InitOutput method) InitOutput.reactionrunerror_level() (InitOutput method) InitOutput.reactionrunerror_message() (InitOutput method) InitOutput.reactionrunerror_reactant() (InitOutput method) InitOutput.reactionrunerror_set() (InitOutput method) InitOutput.reactionrunerror_template() (InitOutput method) InitOutput.reactionrunparams_coordinateSelections() (InitOutput method) InitOutput.reactionrunparams_copyAtomProperties() (InitOutput method) InitOutput.reactionrunparams_maxProducts() (InitOutput method) InitOutput.reactionrunparams_new() (InitOutput method) InitOutput.reactionrunparams_set_coordinateSelections() (InitOutput method) InitOutput.reactionrunparams_set_copyAtomProperties() (InitOutput method) InitOutput.reactionrunparams_set_maxProducts() (InitOutput method) InitOutput.reactionsinglerunparams_coordinateSelection() (InitOutput method) InitOutput.reactionsinglerunparams_new() (InitOutput method) InitOutput.reactionsinglerunparams_set_coordinateSelection() (InitOutput method) InitOutput.reactiontemplateremoval_reaction() (InitOutput method) InitOutput.reactiontemplateremoval_removedTemplates() (InitOutput method) InitOutput.reactiontemplateremovalparams_moveToAgentTemplates() (InitOutput method) InitOutput.reactiontemplateremovalparams_new() (InitOutput method) InitOutput.reactiontemplateremovalparams_set_moveToAgentTemplates() (InitOutput method) InitOutput.reactiontemplateremovalparams_set_thresholdUnmappedAtoms() (InitOutput method) InitOutput.reactiontemplateremovalparams_thresholdUnmappedAtoms() (InitOutput method) InitOutput.reactionvalidationerror_atom() (InitOutput method) InitOutput.reactionvalidationerror_atomCount() (InitOutput method) InitOutput.reactionvalidationerror_cause() (InitOutput method) InitOutput.reactionvalidationerror_kind() (InitOutput method) InitOutput.reactionvalidationerror_map() (InitOutput method) InitOutput.reactionvalidationerror_message() (InitOutput method) InitOutput.reactionvalidationerror_property() (InitOutput method) InitOutput.reactionvalidationerror_role() (InitOutput method) InitOutput.reactionvalidationerror_template() (InitOutput method) InitOutput.reactionvalidationerror_value() (InitOutput method) InitOutput.reactionvalidationissue_atom() (InitOutput method) InitOutput.reactionvalidationissue_detail() (InitOutput method) InitOutput.reactionvalidationissue_kind() (InitOutput method) InitOutput.reactionvalidationissue_map() (InitOutput method) InitOutput.reactionvalidationissue_maps() (InitOutput method) InitOutput.reactionvalidationissue_role() (InitOutput method) InitOutput.reactionvalidationissue_severity() (InitOutput method) InitOutput.reactionvalidationissue_template() (InitOutput method) InitOutput.reactionvalidationparams_new() (InitOutput method) InitOutput.reactionvalidationparams_set_silent() (InitOutput method) InitOutput.reactionvalidationparams_silent() (InitOutput method) InitOutput.reactionvalidationreport_errors() (InitOutput method) InitOutput.reactionvalidationreport_isValid() (InitOutput method) InitOutput.reactionvalidationreport_numErrors() (InitOutput method) InitOutput.reactionvalidationreport_numWarnings() (InitOutput method) InitOutput.reactionvalidationreport_warnings() (InitOutput method) InitOutput.reactionwriteerror_actual() (InitOutput method) InitOutput.reactionwriteerror_cause() (InitOutput method) InitOutput.reactionwriteerror_expected() (InitOutput method) InitOutput.reactionwriteerror_kind() (InitOutput method) InitOutput.reactionwriteerror_message() (InitOutput method) InitOutput.reactionwriteerror_role() (InitOutput method) InitOutput.reactionwriteerror_template() (InitOutput method) InitOutput.reactionwriteparams_canonical() (InitOutput method) InitOutput.reactionwriteparams_coordinateSelections() (InitOutput method) InitOutput.reactionwriteparams_cxFields() (InitOutput method) InitOutput.reactionwriteparams_includeCx() (InitOutput method) InitOutput.reactionwriteparams_includeDativeBonds() (InitOutput method) InitOutput.reactionwriteparams_isomericSmiles() (InitOutput method) InitOutput.reactionwriteparams_new() (InitOutput method) InitOutput.reactionwriteparams_rootedAtAtom() (InitOutput method) InitOutput.reactionwriteparams_set_canonical() (InitOutput method) InitOutput.reactionwriteparams_set_coordinateSelections() (InitOutput method) InitOutput.reactionwriteparams_set_cxFields() (InitOutput method) InitOutput.reactionwriteparams_set_includeCx() (InitOutput method) InitOutput.reactionwriteparams_set_includeDativeBonds() (InitOutput method) InitOutput.reactionwriteparams_set_isomericSmiles() (InitOutput method) InitOutput.reactionwriteparams_set_rootedAtAtom() (InitOutput method) InitOutput.removehsparams_new() (InitOutput method) InitOutput.removehsparams_removeAndTrackIsotopes() (InitOutput method) InitOutput.removehsparams_removeDefiningBondStereo() (InitOutput method) InitOutput.removehsparams_removeDegreeZero() (InitOutput method) InitOutput.removehsparams_removeDummyNeighbors() (InitOutput method) InitOutput.removehsparams_removeHigherDegrees() (InitOutput method) InitOutput.removehsparams_removeHydrides() (InitOutput method) InitOutput.removehsparams_removeInSgroups() (InitOutput method) InitOutput.removehsparams_removeIsotopes() (InitOutput method) InitOutput.removehsparams_removeMapped() (InitOutput method) InitOutput.removehsparams_removeNonimplicit() (InitOutput method) InitOutput.removehsparams_removeNontetrahedralNeighbors() (InitOutput method) InitOutput.removehsparams_removeOnlyHNeighbors() (InitOutput method) InitOutput.removehsparams_removeWithQuery() (InitOutput method) InitOutput.removehsparams_removeWithWedgedBond() (InitOutput method) InitOutput.removehsparams_sanitize() (InitOutput method) InitOutput.removehsparams_set_removeAndTrackIsotopes() (InitOutput method) InitOutput.removehsparams_set_removeDefiningBondStereo() (InitOutput method) InitOutput.removehsparams_set_removeDegreeZero() (InitOutput method) InitOutput.removehsparams_set_removeDummyNeighbors() (InitOutput method) InitOutput.removehsparams_set_removeHigherDegrees() (InitOutput method) InitOutput.removehsparams_set_removeHydrides() (InitOutput method) InitOutput.removehsparams_set_removeInSgroups() (InitOutput method) InitOutput.removehsparams_set_removeIsotopes() (InitOutput method) InitOutput.removehsparams_set_removeMapped() (InitOutput method) InitOutput.removehsparams_set_removeNonimplicit() (InitOutput method) InitOutput.removehsparams_set_removeNontetrahedralNeighbors() (InitOutput method) InitOutput.removehsparams_set_removeOnlyHNeighbors() (InitOutput method) InitOutput.removehsparams_set_removeWithQuery() (InitOutput method) InitOutput.removehsparams_set_removeWithWedgedBond() (InitOutput method) InitOutput.removehsparams_set_sanitize() (InitOutput method) InitOutput.removehsparams_set_showWarnings() (InitOutput method) InitOutput.removehsparams_set_updateExplicitCount() (InitOutput method) InitOutput.removehsparams_showWarnings() (InitOutput method) InitOutput.removehsparams_updateExplicitCount() (InitOutput method) InitOutput.replace3dcoordinatesparams_conformerId() (InitOutput method) InitOutput.replace3dcoordinatesparams_new() (InitOutput method) InitOutput.replace3dcoordinatesparams_set_conformerId() (InitOutput method) InitOutput.residueaddress_insertionCode() (InitOutput method) InitOutput.residueaddress_name() (InitOutput method) InitOutput.residueaddress_segment() (InitOutput method) InitOutput.residueaddress_sequenceNumber() (InitOutput method) InitOutput.residueCode() (InitOutput method) InitOutput.residuecodeparseerror_input() (InitOutput method) InitOutput.residueidentity_code() (InitOutput method) InitOutput.residueidentity_construct() (InitOutput method) InitOutput.residueidentity_info() (InitOutput method) InitOutput.residueidentity_isTabulated() (InitOutput method) InitOutput.residueidentity_name() (InitOutput method) InitOutput.residueidentity_new() (InitOutput method) InitOutput.residueInfo() (InitOutput method) InitOutput.residueinfo_canonicalOneLetterCode() (InitOutput method) InitOutput.residueinfo_code() (InitOutput method) InitOutput.residueinfo_fastaCode() (InitOutput method) InitOutput.residueinfo_found() (InitOutput method) InitOutput.residueinfo_hydrogenCount() (InitOutput method) InitOutput.residueinfo_isAminoAcid() (InitOutput method) InitOutput.residueinfo_isBufferOrWater() (InitOutput method) InitOutput.residueinfo_isDna() (InitOutput method) InitOutput.residueinfo_isModifiedAminoAcid() (InitOutput method) InitOutput.residueinfo_isNaLinking() (InitOutput method) InitOutput.residueinfo_isNucleicAcid() (InitOutput method) InitOutput.residueinfo_isPeptideLinking() (InitOutput method) InitOutput.residueinfo_isRna() (InitOutput method) InitOutput.residueinfo_isStandard() (InitOutput method) InitOutput.residueinfo_isWater() (InitOutput method) InitOutput.residueinfo_kind() (InitOutput method) InitOutput.residueinfo_kindName() (InitOutput method) InitOutput.residueinfo_linkingType() (InitOutput method) InitOutput.residueinfo_name() (InitOutput method) InitOutput.residueinfo_oneLetterCode() (InitOutput method) InitOutput.residueinfo_parentStandardCode() (InitOutput method) InitOutput.residueinfo_weight() (InitOutput method) InitOutput.residueInfoChecked() (InitOutput method) InitOutput.residueinfokind_AA() (InitOutput method) InitOutput.residueinfokind_AAD() (InitOutput method) InitOutput.residueinfokind_BUF() (InitOutput method) InitOutput.residueinfokind_DNA() (InitOutput method) InitOutput.residueinfokind_ELS() (InitOutput method) InitOutput.residueinfokind_HOH() (InitOutput method) InitOutput.residueinfokind_KET() (InitOutput method) InitOutput.residueinfokind_MAA() (InitOutput method) InitOutput.residueinfokind_name() (InitOutput method) InitOutput.residueinfokind_PAA() (InitOutput method) InitOutput.residueinfokind_PYR() (InitOutput method) InitOutput.residueinfokind_RNA() (InitOutput method) InitOutput.residueinfokind_UNKNOWN() (InitOutput method) InitOutput.residueinfokind_value() (InitOutput method) InitOutput.residuename_asBytes() (InitOutput method) InitOutput.residuename_asStr() (InitOutput method) InitOutput.residuename_fromAscii() (InitOutput method) InitOutput.residuesequenceerror_domain() (InitOutput method) InitOutput.residuesequenceerror_kind() (InitOutput method) InitOutput.residuesequenceerror_message() (InitOutput method) InitOutput.residuesourceids_labelEntityId() (InitOutput method) InitOutput.residuesourceids_labelSeqId() (InitOutput method) InitOutput.residuesourceids_segmentId() (InitOutput method) InitOutput.residuesourceids_seqId() (InitOutput method) InitOutput.residuesourceids_subchainId() (InitOutput method) InitOutput.ringsearchparams_includeDativeBonds() (InitOutput method) InitOutput.ringsearchparams_includeHydrogenBonds() (InitOutput method) InitOutput.ringsearchparams_new() (InitOutput method) InitOutput.ringsearchparams_set_includeDativeBonds() (InitOutput method) InitOutput.ringsearchparams_set_includeHydrogenBonds() (InitOutput method) InitOutput.ringstereorelation_atom() (InitOutput method) InitOutput.ringstereorelation_other() (InitOutput method) InitOutput.ringstereorelation_sameOrientation() (InitOutput method) InitOutput.sanitizeerror_bits() (InitOutput method) InitOutput.sanitizeerror_cause() (InitOutput method) InitOutput.sanitizeerror_domain() (InitOutput method) InitOutput.sanitizeerror_kind() (InitOutput method) InitOutput.sanitizeerror_message() (InitOutput method) InitOutput.sanitizeerror_stage() (InitOutput method) InitOutput.sanitizeerror_unknownBits() (InitOutput method) InitOutput.sanitizeoperations_ADJUST_HS() (InitOutput method) InitOutput.sanitizeoperations_ALL() (InitOutput method) InitOutput.sanitizeoperations_and() (InitOutput method) InitOutput.sanitizeoperations_bits() (InitOutput method) InitOutput.sanitizeoperations_CLEANUP() (InitOutput method) InitOutput.sanitizeoperations_CLEANUP_ATROPISOMERS() (InitOutput method) InitOutput.sanitizeoperations_CLEANUP_CHIRALITY() (InitOutput method) InitOutput.sanitizeoperations_CLEANUP_ORGANOMETALLICS() (InitOutput method) InitOutput.sanitizeoperations_contains() (InitOutput method) InitOutput.sanitizeoperations_FIND_RADICALS() (InitOutput method) InitOutput.sanitizeoperations_fromBits() (InitOutput method) InitOutput.sanitizeoperations_isEmpty() (InitOutput method) InitOutput.sanitizeoperations_KEKULIZE() (InitOutput method) InitOutput.sanitizeoperations_NONE() (InitOutput method) InitOutput.sanitizeoperations_or() (InitOutput method) InitOutput.sanitizeoperations_PROPERTIES() (InitOutput method) InitOutput.sanitizeoperations_SET_AROMATICITY() (InitOutput method) InitOutput.sanitizeoperations_SET_CONJUGATION() (InitOutput method) InitOutput.sanitizeoperations_SET_HYBRIDIZATION() (InitOutput method) InitOutput.sanitizeoperations_SYMM_RINGS() (InitOutput method) InitOutput.sanitizeparams_new() (InitOutput method) InitOutput.sanitizeparams_operations() (InitOutput method) InitOutput.sanitizeparams_set_operations() (InitOutput method) InitOutput.sdfbatchiterator_next() (InitOutput method) InitOutput.sdfbatchiterator_nextBatch() (InitOutput method) InitOutput.sdfdataset_batches() (InitOutput method) InitOutput.sdfdataset_isEmpty() (InitOutput method) InitOutput.sdfdataset_iter() (InitOutput method) InitOutput.sdfdataset_len() (InitOutput method) InitOutput.sdfdataset_metadata() (InitOutput method) InitOutput.sdfdataset_open() (InitOutput method) InitOutput.sdfdataset_openWithParams() (InitOutput method) InitOutput.sdfdataset_path() (InitOutput method) InitOutput.sdfdataset_record() (InitOutput method) InitOutput.sdfdataset_recordText() (InitOutput method) InitOutput.sdfdataset_recordWithParams() (InitOutput method) InitOutput.sdfdatasetiterator_next() (InitOutput method) InitOutput.sdferror_actual() (InitOutput method) InitOutput.sdferror_cause() (InitOutput method) InitOutput.sdferror_domain() (InitOutput method) InitOutput.sdferror_expected() (InitOutput method) InitOutput.sdferror_kind() (InitOutput method) InitOutput.sdferror_message() (InitOutput method) InitOutput.sdfgraph_kind() (InitOutput method) InitOutput.sdfgraph_molecule() (InitOutput method) InitOutput.sdfgraph_queryGraph() (InitOutput method) InitOutput.sdfpropertylist_name() (InitOutput method) InitOutput.sdfpropertylist_target() (InitOutput method) InitOutput.sdfpropertylist_values() (InitOutput method) InitOutput.sdfreader_batches() (InitOutput method) InitOutput.sdfreader_open() (InitOutput method) InitOutput.sdfreader_openWithParams() (InitOutput method) InitOutput.sdfreader_params() (InitOutput method) InitOutput.sdfreader_path() (InitOutput method) InitOutput.sdfreaderbatchiterator_next() (InitOutput method) InitOutput.sdfreaderbatchiterator_nextBatch() (InitOutput method) InitOutput.sdfreaderror_cause() (InitOutput method) InitOutput.sdfreaderror_context() (InitOutput method) InitOutput.sdfreaderror_domain() (InitOutput method) InitOutput.sdfreaderror_kind() (InitOutput method) InitOutput.sdfreaderror_message() (InitOutput method) InitOutput.sdfreadparams_coordinateMode() (InitOutput method) InitOutput.sdfreadparams_expandAttachmentPoints() (InitOutput method) InitOutput.sdfreadparams_new() (InitOutput method) InitOutput.sdfreadparams_processPropertyLists() (InitOutput method) InitOutput.sdfreadparams_removeHs() (InitOutput method) InitOutput.sdfreadparams_sanitize() (InitOutput method) InitOutput.sdfreadparams_set_coordinateMode() (InitOutput method) InitOutput.sdfreadparams_set_expandAttachmentPoints() (InitOutput method) InitOutput.sdfreadparams_set_processPropertyLists() (InitOutput method) InitOutput.sdfreadparams_set_removeHs() (InitOutput method) InitOutput.sdfreadparams_set_sanitize() (InitOutput method) InitOutput.sdfreadparams_set_strictParsing() (InitOutput method) InitOutput.sdfreadparams_strictParsing() (InitOutput method) InitOutput.sdfrecord_dataField() (InitOutput method) InitOutput.sdfrecord_dataFields() (InitOutput method) InitOutput.sdfrecord_fromQueryGraph() (InitOutput method) InitOutput.sdfrecord_fromSdf() (InitOutput method) InitOutput.sdfrecord_fromSdfWithParams() (InitOutput method) InitOutput.sdfrecord_graph() (InitOutput method) InitOutput.sdfrecord_index() (InitOutput method) InitOutput.sdfrecord_molecule() (InitOutput method) InitOutput.sdfrecord_properties() (InitOutput method) InitOutput.sdfrecord_queryGraph() (InitOutput method) InitOutput.sdfrecord_sourceCoordinateDim() (InitOutput method) InitOutput.sdfrecord_substanceGroups() (InitOutput method) InitOutput.sdfrecord_title() (InitOutput method) InitOutput.sdfrecord_toMol() (InitOutput method) InitOutput.sdfrecord_toMolWithParams() (InitOutput method) InitOutput.sdfrecord_toSdf() (InitOutput method) InitOutput.sdfrecord_toSdfWithParams() (InitOutput method) InitOutput.sdfrecordmetadata_byteLen() (InitOutput method) InitOutput.sdfrecordmetadata_byteOffset() (InitOutput method) InitOutput.sdfrecordmetadata_byteRange() (InitOutput method) InitOutput.sdfrecordmetadata_index() (InitOutput method) InitOutput.sdfrecordmetadata_lineRange() (InitOutput method) InitOutput.sdfrecordmetadata_title() (InitOutput method) InitOutput.sdfrecordstream_batches() (InitOutput method) InitOutput.sdfrecordstream_bytesConsumed() (InitOutput method) InitOutput.sdfrecordstream_isEnd() (InitOutput method) InitOutput.sdfrecordstream_linesConsumed() (InitOutput method) InitOutput.sdfrecordstream_nextRecord() (InitOutput method) InitOutput.sdfrecordstream_open() (InitOutput method) InitOutput.sdfrecordstream_openWithParams() (InitOutput method) InitOutput.sdfrecordstream_recordsConsumed() (InitOutput method) InitOutput.sgroupbracket_new() (InitOutput method) InitOutput.sgroupbracket_points() (InitOutput method) InitOutput.sgroupcstate_bond() (InitOutput method) InitOutput.sgroupcstate_new() (InitOutput method) InitOutput.sgroupcstate_vector() (InitOutput method) InitOutput.sgroupdisplay_brackets() (InitOutput method) InitOutput.smartsparseerror_atom() (InitOutput method) InitOutput.smartsparseerror_beginAtom() (InitOutput method) InitOutput.smartsparseerror_carrier() (InitOutput method) InitOutput.smartsparseerror_cause() (InitOutput method) InitOutput.smartsparseerror_character() (InitOutput method) InitOutput.smartsparseerror_context() (InitOutput method) InitOutput.smartsparseerror_domain() (InitOutput method) InitOutput.smartsparseerror_endAtom() (InitOutput method) InitOutput.smartsparseerror_feature() (InitOutput method) InitOutput.smartsparseerror_kind() (InitOutput method) InitOutput.smartsparseerror_message() (InitOutput method) InitOutput.smartsparseerror_position() (InitOutput method) InitOutput.smartsparseerror_primitiveDetail() (InitOutput method) InitOutput.smartsparseerror_ring() (InitOutput method) InitOutput.smartsparseparams_allowCxsmiles() (InitOutput method) InitOutput.smartsparseparams_debugParse() (InitOutput method) InitOutput.smartsparseparams_mergeHs() (InitOutput method) InitOutput.smartsparseparams_new() (InitOutput method) InitOutput.smartsparseparams_parseName() (InitOutput method) InitOutput.smartsparseparams_replacements() (InitOutput method) InitOutput.smartsparseparams_set_allowCxsmiles() (InitOutput method) InitOutput.smartsparseparams_set_debugParse() (InitOutput method) InitOutput.smartsparseparams_set_mergeHs() (InitOutput method) InitOutput.smartsparseparams_set_parseName() (InitOutput method) InitOutput.smartsparseparams_set_replacements() (InitOutput method) InitOutput.smartsparseparams_set_skipCleanup() (InitOutput method) InitOutput.smartsparseparams_set_strictCxsmiles() (InitOutput method) InitOutput.smartsparseparams_skipCleanup() (InitOutput method) InitOutput.smartsparseparams_strictCxsmiles() (InitOutput method) InitOutput.smartswriteerror_cause() (InitOutput method) InitOutput.smartswriteerror_domain() (InitOutput method) InitOutput.smartswriteerror_kind() (InitOutput method) InitOutput.smartswriteerror_message() (InitOutput method) InitOutput.smartswriteparams_includeAtomMaps() (InitOutput method) InitOutput.smartswriteparams_includeDativeBonds() (InitOutput method) InitOutput.smartswriteparams_isomericSmiles() (InitOutput method) InitOutput.smartswriteparams_new() (InitOutput method) InitOutput.smartswriteparams_rootedAtAtom() (InitOutput method) InitOutput.smartswriteparams_set_includeAtomMaps() (InitOutput method) InitOutput.smartswriteparams_set_includeDativeBonds() (InitOutput method) InitOutput.smartswriteparams_set_isomericSmiles() (InitOutput method) InitOutput.smartswriteparams_set_rootedAtAtom() (InitOutput method) InitOutput.smileserror_cause() (InitOutput method) InitOutput.smileserror_domain() (InitOutput method) InitOutput.smileserror_kind() (InitOutput method) InitOutput.smileserror_message() (InitOutput method) InitOutput.smilesparseparams_allowCxsmiles() (InitOutput method) InitOutput.smilesparseparams_debugParse() (InitOutput method) InitOutput.smilesparseparams_new() (InitOutput method) InitOutput.smilesparseparams_parseName() (InitOutput method) InitOutput.smilesparseparams_removeHs() (InitOutput method) InitOutput.smilesparseparams_replacements() (InitOutput method) InitOutput.smilesparseparams_sanitize() (InitOutput method) InitOutput.smilesparseparams_set_allowCxsmiles() (InitOutput method) InitOutput.smilesparseparams_set_debugParse() (InitOutput method) InitOutput.smilesparseparams_set_parseName() (InitOutput method) InitOutput.smilesparseparams_set_removeHs() (InitOutput method) InitOutput.smilesparseparams_set_replacements() (InitOutput method) InitOutput.smilesparseparams_set_sanitize() (InitOutput method) InitOutput.smilesparseparams_set_skipCleanup() (InitOutput method) InitOutput.smilesparseparams_set_strictCxsmiles() (InitOutput method) InitOutput.smilesparseparams_skipCleanup() (InitOutput method) InitOutput.smilesparseparams_strictCxsmiles() (InitOutput method) InitOutput.smilesstereoerror_actual() (InitOutput method) InitOutput.smilesstereoerror_cause() (InitOutput method) InitOutput.smilesstereoerror_dimension() (InitOutput method) InitOutput.smilesstereoerror_domain() (InitOutput method) InitOutput.smilesstereoerror_expected() (InitOutput method) InitOutput.smilesstereoerror_field() (InitOutput method) InitOutput.smilesstereoerror_id() (InitOutput method) InitOutput.smilesstereoerror_kind() (InitOutput method) InitOutput.smilesstereoerror_message() (InitOutput method) InitOutput.smileswriteerror_cause() (InitOutput method) InitOutput.smileswriteerror_domain() (InitOutput method) InitOutput.smileswriteerror_kind() (InitOutput method) InitOutput.smileswriteerror_message() (InitOutput method) InitOutput.smileswriteparams_allBondsExplicit() (InitOutput method) InitOutput.smileswriteparams_allHydrogensExplicit() (InitOutput method) InitOutput.smileswriteparams_canonical() (InitOutput method) InitOutput.smileswriteparams_cleanStereo() (InitOutput method) InitOutput.smileswriteparams_ignoreAtomMapNumbers() (InitOutput method) InitOutput.smileswriteparams_includeDativeBonds() (InitOutput method) InitOutput.smileswriteparams_isomericSmiles() (InitOutput method) InitOutput.smileswriteparams_kekule() (InitOutput method) InitOutput.smileswriteparams_new() (InitOutput method) InitOutput.smileswriteparams_rootedAtAtom() (InitOutput method) InitOutput.smileswriteparams_set_allBondsExplicit() (InitOutput method) InitOutput.smileswriteparams_set_allHydrogensExplicit() (InitOutput method) InitOutput.smileswriteparams_set_canonical() (InitOutput method) InitOutput.smileswriteparams_set_cleanStereo() (InitOutput method) InitOutput.smileswriteparams_set_ignoreAtomMapNumbers() (InitOutput method) InitOutput.smileswriteparams_set_includeDativeBonds() (InitOutput method) InitOutput.smileswriteparams_set_isomericSmiles() (InitOutput method) InitOutput.smileswriteparams_set_kekule() (InitOutput method) InitOutput.smileswriteparams_set_rootedAtAtom() (InitOutput method) InitOutput.sparsebitfingerprint_nBits() (InitOutput method) InitOutput.sparsebitfingerprint_onBits() (InitOutput method) InitOutput.sparsecountfingerprint32_fuzzyAnd() (InitOutput method) InitOutput.sparsecountfingerprint32_fuzzyOr() (InitOutput method) InitOutput.sparsecountfingerprint32_length() (InitOutput method) InitOutput.sparsecountfingerprint32_new() (InitOutput method) InitOutput.sparsecountfingerprint32_nonzeroElements() (InitOutput method) InitOutput.sparsecountfingerprint32_setValue() (InitOutput method) InitOutput.sparsecountfingerprint32_totalValue() (InitOutput method) InitOutput.sparsecountfingerprint32_value() (InitOutput method) InitOutput.sparsecountfingerprint32_withAdded() (InitOutput method) InitOutput.sparsecountfingerprint32_withAddedScalar() (InitOutput method) InitOutput.sparsecountfingerprint32_withDividedScalar() (InitOutput method) InitOutput.sparsecountfingerprint32_withMultipliedScalar() (InitOutput method) InitOutput.sparsecountfingerprint32_withSubtracted() (InitOutput method) InitOutput.sparsecountfingerprint32_withSubtractedScalar() (InitOutput method) InitOutput.sparsecountfingerprint_fuzzyAnd() (InitOutput method) InitOutput.sparsecountfingerprint_fuzzyOr() (InitOutput method) InitOutput.sparsecountfingerprint_length() (InitOutput method) InitOutput.sparsecountfingerprint_new() (InitOutput method) InitOutput.sparsecountfingerprint_nonzeroElements() (InitOutput method) InitOutput.sparsecountfingerprint_setValue() (InitOutput method) InitOutput.sparsecountfingerprint_totalValue() (InitOutput method) InitOutput.sparsecountfingerprint_value() (InitOutput method) InitOutput.sparsecountfingerprint_withAdded() (InitOutput method) InitOutput.sparsecountfingerprint_withAddedScalar() (InitOutput method) InitOutput.sparsecountfingerprint_withDividedScalar() (InitOutput method) InitOutput.sparsecountfingerprint_withMultipliedScalar() (InitOutput method) InitOutput.sparsecountfingerprint_withSubtracted() (InitOutput method) InitOutput.sparsecountfingerprint_withSubtractedScalar() (InitOutput method) InitOutput.stereoerror_cause() (InitOutput method) InitOutput.stereoerror_domain() (InitOutput method) InitOutput.stereoerror_kind() (InitOutput method) InitOutput.stereoerror_message() (InitOutput method) InitOutput.stereogroup_atoms() (InitOutput method) InitOutput.stereogroup_bonds() (InitOutput method) InitOutput.stereogroup_kind() (InitOutput method) InitOutput.stereogroup_new() (InitOutput method) InitOutput.stereoisomeriterator_next() (InitOutput method) InitOutput.stereoisomeriterator_yieldedCount() (InitOutput method) InitOutput.stereoisomeroptions_default() (InitOutput method) InitOutput.stereoisomeroptions_maxIsomers() (InitOutput method) InitOutput.stereoisomeroptions_new() (InitOutput method) InitOutput.stereoisomeroptions_onlyStereoGroups() (InitOutput method) InitOutput.stereoisomeroptions_onlyUnassigned() (InitOutput method) InitOutput.stereoisomeroptions_randomSource() (InitOutput method) InitOutput.stereoisomeroptions_set_maxIsomers() (InitOutput method) InitOutput.stereoisomeroptions_set_onlyStereoGroups() (InitOutput method) InitOutput.stereoisomeroptions_set_onlyUnassigned() (InitOutput method) InitOutput.stereoisomeroptions_set_randomSource() (InitOutput method) InitOutput.stereoisomeroptions_set_tryEmbedding() (InitOutput method) InitOutput.stereoisomeroptions_set_unique() (InitOutput method) InitOutput.stereoisomeroptions_setMaxIsomers() (InitOutput method) InitOutput.stereoisomeroptions_setOnlyStereoGroups() (InitOutput method) InitOutput.stereoisomeroptions_setOnlyUnassigned() (InitOutput method) InitOutput.stereoisomeroptions_setRandomSource() (InitOutput method) InitOutput.stereoisomeroptions_setTryEmbedding() (InitOutput method) InitOutput.stereoisomeroptions_setUnique() (InitOutput method) InitOutput.stereoisomeroptions_tryEmbedding() (InitOutput method) InitOutput.stereoisomeroptions_unique() (InitOutput method) InitOutput.stereoisomerrandomsource_fromIntegerSeed() (InitOutput method) InitOutput.stereoisomerrandomsource_fromRandomBits() (InitOutput method) InitOutput.stereoreaderror_cause() (InitOutput method) InitOutput.stereoreaderror_domain() (InitOutput method) InitOutput.stereoreaderror_kind() (InitOutput method) InitOutput.stereoreaderror_message() (InitOutput method) InitOutput.structuretagparams_conformerId() (InitOutput method) InitOutput.structuretagparams_new() (InitOutput method) InitOutput.structuretagparams_replaceExistingTags() (InitOutput method) InitOutput.structuretagparams_set_conformerId() (InitOutput method) InitOutput.structuretagparams_set_replaceExistingTags() (InitOutput method) InitOutput.substancegroup_crossingBondCorrespondence() (InitOutput method) InitOutput.substancegroup_cstates() (InitOutput method) InitOutput.substancegroup_display() (InitOutput method) InitOutput.substancegroup_headCrossingBonds() (InitOutput method) InitOutput.substancegroup_id() (InitOutput method) InitOutput.substancegroup_kind() (InitOutput method) InitOutput.substancegroup_new() (InitOutput method) InitOutput.substancegroupid_index() (InitOutput method) InitOutput.substancegroupid_new() (InitOutput method) InitOutput.substancegroupkind_AnyPolymer() (InitOutput method) InitOutput.substancegroupkind_Copolymer() (InitOutput method) InitOutput.substancegroupkind_Crosslink() (InitOutput method) InitOutput.substancegroupkind_Data() (InitOutput method) InitOutput.substancegroupkind_equals() (InitOutput method) InitOutput.substancegroupkind_Formulation() (InitOutput method) InitOutput.substancegroupkind_Generic() (InitOutput method) InitOutput.substancegroupkind_genericValue() (InitOutput method) InitOutput.substancegroupkind_Graft() (InitOutput method) InitOutput.substancegroupkind_Mer() (InitOutput method) InitOutput.substancegroupkind_Mixture() (InitOutput method) InitOutput.substancegroupkind_MixtureComponent() (InitOutput method) InitOutput.substancegroupkind_Modification() (InitOutput method) InitOutput.substancegroupkind_Monomer() (InitOutput method) InitOutput.substancegroupkind_MultipleGroup() (InitOutput method) InitOutput.substancegroupkind_StructuralRepeatUnit() (InitOutput method) InitOutput.substancegroupkind_Superatom() (InitOutput method) InitOutput.substructmatcherror_branch() (InitOutput method) InitOutput.substructmatcherror_cause() (InitOutput method) InitOutput.substructmatcherror_domain() (InitOutput method) InitOutput.substructmatcherror_kind() (InitOutput method) InitOutput.substructmatcherror_message() (InitOutput method) InitOutput.substructmatcherror_rdkitFunction() (InitOutput method) InitOutput.substructmatchparams_aromaticMatchesConjugated() (InitOutput method) InitOutput.substructmatchparams_aromaticMatchesSingleOrDouble() (InitOutput method) InitOutput.substructmatchparams_atomMatch() (InitOutput method) InitOutput.substructmatchparams_atomProperties() (InitOutput method) InitOutput.substructmatchparams_bondMatch() (InitOutput method) InitOutput.substructmatchparams_bondProperties() (InitOutput method) InitOutput.substructmatchparams_extraAtomCheckOverridesDefaultCheck() (InitOutput method) InitOutput.substructmatchparams_extraBondCheckOverridesDefaultCheck() (InitOutput method) InitOutput.substructmatchparams_finalMatch() (InitOutput method) InitOutput.substructmatchparams_maxMatches() (InitOutput method) InitOutput.substructmatchparams_maxRecursiveMatches() (InitOutput method) InitOutput.substructmatchparams_new() (InitOutput method) InitOutput.substructmatchparams_numThreads() (InitOutput method) InitOutput.substructmatchparams_recursionPossible() (InitOutput method) InitOutput.substructmatchparams_set_aromaticMatchesConjugated() (InitOutput method) InitOutput.substructmatchparams_set_aromaticMatchesSingleOrDouble() (InitOutput method) InitOutput.substructmatchparams_set_atomMatch() (InitOutput method) InitOutput.substructmatchparams_set_atomProperties() (InitOutput method) InitOutput.substructmatchparams_set_bondMatch() (InitOutput method) InitOutput.substructmatchparams_set_bondProperties() (InitOutput method) InitOutput.substructmatchparams_set_extraAtomCheckOverridesDefaultCheck() (InitOutput method) InitOutput.substructmatchparams_set_extraBondCheckOverridesDefaultCheck() (InitOutput method) InitOutput.substructmatchparams_set_finalMatch() (InitOutput method) InitOutput.substructmatchparams_set_maxMatches() (InitOutput method) InitOutput.substructmatchparams_set_maxRecursiveMatches() (InitOutput method) InitOutput.substructmatchparams_set_numThreads() (InitOutput method) InitOutput.substructmatchparams_set_recursionPossible() (InitOutput method) InitOutput.substructmatchparams_set_specifiedStereoQueryMatchesUnspecified() (InitOutput method) InitOutput.substructmatchparams_set_uniquify() (InitOutput method) InitOutput.substructmatchparams_set_useChirality() (InitOutput method) InitOutput.substructmatchparams_set_useEnhancedStereo() (InitOutput method) InitOutput.substructmatchparams_set_useGenericMatchers() (InitOutput method) InitOutput.substructmatchparams_set_useQueryQueryMatches() (InitOutput method) InitOutput.substructmatchparams_specifiedStereoQueryMatchesUnspecified() (InitOutput method) InitOutput.substructmatchparams_uniquify() (InitOutput method) InitOutput.substructmatchparams_useChirality() (InitOutput method) InitOutput.substructmatchparams_useEnhancedStereo() (InitOutput method) InitOutput.substructmatchparams_useGenericMatchers() (InitOutput method) InitOutput.substructmatchparams_useQueryQueryMatches() (InitOutput method) InitOutput.supportMatrix() (InitOutput method) InitOutput.supportmatrixentry_feature() (InitOutput method) InitOutput.supportmatrixentry_operation() (InitOutput method) InitOutput.tautomercatalogerror_cause() (InitOutput method) InitOutput.tautomercatalogerror_domain() (InitOutput method) InitOutput.tautomercatalogerror_kind() (InitOutput method) InitOutput.tautomercatalogerror_message() (InitOutput method) InitOutput.tautomerenumeration_canonicalSmiles() (InitOutput method) InitOutput.tautomerenumeration_canonicalTautomer() (InitOutput method) InitOutput.tautomerenumeration_canonicalTautomerWithParams() (InitOutput method) InitOutput.tautomerenumeration_entries() (InitOutput method) InitOutput.tautomerenumeration_get() (InitOutput method) InitOutput.tautomerenumeration_isEmpty() (InitOutput method) InitOutput.tautomerenumeration_iter() (InitOutput method) InitOutput.tautomerenumeration_len() (InitOutput method) InitOutput.tautomerenumeration_modifiedAtoms() (InitOutput method) InitOutput.tautomerenumeration_modifiedBonds() (InitOutput method) InitOutput.tautomerenumeration_status() (InitOutput method) InitOutput.tautomermoleculeview_atom() (InitOutput method) InitOutput.tautomermoleculeview_atomDegree() (InitOutput method) InitOutput.tautomermoleculeview_atomMetadata() (InitOutput method) InitOutput.tautomermoleculeview_atoms() (InitOutput method) InitOutput.tautomermoleculeview_bond() (InitOutput method) InitOutput.tautomermoleculeview_bonds() (InitOutput method) InitOutput.tautomermoleculeview_numAtoms() (InitOutput method) InitOutput.tautomermoleculeview_numBonds() (InitOutput method) InitOutput.tautomermoleculeview_properties() (InitOutput method) InitOutput.tautomermoleculeview_tautomerScore() (InitOutput method) InitOutput.tautomermoleculeview_toOwned() (InitOutput method) InitOutput.tautomermoleculeview_toSmiles() (InitOutput method) InitOutput.tautomerparams_callback() (InitOutput method) InitOutput.tautomerparams_fromTransformData() (InitOutput method) InitOutput.tautomerparams_fromTransformFile() (InitOutput method) InitOutput.tautomerparams_maxTautomers() (InitOutput method) InitOutput.tautomerparams_maxTransforms() (InitOutput method) InitOutput.tautomerparams_new() (InitOutput method) InitOutput.tautomerparams_reassignStereo() (InitOutput method) InitOutput.tautomerparams_removeBondStereo() (InitOutput method) InitOutput.tautomerparams_removeIsotopicHydrogens() (InitOutput method) InitOutput.tautomerparams_removeSp3Stereo() (InitOutput method) InitOutput.tautomerparams_scoreParams() (InitOutput method) InitOutput.tautomerparams_scorer() (InitOutput method) InitOutput.tautomerparams_set_callback() (InitOutput method) InitOutput.tautomerparams_set_maxTautomers() (InitOutput method) InitOutput.tautomerparams_set_maxTransforms() (InitOutput method) InitOutput.tautomerparams_set_reassignStereo() (InitOutput method) InitOutput.tautomerparams_set_removeBondStereo() (InitOutput method) InitOutput.tautomerparams_set_removeIsotopicHydrogens() (InitOutput method) InitOutput.tautomerparams_set_removeSp3Stereo() (InitOutput method) InitOutput.tautomerparams_set_scoreParams() (InitOutput method) InitOutput.tautomerparams_set_scorer() (InitOutput method) InitOutput.tautomerparams_setCallback() (InitOutput method) InitOutput.tautomerparams_setMaxTautomers() (InitOutput method) InitOutput.tautomerparams_setMaxTransforms() (InitOutput method) InitOutput.tautomerparams_setReassignStereo() (InitOutput method) InitOutput.tautomerparams_setRemoveBondStereo() (InitOutput method) InitOutput.tautomerparams_setRemoveIsotopicHydrogens() (InitOutput method) InitOutput.tautomerparams_setRemoveSp3Stereo() (InitOutput method) InitOutput.tautomerparams_setScorer() (InitOutput method) InitOutput.tautomerparams_transformCount() (InitOutput method) InitOutput.tautomerparams_v1() (InitOutput method) InitOutput.tautomerparams_withMaxTautomers() (InitOutput method) InitOutput.tautomerparams_withMaxTransforms() (InitOutput method) InitOutput.tautomerparams_withReassignStereo() (InitOutput method) InitOutput.tautomerparams_withRemoveBondStereo() (InitOutput method) InitOutput.tautomerparams_withRemoveIsotopicHydrogens() (InitOutput method) InitOutput.tautomerparams_withRemoveSp3Stereo() (InitOutput method) InitOutput.tautomerprogress_entries() (InitOutput method) InitOutput.tautomerprogress_isEmpty() (InitOutput method) InitOutput.tautomerprogress_len() (InitOutput method) InitOutput.tautomerprogress_modifiedAtoms() (InitOutput method) InitOutput.tautomerprogress_modifiedBonds() (InitOutput method) InitOutput.tautomerprogress_numTransforms() (InitOutput method) InitOutput.tautomerprogress_status() (InitOutput method) InitOutput.tautomerprogress_toOwned() (InitOutput method) InitOutput.tautomerrunerror_cause() (InitOutput method) InitOutput.tautomerrunerror_domain() (InitOutput method) InitOutput.tautomerrunerror_kind() (InitOutput method) InitOutput.tautomerrunerror_message() (InitOutput method) InitOutput.tautomerscore_heteroHydrogen() (InitOutput method) InitOutput.tautomerscore_ring() (InitOutput method) InitOutput.tautomerscore_substructure() (InitOutput method) InitOutput.tautomerscore_total() (InitOutput method) InitOutput.tautomerscoreparams_new() (InitOutput method) InitOutput.tautomerscoreparams_set_terms() (InitOutput method) InitOutput.tautomerscoreparams_terms() (InitOutput method) InitOutput.tautomerscoreterm_name() (InitOutput method) InitOutput.tautomerscoreterm_new() (InitOutput method) InitOutput.tautomerscoreterm_score() (InitOutput method) InitOutput.tautomerscoreterm_smarts() (InitOutput method) InitOutput.templateattachment_label() (InitOutput method) InitOutput.templateattachment_new() (InitOutput method) InitOutput.templateattachment_target() (InitOutput method) InitOutput.templateattachmentorder_entries() (InitOutput method) InitOutput.templateattachmentorder_new() (InitOutput method) InitOutput.templateattachmentordererror_atomCount() (InitOutput method) InitOutput.templateattachmentordererror_duplicatePosition() (InitOutput method) InitOutput.templateattachmentordererror_firstPosition() (InitOutput method) InitOutput.templateattachmentordererror_kind() (InitOutput method) InitOutput.templateattachmentordererror_label() (InitOutput method) InitOutput.templateattachmentordererror_mappingLen() (InitOutput method) InitOutput.templateattachmentordererror_message() (InitOutput method) InitOutput.templateattachmentordererror_position() (InitOutput method) InitOutput.templateattachmentordererror_target() (InitOutput method) InitOutput.tetrahedralstereo_center() (InitOutput method) InitOutput.tetrahedralstereo_ligands() (InitOutput method) InitOutput.topologicalfingerprinterror_cause() (InitOutput method) InitOutput.topologicalfingerprinterror_domain() (InitOutput method) InitOutput.topologicalfingerprinterror_field() (InitOutput method) InitOutput.topologicalfingerprinterror_kind() (InitOutput method) InitOutput.topologicalfingerprinterror_message() (InitOutput method) InitOutput.topologicalfingerprinterror_reason() (InitOutput method) InitOutput.topologicalfingerprintoutput_atomBits() (InitOutput method) InitOutput.topologicalfingerprintoutput_bitInfo() (InitOutput method) InitOutput.topologicalfingerprintoutputrequest_atomBits() (InitOutput method) InitOutput.topologicalfingerprintoutputrequest_bitInfo() (InitOutput method) InitOutput.topologicalfingerprintoutputrequest_new() (InitOutput method) InitOutput.topologicalfingerprintoutputrequest_set_atomBits() (InitOutput method) InitOutput.topologicalfingerprintoutputrequest_set_bitInfo() (InitOutput method) InitOutput.topologicalfingerprintparams_atomInvariants() (InitOutput method) InitOutput.topologicalfingerprintparams_branchedPaths() (InitOutput method) InitOutput.topologicalfingerprintparams_fpSize() (InitOutput method) InitOutput.topologicalfingerprintparams_fromAtoms() (InitOutput method) InitOutput.topologicalfingerprintparams_maxPath() (InitOutput method) InitOutput.topologicalfingerprintparams_minPath() (InitOutput method) InitOutput.topologicalfingerprintparams_minSize() (InitOutput method) InitOutput.topologicalfingerprintparams_new() (InitOutput method) InitOutput.topologicalfingerprintparams_numBitsPerFeature() (InitOutput method) InitOutput.topologicalfingerprintparams_set_atomInvariants() (InitOutput method) InitOutput.topologicalfingerprintparams_set_branchedPaths() (InitOutput method) InitOutput.topologicalfingerprintparams_set_fpSize() (InitOutput method) InitOutput.topologicalfingerprintparams_set_fromAtoms() (InitOutput method) InitOutput.topologicalfingerprintparams_set_maxPath() (InitOutput method) InitOutput.topologicalfingerprintparams_set_minPath() (InitOutput method) InitOutput.topologicalfingerprintparams_set_minSize() (InitOutput method) InitOutput.topologicalfingerprintparams_set_numBitsPerFeature() (InitOutput method) InitOutput.topologicalfingerprintparams_set_targetDensity() (InitOutput method) InitOutput.topologicalfingerprintparams_set_useBondOrder() (InitOutput method) InitOutput.topologicalfingerprintparams_set_useHs() (InitOutput method) InitOutput.topologicalfingerprintparams_targetDensity() (InitOutput method) InitOutput.topologicalfingerprintparams_useBondOrder() (InitOutput method) InitOutput.topologicalfingerprintparams_useHs() (InitOutput method) InitOutput.topologicalfingerprintresult_atomBits() (InitOutput method) InitOutput.topologicalfingerprintresult_bitInfo() (InitOutput method) InitOutput.topologicalfingerprintresult_fingerprint() (InitOutput method) InitOutput.topologicaltorsioncallparams_conformerId() (InitOutput method) InitOutput.topologicaltorsioncallparams_construct() (InitOutput method) InitOutput.topologicaltorsioncallparams_customAtomInvariants() (InitOutput method) InitOutput.topologicaltorsioncallparams_customBondInvariants() (InitOutput method) InitOutput.topologicaltorsioncallparams_fromAtoms() (InitOutput method) InitOutput.topologicaltorsioncallparams_ignoreAtoms() (InitOutput method) InitOutput.topologicaltorsioncallparams_set_conformerId() (InitOutput method) InitOutput.topologicaltorsioncallparams_set_customAtomInvariants() (InitOutput method) InitOutput.topologicaltorsioncallparams_set_customBondInvariants() (InitOutput method) InitOutput.topologicaltorsioncallparams_set_fromAtoms() (InitOutput method) InitOutput.topologicaltorsioncallparams_set_ignoreAtoms() (InitOutput method) InitOutput.topologicaltorsioncallparams_set_useLegacyStereoPerception() (InitOutput method) InitOutput.topologicaltorsioncallparams_useLegacyStereoPerception() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_construct() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_counts() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_fingerprints() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_fromJson() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_infoString() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_new() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_settings() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_sparseCounts() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_sparseFingerprints() (InitOutput method) InitOutput.topologicaltorsionfingerprintgenerator_toJson() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_atomInvariantsGenerator() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_conformerId() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_customAtomInvariants() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_customBondInvariants() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_fromAtoms() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_generator() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_ignoreAtoms() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_new() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_set_atomInvariantsGenerator() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_set_conformerId() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_set_customAtomInvariants() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_set_customBondInvariants() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_set_fromAtoms() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_set_generator() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_set_ignoreAtoms() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_set_useLegacyStereoPerception() (InitOutput method) InitOutput.topologicaltorsionfingerprintparams_useLegacyStereoPerception() (InitOutput method) InitOutput.topologicaltorsionparams_bitsPerFeature() (InitOutput method) InitOutput.topologicaltorsionparams_construct() (InitOutput method) InitOutput.topologicaltorsionparams_countBounds() (InitOutput method) InitOutput.topologicaltorsionparams_countSimulation() (InitOutput method) InitOutput.topologicaltorsionparams_fpSize() (InitOutput method) InitOutput.topologicaltorsionparams_includeChirality() (InitOutput method) InitOutput.topologicaltorsionparams_infoString() (InitOutput method) InitOutput.topologicaltorsionparams_onlyShortestPaths() (InitOutput method) InitOutput.topologicaltorsionparams_set_bitsPerFeature() (InitOutput method) InitOutput.topologicaltorsionparams_set_countBounds() (InitOutput method) InitOutput.topologicaltorsionparams_set_countSimulation() (InitOutput method) InitOutput.topologicaltorsionparams_set_fpSize() (InitOutput method) InitOutput.topologicaltorsionparams_set_includeChirality() (InitOutput method) InitOutput.topologicaltorsionparams_set_onlyShortestPaths() (InitOutput method) InitOutput.topologicaltorsionparams_set_torsionAtomCount() (InitOutput method) InitOutput.topologicaltorsionparams_toJson() (InitOutput method) InitOutput.topologicaltorsionparams_torsionAtomCount() (InitOutput method) InitOutput.topologicaltorsionparams_withJson() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_actual() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_atomCount() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_cause() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_code() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_domain() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_index() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_kind() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_message() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_required() (InitOutput method) InitOutput.topologicaltorsionpathscoreerror_subtract() (InitOutput method) InitOutput.topologicaltorsionreaderror_cause() (InitOutput method) InitOutput.topologicaltorsionreaderror_domain() (InitOutput method) InitOutput.topologicaltorsionreaderror_kind() (InitOutput method) InitOutput.topologicaltorsionreaderror_message() (InitOutput method) InitOutput.topologicaltorsionsettings_bitsPerFeature() (InitOutput method) InitOutput.topologicaltorsionsettings_countBounds() (InitOutput method) InitOutput.topologicaltorsionsettings_countSimulation() (InitOutput method) InitOutput.topologicaltorsionsettings_fpSize() (InitOutput method) InitOutput.topologicaltorsionsettings_includeChirality() (InitOutput method) InitOutput.topologicaltorsionsettings_onlyShortestPaths() (InitOutput method) InitOutput.topologicaltorsionsettings_params() (InitOutput method) InitOutput.topologicaltorsionsettings_set_bitsPerFeature() (InitOutput method) InitOutput.topologicaltorsionsettings_set_countBounds() (InitOutput method) InitOutput.topologicaltorsionsettings_set_countSimulation() (InitOutput method) InitOutput.topologicaltorsionsettings_set_fpSize() (InitOutput method) InitOutput.topologicaltorsionsettings_set_includeChirality() (InitOutput method) InitOutput.topologicaltorsionsettings_set_onlyShortestPaths() (InitOutput method) InitOutput.topologicaltorsionsettings_set_torsionAtomCount() (InitOutput method) InitOutput.topologicaltorsionsettings_setBitsPerFeature() (InitOutput method) InitOutput.topologicaltorsionsettings_setCountBounds() (InitOutput method) InitOutput.topologicaltorsionsettings_setCountSimulation() (InitOutput method) InitOutput.topologicaltorsionsettings_setFpSize() (InitOutput method) InitOutput.topologicaltorsionsettings_setIncludeChirality() (InitOutput method) InitOutput.topologicaltorsionsettings_setOnlyShortestPaths() (InitOutput method) InitOutput.topologicaltorsionsettings_setTorsionAtomCount() (InitOutput method) InitOutput.topologicaltorsionsettings_torsionAtomCount() (InitOutput method) InitOutput.topologyblock_atoms() (InitOutput method) InitOutput.topologyblock_bonds() (InitOutput method) InitOutput.topologyblock_stereoGroups() (InitOutput method) InitOutput.topologyblock_substanceGroups() (InitOutput method) InitOutput.transformerror_cause() (InitOutput method) InitOutput.transformerror_domain() (InitOutput method) InitOutput.transformerror_kind() (InitOutput method) InitOutput.transformerror_message() (InitOutput method) InitOutput.uffconformeroptimizationparams_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.uffconformeroptimizationparams_maxIterations() (InitOutput method) InitOutput.uffconformeroptimizationparams_new() (InitOutput method) InitOutput.uffconformeroptimizationparams_numThreads() (InitOutput method) InitOutput.uffconformeroptimizationparams_set_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.uffconformeroptimizationparams_set_maxIterations() (InitOutput method) InitOutput.uffconformeroptimizationparams_set_numThreads() (InitOutput method) InitOutput.uffconformeroptimizationparams_set_vdwThreshold() (InitOutput method) InitOutput.uffconformeroptimizationparams_vdwThreshold() (InitOutput method) InitOutput.uffconformeroptimizationresult_conformerResults() (InitOutput method) InitOutput.uffconformeroptimizationresult_molecule() (InitOutput method) InitOutput.uffconformerresult_conformerId() (InitOutput method) InitOutput.uffconformerresult_energy() (InitOutput method) InitOutput.uffconformerresult_needsMore() (InitOutput method) InitOutput.uffconformerresult_statusCode() (InitOutput method) InitOutput.uffenergygradient_energy() (InitOutput method) InitOutput.uffenergygradient_gradient() (InitOutput method) InitOutput.uffevaluationparams_conformerId() (InitOutput method) InitOutput.uffevaluationparams_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.uffevaluationparams_new() (InitOutput method) InitOutput.uffevaluationparams_set_conformerId() (InitOutput method) InitOutput.uffevaluationparams_set_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.uffevaluationparams_set_vdwThreshold() (InitOutput method) InitOutput.uffevaluationparams_vdwThreshold() (InitOutput method) InitOutput.uffforcefielderror_cause() (InitOutput method) InitOutput.uffforcefielderror_kind() (InitOutput method) InitOutput.uffforcefielderror_message() (InitOutput method) InitOutput.uffforcefielderror_requested() (InitOutput method) InitOutput.uffforcefieldparams_conformerId() (InitOutput method) InitOutput.uffforcefieldparams_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.uffforcefieldparams_new() (InitOutput method) InitOutput.uffforcefieldparams_set_conformerId() (InitOutput method) InitOutput.uffforcefieldparams_set_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.uffforcefieldparams_set_vdwThreshold() (InitOutput method) InitOutput.uffforcefieldparams_vdwThreshold() (InitOutput method) InitOutput.uffoptimizationerror_cause() (InitOutput method) InitOutput.uffoptimizationerror_kind() (InitOutput method) InitOutput.uffoptimizationerror_message() (InitOutput method) InitOutput.uffoptimizationerrorkind_equals() (InitOutput method) InitOutput.uffoptimizationerrorkind_requested() (InitOutput method) InitOutput.uffoptimizationerrorkind_variant() (InitOutput method) InitOutput.uffoptimizationparams_conformerId() (InitOutput method) InitOutput.uffoptimizationparams_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.uffoptimizationparams_maxIterations() (InitOutput method) InitOutput.uffoptimizationparams_new() (InitOutput method) InitOutput.uffoptimizationparams_set_conformerId() (InitOutput method) InitOutput.uffoptimizationparams_set_ignoreInterfragmentInteractions() (InitOutput method) InitOutput.uffoptimizationparams_set_maxIterations() (InitOutput method) InitOutput.uffoptimizationparams_set_vdwThreshold() (InitOutput method) InitOutput.uffoptimizationparams_vdwThreshold() (InitOutput method) InitOutput.uffoptimizationresult_energy() (InitOutput method) InitOutput.uffoptimizationresult_molecule() (InitOutput method) InitOutput.uffoptimizationresult_needsMore() (InitOutput method) InitOutput.uffoptimizationresult_statusCode() (InitOutput method) InitOutput.uffparametererror_cause() (InitOutput method) InitOutput.uffparametererror_kind() (InitOutput method) InitOutput.uffparametererror_message() (InitOutput method) InitOutput.uffparameterqueryerror_cause() (InitOutput method) InitOutput.uffparameterqueryerror_domain() (InitOutput method) InitOutput.uffparameterqueryerror_kind() (InitOutput method) InitOutput.uffparameterqueryerror_message() (InitOutput method) InitOutput.valenceerror_atom() (InitOutput method) InitOutput.valenceerror_atomCount() (InitOutput method) InitOutput.valenceerror_atomicNumber() (InitOutput method) InitOutput.valenceerror_begin() (InitOutput method) InitOutput.valenceerror_bond() (InitOutput method) InitOutput.valenceerror_bondCount() (InitOutput method) InitOutput.valenceerror_calculated() (InitOutput method) InitOutput.valenceerror_cause() (InitOutput method) InitOutput.valenceerror_domain() (InitOutput method) InitOutput.valenceerror_end() (InitOutput method) InitOutput.valenceerror_explicit() (InitOutput method) InitOutput.valenceerror_explicitValence() (InitOutput method) InitOutput.valenceerror_field() (InitOutput method) InitOutput.valenceerror_formalCharge() (InitOutput method) InitOutput.valenceerror_implicit() (InitOutput method) InitOutput.valenceerror_kind() (InitOutput method) InitOutput.valenceerror_message() (InitOutput method) InitOutput.valenceerror_neighborAtom() (InitOutput method) InitOutput.valenceerror_neighborHydrogens() (InitOutput method) InitOutput.valenceerror_order() (InitOutput method) InitOutput.valenceerror_phase() (InitOutput method) InitOutput.valenceerror_physicalBonds() (InitOutput method) InitOutput.valenceerror_reason() (InitOutput method) InitOutput.valenceerror_value() (InitOutput method) InitOutput.valenceparams_model() (InitOutput method) InitOutput.valenceparams_new() (InitOutput method) InitOutput.valenceparams_set_model() (InitOutput method) InitOutput.valenceparams_set_strict() (InitOutput method) InitOutput.valenceparams_strict() (InitOutput method) InitOutput.version() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h05f88ac70f401760() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h08624d7cd030b6a0() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h14118a0e387fd55d() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h19e72435e2b11017() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1f2e9e140386dcff() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_1192() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_3081() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_3115() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_3120() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_3229() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_3230() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_3436() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_3439() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h1fb84771c6d4c7da_535() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h248ca4d0f1d4fa1c() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h268eebdd819191f6() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_1213() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_1214() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_1297() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_1572() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_1736() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_2000() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_2201() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_2202() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_2540() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_2602() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2708d8a2719effc1_3220() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h2cc5e8e47af3b894() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h34612d56d772f01c() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h34612d56d772f01c_3462() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h35cb9bf3c594ee5f() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h38acd83f39f9a161() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h3a81f29a1c9e10be() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h3ff9135752a1f092() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h3ff9135752a1f092_2361() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h4373b30b3ba8a925() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a_1570() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a_1573() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a_1574() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a_2156() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a_2198() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a_2199() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a_2336() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h453b2159268d967a_997() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h45d341170ed13014() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h45d341170ed13014_2976() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h45ebcb141b98b6dd() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h478a223033bd9b1f() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_1352() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_1912() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_2362() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_2740() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_2794() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_3042() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_3070() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_3071() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_3228() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49956dee735bea23_3231() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h49a8825ae387257f() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h4b6da9bc3071ecc9() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h4b6da9bc3071ecc9_2671() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h4b6da9bc3071ecc9_2935() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h4b6da9bc3071ecc9_2936() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h4b6da9bc3071ecc9_2937() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h4db4ab0e05fec32d() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h4dea484daeeed5a3() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h569cdf3f0a66322c() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h569cdf3f0a66322c_3043() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h59baf00393f30cf7() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h614b85946ea67e6c() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h67a2fc157beaf9fd() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h6db98a4cc5df79e0() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h6db98a4cc5df79e0_1571() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h6db98a4cc5df79e0_1735() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h6db98a4cc5df79e0_2200() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h6db98a4cc5df79e0_2541() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h6db98a4cc5df79e0_2545() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h6db98a4cc5df79e0_3051() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h6db98a4cc5df79e0_3311() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h71e91e88d8c4b3f7() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h71e91e88d8c4b3f7_3437() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h71e91e88d8c4b3f7_3438() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h72ca6dab97ecac9e() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h72ca6dab97ecac9e_2885() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h72ca6dab97ecac9e_2886() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h7c59107f9b3cbe63() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h800f6c895d67a2b0() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h8339fab8f3bcda60() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h852738bca8337d35() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h87bc2cc5dae55829() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h8b49ea01c14e3bc2() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h8de728b7fa2df91c() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h9059d7135fd9e11c() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__h9255ce62973f5845() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__ha05b9d9794f8f561() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__ha1b2f829ec646f54() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__ha3f75c99ea49a441() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__ha4a8d6137af526cc() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hae631353995d38ae() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hb82b01e208296be4() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hbaa47e088d36e384() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hbac7c54c94af67c9() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hbb35ae36e72f24fd() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hbd3ee493c359273a() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hc483fc2f39cccc4d() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hc89c1dce75863cbd() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hc9a71a9489900ac4() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hcc0fbd00149512fe() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hcc671454457ab40c() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hd336c339216dfc99() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hd8f113ca221bf109() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hd8f113ca221bf109_2147() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hddbd33dece41c5a1() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__he4f8ec5db018a62d() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__he92c5549aa5e5e18() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__he9c53045f1796d52() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hea34407e9565b8e8() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hec5661b72946c3ef() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hf1d15609af950b6f() (InitOutput method) InitOutput.wasm_bindgen__convert__closures________invoke__hffe1397da5756e64() (InitOutput method) InitOutput.writeCxSmarts() (InitOutput method) InitOutput.writeSmarts() (InitOutput method) InitOutput.xyzreaderror_cause() (InitOutput method) InitOutput.xyzreaderror_domain() (InitOutput method) InitOutput.xyzreaderror_kind() (InitOutput method) InitOutput.xyzreaderror_line() (InitOutput method) InitOutput.xyzreaderror_message() (InitOutput method) InitOutput.xyzreaderror_value() (InitOutput method) InitOutput.xyzwriteerror_cause() (InitOutput method) InitOutput.xyzwriteerror_domain() (InitOutput method) InitOutput.xyzwriteerror_id() (InitOutput method) InitOutput.xyzwriteerror_kind() (InitOutput method) InitOutput.xyzwriteerror_message() (InitOutput method) InitOutput.xyzwriteparams_conformerId() (InitOutput method) InitOutput.xyzwriteparams_new() (InitOutput method) InitOutput.xyzwriteparams_precision() (InitOutput method) InitOutput.xyzwriteparams_set_conformerId() (InitOutput method) InitOutput.xyzwriteparams_set_precision() (InitOutput method) initSync() (built-in function) input() (cosmolkit.ResidueCodeParseError method) input_format (cosmolkit.BioStructureParts attribute) input_format() (cosmolkit.BioStructure method) (cosmolkit.Protein method) ins_code() (cosmolkit.PdbSeqId method) insertion_code (cosmolkit.ResidueAddress attribute) Int (cosmolkit.PropertyValueKind attribute) into_bio_structure() (cosmolkit.Protein method) into_parts() (cosmolkit.BioStructure method) IntVector (cosmolkit.PropertyValueKind attribute) invalid_count() (cosmolkit.MoleculeBatch method) invalid_mask() (cosmolkit.MoleculeBatch method) InvalidAtomIndex (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidFixedAtom (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidInput (cosmolkit.InchiErrorKind attribute) InvalidParameterization (cosmolkit.MolecularForceFieldErrorKind attribute) InvalidSourceOutput (cosmolkit.InchiErrorKind attribute) InvalidTolerance (cosmolkit.MolecularForceFieldErrorKind attribute) invariants (cosmolkit.MorganFingerprintParams property) io_roundtrip (cosmolkit.MoleculeOpSpec attribute) IOD (cosmolkit.ResidueCode attribute) IOH (cosmolkit.ResidueCode attribute) IONIC (cosmolkit.BondOrder attribute) IPA (cosmolkit.ResidueCode attribute) IPH (cosmolkit.ResidueCode attribute) IR (cosmolkit.Element attribute) is_2d (cosmolkit.ReactionCoordinateSelection attribute) is_3d (cosmolkit.Coordinate3DInputParams property) (cosmolkit.ReactionCoordinateSelection attribute) is_3d() (cosmolkit.Conformer3D method) is_amino_acid() (cosmolkit.ResidueInfo method) is_aromatic() (cosmolkit.Atom method) (cosmolkit.Bond method) (cosmolkit.QueryAtom method) is_auto (cosmolkit.ReactionCoordinateSelection attribute) is_buffer_or_water() (cosmolkit.ResidueInfo method) is_conjugated() (cosmolkit.Bond method) is_dna() (cosmolkit.ResidueInfo method) is_empty() (cosmolkit.BioRowSpan method) (cosmolkit.MoleculeBatch method) (cosmolkit.SanitizeOperations method) (cosmolkit.SdfDataset method) (cosmolkit.TautomerEnumeration method) (cosmolkit.TautomerProgress method) is_end() (cosmolkit.SdfRecordStream method) is_implicit_hydrogen (cosmolkit.LigandRef attribute) is_initialized() (cosmolkit.Reaction method) is_modified_amino_acid() (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueInfo method) is_na_linking() (cosmolkit.ResidueInfo method) is_nucleic_acid() (cosmolkit.ResidueInfo method) is_peptide_linking() (cosmolkit.ResidueInfo method) is_prop_computed() (cosmolkit.MoleculeProperties method) is_query (cosmolkit.AvalonFingerprintParams property) is_rna() (cosmolkit.ResidueInfo method) is_standard() (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueInfo method) is_tabulated() (cosmolkit.ResidueIdentity method) is_valid (cosmolkit.ReactionValidationReport attribute) is_valid() (cosmolkit.MmffProperties method) is_water() (cosmolkit.ResidueInfo method) isoform (cosmolkit.BioEntityDbRef attribute) isomeric_smiles (cosmolkit.RandomSmilesWriteParams property) (cosmolkit.ReactionWriteParams property) (cosmolkit.SmartsWriteParams property) (cosmolkit.SmilesWriteParams property) isotope() (cosmolkit.Atom method) (cosmolkit.QueryAtom method) Isotopes (cosmolkit.McsAtomComparator attribute) iter() (cosmolkit.SdfDataset method) (cosmolkit.TautomerEnumeration method) iterations (cosmolkit.ForceFieldMinimizeOutcome attribute) J JEF (cosmolkit.ResidueCode attribute) K K (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) kappa_1() (cosmolkit.Molecule method) kappa_2() (cosmolkit.Molecule method) kappa_3() (cosmolkit.Molecule method) KCX (cosmolkit.ResidueCode attribute) kdg() (cosmolkit.EmbedParams static method) KEEP (cosmolkit.BatchErrorMode attribute) kekule (cosmolkit.RandomSmilesWriteParams property) (cosmolkit.SmilesWriteParams property) kekulize (cosmolkit.MolBlockWriteParams property) KEKULIZE (cosmolkit.SanitizeOperations attribute) Kekulize (cosmolkit.SanitizeStage attribute) kekulize_bonds_() (cosmolkit.Molecule method) kekulize_bonds_with_params_() (cosmolkit.Molecule method) KekulizeError KekulizeError() (class) KekulizeError.[Symbol․dispose]() (KekulizeError method) KekulizeError.actual (KekulizeError attribute) KekulizeError.after (KekulizeError attribute) KekulizeError.atom (KekulizeError attribute) KekulizeError.atomCount (KekulizeError attribute) KekulizeError.before (KekulizeError attribute) KekulizeError.begin (KekulizeError attribute) KekulizeError.bitWidth (KekulizeError attribute) KekulizeError.bond (KekulizeError attribute) KekulizeError.cause (KekulizeError attribute) KekulizeError.domain (KekulizeError attribute) KekulizeError.end (KekulizeError attribute) KekulizeError.expected (KekulizeError attribute) KekulizeError.field (KekulizeError attribute) KekulizeError.free() (KekulizeError method) KekulizeError.kind (KekulizeError attribute) KekulizeError.message (KekulizeError attribute) KekulizeError.problemAtoms (KekulizeError attribute) KekulizeError.questions (KekulizeError attribute) KekulizeError.reason (KekulizeError attribute) KekulizeParams (class in cosmolkit) KekulizeParams() (class) KekulizeParams.[Symbol․dispose]() (KekulizeParams method) KekulizeParams.canonical (KekulizeParams attribute) KekulizeParams.free() (KekulizeParams method) KekulizeParams.markAtomsBonds (KekulizeParams attribute) KekulizeParams.maxBacktracks (KekulizeParams attribute) KekulizeParamsOptions() (interface) KekulizeParamsOptions.canonical? (KekulizeParamsOptions attribute) KekulizeParamsOptions.markAtomsBonds? (KekulizeParamsOptions attribute) KekulizeParamsOptions.maxBacktracks? (KekulizeParamsOptions attribute) Kernel (cosmolkit.MolecularForceFieldErrorKind attribute) KET (cosmolkit.ResidueInfoKind attribute) kind (cosmolkit.BioConnection attribute) (cosmolkit.ForceFieldError property) (cosmolkit.FunctionStatus attribute) (cosmolkit.MmffForceFieldError property) (cosmolkit.MoleculeOpSpec attribute) (cosmolkit.PotentialStereoCenter attribute) (cosmolkit.ReactionValidationIssue attribute) (cosmolkit.SdfGraph attribute) (cosmolkit.UffForceFieldError property) kind() (cosmolkit.BioChainRow method) (cosmolkit.BioEntityRow method) (cosmolkit.BioResidueRow method) (cosmolkit.PropertyStringError method) (cosmolkit.PropertyValue method) (cosmolkit.ProteinChainRef method) (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueInfo method) (cosmolkit.SubstanceGroup method) (cosmolkit.UffOptimizationError method) (cosmolkit.UffParameterError method) kind_name() (cosmolkit.ResidueInfo method) KPI (cosmolkit.ResidueCode attribute) KR (cosmolkit.Element attribute) L l (cosmolkit.BioTlsGroup attribute) LA (cosmolkit.Element attribute) label() (cosmolkit.TemplateAttachment method) label_asym_id() (cosmolkit.ChainSourceIds method) label_entity_id() (cosmolkit.ResidueSourceIds method) label_seq_begin (cosmolkit.BioEntityDbRef attribute) label_seq_end (cosmolkit.BioEntityDbRef attribute) label_seq_id() (cosmolkit.ResidueSourceIds method) labute_asa() (cosmolkit.Molecule method) labute_asa_contributions() (cosmolkit.Molecule method) labute_asa_contributions_with_params() (cosmolkit.Molecule method) labute_asa_with_params() (cosmolkit.Molecule method) LabuteAsaContributions (class in cosmolkit) LabuteAsaContributions() (class) LabuteAsaContributions.[Symbol․dispose]() (LabuteAsaContributions method) LabuteAsaContributions.asa (LabuteAsaContributions attribute) LabuteAsaContributions.atomContributions (LabuteAsaContributions attribute) LabuteAsaContributions.free() (LabuteAsaContributions method) LabuteAsaContributions.hydrogenContribution (LabuteAsaContributions attribute) LAlpha (cosmolkit.BioHelixClass attribute) largest_fragment() (cosmolkit.Molecule method) LAT (cosmolkit.ResidueCode attribute) LayeredFingerprintError LayeredFingerprintError() (class) LayeredFingerprintError.[Symbol․dispose]() (LayeredFingerprintError method) LayeredFingerprintError.cause (LayeredFingerprintError attribute) LayeredFingerprintError.domain (LayeredFingerprintError attribute) LayeredFingerprintError.free() (LayeredFingerprintError method) LayeredFingerprintError.kind (LayeredFingerprintError attribute) LayeredFingerprintError.message (LayeredFingerprintError attribute) LayeredFingerprintLayers (class in cosmolkit) LayeredFingerprintLayers() (class) LayeredFingerprintLayers.[Symbol․dispose]() (LayeredFingerprintLayers method) LayeredFingerprintLayers.bits() (LayeredFingerprintLayers method) LayeredFingerprintLayers.free() (LayeredFingerprintLayers method) LayeredFingerprintLayers.fromBitsRetain() (LayeredFingerprintLayers method) LayeredFingerprintOptions() (interface) LayeredFingerprintOptions.atomCounts? (LayeredFingerprintOptions attribute) LayeredFingerprintOptions.branchedPaths? (LayeredFingerprintOptions attribute) LayeredFingerprintOptions.fpSize? (LayeredFingerprintOptions attribute) LayeredFingerprintOptions.fromAtoms? (LayeredFingerprintOptions attribute) LayeredFingerprintOptions.layers? (LayeredFingerprintOptions attribute) LayeredFingerprintOptions.maxPath? (LayeredFingerprintOptions attribute) LayeredFingerprintOptions.minPath? (LayeredFingerprintOptions attribute) LayeredFingerprintOptions.setOnlyBits? (LayeredFingerprintOptions attribute) LayeredFingerprintParams (class in cosmolkit) LayeredFingerprintParams() (class) LayeredFingerprintParams.[Symbol․dispose]() (LayeredFingerprintParams method) LayeredFingerprintParams.atomCounts (LayeredFingerprintParams attribute) LayeredFingerprintParams.branchedPaths (LayeredFingerprintParams attribute) LayeredFingerprintParams.fpSize (LayeredFingerprintParams attribute) LayeredFingerprintParams.free() (LayeredFingerprintParams method) LayeredFingerprintParams.fromAtoms (LayeredFingerprintParams attribute) LayeredFingerprintParams.layers (LayeredFingerprintParams attribute) LayeredFingerprintParams.maxPath (LayeredFingerprintParams attribute) LayeredFingerprintParams.minPath (LayeredFingerprintParams attribute) LayeredFingerprintParams.setOnlyBits (LayeredFingerprintParams attribute) LayeredFingerprintResult (class in cosmolkit) LayeredFingerprintResult() (class) LayeredFingerprintResult.[Symbol․dispose]() (LayeredFingerprintResult method) LayeredFingerprintResult.atomCounts() (LayeredFingerprintResult method) LayeredFingerprintResult.fingerprint() (LayeredFingerprintResult method) LayeredFingerprintResult.free() (LayeredFingerprintResult method) layers (cosmolkit.LayeredFingerprintParams property) LBT (cosmolkit.ResidueCode attribute) LDA (cosmolkit.ResidueCode attribute) LegacyTopologicalTorsionParams (class in cosmolkit) LegacyTopologicalTorsionParams() (class) LegacyTopologicalTorsionParams.[Symbol․dispose]() (LegacyTopologicalTorsionParams method) LegacyTopologicalTorsionParams.bitsPerEntry (LegacyTopologicalTorsionParams attribute) LegacyTopologicalTorsionParams.customAtomInvariants (LegacyTopologicalTorsionParams attribute) LegacyTopologicalTorsionParams.fpSize (LegacyTopologicalTorsionParams attribute) LegacyTopologicalTorsionParams.free() (LegacyTopologicalTorsionParams method) LegacyTopologicalTorsionParams.fromAtoms (LegacyTopologicalTorsionParams attribute) LegacyTopologicalTorsionParams.ignoreAtoms (LegacyTopologicalTorsionParams attribute) LegacyTopologicalTorsionParams.includeChirality (LegacyTopologicalTorsionParams attribute) LegacyTopologicalTorsionParams.new() (LegacyTopologicalTorsionParams method) LegacyTopologicalTorsionParams.torsionAtomCount (LegacyTopologicalTorsionParams attribute) LegacyTopologicalTorsionParamsOptions() (interface) LegacyTopologicalTorsionParamsOptions.bitsPerEntry? (LegacyTopologicalTorsionParamsOptions attribute) LegacyTopologicalTorsionParamsOptions.customAtomInvariants? (LegacyTopologicalTorsionParamsOptions attribute) LegacyTopologicalTorsionParamsOptions.fpSize? (LegacyTopologicalTorsionParamsOptions attribute) LegacyTopologicalTorsionParamsOptions.fromAtoms? (LegacyTopologicalTorsionParamsOptions attribute) LegacyTopologicalTorsionParamsOptions.ignoreAtoms? (LegacyTopologicalTorsionParamsOptions attribute) LegacyTopologicalTorsionParamsOptions.includeChirality? (LegacyTopologicalTorsionParamsOptions attribute) LegacyTopologicalTorsionParamsOptions.torsionAtomCount? (LegacyTopologicalTorsionParamsOptions attribute) len() (cosmolkit.BioRowSpan method) (cosmolkit.MoleculeBatch method) (cosmolkit.SdfDataset method) (cosmolkit.TautomerEnumeration method) (cosmolkit.TautomerProgress method) length (cosmolkit.BioHelix attribute) length() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) LEU (cosmolkit.ResidueCode attribute) LGamma (cosmolkit.BioHelixClass attribute) LI (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) Ligand (cosmolkit.ResidueKind attribute) LigandOnly (cosmolkit.ChainKind attribute) LigandRef (class in cosmolkit) LigandRef() (class) LigandRef.[Symbol․dispose]() (LigandRef method) LigandRef.atom (LigandRef attribute) LigandRef.free() (LigandRef method) LigandRef.isImplicitHydrogen (LigandRef attribute) ligands (cosmolkit.TetrahedralStereo attribute) line_number() (cosmolkit.BioPdbReadError method) line_range() (cosmolkit.SdfRecordMetadata method) lines_consumed() (cosmolkit.SdfRecordStream method) link_id (cosmolkit.BioConnection attribute) linking_type() (cosmolkit.ResidueInfo method) LINKNODES (cosmolkit.CxSmilesFields attribute) lipinski_hba() (cosmolkit.Molecule method) lipinski_hbd() (cosmolkit.Molecule method) LLP (cosmolkit.ResidueCode attribute) LMT (cosmolkit.ResidueCode attribute) logical_atom_name (cosmolkit.AtomAddress attribute) logp (cosmolkit.CrippenTotals attribute) LOmega (cosmolkit.BioHelixClass attribute) LR (cosmolkit.Element attribute) LU (cosmolkit.Element attribute) luzzati_error (cosmolkit.BioRefinementInfo attribute) LV (cosmolkit.Element attribute) LYS (cosmolkit.ResidueCode attribute) M M (cosmolkit.CipDescriptor attribute) m (cosmolkit.CipDescriptor attribute) M2G (cosmolkit.ResidueCode attribute) M3L (cosmolkit.ResidueCode attribute) MA4 (cosmolkit.ResidueCode attribute) MA6 (cosmolkit.ResidueCode attribute) MAA (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueInfoKind attribute) MaccsFingerprintError MaccsFingerprintError() (class) MaccsFingerprintError.[Symbol․dispose]() (MaccsFingerprintError method) MaccsFingerprintError.bit (MaccsFingerprintError attribute) MaccsFingerprintError.cause (MaccsFingerprintError attribute) MaccsFingerprintError.domain (MaccsFingerprintError attribute) MaccsFingerprintError.free() (MaccsFingerprintError method) MaccsFingerprintError.kind (MaccsFingerprintError attribute) MaccsFingerprintError.message (MaccsFingerprintError attribute) MaccsFingerprintError.option (MaccsFingerprintError attribute) MaccsFingerprintError.reason (MaccsFingerprintError attribute) MaccsFingerprintParams (class in cosmolkit) MaccsFingerprintParams() (class) MaccsFingerprintParams.[Symbol․dispose]() (MaccsFingerprintParams method) MaccsFingerprintParams.free() (MaccsFingerprintParams method) MaccsFingerprintParams.nBits (MaccsFingerprintParams attribute) MaccsFingerprintParamsOptions() (interface) MaccsFingerprintParamsOptions.nBits? (MaccsFingerprintParamsOptions attribute) MAN (cosmolkit.ResidueCode attribute) map (cosmolkit.ReactionValidationIssue attribute) maps (cosmolkit.ReactionValidationIssue attribute) mark_atoms_bonds (cosmolkit.KekulizeParams property) match_chiral_tag (cosmolkit.McsAtomCompareParameters property) match_formal_charge (cosmolkit.McsAtomCompareParameters property) match_fused_rings (cosmolkit.McsBondCompareParameters property) match_fused_rings_strict (cosmolkit.McsBondCompareParameters property) match_isotope (cosmolkit.McsAtomCompareParameters property) match_params() (cosmolkit.Reaction method) match_stereo (cosmolkit.McsBondCompareParameters property) match_valences (cosmolkit.McsAtomCompareParameters property) MatchError MatchError() (class) MatchError.[Symbol․dispose]() (MatchError method) MatchError.cause (MatchError attribute) MatchError.domain (MatchError attribute) MatchError.free() (MatchError method) MatchError.kind (MatchError attribute) MatchError.message (MatchError attribute) MatchResult (class in cosmolkit) MatchResult() (class) MatchResult.[Symbol․dispose]() (MatchResult method) MatchResult.atomMapping() (MatchResult method) MatchResult.atomPairs() (MatchResult method) MatchResult.bondMapping() (MatchResult method) MatchResult.free() (MatchResult method) Materialization (cosmolkit.BioMmcifReadStage attribute) matrix (cosmolkit.BioTransform attribute) matrix() (cosmolkit.AlignmentTransform method) MatrixError MatrixError() (class) MatrixError.[Symbol․dispose]() (MatrixError method) MatrixError.atom (MatrixError attribute) MatrixError.atomCount (MatrixError attribute) MatrixError.bond (MatrixError attribute) MatrixError.bondCount (MatrixError attribute) MatrixError.cause (MatrixError attribute) MatrixError.conformerId (MatrixError attribute) MatrixError.dimension (MatrixError attribute) MatrixError.domain (MatrixError attribute) MatrixError.endpoint (MatrixError attribute) MatrixError.firstPosition (MatrixError attribute) MatrixError.free() (MatrixError method) MatrixError.kind (MatrixError attribute) MatrixError.message (MatrixError attribute) MatrixError.order (MatrixError attribute) MatrixError.position (MatrixError attribute) MatrixError.secondPosition (MatrixError attribute) max_backtracks (cosmolkit.KekulizeParams property) max_distance (cosmolkit.AtomPairParams property) (cosmolkit.McsAtomCompareParameters property) max_isomers (cosmolkit.StereoisomerOptions property) max_iterations (cosmolkit.AlignmentParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.ConformerAlignmentParameters property) (cosmolkit.EmbedParams property) (cosmolkit.ForceFieldMinimizeParams property) (cosmolkit.MmffConformerOptimizationParams property) (cosmolkit.MmffOptimizationParams property) (cosmolkit.UffConformerOptimizationParams property) (cosmolkit.UffOptimizationParams property) max_line_length (cosmolkit.BioPdbReadParams property) max_matches (cosmolkit.AllConformerRmsdParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.CoordinateRmsdParameters property) (cosmolkit.SubstructMatchParams property) max_path (cosmolkit.LayeredFingerprintParams property) (cosmolkit.TopologicalFingerprintParams property) max_path_length() (cosmolkit.AtomPairsParameters static method) max_products (cosmolkit.ReactionRunParams property) max_recursive_iterations (cosmolkit.CipLabelOptions property) max_recursive_matches (cosmolkit.SubstructMatchParams property) max_tautomers (cosmolkit.TautomerParams property) max_transforms (cosmolkit.TautomerParams property) maximize_bonds (cosmolkit.McsParameters property) maximum_common_substructure() (in module cosmolkit) maximum_common_substructure_with_params() (in module cosmolkit) maximumCommonSubstructure() (built-in function) maximumCommonSubstructureWithParams() (built-in function) MaxTautomersReached (cosmolkit.TautomerEnumerationStatus attribute) MaxTransformsReached (cosmolkit.TautomerEnumerationStatus attribute) may_mutate (cosmolkit.MoleculeOpSpec attribute) MC (cosmolkit.Element attribute) McsAtomComparator (class in cosmolkit) (None attribute) McsAtomComparator.Any (McsAtomComparator attribute) McsAtomComparator.AnyHeavyAtom (McsAtomComparator attribute) McsAtomComparator.Elements (McsAtomComparator attribute) McsAtomComparator.Isotopes (McsAtomComparator attribute) McsAtomCompareParameters (class in cosmolkit) McsAtomCompareParameters() (class) McsAtomCompareParameters.[Symbol․dispose]() (McsAtomCompareParameters method) McsAtomCompareParameters.completeRingsOnly (McsAtomCompareParameters attribute) McsAtomCompareParameters.free() (McsAtomCompareParameters method) McsAtomCompareParameters.matchChiralTag (McsAtomCompareParameters attribute) McsAtomCompareParameters.matchFormalCharge (McsAtomCompareParameters attribute) McsAtomCompareParameters.matchIsotope (McsAtomCompareParameters attribute) McsAtomCompareParameters.matchValences (McsAtomCompareParameters attribute) McsAtomCompareParameters.maxDistance (McsAtomCompareParameters attribute) McsAtomCompareParameters.ringMatchesRingOnly (McsAtomCompareParameters attribute) McsAtomCompareParametersOptions() (interface) McsAtomCompareParametersOptions.completeRingsOnly? (McsAtomCompareParametersOptions attribute) McsAtomCompareParametersOptions.matchChiralTag? (McsAtomCompareParametersOptions attribute) McsAtomCompareParametersOptions.matchFormalCharge? (McsAtomCompareParametersOptions attribute) McsAtomCompareParametersOptions.matchIsotope? (McsAtomCompareParametersOptions attribute) McsAtomCompareParametersOptions.matchValences? (McsAtomCompareParametersOptions attribute) McsAtomCompareParametersOptions.maxDistance? (McsAtomCompareParametersOptions attribute) McsAtomCompareParametersOptions.ringMatchesRingOnly? (McsAtomCompareParametersOptions attribute) McsBondComparator (class in cosmolkit) (None attribute) McsBondComparator.Any (McsBondComparator attribute) McsBondComparator.Order (McsBondComparator attribute) McsBondComparator.OrderExact (McsBondComparator attribute) McsBondCompareParameters (class in cosmolkit) McsBondCompareParameters() (class) McsBondCompareParameters.[Symbol․dispose]() (McsBondCompareParameters method) McsBondCompareParameters.completeRingsOnly (McsBondCompareParameters attribute) McsBondCompareParameters.free() (McsBondCompareParameters method) McsBondCompareParameters.matchFusedRings (McsBondCompareParameters attribute) McsBondCompareParameters.matchFusedRingsStrict (McsBondCompareParameters attribute) McsBondCompareParameters.matchStereo (McsBondCompareParameters attribute) McsBondCompareParameters.ringMatchesRingOnly (McsBondCompareParameters attribute) McsBondCompareParametersOptions() (interface) McsBondCompareParametersOptions.completeRingsOnly? (McsBondCompareParametersOptions attribute) McsBondCompareParametersOptions.matchFusedRings? (McsBondCompareParametersOptions attribute) McsBondCompareParametersOptions.matchFusedRingsStrict? (McsBondCompareParametersOptions attribute) McsBondCompareParametersOptions.matchStereo? (McsBondCompareParametersOptions attribute) McsBondCompareParametersOptions.ringMatchesRingOnly? (McsBondCompareParametersOptions attribute) McsError McsError() (class) McsError.[Symbol․dispose]() (McsError method) McsError.domain (McsError attribute) McsError.free() (McsError method) McsError.kind (McsError attribute) McsError.message (McsError attribute) McsParameters (class in cosmolkit) McsParameters() (class) McsParameters.[Symbol․dispose]() (McsParameters method) McsParameters.atomComparator (McsParameters attribute) McsParameters.atomCompareParameters (McsParameters attribute) McsParameters.bondComparator (McsParameters attribute) McsParameters.bondCompareParameters (McsParameters attribute) McsParameters.free() (McsParameters method) McsParameters.initialSeed (McsParameters attribute) McsParameters.maximizeBonds (McsParameters attribute) McsParameters.storeAll (McsParameters attribute) McsParameters.threshold (McsParameters attribute) McsParameters.timeout (McsParameters attribute) McsParameters.verbose (McsParameters attribute) McsParametersOptions() (interface) McsParametersOptions.atomComparator? (McsParametersOptions attribute) McsParametersOptions.atomCompareParameters? (McsParametersOptions attribute) McsParametersOptions.bondComparator? (McsParametersOptions attribute) McsParametersOptions.bondCompareParameters? (McsParametersOptions attribute) McsParametersOptions.initialSeed? (McsParametersOptions attribute) McsParametersOptions.maximizeBonds? (McsParametersOptions attribute) McsParametersOptions.storeAll? (McsParametersOptions attribute) McsParametersOptions.threshold? (McsParametersOptions attribute) McsParametersOptions.timeout? (McsParametersOptions attribute) McsParametersOptions.verbose? (McsParametersOptions attribute) McsResult (class in cosmolkit) McsResult() (class) McsResult.[Symbol․dispose]() (McsResult method) McsResult.atomCount (McsResult attribute) McsResult.bondCount (McsResult attribute) McsResult.completed (McsResult attribute) McsResult.degenerate (McsResult attribute) McsResult.free() (McsResult method) McsResult.query (McsResult attribute) McsResult.smarts (McsResult attribute) MD (cosmolkit.Element attribute) Mdl (cosmolkit.AromaticityModel attribute) MDO (cosmolkit.ResidueCode attribute) MEA (cosmolkit.ResidueCode attribute) mean_b (cosmolkit.BioRefinementInfo attribute) mean_i_over_sigma (cosmolkit.BioReflectionsInfo attribute) MED (cosmolkit.ResidueCode attribute) MEN (cosmolkit.ResidueCode attribute) MEQ (cosmolkit.ResidueCode attribute) Mer (cosmolkit.SubstanceGroupKind attribute) merge_hs (cosmolkit.SmartsParseParams property) MES (cosmolkit.ResidueCode attribute) message() (cosmolkit.BatchError method) MET (cosmolkit.ResidueCode attribute) metadata() (cosmolkit.BioStructure method) (cosmolkit.SdfDataset method) MetalC (cosmolkit.BioConnectionKind attribute) method (cosmolkit.BioExperimentInfo attribute) (cosmolkit.MoleculeOpSpec attribute) MG (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) MG8 (cosmolkit.ResidueCode attribute) MHA (cosmolkit.ResidueCode attribute) MHO (cosmolkit.ResidueCode attribute) MHS (cosmolkit.ResidueCode attribute) MIA (cosmolkit.ResidueCode attribute) min_distance (cosmolkit.AtomPairParams property) min_path (cosmolkit.LayeredFingerprintParams property) (cosmolkit.TopologicalFingerprintParams property) min_size (cosmolkit.TopologicalFingerprintParams property) minimize_() (cosmolkit.MolecularForceField method) minimize_with_params_() (cosmolkit.MolecularForceField method) MissingConformer (cosmolkit.MolecularForceFieldErrorKind attribute) MissingProductMapReactant (cosmolkit.ReactionValidationIssueKind attribute) MissingProducts (cosmolkit.ReactionValidationIssueKind attribute) MissingReactants (cosmolkit.ReactionValidationIssueKind attribute) misuse_hash (cosmolkit.BioMmcifWriteParams property) Mixed (cosmolkit.ChainKind attribute) Mixture (cosmolkit.SubstanceGroupKind attribute) MixtureComponent (cosmolkit.SubstanceGroupKind attribute) MK8 (cosmolkit.ResidueCode attribute) MLE (cosmolkit.ResidueCode attribute) MLU (cosmolkit.ResidueCode attribute) MLY (cosmolkit.ResidueCode attribute) MLZ (cosmolkit.ResidueCode attribute) Mmcif (cosmolkit.BioCoordinateFormat attribute) Mmff94 (cosmolkit.AromaticityModel attribute) (cosmolkit.MmffVariant attribute) Mmff94s (cosmolkit.MmffVariant attribute) mmff_energy_gradient() (cosmolkit.Molecule method) mmff_energy_gradient_with_params() (cosmolkit.Molecule method) mmff_force_field() (cosmolkit.Molecule method) mmff_force_field_with_params() (cosmolkit.Molecule method) mmff_has_all_molecule_params() (cosmolkit.Molecule method) mmff_properties() (cosmolkit.Molecule method) mmff_properties_with_params() (cosmolkit.Molecule method) mmff_variant (cosmolkit.MmffConformerOptimizationParams property) (cosmolkit.MmffEvaluationParams property) (cosmolkit.MmffForceFieldParams property) (cosmolkit.MmffOptimizationParams property) (cosmolkit.MmffPropertiesParams property) MmffAtomProperties (class in cosmolkit) MmffAtomProperties() (class) MmffAtomProperties.[Symbol․dispose]() (MmffAtomProperties method) MmffAtomProperties.atomType() (MmffAtomProperties method) MmffAtomProperties.formalCharge() (MmffAtomProperties method) MmffAtomProperties.free() (MmffAtomProperties method) MmffAtomProperties.partialCharge() (MmffAtomProperties method) MmffConformerOptimizationParams (class in cosmolkit) MmffConformerOptimizationParams() (class) MmffConformerOptimizationParams.[Symbol․dispose]() (MmffConformerOptimizationParams method) MmffConformerOptimizationParams.free() (MmffConformerOptimizationParams method) MmffConformerOptimizationParams.ignoreInterfragmentInteractions (MmffConformerOptimizationParams attribute) MmffConformerOptimizationParams.maxIterations (MmffConformerOptimizationParams attribute) MmffConformerOptimizationParams.mmffVariant (MmffConformerOptimizationParams attribute) MmffConformerOptimizationParams.nonBondedThreshold (MmffConformerOptimizationParams attribute) MmffConformerOptimizationParams.numThreads (MmffConformerOptimizationParams attribute) MmffConformerOptimizationParamsOptions() (interface) MmffConformerOptimizationParamsOptions.ignoreInterfragmentInteractions? (MmffConformerOptimizationParamsOptions attribute) MmffConformerOptimizationParamsOptions.maxIterations? (MmffConformerOptimizationParamsOptions attribute) MmffConformerOptimizationParamsOptions.mmffVariant? (MmffConformerOptimizationParamsOptions attribute) MmffConformerOptimizationParamsOptions.nonBondedThreshold? (MmffConformerOptimizationParamsOptions attribute) MmffConformerOptimizationParamsOptions.numThreads? (MmffConformerOptimizationParamsOptions attribute) MmffEnergyGradient (class in cosmolkit) MmffEnergyGradient() (class) MmffEnergyGradient.[Symbol․dispose]() (MmffEnergyGradient method) MmffEnergyGradient.energy() (MmffEnergyGradient method) MmffEnergyGradient.free() (MmffEnergyGradient method) MmffEnergyGradient.gradient() (MmffEnergyGradient method) MmffEvaluationParams (class in cosmolkit) MmffEvaluationParams() (class) MmffEvaluationParams.[Symbol․dispose]() (MmffEvaluationParams method) MmffEvaluationParams.conformerId (MmffEvaluationParams attribute) MmffEvaluationParams.free() (MmffEvaluationParams method) MmffEvaluationParams.ignoreInterfragmentInteractions (MmffEvaluationParams attribute) MmffEvaluationParams.mmffVariant (MmffEvaluationParams attribute) MmffEvaluationParams.nonBondedThreshold (MmffEvaluationParams attribute) MmffEvaluationParamsOptions() (interface) MmffEvaluationParamsOptions.conformerId? (MmffEvaluationParamsOptions attribute) MmffEvaluationParamsOptions.ignoreInterfragmentInteractions? (MmffEvaluationParamsOptions attribute) MmffEvaluationParamsOptions.mmffVariant? (MmffEvaluationParamsOptions attribute) MmffEvaluationParamsOptions.nonBondedThreshold? (MmffEvaluationParamsOptions attribute) MmffForceFieldError MmffForceFieldError() (class) MmffForceFieldError.[Symbol․dispose]() (MmffForceFieldError method) MmffForceFieldError.actual() (MmffForceFieldError method) MmffForceFieldError.atomIndex() (MmffForceFieldError method) MmffForceFieldError.cause (MmffForceFieldError attribute) MmffForceFieldError.component() (MmffForceFieldError method) MmffForceFieldError.expected() (MmffForceFieldError method) MmffForceFieldError.free() (MmffForceFieldError method) MmffForceFieldError.kind() (MmffForceFieldError method) MmffForceFieldError.message (MmffForceFieldError attribute) MmffForceFieldError.requested() (MmffForceFieldError method) MmffForceFieldParams (class in cosmolkit) MmffForceFieldParams() (class) MmffForceFieldParams.[Symbol․dispose]() (MmffForceFieldParams method) MmffForceFieldParams.conformerId (MmffForceFieldParams attribute) MmffForceFieldParams.free() (MmffForceFieldParams method) MmffForceFieldParams.ignoreInterfragmentInteractions (MmffForceFieldParams attribute) MmffForceFieldParams.mmffVariant (MmffForceFieldParams attribute) MmffForceFieldParams.nonBondedThreshold (MmffForceFieldParams attribute) MmffForceFieldParamsOptions() (interface) MmffForceFieldParamsOptions.conformerId? (MmffForceFieldParamsOptions attribute) MmffForceFieldParamsOptions.ignoreInterfragmentInteractions? (MmffForceFieldParamsOptions attribute) MmffForceFieldParamsOptions.mmffVariant? (MmffForceFieldParamsOptions attribute) MmffForceFieldParamsOptions.nonBondedThreshold? (MmffForceFieldParamsOptions attribute) MmffMolPropertiesError MmffMolPropertiesError() (class) MmffMolPropertiesError.[Symbol․dispose]() (MmffMolPropertiesError method) MmffMolPropertiesError.cause (MmffMolPropertiesError attribute) MmffMolPropertiesError.domain (MmffMolPropertiesError attribute) MmffMolPropertiesError.free() (MmffMolPropertiesError method) MmffMolPropertiesError.kind (MmffMolPropertiesError attribute) MmffMolPropertiesError.message (MmffMolPropertiesError attribute) MmffOptimizationError MmffOptimizationError() (class) MmffOptimizationError.[Symbol․dispose]() (MmffOptimizationError method) MmffOptimizationError.cause (MmffOptimizationError attribute) MmffOptimizationError.free() (MmffOptimizationError method) MmffOptimizationError.message (MmffOptimizationError attribute) MmffOptimizationParams (class in cosmolkit) MmffOptimizationParams() (class) MmffOptimizationParams.[Symbol․dispose]() (MmffOptimizationParams method) MmffOptimizationParams.conformerId (MmffOptimizationParams attribute) MmffOptimizationParams.free() (MmffOptimizationParams method) MmffOptimizationParams.ignoreInterfragmentInteractions (MmffOptimizationParams attribute) MmffOptimizationParams.maxIterations (MmffOptimizationParams attribute) MmffOptimizationParams.mmffVariant (MmffOptimizationParams attribute) MmffOptimizationParams.nonBondedThreshold (MmffOptimizationParams attribute) MmffOptimizationParamsOptions() (interface) MmffOptimizationParamsOptions.conformerId? (MmffOptimizationParamsOptions attribute) MmffOptimizationParamsOptions.ignoreInterfragmentInteractions? (MmffOptimizationParamsOptions attribute) MmffOptimizationParamsOptions.maxIterations? (MmffOptimizationParamsOptions attribute) MmffOptimizationParamsOptions.mmffVariant? (MmffOptimizationParamsOptions attribute) MmffOptimizationParamsOptions.nonBondedThreshold? (MmffOptimizationParamsOptions attribute) MmffOptimizeMoleculeConfResult (class in cosmolkit) MmffOptimizeMoleculeConfResult() (class) MmffOptimizeMoleculeConfResult.[Symbol․dispose]() (MmffOptimizeMoleculeConfResult method) MmffOptimizeMoleculeConfResult.energy() (MmffOptimizeMoleculeConfResult method) MmffOptimizeMoleculeConfResult.free() (MmffOptimizeMoleculeConfResult method) MmffOptimizeMoleculeConfResult.needsMore() (MmffOptimizeMoleculeConfResult method) MmffOptimizeMoleculeConfResult.statusCode() (MmffOptimizeMoleculeConfResult method) MmffOptimizeMoleculeConfsResult (class in cosmolkit) MmffOptimizeMoleculeConfsResult() (class) MmffOptimizeMoleculeConfsResult.[Symbol․dispose]() (MmffOptimizeMoleculeConfsResult method) MmffOptimizeMoleculeConfsResult.conformerResults() (MmffOptimizeMoleculeConfsResult method) MmffOptimizeMoleculeConfsResult.free() (MmffOptimizeMoleculeConfsResult method) MmffOptimizeMoleculeConfsResult.molecule() (MmffOptimizeMoleculeConfsResult method) MmffOptimizeMoleculeResult (class in cosmolkit) MmffOptimizeMoleculeResult() (class) MmffOptimizeMoleculeResult.[Symbol․dispose]() (MmffOptimizeMoleculeResult method) MmffOptimizeMoleculeResult.free() (MmffOptimizeMoleculeResult method) MmffOptimizeMoleculeResult.molecule() (MmffOptimizeMoleculeResult method) MmffOptimizeMoleculeResult.needsMore() (MmffOptimizeMoleculeResult method) MmffOptimizeMoleculeResult.statusCode() (MmffOptimizeMoleculeResult method) MmffProperties (class in cosmolkit) MmffProperties() (class) MmffProperties.[Symbol․dispose]() (MmffProperties method) MmffProperties.atoms() (MmffProperties method) MmffProperties.atomType() (MmffProperties method) MmffProperties.formalCharge() (MmffProperties method) MmffProperties.free() (MmffProperties method) MmffProperties.isValid() (MmffProperties method) MmffProperties.partialCharge() (MmffProperties method) MmffProperties.variant() (MmffProperties method) MmffPropertiesParams (class in cosmolkit) MmffPropertiesParams() (class) MmffPropertiesParams.[Symbol․dispose]() (MmffPropertiesParams method) MmffPropertiesParams.free() (MmffPropertiesParams method) MmffPropertiesParams.mmffVariant (MmffPropertiesParams attribute) MmffPropertiesParamsOptions() (interface) MmffPropertiesParamsOptions.mmffVariant? (MmffPropertiesParamsOptions attribute) MmffVariant (class in cosmolkit) (None attribute) MmffVariant.Mmff94 (MmffVariant attribute) MmffVariant.Mmff94s (MmffVariant attribute) Mmjson (cosmolkit.BioCoordinateFormat attribute) MN (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) MN3 (cosmolkit.ResidueCode attribute) MO (cosmolkit.Element attribute) mod_id (cosmolkit.BioModRes attribute) mod_residues() (cosmolkit.BioStructure method) model (cosmolkit.AromaticityParams property) (cosmolkit.ValenceParams property) model_id() (cosmolkit.BioChainRow method) model_num (cosmolkit.BioCisPep attribute) ModelBuilding (cosmolkit.BioSoftwareClassification attribute) models() (cosmolkit.BioStructure method) Modification (cosmolkit.SubstanceGroupKind attribute) modified_atoms() (cosmolkit.TautomerEnumeration method) (cosmolkit.TautomerProgress method) modified_bonds() (cosmolkit.TautomerEnumeration method) (cosmolkit.TautomerProgress method) ModifiedResidues (cosmolkit.BioMmcifReadStage attribute) modres (cosmolkit.BioMmcifWriteParams property) module cosmolkit MOH (cosmolkit.ResidueCode attribute) Mol2PostError Mol2PostError() (class) Mol2PostError.[Symbol․dispose]() (Mol2PostError method) Mol2PostError.cause (Mol2PostError attribute) Mol2PostError.domain (Mol2PostError attribute) Mol2PostError.free() (Mol2PostError method) Mol2PostError.kind (Mol2PostError attribute) Mol2PostError.message (Mol2PostError attribute) Mol2PostError.stage (Mol2PostError attribute) Mol2ReadError Mol2ReadError() (class) Mol2ReadError.[Symbol․dispose]() (Mol2ReadError method) Mol2ReadError.cause (Mol2ReadError attribute) Mol2ReadError.domain (Mol2ReadError attribute) Mol2ReadError.feature (Mol2ReadError attribute) Mol2ReadError.free() (Mol2ReadError method) Mol2ReadError.kind (Mol2ReadError attribute) Mol2ReadError.message (Mol2ReadError attribute) Mol2ReadError.parseDetail (Mol2ReadError attribute) Mol2ReadParams (class in cosmolkit) Mol2ReadParams() (class) Mol2ReadParams.[Symbol․dispose]() (Mol2ReadParams method) Mol2ReadParams.cleanupSubstructures (Mol2ReadParams attribute) Mol2ReadParams.free() (Mol2ReadParams method) Mol2ReadParams.removeHs (Mol2ReadParams attribute) Mol2ReadParams.sanitize (Mol2ReadParams attribute) Mol2ReadParams.variant (Mol2ReadParams attribute) Mol2ReadParamsOptions() (interface) Mol2ReadParamsOptions.cleanupSubstructures? (Mol2ReadParamsOptions attribute) Mol2ReadParamsOptions.removeHs? (Mol2ReadParamsOptions attribute) Mol2ReadParamsOptions.sanitize? (Mol2ReadParamsOptions attribute) Mol2ReadParamsOptions.variant? (Mol2ReadParamsOptions attribute) Mol2Type (class in cosmolkit) (None attribute) Mol2Type.Corina (Mol2Type attribute) mol_from_binary() (in module cosmolkit) mol_from_inchi() (in module cosmolkit) mol_from_mol() (in module cosmolkit) mol_from_mol2() (in module cosmolkit) mol_from_rdkit() (in module cosmolkit) mol_from_sdf() (in module cosmolkit) mol_from_smiles() (in module cosmolkit) mol_from_xyz_block() (in module cosmolkit) molar_refractivity (cosmolkit.CrippenTotals attribute) MolBlockWriteParams (class in cosmolkit) MolBlockWriteParams() (class) MolBlockWriteParams.[Symbol․dispose]() (MolBlockWriteParams method) MolBlockWriteParams.coordinateSelection (MolBlockWriteParams attribute) MolBlockWriteParams.force2d (MolBlockWriteParams attribute) MolBlockWriteParams.format (MolBlockWriteParams attribute) MolBlockWriteParams.free() (MolBlockWriteParams method) MolBlockWriteParams.includeCoordinates (MolBlockWriteParams attribute) MolBlockWriteParams.includeStereo (MolBlockWriteParams attribute) MolBlockWriteParams.kekulize (MolBlockWriteParams attribute) MolBlockWriteParams.precision (MolBlockWriteParams attribute) MolBlockWriteParamsOptions() (interface) MolBlockWriteParamsOptions.coordinateSelection? (MolBlockWriteParamsOptions attribute) MolBlockWriteParamsOptions.force2d? (MolBlockWriteParamsOptions attribute) MolBlockWriteParamsOptions.format? (MolBlockWriteParamsOptions attribute) MolBlockWriteParamsOptions.includeCoordinates? (MolBlockWriteParamsOptions attribute) MolBlockWriteParamsOptions.includeStereo? (MolBlockWriteParamsOptions attribute) MolBlockWriteParamsOptions.kekulize? (MolBlockWriteParamsOptions attribute) MolBlockWriteParamsOptions.precision? (MolBlockWriteParamsOptions attribute) MolCoordinateSelection (class in cosmolkit) MolCoordinateSelection() (class) MolCoordinateSelection.[Symbol․dispose]() (MolCoordinateSelection method) MolCoordinateSelection.Auto (MolCoordinateSelection attribute) MolCoordinateSelection.free() (MolCoordinateSelection method) MolCoordinateSelection.id (MolCoordinateSelection attribute) MolCoordinateSelection.kind (MolCoordinateSelection attribute) MolCoordinateSelection.ThreeD() (MolCoordinateSelection method) MolCoordinateSelection.TwoD() (MolCoordinateSelection method) molecular_formula() (cosmolkit.Molecule method) molecular_formula_with_params() (cosmolkit.Molecule method) molecular_hash() (cosmolkit.Molecule method) molecular_hash_with_ranks() (cosmolkit.Molecule method) molecular_weight() (cosmolkit.Molecule method) molecular_weight_with_params() (cosmolkit.Molecule method) MolecularForceField (class in cosmolkit) MolecularForceField() (class) MolecularForceField.[Symbol․dispose]() (MolecularForceField method) MolecularForceField.energy() (MolecularForceField method) MolecularForceField.energyGradient() (MolecularForceField method) MolecularForceField.fixedAtoms() (MolecularForceField method) MolecularForceField.free() (MolecularForceField method) MolecularForceField.gradient() (MolecularForceField method) MolecularForceField.gradientUnconstrained() (MolecularForceField method) MolecularForceField.minimize() (MolecularForceField method) MolecularForceField.minimizeWithParams() (MolecularForceField method) MolecularForceField.position() (MolecularForceField method) MolecularForceField.positions() (MolecularForceField method) MolecularForceField.setFixedAtoms() (MolecularForceField method) MolecularForceField.setPosition() (MolecularForceField method) MolecularForceField.setPositions() (MolecularForceField method) MolecularForceFieldErrorKind (class in cosmolkit) (None attribute) MolecularForceFieldErrorKind.Construction (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.CoordinateCount (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.CoordinateShape (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.Initialization (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.InvalidAtomIndex (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.InvalidFixedAtom (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.InvalidParameterization (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.InvalidTolerance (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.Kernel (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.MissingConformer (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.NonFiniteCoordinate (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.Parameterization (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.Preparation (MolecularForceFieldErrorKind attribute) MolecularForceFieldErrorKind.Rings (MolecularForceFieldErrorKind attribute) MolecularIoError MolecularIoError() (class) MolecularIoError.[Symbol․dispose]() (MolecularIoError method) MolecularIoError.cause (MolecularIoError attribute) MolecularIoError.coordinateId (MolecularIoError attribute) MolecularIoError.coordinateKind (MolecularIoError attribute) MolecularIoError.dimension (MolecularIoError attribute) MolecularIoError.domain (MolecularIoError attribute) MolecularIoError.errno (MolecularIoError attribute) MolecularIoError.filename (MolecularIoError attribute) MolecularIoError.format (MolecularIoError attribute) MolecularIoError.free() (MolecularIoError method) MolecularIoError.ioKind (MolecularIoError attribute) MolecularIoError.kind (MolecularIoError attribute) MolecularIoError.message (MolecularIoError attribute) MolecularIoError.parameterDetail (MolecularIoError attribute) MolecularIoError.parameterName (MolecularIoError attribute) MolecularIoError.stage (MolecularIoError attribute) MolecularIoError.threeD (MolecularIoError attribute) MolecularIoError.twoD (MolecularIoError attribute) Molecule (class in cosmolkit) molecule (cosmolkit.AtomPairAtomCodeResult attribute) (cosmolkit.ReactionApplyResult attribute) (cosmolkit.SdfGraph attribute) Molecule() (class) molecule() (cosmolkit.EmbedMoleculeResult method) (cosmolkit.EmbedMultipleConfsResult method) (cosmolkit.MmffOptimizeMoleculeConfsResult method) (cosmolkit.MmffOptimizeMoleculeResult method) (cosmolkit.SdfRecord method) (cosmolkit.UffConformerOptimizationResult method) (cosmolkit.UffOptimizationResult method) Molecule.[Symbol․dispose]() (Molecule method) Molecule.add3dConformer() (Molecule method) Molecule.add3dConformerWithParams() (Molecule method) Molecule.addHydrogens() (Molecule method) Molecule.addHydrogensWithParams() (Molecule method) Molecule.alignConformers() (Molecule method) Molecule.alignConformersWithParams() (Molecule method) Molecule.alignmentTransformTo() (Molecule method) Molecule.alignmentTransformToWithParams() (Molecule method) Molecule.alignTo() (Molecule method) Molecule.alignToWithParams() (Molecule method) Molecule.allConformerBestRmsds() (Molecule method) Molecule.allConformerBestRmsdsWithParams() (Molecule method) Molecule.applyReaction() (Molecule method) Molecule.applyReaction_() (Molecule method) Molecule.applyReactionWithParams() (Molecule method) Molecule.applyReactionWithParams_() (Molecule method) Molecule.assignAromaticity() (Molecule method) Molecule.assignAromaticityWithParams() (Molecule method) Molecule.assignChiralTagsFromStructure() (Molecule method) Molecule.assignChiralTagsFromStructureWithParams() (Molecule method) Molecule.assignCipLabels() (Molecule method) Molecule.assignCipLabelsWithOptions() (Molecule method) Molecule.assignRadicals() (Molecule method) Molecule.assignRingFamilies() (Molecule method) Molecule.assignRingFamiliesWithParams() (Molecule method) Molecule.assignRings() (Molecule method) Molecule.assignValence() (Molecule method) Molecule.assignValenceWithParams() (Molecule method) Molecule.atom() (Molecule method) Molecule.atomicNumbers() (Molecule method) Molecule.atomMetadata() (Molecule method) Molecule.atomProperty() (Molecule method) Molecule.atomPropertyString() (Molecule method) Molecule.atoms() (Molecule method) Molecule.bestAlignmentTo() (Molecule method) Molecule.bestAlignmentToWithParams() (Molecule method) Molecule.bestRmsdTo() (Molecule method) Molecule.bestRmsdToWithParams() (Molecule method) Molecule.bond() (Molecule method) Molecule.bondPropertyString() (Molecule method) Molecule.bonds() (Molecule method) Molecule.canonicalTautomer() (Molecule method) Molecule.canonicalTautomerWithParams() (Molecule method) Molecule.chi0() (Molecule method) Molecule.chi0N() (Molecule method) Molecule.chi0NWithParams() (Molecule method) Molecule.chi0V() (Molecule method) Molecule.chi0VWithParams() (Molecule method) Molecule.chi1() (Molecule method) Molecule.chi1N() (Molecule method) Molecule.chi1NWithParams() (Molecule method) Molecule.chi1V() (Molecule method) Molecule.chi1VWithParams() (Molecule method) Molecule.chi2N() (Molecule method) Molecule.chi2NWithParams() (Molecule method) Molecule.chi2V() (Molecule method) Molecule.chi2VWithParams() (Molecule method) Molecule.chi3N() (Molecule method) Molecule.chi3NWithParams() (Molecule method) Molecule.chi3V() (Molecule method) Molecule.chi3VWithParams() (Molecule method) Molecule.chi4N() (Molecule method) Molecule.chi4NWithParams() (Molecule method) Molecule.chi4V() (Molecule method) Molecule.chi4VWithParams() (Molecule method) Molecule.chiNN() (Molecule method) Molecule.chiNNWithParams() (Molecule method) Molecule.chiNV() (Molecule method) Molecule.chiNVWithParams() (Molecule method) Molecule.cipComputed() (Molecule method) Molecule.clear3dConformers() (Molecule method) Molecule.compute2dCoordinates() (Molecule method) Molecule.compute2dCoordinatesWithParams() (Molecule method) Molecule.conformers3d() (Molecule method) Molecule.coordinateRmsdTo() (Molecule method) Molecule.coordinateRmsdToWithParams() (Molecule method) Molecule.coordinates2d() (Molecule method) Molecule.coordinates3d() (Molecule method) Molecule.crippenDescriptors() (Molecule method) Molecule.crippenDescriptorsWithParams() (Molecule method) Molecule.detectChemistryProblems() (Molecule method) Molecule.detectChemistryProblemsWithParams() (Molecule method) Molecule.dgBoundsMatrix() (Molecule method) Molecule.distanceMatrix() (Molecule method) Molecule.distanceMatrix3d() (Molecule method) Molecule.distanceMatrix3dWithParams() (Molecule method) Molecule.distanceMatrixWithParams() (Molecule method) Molecule.embed3dConformer() (Molecule method) Molecule.embed3dConformerResult() (Molecule method) Molecule.embed3dConformerResultWithParams() (Molecule method) Molecule.embed3dConformers() (Molecule method) Molecule.embed3dConformersResult() (Molecule method) Molecule.embed3dConformersResultWithParams() (Molecule method) Molecule.embed3dConformersWithParams() (Molecule method) Molecule.embed3dConformerWithParams() (Molecule method) Molecule.enumerateStereoisomers() (Molecule method) Molecule.enumerateStereoisomersWithOptions() (Molecule method) Molecule.enumerateStereoisomersWithRandomBits() (Molecule method) Molecule.enumerateTautomers() (Molecule method) Molecule.enumerateTautomersWithParams() (Molecule method) Molecule.exactMolecularWeight() (Molecule method) Molecule.exactMolecularWeightWithParams() (Molecule method) Molecule.findChiralCenters() (Molecule method) Molecule.fingerprintAtomPair() (Molecule method) Molecule.fingerprintAtomPairCount() (Molecule method) Molecule.fingerprintAtomPairCountWithParams() (Molecule method) Molecule.fingerprintAtomPairSparse() (Molecule method) Molecule.fingerprintAtomPairSparseCount() (Molecule method) Molecule.fingerprintAtomPairSparseCountWithParams() (Molecule method) Molecule.fingerprintAtomPairSparseWithParams() (Molecule method) Molecule.fingerprintAtomPairWithParams() (Molecule method) Molecule.fingerprintAvalon() (Molecule method) Molecule.fingerprintAvalonWithParams() (Molecule method) Molecule.fingerprintLayered() (Molecule method) Molecule.fingerprintLayeredWithOutput() (Molecule method) Molecule.fingerprintLayeredWithOutputWithParams() (Molecule method) Molecule.fingerprintLayeredWithParams() (Molecule method) Molecule.fingerprintMaccs() (Molecule method) Molecule.fingerprintMaccsRaw() (Molecule method) Molecule.fingerprintMaccsWithParams() (Molecule method) Molecule.fingerprintMorgan() (Molecule method) Molecule.fingerprintMorganCount() (Molecule method) Molecule.fingerprintMorganCountWithGenerator() (Molecule method) Molecule.fingerprintMorganCountWithParams() (Molecule method) Molecule.fingerprintMorganSparse() (Molecule method) Molecule.fingerprintMorganSparseCount() (Molecule method) Molecule.fingerprintMorganSparseCountWithGenerator() (Molecule method) Molecule.fingerprintMorganSparseCountWithParams() (Molecule method) Molecule.fingerprintMorganSparseWithGenerator() (Molecule method) Molecule.fingerprintMorganSparseWithParams() (Molecule method) Molecule.fingerprintMorganWithGenerator() (Molecule method) Molecule.fingerprintMorganWithParams() (Molecule method) Molecule.fingerprintPattern() (Molecule method) Molecule.fingerprintPatternWithParams() (Molecule method) Molecule.fingerprintTopological() (Molecule method) Molecule.fingerprintTopologicalTorsion() (Molecule method) Molecule.fingerprintTopologicalTorsionCount() (Molecule method) Molecule.fingerprintTopologicalTorsionCountLegacy() (Molecule method) Molecule.fingerprintTopologicalTorsionCountLegacyWithParams() (Molecule method) Molecule.fingerprintTopologicalTorsionCountWithGenerator() (Molecule method) Molecule.fingerprintTopologicalTorsionCountWithParams() (Molecule method) Molecule.fingerprintTopologicalTorsionLegacy() (Molecule method) Molecule.fingerprintTopologicalTorsionLegacyWithParams() (Molecule method) Molecule.fingerprintTopologicalTorsionSparse() (Molecule method) Molecule.fingerprintTopologicalTorsionSparseCount() (Molecule method) Molecule.fingerprintTopologicalTorsionSparseCountLegacy() (Molecule method) Molecule.fingerprintTopologicalTorsionSparseCountLegacyWithParams() (Molecule method) Molecule.fingerprintTopologicalTorsionSparseCountWithGenerator() (Molecule method) Molecule.fingerprintTopologicalTorsionSparseCountWithParams() (Molecule method) Molecule.fingerprintTopologicalTorsionSparseWithGenerator() (Molecule method) Molecule.fingerprintTopologicalTorsionSparseWithParams() (Molecule method) Molecule.fingerprintTopologicalTorsionWithGenerator() (Molecule method) Molecule.fingerprintTopologicalTorsionWithParams() (Molecule method) Molecule.fingerprintTopologicalWithOutput() (Molecule method) Molecule.fingerprintTopologicalWithOutputWithParams() (Molecule method) Molecule.fingerprintTopologicalWithParams() (Molecule method) Molecule.fractionCsp3() (Molecule method) Molecule.fragments() (Molecule method) Molecule.free() (Molecule method) Molecule.fromInchi() (Molecule method) Molecule.fromInchiWithParams() (Molecule method) Molecule.fromMol() (Molecule method) Molecule.fromMol2() (Molecule method) Molecule.fromMol2WithParams() (Molecule method) Molecule.fromMolWithParams() (Molecule method) Molecule.fromParts() (Molecule method) Molecule.fromSdf() (Molecule method) Molecule.fromSdfWithParams() (Molecule method) Molecule.fromSmiles() (Molecule method) Molecule.fromSmilesWithParams() (Molecule method) Molecule.fromSmilesWithSanitize() (Molecule method) Molecule.fromXyzBlock() (Molecule method) Molecule.hallKierAlpha() (Molecule method) Molecule.hallKierAlphaWithContributions() (Molecule method) Molecule.has2dCoordinates() (Molecule method) Molecule.hasSubstructMatch() (Molecule method) Molecule.hasSubstructMatchWithParams() (Molecule method) Molecule.hasValenceViolation() (Molecule method) Molecule.kappa1() (Molecule method) Molecule.kappa2() (Molecule method) Molecule.kappa3() (Molecule method) Molecule.kekulizeBonds() (Molecule method) Molecule.kekulizeBondsWithParams() (Molecule method) Molecule.labuteAsa() (Molecule method) Molecule.labuteAsaContributions() (Molecule method) Molecule.labuteAsaContributionsWithParams() (Molecule method) Molecule.labuteAsaWithParams() (Molecule method) Molecule.largestFragment() (Molecule method) Molecule.lipinskiHba() (Molecule method) Molecule.lipinskiHbd() (Molecule method) Molecule.mmffEnergyGradient() (Molecule method) Molecule.mmffEnergyGradientWithParams() (Molecule method) Molecule.mmffForceField() (Molecule method) Molecule.mmffForceFieldWithParams() (Molecule method) Molecule.mmffHasAllMoleculeParams() (Molecule method) Molecule.mmffProperties() (Molecule method) Molecule.mmffPropertiesWithParams() (Molecule method) Molecule.molecularFormula() (Molecule method) Molecule.molecularFormulaWithParams() (Molecule method) Molecule.molecularHash() (Molecule method) Molecule.molecularHashWithRanks() (Molecule method) Molecule.molecularWeight() (Molecule method) Molecule.molecularWeightWithParams() (Molecule method) Molecule.mqns() (Molecule method) Molecule.murckoDecompose() (Molecule method) Molecule.murckoScaffold() (Molecule method) Molecule.nameOrEmpty() (Molecule method) Molecule.netScaffold() (Molecule method) Molecule.new() (Molecule method) Molecule.num3dConformers() (Molecule method) Molecule.numAliphaticCarbocycles() (Molecule method) Molecule.numAliphaticHeterocycles() (Molecule method) Molecule.numAliphaticRings() (Molecule method) Molecule.numAmideBonds() (Molecule method) Molecule.numAromaticCarbocycles() (Molecule method) Molecule.numAromaticHeterocycles() (Molecule method) Molecule.numAromaticRings() (Molecule method) Molecule.numAtoms() (Molecule method) Molecule.numAtomStereoCenters() (Molecule method) Molecule.numBonds() (Molecule method) Molecule.numBridgeheadAtoms() (Molecule method) Molecule.numConformers3d() (Molecule method) Molecule.numHba() (Molecule method) Molecule.numHbd() (Molecule method) Molecule.numHeavyAtoms() (Molecule method) Molecule.numHeteroatoms() (Molecule method) Molecule.numHeterocycles() (Molecule method) Molecule.numRings() (Molecule method) Molecule.numRotatableBonds() (Molecule method) Molecule.numRotatableBondsWithParams() (Molecule method) Molecule.numSaturatedCarbocycles() (Molecule method) Molecule.numSaturatedHeterocycles() (Molecule method) Molecule.numSaturatedRings() (Molecule method) Molecule.numSpiroAtoms() (Molecule method) Molecule.numUnspecifiedAtomStereoCenters() (Molecule method) Molecule.perceiveStereochemistry() (Molecule method) Molecule.phi() (Molecule method) Molecule.potentialStereo() (Molecule method) Molecule.potentialStereoWithParams() (Molecule method) Molecule.properties() (Molecule method) Molecule.property() (Molecule method) Molecule.propertyKeys() (Molecule method) Molecule.propertyOrEmpty() (Molecule method) Molecule.qed() (Molecule method) Molecule.reactionProducts() (Molecule method) Molecule.reactionProductsFromInputs() (Molecule method) Molecule.reactionProductsWithParams() (Molecule method) Molecule.readMol() (Molecule method) Molecule.readMol2() (Molecule method) Molecule.readMol2WithParams() (Molecule method) Molecule.readMolWithParams() (Molecule method) Molecule.readSdf() (Molecule method) Molecule.readSdfWithParams() (Molecule method) Molecule.readXyz() (Molecule method) Molecule.removeHydrogens() (Molecule method) Molecule.removeHydrogensWithParams() (Molecule method) Molecule.sanitize() (Molecule method) Molecule.sanitize_() (Molecule method) Molecule.sanitizeWithParams() (Molecule method) Molecule.sanitizeWithParams_() (Molecule method) Molecule.sdfDataFieldNames() (Molecule method) Molecule.sdfDataFieldOrEmpty() (Molecule method) Molecule.set2dCoordinates() (Molecule method) Molecule.set2dCoordinatesWithParams() (Molecule method) Molecule.set3dCoordinates() (Molecule method) Molecule.set3dCoordinatesWithParams() (Molecule method) Molecule.setAtomPosition() (Molecule method) Molecule.setAtomPositionWithParams() (Molecule method) Molecule.setAtomProperty() (Molecule method) Molecule.setOnly3dConformer() (Molecule method) Molecule.setOnly3dConformerWithParams() (Molecule method) Molecule.slogpVsa() (Molecule method) Molecule.slogpVsa1() (Molecule method) Molecule.slogpVsa10() (Molecule method) Molecule.slogpVsa11() (Molecule method) Molecule.slogpVsa12() (Molecule method) Molecule.slogpVsa2() (Molecule method) Molecule.slogpVsa3() (Molecule method) Molecule.slogpVsa4() (Molecule method) Molecule.slogpVsa5() (Molecule method) Molecule.slogpVsa6() (Molecule method) Molecule.slogpVsa7() (Molecule method) Molecule.slogpVsa8() (Molecule method) Molecule.slogpVsa9() (Molecule method) Molecule.slogpVsaWithParams() (Molecule method) Molecule.smrVsa() (Molecule method) Molecule.smrVsa1() (Molecule method) Molecule.smrVsa10() (Molecule method) Molecule.smrVsa2() (Molecule method) Molecule.smrVsa3() (Molecule method) Molecule.smrVsa4() (Molecule method) Molecule.smrVsa5() (Molecule method) Molecule.smrVsa6() (Molecule method) Molecule.smrVsa7() (Molecule method) Molecule.smrVsa8() (Molecule method) Molecule.smrVsa9() (Molecule method) Molecule.smrVsaWithParams() (Molecule method) Molecule.stereoisomerCount() (Molecule method) Molecule.stereoisomerCountWithOptions() (Molecule method) Molecule.substructMatch() (Molecule method) Molecule.substructMatches() (Molecule method) Molecule.substructMatchesCompiled() (Molecule method) Molecule.substructMatchesWithParams() (Molecule method) Molecule.substructMatchWithParams() (Molecule method) Molecule.tautomerScore() (Molecule method) Molecule.tautomerScoreWithParams() (Molecule method) Molecule.tetrahedralStereo() (Molecule method) Molecule.toBuilder() (Molecule method) Molecule.toCxSmarts() (Molecule method) Molecule.toCxSmartsWithParams() (Molecule method) Molecule.toCxSmiles() (Molecule method) Molecule.toCxSmilesWithParams() (Molecule method) Molecule.toFragmentCxSmiles() (Molecule method) Molecule.toFragmentCxSmilesWithParams() (Molecule method) Molecule.toFragmentSmiles() (Molecule method) Molecule.toFragmentSmilesWithParams() (Molecule method) Molecule.toInchi() (Molecule method) Molecule.toInchiKey() (Molecule method) Molecule.toInchiKeyWithParams() (Molecule method) Molecule.toInchiWithParams() (Molecule method) Molecule.toMol() (Molecule method) Molecule.toMolWithParams() (Molecule method) Molecule.toPng() (Molecule method) Molecule.topologicalTorsionIds() (Molecule method) Molecule.topologicalTorsionIdsWithParams() (Molecule method) Molecule.topologicalTorsionPathScore() (Molecule method) Molecule.topology() (Molecule method) Molecule.toRandomSmiles() (Molecule method) Molecule.toRandomSmilesWithParams() (Molecule method) Molecule.toSdf() (Molecule method) Molecule.toSdf2d() (Molecule method) Molecule.toSdf2dWithParams() (Molecule method) Molecule.toSdf3d() (Molecule method) Molecule.toSdf3dWithParams() (Molecule method) Molecule.toSdfWithParams() (Molecule method) Molecule.toSmarts() (Molecule method) Molecule.toSmartsWithParams() (Molecule method) Molecule.toSmiles() (Molecule method) Molecule.toSmilesWithParams() (Molecule method) Molecule.toSvg() (Molecule method) Molecule.totalAtomCount() (Molecule method) Molecule.toXyz() (Molecule method) Molecule.toXyzWithParams() (Molecule method) Molecule.tpsa() (Molecule method) Molecule.tpsaWithParams() (Molecule method) Molecule.uffEnergyGradient() (Molecule method) Molecule.uffEnergyGradientWithParams() (Molecule method) Molecule.uffForceField() (Molecule method) Molecule.uffForceFieldWithParams() (Molecule method) Molecule.uffHasAllMoleculeParams() (Molecule method) Molecule.with2dCoordinateBlock() (Molecule method) Molecule.with2dCoordinateBlockWithParams() (Molecule method) Molecule.with2dCoordinates() (Molecule method) Molecule.with2dCoordinatesWithParams() (Molecule method) Molecule.with3dConformer() (Molecule method) Molecule.with3dConformerResult() (Molecule method) Molecule.with3dConformerResultWithParams() (Molecule method) Molecule.with3dConformers() (Molecule method) Molecule.with3dConformersResult() (Molecule method) Molecule.with3dConformersResultWithParams() (Molecule method) Molecule.with3dConformersWithParams() (Molecule method) Molecule.with3dConformerWithParams() (Molecule method) Molecule.with3dCoordinates() (Molecule method) Molecule.with3dCoordinatesWithParams() (Molecule method) Molecule.withAdded3dConformer() (Molecule method) Molecule.withAdded3dConformerWithParams() (Molecule method) Molecule.withAlignedConformers() (Molecule method) Molecule.withAlignedConformersWithParams() (Molecule method) Molecule.withAlignmentTo() (Molecule method) Molecule.withAlignmentToWithParams() (Molecule method) Molecule.withAssignedAromaticity() (Molecule method) Molecule.withAssignedAromaticityWithParams() (Molecule method) Molecule.withAssignedRadicals() (Molecule method) Molecule.withAssignedRingFamilies() (Molecule method) Molecule.withAssignedRingFamiliesWithParams() (Molecule method) Molecule.withAssignedRings() (Molecule method) Molecule.withAssignedValence() (Molecule method) Molecule.withAssignedValenceWithParams() (Molecule method) Molecule.withAtomPairAtomCode() (Molecule method) Molecule.withAtomPosition() (Molecule method) Molecule.withAtomPositionWithParams() (Molecule method) Molecule.withAtomProperty() (Molecule method) Molecule.withChiralTagsFromStructure() (Molecule method) Molecule.withChiralTagsFromStructureWithParams() (Molecule method) Molecule.withCipLabels() (Molecule method) Molecule.withCipLabelsWithOptions() (Molecule method) Molecule.withCleared3dConformers() (Molecule method) Molecule.withHydrogens() (Molecule method) Molecule.withHydrogensWithParams() (Molecule method) Molecule.withKekulizedBonds() (Molecule method) Molecule.withKekulizedBondsWithParams() (Molecule method) Molecule.withMmffOptimized() (Molecule method) Molecule.withMmffOptimizedConformers() (Molecule method) Molecule.withMmffOptimizedConformersWithParams() (Molecule method) Molecule.withMmffOptimizedWithParams() (Molecule method) Molecule.withName() (Molecule method) Molecule.withOnly3dConformer() (Molecule method) Molecule.withOnly3dConformerWithParams() (Molecule method) Molecule.withoutHydrogens() (Molecule method) Molecule.withoutHydrogensWithParams() (Molecule method) Molecule.withProperty() (Molecule method) Molecule.withSdfDataField() (Molecule method) Molecule.withUffOptimized() (Molecule method) Molecule.withUffOptimizedConformers() (Molecule method) Molecule.withUffOptimizedConformersWithParams() (Molecule method) Molecule.withUffOptimizedWithParams() (Molecule method) Molecule.writeMol() (Molecule method) Molecule.writeMolWithParams() (Molecule method) Molecule.writePng() (Molecule method) Molecule.writeSdf() (Molecule method) Molecule.writeSdfFiles() (Molecule method) Molecule.writeSdfFilesWithParams() (Molecule method) Molecule.writeSdfWithParams() (Molecule method) Molecule.writeSvg() (Molecule method) Molecule.writeXyz() (Molecule method) Molecule.writeXyzWithParams() (Molecule method) MoleculeBatch (class in cosmolkit) MoleculeBatch() (class) MoleculeBatch.[Symbol․dispose]() (MoleculeBatch method) MoleculeBatch.dgBoundsMatrixList() (MoleculeBatch method) MoleculeBatch.dgBoundsMatrixListWithParams() (MoleculeBatch method) MoleculeBatch.errorMode() (MoleculeBatch method) MoleculeBatch.errors() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairCountList() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairCountListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairList() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairSparseBitsList() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairSparseBitsListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairSparseCountList() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairSparseCountListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairWithOutputList() (MoleculeBatch method) MoleculeBatch.fingerprintAtomPairWithOutputListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintLayeredList() (MoleculeBatch method) MoleculeBatch.fingerprintLayeredListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintLayeredWithOutputList() (MoleculeBatch method) MoleculeBatch.fingerprintLayeredWithOutputListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintMorganList() (MoleculeBatch method) MoleculeBatch.fingerprintMorganListWithGeneratorParams() (MoleculeBatch method) MoleculeBatch.fingerprintMorganListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintMorganWithOutputList() (MoleculeBatch method) MoleculeBatch.fingerprintMorganWithOutputListWithGeneratorParams() (MoleculeBatch method) MoleculeBatch.fingerprintMorganWithOutputListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintPatternList() (MoleculeBatch method) MoleculeBatch.fingerprintPatternListWithParams() (MoleculeBatch method) MoleculeBatch.fingerprintTopologicalTorsionList() (MoleculeBatch method) MoleculeBatch.fingerprintTopologicalTorsionListWithParams() (MoleculeBatch method) MoleculeBatch.free() (MoleculeBatch method) MoleculeBatch.fromDatasetIndices() (MoleculeBatch method) MoleculeBatch.fromRecords() (MoleculeBatch method) MoleculeBatch.fromSdfRecords() (MoleculeBatch method) MoleculeBatch.fromSdfRecordsWithParams() (MoleculeBatch method) MoleculeBatch.fromSmilesList() (MoleculeBatch method) MoleculeBatch.fromSmilesListWithParams() (MoleculeBatch method) MoleculeBatch.get() (MoleculeBatch method) MoleculeBatch.invalidCount() (MoleculeBatch method) MoleculeBatch.invalidMask() (MoleculeBatch method) MoleculeBatch.isEmpty() (MoleculeBatch method) MoleculeBatch.len() (MoleculeBatch method) MoleculeBatch.parallelJobs() (MoleculeBatch method) MoleculeBatch.progressBar() (MoleculeBatch method) MoleculeBatch.readSdf() (MoleculeBatch method) MoleculeBatch.readSdfWithParams() (MoleculeBatch method) MoleculeBatch.records() (MoleculeBatch method) MoleculeBatch.sanitize() (MoleculeBatch method) MoleculeBatch.sanitizeWithParams() (MoleculeBatch method) MoleculeBatch.toList() (MoleculeBatch method) MoleculeBatch.toSmilesList() (MoleculeBatch method) MoleculeBatch.toSmilesListWithParams() (MoleculeBatch method) MoleculeBatch.toSvgList() (MoleculeBatch method) MoleculeBatch.toSvgListWithParams() (MoleculeBatch method) MoleculeBatch.validCount() (MoleculeBatch method) MoleculeBatch.validMask() (MoleculeBatch method) MoleculeBatch.with2dCoordinates() (MoleculeBatch method) MoleculeBatch.with2dCoordinatesWithParams() (MoleculeBatch method) MoleculeBatch.withHydrogens() (MoleculeBatch method) MoleculeBatch.withHydrogensWithParams() (MoleculeBatch method) MoleculeBatch.withKekulizedBonds() (MoleculeBatch method) MoleculeBatch.withKekulizedBondsWithParams() (MoleculeBatch method) MoleculeBatch.withoutHydrogens() (MoleculeBatch method) MoleculeBatch.withoutHydrogensWithParams() (MoleculeBatch method) MoleculeBatch.withParallelJobs() (MoleculeBatch method) MoleculeBatch.withProgressBar() (MoleculeBatch method) MoleculeBatch.withValidRecords() (MoleculeBatch method) MoleculeBatch.writeImages() (MoleculeBatch method) MoleculeBatch.writeImagesWithParams() (MoleculeBatch method) MoleculeBatch.writeSdf() (MoleculeBatch method) MoleculeBatch.writeSdfFiles() (MoleculeBatch method) MoleculeBatch.writeSdfFilesWithParams() (MoleculeBatch method) MoleculeBatch.writeSdfWithParams() (MoleculeBatch method) MoleculeBuilder (class in cosmolkit) MoleculeBuilder() (class) MoleculeBuilder.[Symbol․dispose]() (MoleculeBuilder method) MoleculeBuilder.add2dConformer() (MoleculeBuilder method) MoleculeBuilder.add3dConformer() (MoleculeBuilder method) MoleculeBuilder.addAtom() (MoleculeBuilder method) MoleculeBuilder.addBond() (MoleculeBuilder method) MoleculeBuilder.addStereoGroup() (MoleculeBuilder method) MoleculeBuilder.addSubstanceGroup() (MoleculeBuilder method) MoleculeBuilder.atoms() (MoleculeBuilder method) MoleculeBuilder.bondBetweenAtoms() (MoleculeBuilder method) MoleculeBuilder.bonds() (MoleculeBuilder method) MoleculeBuilder.build() (MoleculeBuilder method) MoleculeBuilder.coordinates() (MoleculeBuilder method) MoleculeBuilder.degree() (MoleculeBuilder method) MoleculeBuilder.free() (MoleculeBuilder method) MoleculeBuilder.fromParts() (MoleculeBuilder method) MoleculeBuilder.neighborBonds() (MoleculeBuilder method) MoleculeBuilder.properties() (MoleculeBuilder method) MoleculeBuilder.removeBondBetweenAtoms() (MoleculeBuilder method) MoleculeBuilder.set2dCoordinates() (MoleculeBuilder method) MoleculeBuilder.setAtomFormalCharge() (MoleculeBuilder method) MoleculeBuilder.setBondOrder() (MoleculeBuilder method) MoleculeBuilder.stereoGroups() (MoleculeBuilder method) MoleculeBuilder.substanceGroups() (MoleculeBuilder method) MoleculeBuilder.withName() (MoleculeBuilder method) MoleculeBuilder.withProperties() (MoleculeBuilder method) MoleculeBuilder.withProperty() (MoleculeBuilder method) MoleculeBuilder.withSdfDataField() (MoleculeBuilder method) MoleculeHashError MoleculeHashError() (class) MoleculeHashError.[Symbol․dispose]() (MoleculeHashError method) MoleculeHashError.actual (MoleculeHashError attribute) MoleculeHashError.atomCount (MoleculeHashError attribute) MoleculeHashError.cause (MoleculeHashError attribute) MoleculeHashError.domain (MoleculeHashError attribute) MoleculeHashError.free() (MoleculeHashError method) MoleculeHashError.kind (MoleculeHashError attribute) MoleculeHashError.message (MoleculeHashError attribute) MoleculeOpSpec (class in cosmolkit) MoleculeOpSpec() (class) MoleculeOpSpec.[Symbol․dispose]() (MoleculeOpSpec method) MoleculeOpSpec.access (MoleculeOpSpec attribute) MoleculeOpSpec.autoRemap (MoleculeOpSpec attribute) MoleculeOpSpec.cipState (MoleculeOpSpec attribute) MoleculeOpSpec.derivedEffects (MoleculeOpSpec attribute) MoleculeOpSpec.domain (MoleculeOpSpec attribute) MoleculeOpSpec.free() (MoleculeOpSpec method) MoleculeOpSpec.implFn (MoleculeOpSpec attribute) MoleculeOpSpec.ioRoundtrip (MoleculeOpSpec attribute) MoleculeOpSpec.kind (MoleculeOpSpec attribute) MoleculeOpSpec.mayMutate (MoleculeOpSpec attribute) MoleculeOpSpec.method (MoleculeOpSpec attribute) MoleculeOpSpec.output (MoleculeOpSpec attribute) MoleculeOpSpec.parity (MoleculeOpSpec attribute) MoleculeOpSpec.requiresMapping (MoleculeOpSpec attribute) MoleculeOpSpec.resultType (MoleculeOpSpec attribute) MoleculeOpSpec.semanticPreconditions (MoleculeOpSpec attribute) MoleculeOpSpec.status (MoleculeOpSpec attribute) MoleculeOpSpec.topologyEdit (MoleculeOpSpec attribute) MoleculeProperties (class in cosmolkit) MoleculeProperties() (class) MoleculeProperties.[Symbol․dispose]() (MoleculeProperties method) MoleculeProperties.computedPropNames() (MoleculeProperties method) MoleculeProperties.free() (MoleculeProperties method) MoleculeProperties.isPropComputed() (MoleculeProperties method) MoleculeProperties.name() (MoleculeProperties method) MoleculeProperties.prop() (MoleculeProperties method) MoleculeProperties.props() (MoleculeProperties method) MoleculeProperties.sdfDataFields() (MoleculeProperties method) MoleculeProperties.sdfPropertyLists() (MoleculeProperties method) MOLFILE_VALUES (cosmolkit.CxSmilesFields attribute) mols_from_records() (in module cosmolkit) mols_from_sdf_records() (in module cosmolkit) mols_from_smiles_list() (in module cosmolkit) MolWriteError MolWriteError() (class) MolWriteError.[Symbol․dispose]() (MolWriteError method) MolWriteError.capability (MolWriteError attribute) MolWriteError.cause (MolWriteError attribute) MolWriteError.dimension (MolWriteError attribute) MolWriteError.domain (MolWriteError attribute) MolWriteError.free() (MolWriteError method) MolWriteError.id (MolWriteError attribute) MolWriteError.kind (MolWriteError attribute) MolWriteError.message (MolWriteError attribute) MolWriteError.subset (MolWriteError attribute) MolWriteError.threeD (MolWriteError attribute) MolWriteError.twoD (MolWriteError attribute) MolWriteError.valueDetail (MolWriteError attribute) mono_or_laue (cosmolkit.BioDiffractionInfo attribute) monochromator (cosmolkit.BioDiffractionInfo attribute) Monomer (cosmolkit.SubstanceGroupKind attribute) MorganAtomInvariantsGenerator (class in cosmolkit) MorganAtomInvariantsGenerator() (class) MorganAtomInvariantsGenerator.[Symbol․dispose]() (MorganAtomInvariantsGenerator method) MorganAtomInvariantsGenerator.atomPair() (MorganAtomInvariantsGenerator method) MorganAtomInvariantsGenerator.connectivity() (MorganAtomInvariantsGenerator method) MorganAtomInvariantsGenerator.features() (MorganAtomInvariantsGenerator method) MorganAtomInvariantsGenerator.free() (MorganAtomInvariantsGenerator method) MorganBondInvariantsGenerator (class in cosmolkit) MorganBondInvariantsGenerator() (class) MorganBondInvariantsGenerator.[Symbol․dispose]() (MorganBondInvariantsGenerator method) MorganBondInvariantsGenerator.free() (MorganBondInvariantsGenerator method) MorganBondInvariantsGenerator.includeChirality (MorganBondInvariantsGenerator attribute) MorganBondInvariantsGenerator.new() (MorganBondInvariantsGenerator method) MorganBondInvariantsGenerator.useBondTypes (MorganBondInvariantsGenerator attribute) MorganBondInvariantsGeneratorOptions() (interface) MorganBondInvariantsGeneratorOptions.includeChirality? (MorganBondInvariantsGeneratorOptions attribute) MorganBondInvariantsGeneratorOptions.useBondTypes? (MorganBondInvariantsGeneratorOptions attribute) MorganCallParams (class in cosmolkit) MorganCallParams() (class) MorganCallParams.[Symbol․dispose]() (MorganCallParams method) MorganCallParams.conformerId (MorganCallParams attribute) MorganCallParams.customAtomInvariants (MorganCallParams attribute) MorganCallParams.customBondInvariants (MorganCallParams attribute) MorganCallParams.free() (MorganCallParams method) MorganCallParams.fromAtoms (MorganCallParams attribute) MorganCallParams.ignoreAtoms (MorganCallParams attribute) MorganCallParams.new() (MorganCallParams method) MorganCallParamsOptions() (interface) MorganCallParamsOptions.conformerId? (MorganCallParamsOptions attribute) MorganCallParamsOptions.customAtomInvariants? (MorganCallParamsOptions attribute) MorganCallParamsOptions.customBondInvariants? (MorganCallParamsOptions attribute) MorganCallParamsOptions.fromAtoms? (MorganCallParamsOptions attribute) MorganCallParamsOptions.ignoreAtoms? (MorganCallParamsOptions attribute) MorganFingerprintGenerator (class in cosmolkit) MorganFingerprintGenerator() (class) MorganFingerprintGenerator.[Symbol․dispose]() (MorganFingerprintGenerator method) MorganFingerprintGenerator.counts() (MorganFingerprintGenerator method) MorganFingerprintGenerator.fingerprints() (MorganFingerprintGenerator method) MorganFingerprintGenerator.free() (MorganFingerprintGenerator method) MorganFingerprintGenerator.fromJson() (MorganFingerprintGenerator method) MorganFingerprintGenerator.infoString() (MorganFingerprintGenerator method) MorganFingerprintGenerator.new() (MorganFingerprintGenerator method) MorganFingerprintGenerator.settings() (MorganFingerprintGenerator method) MorganFingerprintGenerator.sparseCounts() (MorganFingerprintGenerator method) MorganFingerprintGenerator.sparseFingerprints() (MorganFingerprintGenerator method) MorganFingerprintGenerator.toJson() (MorganFingerprintGenerator method) MorganFingerprintParams (class in cosmolkit) MorganFingerprintParams() (class) MorganFingerprintParams.[Symbol․dispose]() (MorganFingerprintParams method) MorganFingerprintParams.conformerId (MorganFingerprintParams attribute) MorganFingerprintParams.customAtomInvariants (MorganFingerprintParams attribute) MorganFingerprintParams.customBondInvariants (MorganFingerprintParams attribute) MorganFingerprintParams.free() (MorganFingerprintParams method) MorganFingerprintParams.fromAtoms (MorganFingerprintParams attribute) MorganFingerprintParams.generator (MorganFingerprintParams attribute) MorganFingerprintParams.ignoreAtoms (MorganFingerprintParams attribute) MorganFingerprintParams.invariants (MorganFingerprintParams attribute) MorganFingerprintParamsOptions() (interface) MorganFingerprintParamsOptions.conformerId? (MorganFingerprintParamsOptions attribute) MorganFingerprintParamsOptions.customAtomInvariants? (MorganFingerprintParamsOptions attribute) MorganFingerprintParamsOptions.customBondInvariants? (MorganFingerprintParamsOptions attribute) MorganFingerprintParamsOptions.fromAtoms? (MorganFingerprintParamsOptions attribute) MorganFingerprintParamsOptions.generator? (MorganFingerprintParamsOptions attribute) MorganFingerprintParamsOptions.ignoreAtoms? (MorganFingerprintParamsOptions attribute) MorganFingerprintParamsOptions.invariants? (MorganFingerprintParamsOptions attribute) MorganInvariants (class in cosmolkit) MorganInvariants() (class) MorganInvariants.[Symbol․dispose]() (MorganInvariants method) MorganInvariants.connectivity() (MorganInvariants method) MorganInvariants.features() (MorganInvariants method) MorganInvariants.free() (MorganInvariants method) MorganParams (class in cosmolkit) MorganParams() (class) MorganParams.[Symbol․dispose]() (MorganParams method) MorganParams.bitsPerFeature (MorganParams attribute) MorganParams.countBounds (MorganParams attribute) MorganParams.countSimulation (MorganParams attribute) MorganParams.fpSize (MorganParams attribute) MorganParams.free() (MorganParams method) MorganParams.includeChirality (MorganParams attribute) MorganParams.includeRedundantEnvironments (MorganParams attribute) MorganParams.includeRingMembership (MorganParams attribute) MorganParams.infoString() (MorganParams method) MorganParams.onlyNonzeroInvariants (MorganParams attribute) MorganParams.radius (MorganParams attribute) MorganParams.toJson() (MorganParams method) MorganParams.useBondTypes (MorganParams attribute) MorganParams.withJson() (MorganParams method) MorganParamsOptions() (interface) MorganParamsOptions.bitsPerFeature? (MorganParamsOptions attribute) MorganParamsOptions.countBounds? (MorganParamsOptions attribute) MorganParamsOptions.countSimulation? (MorganParamsOptions attribute) MorganParamsOptions.fpSize? (MorganParamsOptions attribute) MorganParamsOptions.includeChirality? (MorganParamsOptions attribute) MorganParamsOptions.includeRedundantEnvironments? (MorganParamsOptions attribute) MorganParamsOptions.includeRingMembership? (MorganParamsOptions attribute) MorganParamsOptions.onlyNonzeroInvariants? (MorganParamsOptions attribute) MorganParamsOptions.radius? (MorganParamsOptions attribute) MorganParamsOptions.useBondTypes? (MorganParamsOptions attribute) MorganReadError MorganReadError() (class) MorganReadError.[Symbol․dispose]() (MorganReadError method) MorganReadError.cause (MorganReadError attribute) MorganReadError.domain (MorganReadError attribute) MorganReadError.free() (MorganReadError method) MorganReadError.kind (MorganReadError attribute) MorganReadError.message (MorganReadError attribute) MorganSettings (class in cosmolkit) MorganSettings() (class) MorganSettings.[Symbol․dispose]() (MorganSettings method) MorganSettings.bitsPerFeature (MorganSettings attribute) MorganSettings.countBounds (MorganSettings attribute) MorganSettings.countSimulation (MorganSettings attribute) MorganSettings.fpSize (MorganSettings attribute) MorganSettings.free() (MorganSettings method) MorganSettings.includeChirality (MorganSettings attribute) MorganSettings.includeRedundantEnvironments (MorganSettings attribute) MorganSettings.onlyNonzeroInvariants (MorganSettings attribute) MorganSettings.params() (MorganSettings method) MorganSettings.radius (MorganSettings attribute) MorganSettings.setBitsPerFeature() (MorganSettings method) MorganSettings.setCountBounds() (MorganSettings method) MorganSettings.setCountSimulation() (MorganSettings method) MorganSettings.setFpSize() (MorganSettings method) MorganSettings.setIncludeChirality() (MorganSettings method) MorganSettings.setIncludeRedundantEnvironments() (MorganSettings method) MorganSettings.setOnlyNonzeroInvariants() (MorganSettings method) MorganSettings.setRadius() (MorganSettings method) move_to_agent_templates (cosmolkit.ReactionTemplateRemovalParams property) MPD (cosmolkit.ResidueCode attribute) MPO (cosmolkit.ResidueCode attribute) mqns() (cosmolkit.Molecule method) MRD (cosmolkit.ResidueCode attribute) MRY (cosmolkit.ResidueCode attribute) MSE (cosmolkit.ResidueCode attribute) MT (cosmolkit.Element attribute) MTL (cosmolkit.ResidueCode attribute) MultipleCharge (cosmolkit.ReactionValidationIssueKind attribute) MultipleGroup (cosmolkit.SubstanceGroupKind attribute) MultipleHydrogenCount (cosmolkit.ReactionValidationIssueKind attribute) MultipleIsotope (cosmolkit.ReactionValidationIssueKind attribute) MultipleMass (cosmolkit.ReactionValidationIssueKind attribute) murcko_decompose() (cosmolkit.Molecule method) murcko_scaffold() (cosmolkit.Molecule method) MVA (cosmolkit.ResidueCode attribute) N N (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) N8E (cosmolkit.ResidueCode attribute) n_bits (cosmolkit.AvalonFingerprintParams property) (cosmolkit.MaccsFingerprintParams property) (cosmolkit.PatternFingerprintParams property) n_bits() (cosmolkit.Fingerprint method) (cosmolkit.SparseBitFingerprint method) n_jobs (cosmolkit.BatchExportParams property) (cosmolkit.BatchParams property) (cosmolkit.BatchQueryParams property) NA (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) NAD (cosmolkit.ResidueCode attribute) NAG (cosmolkit.ResidueCode attribute) name (cosmolkit.BioAssembly attribute) (cosmolkit.BioAssemblyOperator attribute) (cosmolkit.BioConnection attribute) (cosmolkit.BioRefinementRestraint attribute) (cosmolkit.BioSheet attribute) (cosmolkit.BioSoftwareItem attribute) (cosmolkit.BioStrand attribute) (cosmolkit.BioStructureSourceState attribute) (cosmolkit.FeatureSpec attribute) (cosmolkit.ResidueAddress attribute) name() (cosmolkit.BioAtomRow method) (cosmolkit.BioResidueRow method) (cosmolkit.BioStructure method) (cosmolkit.MoleculeProperties method) (cosmolkit.ProteinAtomRef method) (cosmolkit.ProteinResidueRef method) (cosmolkit.QueryGraph method) (cosmolkit.ResidueIdentity method) (cosmolkit.ResidueInfo method) (cosmolkit.SdfPropertyList method) (cosmolkit.TautomerScoreTerm method) NAP (cosmolkit.ResidueCode attribute) NB (cosmolkit.Element attribute) NCO (cosmolkit.ResidueCode attribute) Ncs (cosmolkit.BioMmcifReadStage attribute) ncs (cosmolkit.BioMmcifWriteParams property) ncs_oper_identity_id() (cosmolkit.BioStructure method) ncs_operators() (cosmolkit.BioStructure method) ND (cosmolkit.Element attribute) NDG (cosmolkit.ResidueCode attribute) NE (cosmolkit.Element attribute) needs_more() (cosmolkit.MmffOptimizeMoleculeConfResult method) (cosmolkit.MmffOptimizeMoleculeResult method) (cosmolkit.UffConformerResult method) (cosmolkit.UffOptimizationResult method) neighbor_bonds() (cosmolkit.MoleculeBuilder method) NEP (cosmolkit.ResidueCode attribute) net_scaffold() (cosmolkit.Molecule method) new() (cosmolkit.AlignmentAtomMap static method) (cosmolkit.AlignmentParameters static method) (cosmolkit.AllConformerRmsdParameters static method) (cosmolkit.AtomSpec static method) (cosmolkit.BestAlignmentParameters static method) (cosmolkit.BondSpec static method) (cosmolkit.ConformerAlignmentParameters static method) (cosmolkit.CoordinateRmsdParameters static method) (cosmolkit.EmbedParams static method) (cosmolkit.FingerprintAdditionalOutput static method) (cosmolkit.LegacyTopologicalTorsionParams static method) (cosmolkit.Molecule static method) (cosmolkit.MoleculeBuilder static method) (cosmolkit.MorganBondInvariantsGenerator static method) (cosmolkit.MorganCallParams static method) (cosmolkit.MorganFingerprintGenerator static method) (cosmolkit.ResidueIdentity static method) (cosmolkit.SGroupBracket static method) (cosmolkit.SGroupCState static method) (cosmolkit.SparseCountFingerprint static method) (cosmolkit.SparseCountFingerprint32 static method) (cosmolkit.SubstanceGroup static method) (cosmolkit.SubstanceGroupId static method) (cosmolkit.TautomerScoreTerm static method) (cosmolkit.TopologicalTorsionFingerprintGenerator static method) next() (cosmolkit.StereoisomerIterator method) next_batch() (cosmolkit.SdfBatchIterator method) (cosmolkit.SdfReaderBatchIterator method) next_record() (cosmolkit.SdfRecordStream method) NGA (cosmolkit.ResidueCode attribute) NH (cosmolkit.Element attribute) NH2 (cosmolkit.ResidueCode attribute) NH4 (cosmolkit.ResidueCode attribute) NHE (cosmolkit.ResidueCode attribute) NI (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) NLE (cosmolkit.ResidueCode attribute) NO (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) NO3 (cosmolkit.ResidueCode attribute) no_implicit() (cosmolkit.Atom method) (cosmolkit.QueryAtom method) NoHydrogen (cosmolkit.BioCalcFlag attribute) non_ascii_line (cosmolkit.BioStructureSourceState attribute) non_bonded_threshold (cosmolkit.MmffConformerOptimizationParams property) (cosmolkit.MmffEvaluationParams property) (cosmolkit.MmffForceFieldParams property) (cosmolkit.MmffOptimizationParams property) NONE (cosmolkit.BondDirection attribute) (cosmolkit.CxSmilesFields attribute) (cosmolkit.PotentialStereoDescriptor attribute) (cosmolkit.SanitizeOperations attribute) None_ (cosmolkit.SanitizeStage attribute) NonFiniteCoordinate (cosmolkit.MolecularForceFieldErrorKind attribute) NonPolymer (cosmolkit.EntityKind attribute) NonStrict (cosmolkit.RotatableBondsOptions attribute) nonzero_elements() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) NotApplicable (cosmolkit.BioAssemblySpecialKind attribute) (cosmolkit.ParityPolicy attribute) NotSet (cosmolkit.BioCalcFlag attribute) NP (cosmolkit.Element attribute) NRQ (cosmolkit.ResidueCode attribute) num_3d_conformers() (cosmolkit.Molecule method) num_agent_templates() (cosmolkit.Reaction method) num_aliphatic_carbocycles() (cosmolkit.Molecule method) num_aliphatic_heterocycles() (cosmolkit.Molecule method) num_aliphatic_rings() (cosmolkit.Molecule method) num_amide_bonds() (cosmolkit.Molecule method) num_aromatic_carbocycles() (cosmolkit.Molecule method) num_aromatic_heterocycles() (cosmolkit.Molecule method) num_aromatic_rings() (cosmolkit.Molecule method) num_atom_pair_fingerprint_bits() (cosmolkit.AtomPairsParameters static method) num_atom_stereo_centers() (cosmolkit.Molecule method) num_atoms() (cosmolkit.BioStructure method) (cosmolkit.CompiledQuery method) (cosmolkit.Molecule method) (cosmolkit.Protein method) (cosmolkit.QueryGraph method) (cosmolkit.TautomerMoleculeView method) num_bits_per_feature (cosmolkit.TopologicalFingerprintParams property) num_bonds() (cosmolkit.CompiledQuery method) (cosmolkit.Molecule method) (cosmolkit.QueryGraph method) (cosmolkit.TautomerMoleculeView method) num_branch_bits() (cosmolkit.AtomPairsParameters static method) num_bridgehead_atoms() (cosmolkit.Molecule method) num_chains() (cosmolkit.BioStructure method) (cosmolkit.Protein method) num_chiral_bits() (cosmolkit.AtomPairsParameters static method) num_entities() (cosmolkit.BioStructure method) num_errors (cosmolkit.ReactionValidationReport attribute) num_hba() (cosmolkit.Molecule method) num_hbd() (cosmolkit.Molecule method) num_heavy_atoms() (cosmolkit.Molecule method) num_heteroatoms() (cosmolkit.Molecule method) num_heterocycles() (cosmolkit.Molecule method) num_id (cosmolkit.BioTlsGroup attribute) num_models() (cosmolkit.BioStructure method) (cosmolkit.Protein method) num_path_bits() (cosmolkit.AtomPairsParameters static method) num_pi_bits() (cosmolkit.AtomPairsParameters static method) num_product_templates() (cosmolkit.Reaction method) num_reactant_templates() (cosmolkit.Reaction method) num_residues() (cosmolkit.BioStructure method) (cosmolkit.Protein method) num_rings() (cosmolkit.Molecule method) num_rotatable_bonds() (cosmolkit.Molecule method) num_rotatable_bonds_with_params() (cosmolkit.Molecule method) num_saturated_carbocycles() (cosmolkit.Molecule method) num_saturated_heterocycles() (cosmolkit.Molecule method) num_saturated_rings() (cosmolkit.Molecule method) num_spiro_atoms() (cosmolkit.Molecule method) num_threads (cosmolkit.AllConformerRmsdParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.EmbedParams property) (cosmolkit.MmffConformerOptimizationParams property) (cosmolkit.SubstructMatchParams property) (cosmolkit.UffConformerOptimizationParams property) num_transforms() (cosmolkit.TautomerProgress method) num_type_bits() (cosmolkit.AtomPairsParameters static method) num_unspecified_atom_stereo_centers() (cosmolkit.Molecule method) num_warnings (cosmolkit.ReactionValidationReport attribute) num_zero_fail (cosmolkit.EmbedParams property) number (cosmolkit.BioSiftsUnpResidue attribute) number_of_crystals (cosmolkit.BioExperimentInfo attribute) numbered_ter (cosmolkit.BioPdbWriteParams property) O O (cosmolkit.Element attribute) OAS (cosmolkit.ResidueCode attribute) occupancy() (cosmolkit.BioAtomRow method) OCS (cosmolkit.ResidueCode attribute) OG (cosmolkit.Element attribute) ok() (cosmolkit.EmbedMoleculeResult method) oligomeric_count (cosmolkit.BioAssembly attribute) oligomeric_details (cosmolkit.BioAssembly attribute) OMC (cosmolkit.ResidueCode attribute) OMG (cosmolkit.ResidueCode attribute) OMU (cosmolkit.ResidueCode attribute) OMY (cosmolkit.ResidueCode attribute) OMZ (cosmolkit.ResidueCode attribute) on_bits() (cosmolkit.Fingerprint method) (cosmolkit.SparseBitFingerprint method) one_letter_code() (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueInfo method) ONEANDAHALF (cosmolkit.BondOrder attribute) only_altloc (cosmolkit.BioCisPep attribute) only_heavy_atoms_for_rms (cosmolkit.EmbedParams property) only_nonzero_invariants (cosmolkit.MorganParams property) (cosmolkit.MorganSettings attribute) only_on_atoms (cosmolkit.AddHsParams property) only_shortest_paths (cosmolkit.TopologicalTorsionParams property) (cosmolkit.TopologicalTorsionSettings attribute) only_stereo_groups (cosmolkit.StereoisomerOptions property) only_unassigned (cosmolkit.StereoisomerOptions property) open() (cosmolkit.SdfDataset static method) (cosmolkit.SdfReader static method) (cosmolkit.SdfRecordStream static method) open_with_params() (cosmolkit.SdfDataset static method) (cosmolkit.SdfReader static method) (cosmolkit.SdfRecordStream static method) operation (cosmolkit.ChemistryProblem attribute) (cosmolkit.OperationInvariantEntry attribute) (cosmolkit.ParityMatrixEntry attribute) (cosmolkit.SupportMatrixEntry attribute) operation() (cosmolkit.BatchError method) operation_invariant() (in module cosmolkit) operation_invariant_matrix() (in module cosmolkit) operation_parity() (in module cosmolkit) operation_spec() (in module cosmolkit) operation_specs() (in module cosmolkit) OperationError OperationError() (class) OperationError.[Symbol․dispose]() (OperationError method) OperationError.cause (OperationError attribute) OperationError.domain (OperationError attribute) OperationError.free() (OperationError method) OperationError.kind (OperationError attribute) OperationError.message (OperationError attribute) operationInvariant() (built-in function) OperationInvariantEntry (class in cosmolkit) OperationInvariantEntry() (class) OperationInvariantEntry.[Symbol․dispose]() (OperationInvariantEntry method) OperationInvariantEntry.free() (OperationInvariantEntry method) OperationInvariantEntry.operation (OperationInvariantEntry attribute) OperationInvariantEntry.profile (OperationInvariantEntry attribute) operationInvariantMatrix() (built-in function) operationParity() (built-in function) operations (cosmolkit.SanitizeParams property) operationSpec() (built-in function) operationSpecs() (built-in function) operator_type (cosmolkit.BioAssemblyOperator attribute) operators (cosmolkit.BioAssemblyGenerator attribute) optics (cosmolkit.BioDiffractionInfo attribute) optimizer_force_tol (cosmolkit.EmbedParams property) options (cosmolkit.InchiWriteParams property) Order (cosmolkit.McsBondComparator attribute) order() (cosmolkit.Bond method) order_code() (cosmolkit.Bond method) order_name() (cosmolkit.Bond method) OrderExact (cosmolkit.McsBondComparator attribute) origin (cosmolkit.BioTlsGroup attribute) Origx (cosmolkit.BioMmcifReadStage attribute) origx (cosmolkit.BioMmcifWriteParams property) (cosmolkit.BioStructureSourceState attribute) origx() (cosmolkit.BioStructure method) ORN (cosmolkit.ResidueCode attribute) OS (cosmolkit.Element attribute) OTE (cosmolkit.ResidueCode attribute) OTHER (cosmolkit.BondOrder attribute) (cosmolkit.Hybridization attribute) Other (cosmolkit.PolymerKind attribute) other (cosmolkit.RingStereoRelation attribute) outer_electrons() (cosmolkit.ElementInfo method) output (cosmolkit.MoleculeOpSpec attribute) P P (cosmolkit.CipDescriptor attribute) p (cosmolkit.CipDescriptor attribute) P (cosmolkit.Element attribute) P33 (cosmolkit.ResidueCode attribute) P4C (cosmolkit.ResidueCode attribute) PA (cosmolkit.Element attribute) PAA (cosmolkit.ResidueInfoKind attribute) parallel_jobs() (cosmolkit.MoleculeBatch method) Parameterization (cosmolkit.MolecularForceFieldErrorKind attribute) ParameterTable (cosmolkit.UffParameterErrorKind attribute) params() (cosmolkit.EmbedMoleculeResult method) (cosmolkit.EmbedMultipleConfsResult method) (cosmolkit.MorganSettings method) (cosmolkit.SdfReader method) (cosmolkit.TopologicalTorsionSettings method) parent_comp_id (cosmolkit.BioModRes attribute) parent_standard_code() (cosmolkit.ProteinResidueRef method) (cosmolkit.ResidueInfo method) parity (cosmolkit.MoleculeOpSpec attribute) parity_matrix() (in module cosmolkit) parityMatrix() (built-in function) ParityMatrixEntry (class in cosmolkit) ParityMatrixEntry() (class) ParityMatrixEntry.[Symbol․dispose]() (ParityMatrixEntry method) ParityMatrixEntry.feature (ParityMatrixEntry attribute) ParityMatrixEntry.free() (ParityMatrixEntry method) ParityMatrixEntry.operation (ParityMatrixEntry attribute) ParityMatrixEntry.profile (ParityMatrixEntry attribute) ParityMatrixEntry.rdkitVersion (ParityMatrixEntry attribute) ParityPolicy (class in cosmolkit) (None attribute) ParityPolicy.NotApplicable (ParityPolicy attribute) ParityPolicy.RequiredNow (ParityPolicy attribute) ParityPolicy.RequiredWhenSupported (ParityPolicy attribute) parse_name (cosmolkit.SmartsParseParams property) (cosmolkit.SmilesParseParams property) parse_smarts() (in module cosmolkit) parse_smarts_with_params() (in module cosmolkit) parse_smirks() (in module cosmolkit) parse_smirks_with_params() (in module cosmolkit) parseSmarts() (built-in function) parseSmartsWithParams() (built-in function) parseSmirks() (built-in function) parseSmirksWithParams() (built-in function) partial_charge() (cosmolkit.MmffAtomProperties method) (cosmolkit.MmffProperties method) partner1 (cosmolkit.BioConnection attribute) partner2 (cosmolkit.BioConnection attribute) partner_c (cosmolkit.BioCisPep attribute) partner_n (cosmolkit.BioCisPep attribute) path() (cosmolkit.SdfDataset method) (cosmolkit.SdfReader method) PatternFingerprintError PatternFingerprintError() (class) PatternFingerprintError.[Symbol․dispose]() (PatternFingerprintError method) PatternFingerprintError.cause (PatternFingerprintError attribute) PatternFingerprintError.domain (PatternFingerprintError attribute) PatternFingerprintError.free() (PatternFingerprintError method) PatternFingerprintError.kind (PatternFingerprintError attribute) PatternFingerprintError.message (PatternFingerprintError attribute) PatternFingerprintParams (class in cosmolkit) PatternFingerprintParams() (class) PatternFingerprintParams.[Symbol․dispose]() (PatternFingerprintParams method) PatternFingerprintParams.free() (PatternFingerprintParams method) PatternFingerprintParams.nBits (PatternFingerprintParams attribute) PatternFingerprintParams.tautomeric (PatternFingerprintParams attribute) PatternFingerprintParamsOptions() (interface) PatternFingerprintParamsOptions.nBits? (PatternFingerprintParamsOptions attribute) PatternFingerprintParamsOptions.tautomeric? (PatternFingerprintParamsOptions attribute) PB (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) PCA (cosmolkit.ResidueCode attribute) PD (cosmolkit.Element attribute) Pdb (cosmolkit.BioCoordinateFormat attribute) pdb_helix_class (cosmolkit.BioHelix attribute) PdbAtomSerial() (class) PdbAtomSerial.[Symbol․dispose]() (PdbAtomSerial method) PdbAtomSerial.free() (PdbAtomSerial method) PdbAtomSerial.value() (PdbAtomSerial method) PdbChainId() (class) PdbChainId.[Symbol․dispose]() (PdbChainId method) PdbChainId.asBytes() (PdbChainId method) PdbChainId.asStr() (PdbChainId method) PdbChainId.free() (PdbChainId method) PdbChainId.fromAscii() (PdbChainId method) PdbSeqId (class in cosmolkit) PdbSeqId() (class) PdbSeqId.[Symbol․dispose]() (PdbSeqId method) PdbSeqId.free() (PdbSeqId method) PdbSeqId.insCode() (PdbSeqId method) PdbSeqId.seqNum() (PdbSeqId method) PDO (cosmolkit.ResidueCode attribute) PE4 (cosmolkit.ResidueCode attribute) PE7 (cosmolkit.ResidueCode attribute) PE8 (cosmolkit.ResidueCode attribute) PEG (cosmolkit.ResidueCode attribute) PeptideD (cosmolkit.PolymerKind attribute) PeptideL (cosmolkit.PolymerKind attribute) perceive_stereochemistry() (cosmolkit.Molecule method) period() (cosmolkit.ElementInfo method) permutation (cosmolkit.PotentialStereoInfo attribute) permute_degree_four (cosmolkit.Coordinate2DParams property) PEU (cosmolkit.ResidueCode attribute) PG4 (cosmolkit.ResidueCode attribute) PG5 (cosmolkit.ResidueCode attribute) PG6 (cosmolkit.ResidueCode attribute) PGE (cosmolkit.ResidueCode attribute) PGO (cosmolkit.ResidueCode attribute) PGQ (cosmolkit.ResidueCode attribute) PGR (cosmolkit.ResidueCode attribute) ph (cosmolkit.BioExperimentalCrystalInfo attribute) ph_range (cosmolkit.BioExperimentalCrystalInfo attribute) Phasing (cosmolkit.BioSoftwareClassification attribute) PHD (cosmolkit.ResidueCode attribute) PHE (cosmolkit.ResidueCode attribute) PHI (cosmolkit.ResidueCode attribute) phi() (cosmolkit.Molecule method) PHL (cosmolkit.ResidueCode attribute) pi_electrons() (cosmolkit.AtomCodeExplanation method) PickleError PIG (cosmolkit.ResidueCode attribute) PIN (cosmolkit.ResidueCode attribute) PLP (cosmolkit.ResidueCode attribute) PM (cosmolkit.Element attribute) Pna (cosmolkit.PolymerKind attribute) PO (cosmolkit.Element attribute) PO4 (cosmolkit.ResidueCode attribute) points() (cosmolkit.SGroupBracket method) POL (cosmolkit.ResidueCode attribute) POLYMER (cosmolkit.CxSmilesFields attribute) Polymer (cosmolkit.EntityKind attribute) polymer_kind() (cosmolkit.BioEntityRow method) PolymerKind (class in cosmolkit) (None attribute) PolymerKind.CyclicPseudoPeptide (PolymerKind attribute) PolymerKind.Dna (PolymerKind attribute) PolymerKind.DnaRnaHybrid (PolymerKind attribute) PolymerKind.Other (PolymerKind attribute) PolymerKind.PeptideD (PolymerKind attribute) PolymerKind.PeptideL (PolymerKind attribute) PolymerKind.Pna (PolymerKind attribute) PolymerKind.Rna (PolymerKind attribute) PolymerKind.SaccharideD (PolymerKind attribute) PolymerKind.SaccharideL (PolymerKind attribute) PolymerKind.Unknown (PolymerKind attribute) position() (cosmolkit.BioAtomRow method) (cosmolkit.MolecularForceField method) (cosmolkit.ProteinAtomRef method) positions (cosmolkit.BioCoordinateBlock attribute) positions() (cosmolkit.MolecularForceField method) potential_stereo() (cosmolkit.Molecule method) potential_stereo_with_params() (cosmolkit.Molecule method) PotentialStereoCenter (class in cosmolkit) PotentialStereoCenter() (class) PotentialStereoCenter.[Symbol․dispose]() (PotentialStereoCenter method) PotentialStereoCenter.free() (PotentialStereoCenter method) PotentialStereoCenter.index (PotentialStereoCenter attribute) PotentialStereoCenter.kind (PotentialStereoCenter attribute) PotentialStereoDescriptor (class in cosmolkit) (None attribute) PotentialStereoDescriptor.BondAtropCcw (PotentialStereoDescriptor attribute) PotentialStereoDescriptor.BondAtropCw (PotentialStereoDescriptor attribute) PotentialStereoDescriptor.BondCis (PotentialStereoDescriptor attribute) PotentialStereoDescriptor.BondTrans (PotentialStereoDescriptor attribute) PotentialStereoDescriptor.None (PotentialStereoDescriptor attribute) PotentialStereoDescriptor.TetrahedralClockwise (PotentialStereoDescriptor attribute) PotentialStereoDescriptor.TetrahedralCounterclockwise (PotentialStereoDescriptor attribute) PotentialStereoError PotentialStereoError() (class) PotentialStereoError.[Symbol․dispose]() (PotentialStereoError method) PotentialStereoError.cause (PotentialStereoError attribute) PotentialStereoError.domain (PotentialStereoError attribute) PotentialStereoError.free() (PotentialStereoError method) PotentialStereoError.kind (PotentialStereoError attribute) PotentialStereoError.message (PotentialStereoError attribute) PotentialStereoInfo (class in cosmolkit) PotentialStereoInfo() (class) PotentialStereoInfo.[Symbol․dispose]() (PotentialStereoInfo method) PotentialStereoInfo.centeredOn (PotentialStereoInfo attribute) PotentialStereoInfo.controllingAtoms (PotentialStereoInfo attribute) PotentialStereoInfo.descriptor (PotentialStereoInfo attribute) PotentialStereoInfo.free() (PotentialStereoInfo method) PotentialStereoInfo.permutation (PotentialStereoInfo attribute) PotentialStereoInfo.specified (PotentialStereoInfo attribute) PotentialStereoInfo.stereoType (PotentialStereoInfo attribute) PotentialStereoParams (class in cosmolkit) PotentialStereoParams() (class) PotentialStereoParams.[Symbol․dispose]() (PotentialStereoParams method) PotentialStereoParams.allowNontetrahedral (PotentialStereoParams attribute) PotentialStereoParams.clean (PotentialStereoParams attribute) PotentialStereoParams.flagPossible (PotentialStereoParams attribute) PotentialStereoParams.free() (PotentialStereoParams method) PotentialStereoParamsOptions() (interface) PotentialStereoParamsOptions.allowNontetrahedral? (PotentialStereoParamsOptions attribute) PotentialStereoParamsOptions.clean? (PotentialStereoParamsOptions attribute) PotentialStereoParamsOptions.flagPossible? (PotentialStereoParamsOptions attribute) PotentialStereoResult (class in cosmolkit) PotentialStereoResult() (class) PotentialStereoResult.[Symbol․dispose]() (PotentialStereoResult method) PotentialStereoResult.atomRanks (PotentialStereoResult attribute) PotentialStereoResult.cleanedMolecule (PotentialStereoResult attribute) PotentialStereoResult.free() (PotentialStereoResult method) PotentialStereoResult.ringRelations (PotentialStereoResult attribute) PotentialStereoResult.stereo (PotentialStereoResult attribute) PotentialStereoSpecified (class in cosmolkit) (None attribute) PotentialStereoSpecified.Specified (PotentialStereoSpecified attribute) PotentialStereoSpecified.Unknown (PotentialStereoSpecified attribute) PotentialStereoSpecified.Unspecified (PotentialStereoSpecified attribute) PotentialStereoType (class in cosmolkit) (None attribute) PotentialStereoType.AtomOctahedral (PotentialStereoType attribute) PotentialStereoType.AtomSquarePlanar (PotentialStereoType attribute) PotentialStereoType.AtomTetrahedral (PotentialStereoType attribute) PotentialStereoType.AtomTrigonalBipyramidal (PotentialStereoType attribute) PotentialStereoType.BondAtropisomer (PotentialStereoType attribute) PotentialStereoType.BondCumuleneEven (PotentialStereoType attribute) PotentialStereoType.BondDouble (PotentialStereoType attribute) PR (cosmolkit.Element attribute) precision (cosmolkit.MolBlockWriteParams property) (cosmolkit.XyzWriteParams property) prefer_pairs (cosmolkit.BioMmcifWriteParams property) Preparation (cosmolkit.MolecularForceFieldErrorKind attribute) (cosmolkit.UffParameterErrorKind attribute) Preserve (cosmolkit.SdfCoordinateMode attribute) preserve_serial (cosmolkit.BioPdbWriteParams property) PRO (cosmolkit.ResidueCode attribute) probe_atom (cosmolkit.AlignmentAtomMap attribute) probe_conformer_id (cosmolkit.AlignmentParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.CoordinateRmsdParameters property) probe_conformer_id() (cosmolkit.ConformerRmsd method) problems (cosmolkit.ChemistryProblemReport attribute) process_property_lists (cosmolkit.SdfReadParams property) Product (cosmolkit.ReactionRole attribute) product_template() (cosmolkit.Reaction method) product_templates() (cosmolkit.Reaction method) profile (cosmolkit.OperationInvariantEntry attribute) (cosmolkit.ParityMatrixEntry attribute) progress_bar (cosmolkit.BatchExportParams property) (cosmolkit.BatchParams property) (cosmolkit.BatchQueryParams property) progress_bar() (cosmolkit.MoleculeBatch method) progress_callback (cosmolkit.BatchQueryParams property) prop() (cosmolkit.MoleculeProperties method) PROPERTIES (cosmolkit.SanitizeOperations attribute) Properties (cosmolkit.SanitizeStage attribute) properties() (cosmolkit.Molecule method) (cosmolkit.MoleculeBuilder method) (cosmolkit.SdfRecord method) (cosmolkit.TautomerMoleculeView method) property() (cosmolkit.Molecule method) property_value_to_text() (in module cosmolkit) PropertyStringError PropertyStringError() (class) PropertyStringError.[Symbol․dispose]() (PropertyStringError method) PropertyStringError.cause (PropertyStringError attribute) PropertyStringError.domain (PropertyStringError attribute) PropertyStringError.free() (PropertyStringError method) PropertyStringError.kind() (PropertyStringError method) PropertyStringError.message (PropertyStringError attribute) PropertyValue (class in cosmolkit) PropertyValue() (class) PropertyValue.[Symbol․dispose]() (PropertyValue method) PropertyValue.asBool() (PropertyValue method) PropertyValue.asDouble() (PropertyValue method) PropertyValue.asInt() (PropertyValue method) PropertyValue.asIntVector() (PropertyValue method) PropertyValue.asString() (PropertyValue method) PropertyValue.asStringVector() (PropertyValue method) PropertyValue.asUint() (PropertyValue method) PropertyValue.free() (PropertyValue method) PropertyValue.kind() (PropertyValue method) PropertyValueError PropertyValueError() (class) PropertyValueError.[Symbol․dispose]() (PropertyValueError method) PropertyValueError.actual() (PropertyValueError method) PropertyValueError.cause (PropertyValueError attribute) PropertyValueError.domain (PropertyValueError attribute) PropertyValueError.expected() (PropertyValueError method) PropertyValueError.free() (PropertyValueError method) PropertyValueError.kind (PropertyValueError attribute) PropertyValueError.message (PropertyValueError attribute) PropertyValueKind (class in cosmolkit) (None attribute) PropertyValueKind.Bool (PropertyValueKind attribute) PropertyValueKind.Double (PropertyValueKind attribute) PropertyValueKind.Int (PropertyValueKind attribute) PropertyValueKind.IntVector (PropertyValueKind attribute) PropertyValueKind.String (PropertyValueKind attribute) PropertyValueKind.StringVector (PropertyValueKind attribute) PropertyValueKind.UInt (PropertyValueKind attribute) propertyValueToText() (built-in function) props() (cosmolkit.Conformer2D method) (cosmolkit.Conformer3D method) (cosmolkit.MoleculeProperties method) Protein (class in cosmolkit) (cosmolkit.ChainKind attribute) Protein() (class) protein() (cosmolkit.BioStructure method) Protein.[Symbol․dispose]() (Protein method) Protein.asBioStructure() (Protein method) Protein.atoms() (Protein method) Protein.chain() (Protein method) Protein.chains() (Protein method) Protein.free() (Protein method) Protein.fromMmcif() (Protein method) Protein.fromPdb() (Protein method) Protein.fromPdbWithParams() (Protein method) Protein.fromText() (Protein method) Protein.fromTextWithParams() (Protein method) Protein.inputFormat() (Protein method) Protein.intoBioStructure() (Protein method) Protein.len() (Protein method) Protein.numAtoms() (Protein method) Protein.numChains() (Protein method) Protein.numModels() (Protein method) Protein.numResidues() (Protein method) Protein.read() (Protein method) Protein.readWithFormat() (Protein method) Protein.residues() (Protein method) Protein.retainSelection() (Protein method) Protein.selectedAtomIds() (Protein method) Protein.selectionSummary() (Protein method) Protein.toMolecule() (Protein method) Protein.toMoleculeWithParams() (Protein method) Protein.translate() (Protein method) Protein.withSelection() (Protein method) Protein.withTranslatedCoordinates() (Protein method) protein_from_mmcif() (in module cosmolkit) protein_from_pdb() (in module cosmolkit) ProteinAtomIter() (class) ProteinAtomIter.[Symbol․dispose]() (ProteinAtomIter method) ProteinAtomIter.free() (ProteinAtomIter method) ProteinAtomIter.len() (ProteinAtomIter method) ProteinAtomRef (class in cosmolkit) ProteinAtomRef() (class) ProteinAtomRef.[Symbol․dispose]() (ProteinAtomRef method) ProteinAtomRef.altloc() (ProteinAtomRef method) ProteinAtomRef.atomicNumber() (ProteinAtomRef method) ProteinAtomRef.element() (ProteinAtomRef method) ProteinAtomRef.elementSymbol() (ProteinAtomRef method) ProteinAtomRef.free() (ProteinAtomRef method) ProteinAtomRef.id() (ProteinAtomRef method) ProteinAtomRef.name() (ProteinAtomRef method) ProteinAtomRef.position() (ProteinAtomRef method) ProteinAtomRef.residue() (ProteinAtomRef method) ProteinAtomRef.row() (ProteinAtomRef method) ProteinChainIter() (class) ProteinChainIter.[Symbol․dispose]() (ProteinChainIter method) ProteinChainIter.free() (ProteinChainIter method) ProteinChainIter.len() (ProteinChainIter method) ProteinChainRef (class in cosmolkit) ProteinChainRef() (class) ProteinChainRef.[Symbol․dispose]() (ProteinChainRef method) ProteinChainRef.atoms() (ProteinChainRef method) ProteinChainRef.free() (ProteinChainRef method) ProteinChainRef.id() (ProteinChainRef method) ProteinChainRef.kind() (ProteinChainRef method) ProteinChainRef.len() (ProteinChainRef method) ProteinChainRef.residues() (ProteinChainRef method) ProteinChainRef.row() (ProteinChainRef method) ProteinChainRef.source() (ProteinChainRef method) ProteinDnaComplex (cosmolkit.ChainKind attribute) ProteinProjectionError ProteinProjectionError() (class) ProteinProjectionError.[Symbol․dispose]() (ProteinProjectionError method) ProteinProjectionError.cause (ProteinProjectionError attribute) ProteinProjectionError.domain (ProteinProjectionError attribute) ProteinProjectionError.free() (ProteinProjectionError method) ProteinProjectionError.index (ProteinProjectionError attribute) ProteinProjectionError.kind (ProteinProjectionError attribute) ProteinProjectionError.message (ProteinProjectionError attribute) ProteinProjectionError.source (ProteinProjectionError attribute) ProteinReadError ProteinReadError() (class) ProteinReadError.[Symbol․dispose]() (ProteinReadError method) ProteinReadError.cause (ProteinReadError attribute) ProteinReadError.domain (ProteinReadError attribute) ProteinReadError.free() (ProteinReadError method) ProteinReadError.kind (ProteinReadError attribute) ProteinReadError.message (ProteinReadError attribute) ProteinResidueIter() (class) ProteinResidueIter.[Symbol․dispose]() (ProteinResidueIter method) ProteinResidueIter.free() (ProteinResidueIter method) ProteinResidueIter.len() (ProteinResidueIter method) ProteinResidueRef (class in cosmolkit) ProteinResidueRef() (class) ProteinResidueRef.[Symbol․dispose]() (ProteinResidueRef method) ProteinResidueRef.atoms() (ProteinResidueRef method) ProteinResidueRef.canonicalOneLetterCode() (ProteinResidueRef method) ProteinResidueRef.chain() (ProteinResidueRef method) ProteinResidueRef.code() (ProteinResidueRef method) ProteinResidueRef.fastaCode() (ProteinResidueRef method) ProteinResidueRef.free() (ProteinResidueRef method) ProteinResidueRef.id() (ProteinResidueRef method) ProteinResidueRef.info() (ProteinResidueRef method) ProteinResidueRef.isModifiedAminoAcid() (ProteinResidueRef method) ProteinResidueRef.isStandard() (ProteinResidueRef method) ProteinResidueRef.kind() (ProteinResidueRef method) ProteinResidueRef.len() (ProteinResidueRef method) ProteinResidueRef.name() (ProteinResidueRef method) ProteinResidueRef.oneLetterCode() (ProteinResidueRef method) ProteinResidueRef.parentStandardCode() (ProteinResidueRef method) ProteinResidueRef.row() (ProteinResidueRef method) ProteinRnaComplex (cosmolkit.ChainKind attribute) ProteinSelectionSummary (class in cosmolkit) ProteinSelectionSummary() (class) ProteinSelectionSummary.[Symbol․dispose]() (ProteinSelectionSummary method) ProteinSelectionSummary.atoms (ProteinSelectionSummary attribute) ProteinSelectionSummary.chains (ProteinSelectionSummary attribute) ProteinSelectionSummary.free() (ProteinSelectionSummary method) ProteinSelectionSummary.residues (ProteinSelectionSummary attribute) proximity_bonding (cosmolkit.BioMoleculeParams property) prune_rms_thresh (cosmolkit.EmbedParams property) PSU (cosmolkit.ResidueCode attribute) PT (cosmolkit.Element attribute) PTR (cosmolkit.ResidueCode attribute) PU (cosmolkit.Element attribute) PYL (cosmolkit.ResidueCode attribute) PYR (cosmolkit.ResidueInfoKind attribute) Q qed() (cosmolkit.Molecule method) QUADRUPLE (cosmolkit.BondOrder attribute) query (cosmolkit.McsResult attribute) query() (cosmolkit.CompiledQuery method) query_graph (cosmolkit.SdfGraph attribute) query_graph() (cosmolkit.SdfRecord method) QueryAtom (class in cosmolkit) QueryAtom() (class) QueryAtom.[Symbol․dispose]() (QueryAtom method) QueryAtom.atomicNumber() (QueryAtom method) QueryAtom.atomMap() (QueryAtom method) QueryAtom.explicitHydrogens() (QueryAtom method) QueryAtom.formalCharge() (QueryAtom method) QueryAtom.free() (QueryAtom method) QueryAtom.id() (QueryAtom method) QueryAtom.isAromatic() (QueryAtom method) QueryAtom.isotope() (QueryAtom method) QueryAtom.noImplicit() (QueryAtom method) QueryAtom.radicalElectrons() (QueryAtom method) QueryCompileError QueryCompileError() (class) QueryCompileError.[Symbol․dispose]() (QueryCompileError method) QueryCompileError.cause (QueryCompileError attribute) QueryCompileError.domain (QueryCompileError attribute) QueryCompileError.free() (QueryCompileError method) QueryCompileError.kind (QueryCompileError attribute) QueryCompileError.message (QueryCompileError attribute) QueryGraph (class in cosmolkit) QueryGraph() (class) QueryGraph.[Symbol․dispose]() (QueryGraph method) QueryGraph.free() (QueryGraph method) QueryGraph.fromSmarts() (QueryGraph method) QueryGraph.fromSmartsWithParams() (QueryGraph method) QueryGraph.name() (QueryGraph method) QueryGraph.numAtoms() (QueryGraph method) QueryGraph.numBonds() (QueryGraph method) QUINTUPLE (cosmolkit.BondOrder attribute) R R (cosmolkit.CipDescriptor attribute) r (cosmolkit.CipDescriptor attribute) R0AF (cosmolkit.ResidueCode attribute) R0TD (cosmolkit.ResidueCode attribute) R12P (cosmolkit.ResidueCode attribute) R144 (cosmolkit.ResidueCode attribute) R15P (cosmolkit.ResidueCode attribute) R16D (cosmolkit.ResidueCode attribute) R1BO (cosmolkit.ResidueCode attribute) R1MA (cosmolkit.ResidueCode attribute) R1MG (cosmolkit.ResidueCode attribute) R1PS (cosmolkit.ResidueCode attribute) R2MA (cosmolkit.ResidueCode attribute) R2MG (cosmolkit.ResidueCode attribute) R2OS (cosmolkit.ResidueCode attribute) R310 (cosmolkit.BioHelixClass attribute) R3CO (cosmolkit.ResidueCode attribute) R3DR (cosmolkit.ResidueCode attribute) R3FG (cosmolkit.ResidueCode attribute) R3NI (cosmolkit.ResidueCode attribute) R4OC (cosmolkit.ResidueCode attribute) R4SU (cosmolkit.ResidueCode attribute) R5BU (cosmolkit.ResidueCode attribute) R5CM (cosmolkit.ResidueCode attribute) R5MU (cosmolkit.ResidueCode attribute) R6MZ (cosmolkit.ResidueCode attribute) R7MG (cosmolkit.ResidueCode attribute) R8OG (cosmolkit.ResidueCode attribute) r_all (cosmolkit.BioBasicRefinementInfo attribute) r_free (cosmolkit.BioBasicRefinementInfo attribute) r_merge (cosmolkit.BioReflectionsInfo attribute) r_sym (cosmolkit.BioReflectionsInfo attribute) r_work (cosmolkit.BioBasicRefinementInfo attribute) RA (cosmolkit.Element attribute) radical_electrons() (cosmolkit.Atom method) (cosmolkit.QueryAtom method) RADICALS (cosmolkit.CxSmilesFields attribute) radius (cosmolkit.MorganParams property) (cosmolkit.MorganSettings attribute) RAISE (cosmolkit.BatchErrorMode attribute) RAlpha (cosmolkit.BioHelixClass attribute) rand_neg_eig (cosmolkit.EmbedParams property) random_seed (cosmolkit.EmbedParams property) random_source (cosmolkit.StereoisomerOptions property) RandomSmilesWriteParams (class in cosmolkit) RandomSmilesWriteParams() (class) RandomSmilesWriteParams.[Symbol․dispose]() (RandomSmilesWriteParams method) RandomSmilesWriteParams.allBondsExplicit (RandomSmilesWriteParams attribute) RandomSmilesWriteParams.allHydrogensExplicit (RandomSmilesWriteParams attribute) RandomSmilesWriteParams.free() (RandomSmilesWriteParams method) RandomSmilesWriteParams.isomericSmiles (RandomSmilesWriteParams attribute) RandomSmilesWriteParams.kekule (RandomSmilesWriteParams attribute) RandomSmilesWriteParamsOptions() (interface) RandomSmilesWriteParamsOptions.allBondsExplicit? (RandomSmilesWriteParamsOptions attribute) RandomSmilesWriteParamsOptions.allHydrogensExplicit? (RandomSmilesWriteParamsOptions attribute) RandomSmilesWriteParamsOptions.isomericSmiles? (RandomSmilesWriteParamsOptions attribute) RandomSmilesWriteParamsOptions.kekule? (RandomSmilesWriteParamsOptions attribute) raw_remarks (cosmolkit.BioStructureSourceState attribute) RB (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) rb0() (cosmolkit.ElementInfo method) Rdkit (cosmolkit.AromaticityModel attribute) rdkit_version (cosmolkit.ParityMatrixEntry attribute) RdkitLike (cosmolkit.ValenceModel attribute) RE (cosmolkit.Element attribute) Reactant (cosmolkit.ReactionRole attribute) reactant_template() (cosmolkit.Reaction method) reactant_templates() (cosmolkit.Reaction method) Reaction (class in cosmolkit) reaction (cosmolkit.ReactionTemplateRemoval attribute) Reaction() (class) Reaction.[Symbol․dispose]() (Reaction method) Reaction.agentTemplate() (Reaction method) Reaction.agentTemplates() (Reaction method) Reaction.free() (Reaction method) Reaction.fromSmirks() (Reaction method) Reaction.fromSmirksWithParams() (Reaction method) Reaction.fromTemplates() (Reaction method) Reaction.implicitProperties() (Reaction method) Reaction.isInitialized() (Reaction method) Reaction.matchParams() (Reaction method) Reaction.numAgentTemplates() (Reaction method) Reaction.numProductTemplates() (Reaction method) Reaction.numReactantTemplates() (Reaction method) Reaction.productTemplate() (Reaction method) Reaction.productTemplates() (Reaction method) Reaction.reactantTemplate() (Reaction method) Reaction.reactantTemplates() (Reaction method) Reaction.run() (Reaction method) Reaction.toCxSmirks() (Reaction method) Reaction.toCxSmirksWithParams() (Reaction method) Reaction.toSmirks() (Reaction method) Reaction.toSmirksWithParams() (Reaction method) Reaction.validate() (Reaction method) Reaction.validateWithParams() (Reaction method) Reaction.withAgentTemplate() (Reaction method) Reaction.withImplicitProperties() (Reaction method) Reaction.withInitialized() (Reaction method) Reaction.withInitializedWithParams() (Reaction method) Reaction.withMatchParams() (Reaction method) Reaction.withoutAgents() (Reaction method) Reaction.withoutUnmappedProducts() (Reaction method) Reaction.withoutUnmappedProductsWithParams() (Reaction method) Reaction.withoutUnmappedReactants() (Reaction method) Reaction.withoutUnmappedReactantsWithParams() (Reaction method) Reaction.withProductTemplate() (Reaction method) Reaction.withReactantTemplate() (Reaction method) reaction_from_smirks() (in module cosmolkit) reaction_products() (cosmolkit.Molecule method) reaction_products_from_inputs() (cosmolkit.Molecule method) reaction_products_with_params() (cosmolkit.Molecule method) ReactionApplyError ReactionApplyError() (class) ReactionApplyError.[Symbol․dispose]() (ReactionApplyError method) ReactionApplyError.atom (ReactionApplyError attribute) ReactionApplyError.cause (ReactionApplyError attribute) ReactionApplyError.free() (ReactionApplyError method) ReactionApplyError.kind (ReactionApplyError attribute) ReactionApplyError.message (ReactionApplyError attribute) ReactionApplyError.products (ReactionApplyError attribute) ReactionApplyError.reactants (ReactionApplyError attribute) ReactionApplyParams (class in cosmolkit) ReactionApplyParams() (class) ReactionApplyParams.[Symbol․dispose]() (ReactionApplyParams method) ReactionApplyParams.free() (ReactionApplyParams method) ReactionApplyParams.removeUnmatchedAtoms (ReactionApplyParams attribute) ReactionApplyParamsOptions() (interface) ReactionApplyParamsOptions.removeUnmatchedAtoms? (ReactionApplyParamsOptions attribute) ReactionApplyResult (class in cosmolkit) ReactionApplyResult() (class) ReactionApplyResult.[Symbol․dispose]() (ReactionApplyResult method) ReactionApplyResult.changed (ReactionApplyResult attribute) ReactionApplyResult.free() (ReactionApplyResult method) ReactionApplyResult.molecule (ReactionApplyResult attribute) ReactionCoordinateSelection (class in cosmolkit) ReactionCoordinateSelection() (class) ReactionCoordinateSelection.[Symbol․dispose]() (ReactionCoordinateSelection method) ReactionCoordinateSelection.auto() (ReactionCoordinateSelection method) ReactionCoordinateSelection.free() (ReactionCoordinateSelection method) ReactionCoordinateSelection.id (ReactionCoordinateSelection attribute) ReactionCoordinateSelection.is2d (ReactionCoordinateSelection attribute) ReactionCoordinateSelection.is3d (ReactionCoordinateSelection attribute) ReactionCoordinateSelection.isAuto (ReactionCoordinateSelection attribute) ReactionCoordinateSelection.threeD() (ReactionCoordinateSelection method) ReactionCoordinateSelection.twoD() (ReactionCoordinateSelection method) ReactionInitializationError ReactionInitializationError() (class) ReactionInitializationError.[Symbol․dispose]() (ReactionInitializationError method) ReactionInitializationError.cause (ReactionInitializationError attribute) ReactionInitializationError.free() (ReactionInitializationError method) ReactionInitializationError.kind (ReactionInitializationError attribute) ReactionInitializationError.message (ReactionInitializationError attribute) ReactionInitializationError.report (ReactionInitializationError attribute) ReactionModelError ReactionModelError() (class) ReactionModelError.[Symbol․dispose]() (ReactionModelError method) ReactionModelError.cause (ReactionModelError attribute) ReactionModelError.count (ReactionModelError attribute) ReactionModelError.free() (ReactionModelError method) ReactionModelError.index (ReactionModelError attribute) ReactionModelError.kind (ReactionModelError attribute) ReactionModelError.message (ReactionModelError attribute) ReactionModelError.role (ReactionModelError attribute) ReactionModelError.template (ReactionModelError attribute) ReactionParseError ReactionParseError() (class) ReactionParseError.[Symbol․dispose]() (ReactionParseError method) ReactionParseError.atom (ReactionParseError attribute) ReactionParseError.atomCount (ReactionParseError attribute) ReactionParseError.cause (ReactionParseError attribute) ReactionParseError.count (ReactionParseError attribute) ReactionParseError.end (ReactionParseError attribute) ReactionParseError.flag (ReactionParseError attribute) ReactionParseError.free() (ReactionParseError method) ReactionParseError.kind (ReactionParseError attribute) ReactionParseError.message (ReactionParseError attribute) ReactionParseError.product (ReactionParseError attribute) ReactionParseError.reactant (ReactionParseError attribute) ReactionParseError.role (ReactionParseError attribute) ReactionParseError.start (ReactionParseError attribute) ReactionParseError.startAtom (ReactionParseError attribute) ReactionParseError.startBond (ReactionParseError attribute) ReactionParseError.template (ReactionParseError attribute) ReactionParseError.text (ReactionParseError attribute) ReactionParseParams (class in cosmolkit) ReactionParseParams() (class) ReactionParseParams.[Symbol․dispose]() (ReactionParseParams method) ReactionParseParams.allowCxsmiles (ReactionParseParams attribute) ReactionParseParams.free() (ReactionParseParams method) ReactionParseParams.replacements (ReactionParseParams attribute) ReactionParseParams.sanitize (ReactionParseParams attribute) ReactionParseParams.strictCxsmiles (ReactionParseParams attribute) ReactionParseParams.useSmiles (ReactionParseParams attribute) ReactionParseParamsOptions() (interface) ReactionParseParamsOptions.allowCxsmiles? (ReactionParseParamsOptions attribute) ReactionParseParamsOptions.replacements? (ReactionParseParamsOptions attribute) ReactionParseParamsOptions.sanitize? (ReactionParseParamsOptions attribute) ReactionParseParamsOptions.strictCxsmiles? (ReactionParseParamsOptions attribute) ReactionParseParamsOptions.useSmiles? (ReactionParseParamsOptions attribute) ReactionProductError ReactionProductError() (class) ReactionProductError.[Symbol․dispose]() (ReactionProductError method) ReactionProductError.atom (ReactionProductError attribute) ReactionProductError.bond (ReactionProductError attribute) ReactionProductError.cause (ReactionProductError attribute) ReactionProductError.detail (ReactionProductError attribute) ReactionProductError.free() (ReactionProductError method) ReactionProductError.index (ReactionProductError attribute) ReactionProductError.key (ReactionProductError attribute) ReactionProductError.kind (ReactionProductError attribute) ReactionProductError.message (ReactionProductError attribute) ReactionProductError.productAtom (ReactionProductError attribute) ReactionProductError.reactantAtom (ReactionProductError attribute) ReactionProductError.rowKind (ReactionProductError attribute) ReactionProductError.stage (ReactionProductError attribute) ReactionRole (class in cosmolkit) (None attribute) ReactionRole.Agent (ReactionRole attribute) ReactionRole.Product (ReactionRole attribute) ReactionRole.Reactant (ReactionRole attribute) ReactionRunError ReactionRunError() (class) ReactionRunError.[Symbol․dispose]() (ReactionRunError method) ReactionRunError.actual (ReactionRunError attribute) ReactionRunError.atom (ReactionRunError attribute) ReactionRunError.atomCount (ReactionRunError attribute) ReactionRunError.cause (ReactionRunError attribute) ReactionRunError.count (ReactionRunError attribute) ReactionRunError.expected (ReactionRunError attribute) ReactionRunError.free() (ReactionRunError method) ReactionRunError.index (ReactionRunError attribute) ReactionRunError.kind (ReactionRunError attribute) ReactionRunError.level (ReactionRunError attribute) ReactionRunError.message (ReactionRunError attribute) ReactionRunError.reactant (ReactionRunError attribute) ReactionRunError.set (ReactionRunError attribute) ReactionRunError.template (ReactionRunError attribute) ReactionRunParams (class in cosmolkit) ReactionRunParams() (class) ReactionRunParams.[Symbol․dispose]() (ReactionRunParams method) ReactionRunParams.coordinateSelections (ReactionRunParams attribute) ReactionRunParams.copyAtomProperties (ReactionRunParams attribute) ReactionRunParams.free() (ReactionRunParams method) ReactionRunParams.maxProducts (ReactionRunParams attribute) ReactionRunParamsOptions() (interface) ReactionRunParamsOptions.coordinateSelections? (ReactionRunParamsOptions attribute) ReactionRunParamsOptions.copyAtomProperties? (ReactionRunParamsOptions attribute) ReactionRunParamsOptions.maxProducts? (ReactionRunParamsOptions attribute) ReactionSingleRunParams (class in cosmolkit) ReactionSingleRunParams() (class) ReactionSingleRunParams.[Symbol․dispose]() (ReactionSingleRunParams method) ReactionSingleRunParams.coordinateSelection (ReactionSingleRunParams attribute) ReactionSingleRunParams.free() (ReactionSingleRunParams method) ReactionSingleRunParamsOptions() (interface) ReactionSingleRunParamsOptions.coordinateSelection? (ReactionSingleRunParamsOptions attribute) ReactionTemplateRemoval (class in cosmolkit) ReactionTemplateRemoval() (class) ReactionTemplateRemoval.[Symbol․dispose]() (ReactionTemplateRemoval method) ReactionTemplateRemoval.free() (ReactionTemplateRemoval method) ReactionTemplateRemoval.reaction (ReactionTemplateRemoval attribute) ReactionTemplateRemoval.removedTemplates (ReactionTemplateRemoval attribute) ReactionTemplateRemovalParams (class in cosmolkit) ReactionTemplateRemovalParams() (class) ReactionTemplateRemovalParams.[Symbol․dispose]() (ReactionTemplateRemovalParams method) ReactionTemplateRemovalParams.free() (ReactionTemplateRemovalParams method) ReactionTemplateRemovalParams.moveToAgentTemplates (ReactionTemplateRemovalParams attribute) ReactionTemplateRemovalParams.thresholdUnmappedAtoms (ReactionTemplateRemovalParams attribute) ReactionTemplateRemovalParamsOptions() (interface) ReactionTemplateRemovalParamsOptions.moveToAgentTemplates? (ReactionTemplateRemovalParamsOptions attribute) ReactionTemplateRemovalParamsOptions.thresholdUnmappedAtoms? (ReactionTemplateRemovalParamsOptions attribute) ReactionValidationError ReactionValidationError() (class) ReactionValidationError.[Symbol․dispose]() (ReactionValidationError method) ReactionValidationError.atom (ReactionValidationError attribute) ReactionValidationError.atomCount (ReactionValidationError attribute) ReactionValidationError.cause (ReactionValidationError attribute) ReactionValidationError.free() (ReactionValidationError method) ReactionValidationError.kind (ReactionValidationError attribute) ReactionValidationError.map (ReactionValidationError attribute) ReactionValidationError.message (ReactionValidationError attribute) ReactionValidationError.property (ReactionValidationError attribute) ReactionValidationError.role (ReactionValidationError attribute) ReactionValidationError.template (ReactionValidationError attribute) ReactionValidationError.value (ReactionValidationError attribute) ReactionValidationIssue (class in cosmolkit) ReactionValidationIssue() (class) ReactionValidationIssue.[Symbol․dispose]() (ReactionValidationIssue method) ReactionValidationIssue.atom (ReactionValidationIssue attribute) ReactionValidationIssue.detail (ReactionValidationIssue attribute) ReactionValidationIssue.free() (ReactionValidationIssue method) ReactionValidationIssue.kind (ReactionValidationIssue attribute) ReactionValidationIssue.map (ReactionValidationIssue attribute) ReactionValidationIssue.maps (ReactionValidationIssue attribute) ReactionValidationIssue.role (ReactionValidationIssue attribute) ReactionValidationIssue.severity (ReactionValidationIssue attribute) ReactionValidationIssue.template (ReactionValidationIssue attribute) ReactionValidationIssueKind (class in cosmolkit) (None attribute) ReactionValidationIssueKind.DuplicateProductMap (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.DuplicateReactantMap (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.MissingProductMapReactant (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.MissingProducts (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.MissingReactants (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.MultipleCharge (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.MultipleHydrogenCount (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.MultipleIsotope (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.MultipleMass (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.UnmappedProduct (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.UnmappedReactant (ReactionValidationIssueKind attribute) ReactionValidationIssueKind.UnmappedReactantMaps (ReactionValidationIssueKind attribute) ReactionValidationParams (class in cosmolkit) ReactionValidationParams() (class) ReactionValidationParams.[Symbol․dispose]() (ReactionValidationParams method) ReactionValidationParams.free() (ReactionValidationParams method) ReactionValidationParams.silent (ReactionValidationParams attribute) ReactionValidationParamsOptions() (interface) ReactionValidationParamsOptions.silent? (ReactionValidationParamsOptions attribute) ReactionValidationReport (class in cosmolkit) ReactionValidationReport() (class) ReactionValidationReport.[Symbol․dispose]() (ReactionValidationReport method) ReactionValidationReport.errors (ReactionValidationReport attribute) ReactionValidationReport.free() (ReactionValidationReport method) ReactionValidationReport.isValid (ReactionValidationReport attribute) ReactionValidationReport.numErrors (ReactionValidationReport attribute) ReactionValidationReport.numWarnings (ReactionValidationReport attribute) ReactionValidationReport.warnings (ReactionValidationReport attribute) ReactionValidationSeverity (class in cosmolkit) (None attribute) ReactionValidationSeverity.Error (ReactionValidationSeverity attribute) ReactionValidationSeverity.Warning (ReactionValidationSeverity attribute) ReactionWriteError ReactionWriteError() (class) ReactionWriteError.[Symbol․dispose]() (ReactionWriteError method) ReactionWriteError.actual (ReactionWriteError attribute) ReactionWriteError.cause (ReactionWriteError attribute) ReactionWriteError.expected (ReactionWriteError attribute) ReactionWriteError.free() (ReactionWriteError method) ReactionWriteError.kind (ReactionWriteError attribute) ReactionWriteError.message (ReactionWriteError attribute) ReactionWriteError.role (ReactionWriteError attribute) ReactionWriteError.template (ReactionWriteError attribute) ReactionWriteParams (class in cosmolkit) ReactionWriteParams() (class) ReactionWriteParams.[Symbol․dispose]() (ReactionWriteParams method) ReactionWriteParams.canonical (ReactionWriteParams attribute) ReactionWriteParams.coordinateSelections (ReactionWriteParams attribute) ReactionWriteParams.cxFields (ReactionWriteParams attribute) ReactionWriteParams.free() (ReactionWriteParams method) ReactionWriteParams.includeCx (ReactionWriteParams attribute) ReactionWriteParams.includeDativeBonds (ReactionWriteParams attribute) ReactionWriteParams.isomericSmiles (ReactionWriteParams attribute) ReactionWriteParams.rootedAtAtom (ReactionWriteParams attribute) ReactionWriteParamsOptions() (interface) ReactionWriteParamsOptions.canonical? (ReactionWriteParamsOptions attribute) ReactionWriteParamsOptions.coordinateSelections? (ReactionWriteParamsOptions attribute) ReactionWriteParamsOptions.cxFields? (ReactionWriteParamsOptions attribute) ReactionWriteParamsOptions.includeCx? (ReactionWriteParamsOptions attribute) ReactionWriteParamsOptions.includeDativeBonds? (ReactionWriteParamsOptions attribute) ReactionWriteParamsOptions.isomericSmiles? (ReactionWriteParamsOptions attribute) ReactionWriteParamsOptions.rootedAtAtom? (ReactionWriteParamsOptions attribute) read() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) read_mol() (cosmolkit.Molecule static method) read_mol2() (cosmolkit.Molecule static method) read_mol2_with_params() (cosmolkit.Molecule static method) read_mol_with_params() (cosmolkit.Molecule static method) read_sdf() (cosmolkit.Molecule static method) (cosmolkit.MoleculeBatch static method) read_sdf_with_params() (cosmolkit.Molecule static method) (cosmolkit.MoleculeBatch static method) read_with_format() (cosmolkit.BioStructure static method) (cosmolkit.Protein static method) read_xyz() (cosmolkit.Molecule static method) reassign_stereo (cosmolkit.TautomerParams property) Record (cosmolkit.BioPdbReadStage attribute) record() (cosmolkit.SdfDataset method) record_tag() (cosmolkit.BioPdbReadError method) record_text() (cosmolkit.SdfDataset method) record_with_params() (cosmolkit.SdfDataset method) records() (cosmolkit.MoleculeBatch method) records_consumed() (cosmolkit.SdfRecordStream method) recursion_possible (cosmolkit.SubstructMatchParams property) redundancy (cosmolkit.BioReflectionsInfo attribute) reference (cosmolkit.FunctionStatus attribute) reference_atom (cosmolkit.AlignmentAtomMap attribute) reference_conformer_id (cosmolkit.AlignmentParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.CoordinateRmsdParameters property) reference_conformer_id() (cosmolkit.ConformerRmsd method) refine (cosmolkit.BioMmcifWriteParams property) refinement (cosmolkit.BioMetadata attribute) Refinement (cosmolkit.BioMmcifReadStage attribute) (cosmolkit.BioSoftwareClassification attribute) reflect (cosmolkit.AlignmentParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.ConformerAlignmentParameters property) reflection_count (cosmolkit.BioBasicRefinementInfo attribute) reflections (cosmolkit.BioExperimentInfo attribute) Reflections (cosmolkit.BioMmcifReadStage attribute) reflns (cosmolkit.BioMmcifWriteParams property) remark_300_detail (cosmolkit.BioMetadata attribute) remarks (cosmolkit.BioRefinementInfo attribute) remove_and_track_isotopes (cosmolkit.RemoveHsParams property) remove_bond_between_atoms() (cosmolkit.MoleculeBuilder method) remove_bond_stereo (cosmolkit.TautomerParams property) remove_defining_bond_stereo (cosmolkit.RemoveHsParams property) remove_degree_zero (cosmolkit.RemoveHsParams property) remove_dummy_neighbors (cosmolkit.RemoveHsParams property) remove_higher_degrees (cosmolkit.RemoveHsParams property) remove_hs (cosmolkit.BioMoleculeParams property) (cosmolkit.InchiReadParams property) (cosmolkit.Mol2ReadParams property) (cosmolkit.SdfReadParams property) (cosmolkit.SmilesParseParams property) remove_hydrides (cosmolkit.RemoveHsParams property) remove_hydrogens_() (cosmolkit.Molecule method) remove_hydrogens_with_params_() (cosmolkit.Molecule method) remove_in_sgroups (cosmolkit.RemoveHsParams property) remove_isotopes (cosmolkit.RemoveHsParams property) remove_isotopic_hydrogens (cosmolkit.TautomerParams property) remove_mapped (cosmolkit.RemoveHsParams property) remove_nonimplicit (cosmolkit.RemoveHsParams property) remove_nontetrahedral_neighbors (cosmolkit.RemoveHsParams property) remove_only_h_neighbors (cosmolkit.RemoveHsParams property) remove_sp3_stereo (cosmolkit.TautomerParams property) remove_unmatched_atoms (cosmolkit.ReactionApplyParams property) remove_with_query (cosmolkit.RemoveHsParams property) remove_with_wedged_bond (cosmolkit.RemoveHsParams property) removed_templates (cosmolkit.ReactionTemplateRemoval attribute) RemoveHsParams (class in cosmolkit) RemoveHsParams() (class) RemoveHsParams.[Symbol․dispose]() (RemoveHsParams method) RemoveHsParams.free() (RemoveHsParams method) RemoveHsParams.removeAndTrackIsotopes (RemoveHsParams attribute) RemoveHsParams.removeDefiningBondStereo (RemoveHsParams attribute) RemoveHsParams.removeDegreeZero (RemoveHsParams attribute) RemoveHsParams.removeDummyNeighbors (RemoveHsParams attribute) RemoveHsParams.removeHigherDegrees (RemoveHsParams attribute) RemoveHsParams.removeHydrides (RemoveHsParams attribute) RemoveHsParams.removeInSgroups (RemoveHsParams attribute) RemoveHsParams.removeIsotopes (RemoveHsParams attribute) RemoveHsParams.removeMapped (RemoveHsParams attribute) RemoveHsParams.removeNonimplicit (RemoveHsParams attribute) RemoveHsParams.removeNontetrahedralNeighbors (RemoveHsParams attribute) RemoveHsParams.removeOnlyHNeighbors (RemoveHsParams attribute) RemoveHsParams.removeWithQuery (RemoveHsParams attribute) RemoveHsParams.removeWithWedgedBond (RemoveHsParams attribute) RemoveHsParams.sanitize (RemoveHsParams attribute) RemoveHsParams.showWarnings (RemoveHsParams attribute) RemoveHsParams.updateExplicitCount (RemoveHsParams attribute) RemoveHsParamsOptions() (interface) RemoveHsParamsOptions.removeAndTrackIsotopes? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeDefiningBondStereo? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeDegreeZero? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeDummyNeighbors? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeHigherDegrees? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeHydrides? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeInSgroups? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeIsotopes? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeMapped? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeNonimplicit? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeNontetrahedralNeighbors? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeOnlyHNeighbors? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeWithQuery? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.removeWithWedgedBond? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.sanitize? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.showWarnings? (RemoveHsParamsOptions attribute) RemoveHsParamsOptions.updateExplicitCount? (RemoveHsParamsOptions attribute) Replace3DCoordinatesParams (class in cosmolkit) Replace3DCoordinatesParams() (class) Replace3DCoordinatesParams.[Symbol․dispose]() (Replace3DCoordinatesParams method) Replace3DCoordinatesParams.conformerId (Replace3DCoordinatesParams attribute) Replace3DCoordinatesParams.free() (Replace3DCoordinatesParams method) Replace3DCoordinatesParamsOptions() (interface) Replace3DCoordinatesParamsOptions.conformerId? (Replace3DCoordinatesParamsOptions attribute) replace_existing_tags (cosmolkit.StructureTagParams property) replacements (cosmolkit.ReactionParseParams property) (cosmolkit.SmartsParseParams property) (cosmolkit.SmilesParseParams property) report_path (cosmolkit.BatchImageParams property) reported_angle (cosmolkit.BioCisPep attribute) reported_distance (cosmolkit.BioConnection attribute) reported_sym (cosmolkit.BioConnection attribute) RepresentativeHelical (cosmolkit.BioAssemblySpecialKind attribute) requested (cosmolkit.ForceFieldError property) (cosmolkit.MmffForceFieldError property) (cosmolkit.UffForceFieldError property) (cosmolkit.UffOptimizationErrorKind attribute) requested_num_confs() (cosmolkit.EmbedMultipleConfsResult method) Require2D (cosmolkit.SdfCoordinateMode attribute) Require3D (cosmolkit.SdfCoordinateMode attribute) RequiredNow (cosmolkit.ParityPolicy attribute) RequiredWhenSupported (cosmolkit.ParityPolicy attribute) requires_mapping (cosmolkit.MoleculeOpSpec attribute) RequireZero (cosmolkit.CoordinateZPolicy attribute) res_begin (cosmolkit.BioTlsSelection attribute) res_end (cosmolkit.BioTlsSelection attribute) res_id (cosmolkit.BioModRes attribute) residue (cosmolkit.AtomAddress attribute) (cosmolkit.BioSiftsUnpResidue attribute) residue() (cosmolkit.ProteinAtomRef method) residue_atoms() (cosmolkit.BioStructure method) residue_code() (in module cosmolkit) RESIDUE_CODE_MAP (in module cosmolkit) residue_id() (cosmolkit.BioAtomRow method) residue_info() (in module cosmolkit) residue_info_checked() (in module cosmolkit) RESIDUE_INFO_KIND_MAP (in module cosmolkit) ResidueAddress (class in cosmolkit) ResidueAddress() (class) ResidueAddress.[Symbol․dispose]() (ResidueAddress method) ResidueAddress.free() (ResidueAddress method) ResidueAddress.insertionCode (ResidueAddress attribute) ResidueAddress.name (ResidueAddress attribute) ResidueAddress.segment (ResidueAddress attribute) ResidueAddress.sequenceNumber (ResidueAddress attribute) ResidueCode (class in cosmolkit) (None attribute) residueCode() (built-in function) ResidueCode.A (ResidueCode attribute) ResidueCode.A2G (ResidueCode attribute) ResidueCode.ABA (ResidueCode attribute) ResidueCode.ACA (ResidueCode attribute) ResidueCode.ACE (ResidueCode attribute) ResidueCode.ACN (ResidueCode attribute) ResidueCode.ACT (ResidueCode attribute) ResidueCode.ACY (ResidueCode attribute) ResidueCode.ADP (ResidueCode attribute) ResidueCode.AG (ResidueCode attribute) ResidueCode.AGM (ResidueCode attribute) ResidueCode.AIB (ResidueCode attribute) ResidueCode.AL (ResidueCode attribute) ResidueCode.ALA (ResidueCode attribute) ResidueCode.ALC (ResidueCode attribute) ResidueCode.ALY (ResidueCode attribute) ResidueCode.ARG (ResidueCode attribute) ResidueCode.ASN (ResidueCode attribute) ResidueCode.ASP (ResidueCode attribute) ResidueCode.ASX (ResidueCode attribute) ResidueCode.ATP (ResidueCode attribute) ResidueCode.AZI (ResidueCode attribute) ResidueCode.B3E (ResidueCode attribute) ResidueCode.B3P (ResidueCode attribute) ResidueCode.B7G (ResidueCode attribute) ResidueCode.BA (ResidueCode attribute) ResidueCode.BCN (ResidueCode attribute) ResidueCode.BE7 (ResidueCode attribute) ResidueCode.BEQ (ResidueCode attribute) ResidueCode.BFD (ResidueCode attribute) ResidueCode.BGC (ResidueCode attribute) ResidueCode.BMA (ResidueCode attribute) ResidueCode.BME (ResidueCode attribute) ResidueCode.BMT (ResidueCode attribute) ResidueCode.BNG (ResidueCode attribute) ResidueCode.BOG (ResidueCode attribute) ResidueCode.BR (ResidueCode attribute) ResidueCode.BRO (ResidueCode attribute) ResidueCode.BRU (ResidueCode attribute) ResidueCode.BTB (ResidueCode attribute) ResidueCode.BU1 (ResidueCode attribute) ResidueCode.BU2 (ResidueCode attribute) ResidueCode.BU3 (ResidueCode attribute) ResidueCode.C (ResidueCode attribute) ResidueCode.C10 (ResidueCode attribute) ResidueCode.C15 (ResidueCode attribute) ResidueCode.C8E (ResidueCode attribute) ResidueCode.CA (ResidueCode attribute) ResidueCode.CAC (ResidueCode attribute) ResidueCode.CAF (ResidueCode attribute) ResidueCode.CAS (ResidueCode attribute) ResidueCode.CBM (ResidueCode attribute) ResidueCode.CBR (ResidueCode attribute) ResidueCode.CBX (ResidueCode attribute) ResidueCode.CCC (ResidueCode attribute) ResidueCode.CCN (ResidueCode attribute) ResidueCode.CD (ResidueCode attribute) ResidueCode.CE1 (ResidueCode attribute) ResidueCode.CGU (ResidueCode attribute) ResidueCode.CIR (ResidueCode attribute) ResidueCode.CIT (ResidueCode attribute) ResidueCode.CL (ResidueCode attribute) ResidueCode.CLO (ResidueCode attribute) ResidueCode.CM (ResidueCode attribute) ResidueCode.CM5 (ResidueCode attribute) ResidueCode.CME (ResidueCode attribute) ResidueCode.CN (ResidueCode attribute) ResidueCode.CO (ResidueCode attribute) ResidueCode.CPS (ResidueCode attribute) ResidueCode.CR2 (ResidueCode attribute) ResidueCode.CR8 (ResidueCode attribute) ResidueCode.CRF (ResidueCode attribute) ResidueCode.CRO (ResidueCode attribute) ResidueCode.CRQ (ResidueCode attribute) ResidueCode.CRY (ResidueCode attribute) ResidueCode.CS (ResidueCode attribute) ResidueCode.CSD (ResidueCode attribute) ResidueCode.CSH (ResidueCode attribute) ResidueCode.CSO (ResidueCode attribute) ResidueCode.CSS (ResidueCode attribute) ResidueCode.CSX (ResidueCode attribute) ResidueCode.CU (ResidueCode attribute) ResidueCode.CU1 (ResidueCode attribute) ResidueCode.CXE (ResidueCode attribute) ResidueCode.CXM (ResidueCode attribute) ResidueCode.CYN (ResidueCode attribute) ResidueCode.CYS (ResidueCode attribute) ResidueCode.DA (ResidueCode attribute) ResidueCode.DAB (ResidueCode attribute) ResidueCode.DAL (ResidueCode attribute) ResidueCode.DAR (ResidueCode attribute) ResidueCode.DAS (ResidueCode attribute) ResidueCode.DC (ResidueCode attribute) ResidueCode.DCY (ResidueCode attribute) ResidueCode.DDQ (ResidueCode attribute) ResidueCode.DG (ResidueCode attribute) ResidueCode.DGL (ResidueCode attribute) ResidueCode.DGN (ResidueCode attribute) ResidueCode.DHA (ResidueCode attribute) ResidueCode.DHD (ResidueCode attribute) ResidueCode.DHI (ResidueCode attribute) ResidueCode.DI (ResidueCode attribute) ResidueCode.DIA (ResidueCode attribute) ResidueCode.DIL (ResidueCode attribute) ResidueCode.DIO (ResidueCode attribute) ResidueCode.DLE (ResidueCode attribute) ResidueCode.DLY (ResidueCode attribute) ResidueCode.DMF (ResidueCode attribute) ResidueCode.DMS (ResidueCode attribute) ResidueCode.DMU (ResidueCode attribute) ResidueCode.DMX (ResidueCode attribute) ResidueCode.DN (ResidueCode attribute) ResidueCode.DOC (ResidueCode attribute) ResidueCode.DOD (ResidueCode attribute) ResidueCode.DOX (ResidueCode attribute) ResidueCode.DPN (ResidueCode attribute) ResidueCode.DPR (ResidueCode attribute) ResidueCode.DR6 (ResidueCode attribute) ResidueCode.DSG (ResidueCode attribute) ResidueCode.DSN (ResidueCode attribute) ResidueCode.DT (ResidueCode attribute) ResidueCode.DTH (ResidueCode attribute) ResidueCode.DTR (ResidueCode attribute) ResidueCode.DTY (ResidueCode attribute) ResidueCode.DU (ResidueCode attribute) ResidueCode.DVA (ResidueCode attribute) ResidueCode.DXG (ResidueCode attribute) ResidueCode.EDO (ResidueCode attribute) ResidueCode.EEE (ResidueCode attribute) ResidueCode.EGL (ResidueCode attribute) ResidueCode.EOH (ResidueCode attribute) ResidueCode.EPE (ResidueCode attribute) ResidueCode.ETF (ResidueCode attribute) ResidueCode.F (ResidueCode attribute) ResidueCode.FAD (ResidueCode attribute) ResidueCode.FCY (ResidueCode attribute) ResidueCode.FE (ResidueCode attribute) ResidueCode.FE2 (ResidueCode attribute) ResidueCode.FGA (ResidueCode attribute) ResidueCode.FLO (ResidueCode attribute) ResidueCode.FME (ResidueCode attribute) ResidueCode.FMN (ResidueCode attribute) ResidueCode.FMT (ResidueCode attribute) ResidueCode.FRU (ResidueCode attribute) ResidueCode.FUC (ResidueCode attribute) ResidueCode.FVA (ResidueCode attribute) ResidueCode.G (ResidueCode attribute) ResidueCode.GAL (ResidueCode attribute) ResidueCode.GBL (ResidueCode attribute) ResidueCode.GCD (ResidueCode attribute) ResidueCode.GDP (ResidueCode attribute) ResidueCode.GHP (ResidueCode attribute) ResidueCode.GL3 (ResidueCode attribute) ResidueCode.GLA (ResidueCode attribute) ResidueCode.GLC (ResidueCode attribute) ResidueCode.GLN (ResidueCode attribute) ResidueCode.GLO (ResidueCode attribute) ResidueCode.GLU (ResidueCode attribute) ResidueCode.GLX (ResidueCode attribute) ResidueCode.GLY (ResidueCode attribute) ResidueCode.GOL (ResidueCode attribute) ResidueCode.GPX (ResidueCode attribute) ResidueCode.GYS (ResidueCode attribute) ResidueCode.H2U (ResidueCode attribute) ResidueCode.HEM (ResidueCode attribute) ResidueCode.HEZ (ResidueCode attribute) ResidueCode.HG (ResidueCode attribute) ResidueCode.HIC (ResidueCode attribute) ResidueCode.HIS (ResidueCode attribute) ResidueCode.HOH (ResidueCode attribute) ResidueCode.HTG (ResidueCode attribute) ResidueCode.HTO (ResidueCode attribute) ResidueCode.HYP (ResidueCode attribute) ResidueCode.I (ResidueCode attribute) ResidueCode.IAS (ResidueCode attribute) ResidueCode.ICI (ResidueCode attribute) ResidueCode.ICT (ResidueCode attribute) ResidueCode.IDO (ResidueCode attribute) ResidueCode.ILE (ResidueCode attribute) ResidueCode.IOD (ResidueCode attribute) ResidueCode.IOH (ResidueCode attribute) ResidueCode.IPA (ResidueCode attribute) ResidueCode.IPH (ResidueCode attribute) ResidueCode.JEF (ResidueCode attribute) ResidueCode.K (ResidueCode attribute) ResidueCode.KCX (ResidueCode attribute) ResidueCode.KPI (ResidueCode attribute) ResidueCode.LAT (ResidueCode attribute) ResidueCode.LBT (ResidueCode attribute) ResidueCode.LDA (ResidueCode attribute) ResidueCode.LEU (ResidueCode attribute) ResidueCode.LI (ResidueCode attribute) ResidueCode.LLP (ResidueCode attribute) ResidueCode.LMT (ResidueCode attribute) ResidueCode.LYS (ResidueCode attribute) ResidueCode.M2G (ResidueCode attribute) ResidueCode.M3L (ResidueCode attribute) ResidueCode.MA4 (ResidueCode attribute) ResidueCode.MA6 (ResidueCode attribute) ResidueCode.MAA (ResidueCode attribute) ResidueCode.MAN (ResidueCode attribute) ResidueCode.MDO (ResidueCode attribute) ResidueCode.MEA (ResidueCode attribute) ResidueCode.MED (ResidueCode attribute) ResidueCode.MEN (ResidueCode attribute) ResidueCode.MEQ (ResidueCode attribute) ResidueCode.MES (ResidueCode attribute) ResidueCode.MET (ResidueCode attribute) ResidueCode.MG (ResidueCode attribute) ResidueCode.MG8 (ResidueCode attribute) ResidueCode.MHA (ResidueCode attribute) ResidueCode.MHO (ResidueCode attribute) ResidueCode.MHS (ResidueCode attribute) ResidueCode.MIA (ResidueCode attribute) ResidueCode.MK8 (ResidueCode attribute) ResidueCode.MLE (ResidueCode attribute) ResidueCode.MLU (ResidueCode attribute) ResidueCode.MLY (ResidueCode attribute) ResidueCode.MLZ (ResidueCode attribute) ResidueCode.MN (ResidueCode attribute) ResidueCode.MN3 (ResidueCode attribute) ResidueCode.MOH (ResidueCode attribute) ResidueCode.MPD (ResidueCode attribute) ResidueCode.MPO (ResidueCode attribute) ResidueCode.MRD (ResidueCode attribute) ResidueCode.MRY (ResidueCode attribute) ResidueCode.MSE (ResidueCode attribute) ResidueCode.MTL (ResidueCode attribute) ResidueCode.MVA (ResidueCode attribute) ResidueCode.N (ResidueCode attribute) ResidueCode.N8E (ResidueCode attribute) ResidueCode.NA (ResidueCode attribute) ResidueCode.NAD (ResidueCode attribute) ResidueCode.NAG (ResidueCode attribute) ResidueCode.NAP (ResidueCode attribute) ResidueCode.NCO (ResidueCode attribute) ResidueCode.NDG (ResidueCode attribute) ResidueCode.NEP (ResidueCode attribute) ResidueCode.NGA (ResidueCode attribute) ResidueCode.NH2 (ResidueCode attribute) ResidueCode.NH4 (ResidueCode attribute) ResidueCode.NHE (ResidueCode attribute) ResidueCode.NI (ResidueCode attribute) ResidueCode.NLE (ResidueCode attribute) ResidueCode.NO (ResidueCode attribute) ResidueCode.NO3 (ResidueCode attribute) ResidueCode.NRQ (ResidueCode attribute) ResidueCode.OAS (ResidueCode attribute) ResidueCode.OCS (ResidueCode attribute) ResidueCode.OMC (ResidueCode attribute) ResidueCode.OMG (ResidueCode attribute) ResidueCode.OMU (ResidueCode attribute) ResidueCode.OMY (ResidueCode attribute) ResidueCode.OMZ (ResidueCode attribute) ResidueCode.ORN (ResidueCode attribute) ResidueCode.OTE (ResidueCode attribute) ResidueCode.P33 (ResidueCode attribute) ResidueCode.P4C (ResidueCode attribute) ResidueCode.PB (ResidueCode attribute) ResidueCode.PCA (ResidueCode attribute) ResidueCode.PDO (ResidueCode attribute) ResidueCode.PE4 (ResidueCode attribute) ResidueCode.PE7 (ResidueCode attribute) ResidueCode.PE8 (ResidueCode attribute) ResidueCode.PEG (ResidueCode attribute) ResidueCode.PEU (ResidueCode attribute) ResidueCode.PG4 (ResidueCode attribute) ResidueCode.PG5 (ResidueCode attribute) ResidueCode.PG6 (ResidueCode attribute) ResidueCode.PGE (ResidueCode attribute) ResidueCode.PGO (ResidueCode attribute) ResidueCode.PGQ (ResidueCode attribute) ResidueCode.PGR (ResidueCode attribute) ResidueCode.PHD (ResidueCode attribute) ResidueCode.PHE (ResidueCode attribute) ResidueCode.PHI (ResidueCode attribute) ResidueCode.PHL (ResidueCode attribute) ResidueCode.PIG (ResidueCode attribute) ResidueCode.PIN (ResidueCode attribute) ResidueCode.PLP (ResidueCode attribute) ResidueCode.PO4 (ResidueCode attribute) ResidueCode.POL (ResidueCode attribute) ResidueCode.PRO (ResidueCode attribute) ResidueCode.PSU (ResidueCode attribute) ResidueCode.PTR (ResidueCode attribute) ResidueCode.PYL (ResidueCode attribute) ResidueCode.R0AF (ResidueCode attribute) ResidueCode.R0TD (ResidueCode attribute) ResidueCode.R12P (ResidueCode attribute) ResidueCode.R144 (ResidueCode attribute) ResidueCode.R15P (ResidueCode attribute) ResidueCode.R16D (ResidueCode attribute) ResidueCode.R1BO (ResidueCode attribute) ResidueCode.R1MA (ResidueCode attribute) ResidueCode.R1MG (ResidueCode attribute) ResidueCode.R1PS (ResidueCode attribute) ResidueCode.R2MA (ResidueCode attribute) ResidueCode.R2MG (ResidueCode attribute) ResidueCode.R2OS (ResidueCode attribute) ResidueCode.R3CO (ResidueCode attribute) ResidueCode.R3DR (ResidueCode attribute) ResidueCode.R3FG (ResidueCode attribute) ResidueCode.R3NI (ResidueCode attribute) ResidueCode.R4OC (ResidueCode attribute) ResidueCode.R4SU (ResidueCode attribute) ResidueCode.R5BU (ResidueCode attribute) ResidueCode.R5CM (ResidueCode attribute) ResidueCode.R5MU (ResidueCode attribute) ResidueCode.R6MZ (ResidueCode attribute) ResidueCode.R7MG (ResidueCode attribute) ResidueCode.R8OG (ResidueCode attribute) ResidueCode.RB (ResidueCode attribute) ResidueCode.SAC (ResidueCode attribute) ResidueCode.SAL (ResidueCode attribute) ResidueCode.SAR (ResidueCode attribute) ResidueCode.SBT (ResidueCode attribute) ResidueCode.SCH (ResidueCode attribute) ResidueCode.SCN (ResidueCode attribute) ResidueCode.SCY (ResidueCode attribute) ResidueCode.SDS (ResidueCode attribute) ResidueCode.SEC (ResidueCode attribute) ResidueCode.SEP (ResidueCode attribute) ResidueCode.SER (ResidueCode attribute) ResidueCode.SF4 (ResidueCode attribute) ResidueCode.SIA (ResidueCode attribute) ResidueCode.SMC (ResidueCode attribute) ResidueCode.SME (ResidueCode attribute) ResidueCode.SNC (ResidueCode attribute) ResidueCode.SNN (ResidueCode attribute) ResidueCode.SO4 (ResidueCode attribute) ResidueCode.SOR (ResidueCode attribute) ResidueCode.SPD (ResidueCode attribute) ResidueCode.SPK (ResidueCode attribute) ResidueCode.SPM (ResidueCode attribute) ResidueCode.SR (ResidueCode attribute) ResidueCode.SUC (ResidueCode attribute) ResidueCode.TAR (ResidueCode attribute) ResidueCode.TAU (ResidueCode attribute) ResidueCode.TBU (ResidueCode attribute) ResidueCode.TEP (ResidueCode attribute) ResidueCode.TFP (ResidueCode attribute) ResidueCode.THR (ResidueCode attribute) ResidueCode.TLA (ResidueCode attribute) ResidueCode.TMA (ResidueCode attribute) ResidueCode.TOX (ResidueCode attribute) ResidueCode.TPO (ResidueCode attribute) ResidueCode.TPQ (ResidueCode attribute) ResidueCode.TRE (ResidueCode attribute) ResidueCode.TRP (ResidueCode attribute) ResidueCode.TRQ (ResidueCode attribute) ResidueCode.TRS (ResidueCode attribute) ResidueCode.TRT (ResidueCode attribute) ResidueCode.TYR (ResidueCode attribute) ResidueCode.TYS (ResidueCode attribute) ResidueCode.U (ResidueCode attribute) ResidueCode.UMQ (ResidueCode attribute) ResidueCode.UNK (ResidueCode attribute) ResidueCode.UNKNOWN (ResidueCode attribute) ResidueCode.UR3 (ResidueCode attribute) ResidueCode.URE (ResidueCode attribute) ResidueCode.VAL (ResidueCode attribute) ResidueCode.XPE (ResidueCode attribute) ResidueCode.XYP (ResidueCode attribute) ResidueCode.Y1 (ResidueCode attribute) ResidueCode.YCM (ResidueCode attribute) ResidueCode.YT3 (ResidueCode attribute) ResidueCode.ZN (ResidueCode attribute) ResidueCode.ZN2 (ResidueCode attribute) ResidueCodeParseError ResidueCodeParseError() (class) ResidueCodeParseError.[Symbol․dispose]() (ResidueCodeParseError method) ResidueCodeParseError.free() (ResidueCodeParseError method) ResidueCodeParseError.input() (ResidueCodeParseError method) ResidueIdentity (class in cosmolkit) ResidueIdentity() (class) ResidueIdentity.[Symbol․dispose]() (ResidueIdentity method) ResidueIdentity.code() (ResidueIdentity method) ResidueIdentity.free() (ResidueIdentity method) ResidueIdentity.info() (ResidueIdentity method) ResidueIdentity.isTabulated() (ResidueIdentity method) ResidueIdentity.name() (ResidueIdentity method) ResidueIdentity.new() (ResidueIdentity method) ResidueInfo (class in cosmolkit) residueInfo() (built-in function) ResidueInfo() (class) ResidueInfo.[Symbol․dispose]() (ResidueInfo method) ResidueInfo.canonicalOneLetterCode() (ResidueInfo method) ResidueInfo.code() (ResidueInfo method) ResidueInfo.fastaCode() (ResidueInfo method) ResidueInfo.found() (ResidueInfo method) ResidueInfo.free() (ResidueInfo method) ResidueInfo.hydrogenCount() (ResidueInfo method) ResidueInfo.isAminoAcid() (ResidueInfo method) ResidueInfo.isBufferOrWater() (ResidueInfo method) ResidueInfo.isDna() (ResidueInfo method) ResidueInfo.isModifiedAminoAcid() (ResidueInfo method) ResidueInfo.isNaLinking() (ResidueInfo method) ResidueInfo.isNucleicAcid() (ResidueInfo method) ResidueInfo.isPeptideLinking() (ResidueInfo method) ResidueInfo.isRna() (ResidueInfo method) ResidueInfo.isStandard() (ResidueInfo method) ResidueInfo.isWater() (ResidueInfo method) ResidueInfo.kind() (ResidueInfo method) ResidueInfo.kindName() (ResidueInfo method) ResidueInfo.linkingType() (ResidueInfo method) ResidueInfo.name() (ResidueInfo method) ResidueInfo.oneLetterCode() (ResidueInfo method) ResidueInfo.parentStandardCode() (ResidueInfo method) ResidueInfo.weight() (ResidueInfo method) residueInfoChecked() (built-in function) ResidueInfoKind (class in cosmolkit) ResidueInfoKind() (class) ResidueInfoKind.[Symbol․dispose]() (ResidueInfoKind method) ResidueInfoKind.AA (ResidueInfoKind attribute) ResidueInfoKind.AAD (ResidueInfoKind attribute) ResidueInfoKind.BUF (ResidueInfoKind attribute) ResidueInfoKind.DNA (ResidueInfoKind attribute) ResidueInfoKind.ELS (ResidueInfoKind attribute) ResidueInfoKind.free() (ResidueInfoKind method) ResidueInfoKind.HOH (ResidueInfoKind attribute) ResidueInfoKind.KET (ResidueInfoKind attribute) ResidueInfoKind.MAA (ResidueInfoKind attribute) ResidueInfoKind.name() (ResidueInfoKind method) ResidueInfoKind.PAA (ResidueInfoKind attribute) ResidueInfoKind.PYR (ResidueInfoKind attribute) ResidueInfoKind.RNA (ResidueInfoKind attribute) ResidueInfoKind.UNKNOWN (ResidueInfoKind attribute) ResidueInfoKind.value (ResidueInfoKind attribute) ResidueKind (class in cosmolkit) (None attribute) ResidueKind.AminoAcid (ResidueKind attribute) ResidueKind.Buffer (ResidueKind attribute) ResidueKind.Dna (ResidueKind attribute) ResidueKind.Ligand (ResidueKind attribute) ResidueKind.Rna (ResidueKind attribute) ResidueKind.Saccharide (ResidueKind attribute) ResidueKind.Unknown (ResidueKind attribute) ResidueKind.Water (ResidueKind attribute) ResidueName() (class) ResidueName.[Symbol․dispose]() (ResidueName method) ResidueName.asBytes() (ResidueName method) ResidueName.asStr() (ResidueName method) ResidueName.free() (ResidueName method) ResidueName.fromAscii() (ResidueName method) residues (cosmolkit.ProteinSelectionSummary attribute) residues() (cosmolkit.BioChainRow method) (cosmolkit.BioStructure method) (cosmolkit.Protein method) (cosmolkit.ProteinChainRef method) ResidueSequenceError ResidueSequenceError() (class) ResidueSequenceError.[Symbol․dispose]() (ResidueSequenceError method) ResidueSequenceError.domain (ResidueSequenceError attribute) ResidueSequenceError.free() (ResidueSequenceError method) ResidueSequenceError.kind (ResidueSequenceError attribute) ResidueSequenceError.message (ResidueSequenceError attribute) ResidueSourceIds (class in cosmolkit) ResidueSourceIds() (class) ResidueSourceIds.[Symbol․dispose]() (ResidueSourceIds method) ResidueSourceIds.free() (ResidueSourceIds method) ResidueSourceIds.labelEntityId() (ResidueSourceIds method) ResidueSourceIds.labelSeqId() (ResidueSourceIds method) ResidueSourceIds.segmentId() (ResidueSourceIds method) ResidueSourceIds.seqId() (ResidueSourceIds method) ResidueSourceIds.subchainId() (ResidueSourceIds method) resolution (cosmolkit.BioStructureSourceState attribute) resolution() (cosmolkit.BioStructure method) resolution_high (cosmolkit.BioBasicRefinementInfo attribute) (cosmolkit.BioReflectionsInfo attribute) resolution_low (cosmolkit.BioBasicRefinementInfo attribute) (cosmolkit.BioReflectionsInfo attribute) restr_stats (cosmolkit.BioRefinementInfo attribute) result_type (cosmolkit.MoleculeOpSpec attribute) retain_selection_() (cosmolkit.BioStructure method) (cosmolkit.Protein method) RF (cosmolkit.Element attribute) rfree_selection_method (cosmolkit.BioRefinementInfo attribute) rfree_set_count (cosmolkit.BioBasicRefinementInfo attribute) RG (cosmolkit.Element attribute) RGamma (cosmolkit.BioHelixClass attribute) RH (cosmolkit.Element attribute) ring() (cosmolkit.TautomerScore method) ring_matches_ring_only (cosmolkit.McsAtomCompareParameters property) (cosmolkit.McsBondCompareParameters property) ring_relations (cosmolkit.PotentialStereoResult attribute) Rings (cosmolkit.MolecularForceFieldErrorKind attribute) RingSearchParams (class in cosmolkit) RingSearchParams() (class) RingSearchParams.[Symbol․dispose]() (RingSearchParams method) RingSearchParams.free() (RingSearchParams method) RingSearchParams.includeDativeBonds (RingSearchParams attribute) RingSearchParams.includeHydrogenBonds (RingSearchParams attribute) RingSearchParamsOptions() (interface) RingSearchParamsOptions.includeDativeBonds? (RingSearchParamsOptions attribute) RingSearchParamsOptions.includeHydrogenBonds? (RingSearchParamsOptions attribute) RingStereoRelation (class in cosmolkit) RingStereoRelation() (class) RingStereoRelation.[Symbol․dispose]() (RingStereoRelation method) RingStereoRelation.atom (RingStereoRelation attribute) RingStereoRelation.free() (RingStereoRelation method) RingStereoRelation.other (RingStereoRelation attribute) RingStereoRelation.sameOrientation (RingStereoRelation attribute) rmsd() (cosmolkit.AlignmentResult method) (cosmolkit.ConformerRmsd method) rmsds() (cosmolkit.ConformerAlignmentReport method) RN (cosmolkit.Element attribute) Rna (cosmolkit.ChainKind attribute) (cosmolkit.PolymerKind attribute) RNA (cosmolkit.ResidueInfoKind attribute) Rna (cosmolkit.ResidueKind attribute) role (cosmolkit.ReactionValidationIssue attribute) ROmega (cosmolkit.BioHelixClass attribute) rooted_at_atom (cosmolkit.ReactionWriteParams property) (cosmolkit.SmartsWriteParams property) (cosmolkit.SmilesWriteParams property) RotatableBondsOptions (class in cosmolkit) (None attribute) RotatableBondsOptions.Default (RotatableBondsOptions attribute) RotatableBondsOptions.NonStrict (RotatableBondsOptions attribute) RotatableBondsOptions.Strict (RotatableBondsOptions attribute) RotatableBondsOptions.StrictLinkages (RotatableBondsOptions attribute) row() (cosmolkit.ProteinAtomRef method) (cosmolkit.ProteinChainRef method) (cosmolkit.ProteinResidueRef method) RPi (cosmolkit.BioHelixClass attribute) RU (cosmolkit.Element attribute) run() (cosmolkit.Reaction method) S s (cosmolkit.BioTlsGroup attribute) S (cosmolkit.CipDescriptor attribute) s (cosmolkit.CipDescriptor attribute) S (cosmolkit.Element attribute) (cosmolkit.Hybridization attribute) SAC (cosmolkit.ResidueCode attribute) Saccharide (cosmolkit.ResidueKind attribute) SaccharideD (cosmolkit.PolymerKind attribute) SaccharideL (cosmolkit.PolymerKind attribute) SAL (cosmolkit.ResidueCode attribute) Same (cosmolkit.BioAsu attribute) same_orientation (cosmolkit.RingStereoRelation attribute) sample_seed (cosmolkit.Coordinate2DParams property) samples (cosmolkit.Coordinate2DParams property) sanitize (cosmolkit.BioMoleculeParams property) (cosmolkit.InchiReadParams property) (cosmolkit.Mol2ReadParams property) (cosmolkit.ReactionParseParams property) (cosmolkit.RemoveHsParams property) (cosmolkit.SdfReadParams property) (cosmolkit.SmilesParseParams property) sanitize() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) sanitize_() (cosmolkit.Molecule method) sanitize_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) sanitize_with_params_() (cosmolkit.Molecule method) SanitizeError SanitizeError() (class) SanitizeError.[Symbol․dispose]() (SanitizeError method) SanitizeError.bits (SanitizeError attribute) SanitizeError.cause (SanitizeError attribute) SanitizeError.domain (SanitizeError attribute) SanitizeError.free() (SanitizeError method) SanitizeError.kind (SanitizeError attribute) SanitizeError.message (SanitizeError attribute) SanitizeError.stage (SanitizeError attribute) SanitizeError.unknownBits (SanitizeError attribute) SanitizeFailed (cosmolkit.InchiErrorKind attribute) SanitizeOperations (class in cosmolkit) SanitizeOperations() (class) SanitizeOperations.[Symbol․dispose]() (SanitizeOperations method) SanitizeOperations.ADJUST_HS (SanitizeOperations attribute) SanitizeOperations.ALL (SanitizeOperations attribute) SanitizeOperations.and() (SanitizeOperations method) SanitizeOperations.bits() (SanitizeOperations method) SanitizeOperations.CLEANUP (SanitizeOperations attribute) SanitizeOperations.CLEANUP_ATROPISOMERS (SanitizeOperations attribute) SanitizeOperations.CLEANUP_CHIRALITY (SanitizeOperations attribute) SanitizeOperations.CLEANUP_ORGANOMETALLICS (SanitizeOperations attribute) SanitizeOperations.contains() (SanitizeOperations method) SanitizeOperations.FIND_RADICALS (SanitizeOperations attribute) SanitizeOperations.free() (SanitizeOperations method) SanitizeOperations.fromBits() (SanitizeOperations method) SanitizeOperations.isEmpty() (SanitizeOperations method) SanitizeOperations.KEKULIZE (SanitizeOperations attribute) SanitizeOperations.NONE (SanitizeOperations attribute) SanitizeOperations.or() (SanitizeOperations method) SanitizeOperations.PROPERTIES (SanitizeOperations attribute) SanitizeOperations.SET_AROMATICITY (SanitizeOperations attribute) SanitizeOperations.SET_CONJUGATION (SanitizeOperations attribute) SanitizeOperations.SET_HYBRIDIZATION (SanitizeOperations attribute) SanitizeOperations.SYMM_RINGS (SanitizeOperations attribute) SanitizeParams (class in cosmolkit) SanitizeParams() (class) SanitizeParams.[Symbol․dispose]() (SanitizeParams method) SanitizeParams.free() (SanitizeParams method) SanitizeParams.operations (SanitizeParams attribute) SanitizeParamsOptions() (interface) SanitizeParamsOptions.operations? (SanitizeParamsOptions attribute) SanitizeStage (class in cosmolkit) (None attribute) SanitizeStage.AdjustHs (SanitizeStage attribute) SanitizeStage.Cleanup (SanitizeStage attribute) SanitizeStage.CleanupAtropisomers (SanitizeStage attribute) SanitizeStage.CleanupChirality (SanitizeStage attribute) SanitizeStage.CleanupOrganometallics (SanitizeStage attribute) SanitizeStage.FindRadicals (SanitizeStage attribute) SanitizeStage.Kekulize (SanitizeStage attribute) SanitizeStage.None (SanitizeStage attribute) SanitizeStage.Properties (SanitizeStage attribute) SanitizeStage.SetAromaticity (SanitizeStage attribute) SanitizeStage.SetConjugation (SanitizeStage attribute) SanitizeStage.SetHybridization (SanitizeStage attribute) SanitizeStage.SymmRings (SanitizeStage attribute) SAR (cosmolkit.ResidueCode attribute) SB (cosmolkit.Element attribute) SBT (cosmolkit.ResidueCode attribute) SC (cosmolkit.Element attribute) scale (cosmolkit.BioMmcifWriteParams property) scattering_type (cosmolkit.BioDiffractionInfo attribute) SCH (cosmolkit.ResidueCode attribute) SCN (cosmolkit.ResidueCode attribute) score() (cosmolkit.TautomerScoreTerm method) score_params (cosmolkit.TautomerParams property) scorer (cosmolkit.TautomerParams property) SCY (cosmolkit.ResidueCode attribute) sdf_data_fields() (cosmolkit.MoleculeProperties method) sdf_property_lists() (cosmolkit.MoleculeProperties method) SdfBatchIterator (class in cosmolkit) SdfBatchIterator() (class) SdfBatchIterator.[Symbol․dispose]() (SdfBatchIterator method) SdfBatchIterator.free() (SdfBatchIterator method) SdfBatchIterator.nextBatch() (SdfBatchIterator method) SdfCoordinateMode (class in cosmolkit) (None attribute) SdfCoordinateMode.Preserve (SdfCoordinateMode attribute) SdfCoordinateMode.Require2D (SdfCoordinateMode attribute) SdfCoordinateMode.Require3D (SdfCoordinateMode attribute) SdfDataset (class in cosmolkit) SdfDataset() (class) SdfDataset.[Symbol․dispose]() (SdfDataset method) SdfDataset.batches() (SdfDataset method) SdfDataset.free() (SdfDataset method) SdfDataset.isEmpty() (SdfDataset method) SdfDataset.iter() (SdfDataset method) SdfDataset.len() (SdfDataset method) SdfDataset.metadata() (SdfDataset method) SdfDataset.open() (SdfDataset method) SdfDataset.openWithParams() (SdfDataset method) SdfDataset.path() (SdfDataset method) SdfDataset.record() (SdfDataset method) SdfDataset.recordText() (SdfDataset method) SdfDataset.recordWithParams() (SdfDataset method) SdfDatasetIterator (class in cosmolkit) SdfDatasetIterator() (class) SdfDatasetIterator.[Symbol․dispose]() (SdfDatasetIterator method) SdfDatasetIterator.free() (SdfDatasetIterator method) SdfError SdfError() (class) SdfError.[Symbol․dispose]() (SdfError method) SdfError.actual (SdfError attribute) SdfError.cause (SdfError attribute) SdfError.domain (SdfError attribute) SdfError.expected (SdfError attribute) SdfError.free() (SdfError method) SdfError.kind (SdfError attribute) SdfError.message (SdfError attribute) SdfFormat (class in cosmolkit) (None attribute) SdfFormat.V2000 (SdfFormat attribute) SdfFormat.V3000 (SdfFormat attribute) SdfGraph (class in cosmolkit) SdfGraph() (class) SdfGraph.[Symbol․dispose]() (SdfGraph method) SdfGraph.free() (SdfGraph method) SdfGraph.kind (SdfGraph attribute) SdfGraph.molecule (SdfGraph attribute) SdfGraph.queryGraph (SdfGraph attribute) SdfPropertyList (class in cosmolkit) SdfPropertyList() (class) SdfPropertyList.[Symbol․dispose]() (SdfPropertyList method) SdfPropertyList.free() (SdfPropertyList method) SdfPropertyList.name() (SdfPropertyList method) SdfPropertyList.target() (SdfPropertyList method) SdfPropertyList.values() (SdfPropertyList method) SdfPropertyListTarget (class in cosmolkit) (None attribute) SdfPropertyListTarget.Atom (SdfPropertyListTarget attribute) SdfPropertyListTarget.Bond (SdfPropertyListTarget attribute) SdfReader (class in cosmolkit) SdfReader() (class) SdfReader.[Symbol․dispose]() (SdfReader method) SdfReader.batches() (SdfReader method) SdfReader.free() (SdfReader method) SdfReader.open() (SdfReader method) SdfReader.openWithParams() (SdfReader method) SdfReader.params() (SdfReader method) SdfReader.path() (SdfReader method) SdfReaderBatchIterator (class in cosmolkit) SdfReaderBatchIterator() (class) SdfReaderBatchIterator.[Symbol․dispose]() (SdfReaderBatchIterator method) SdfReaderBatchIterator.free() (SdfReaderBatchIterator method) SdfReaderBatchIterator.nextBatch() (SdfReaderBatchIterator method) SdfReadError SdfReadError() (class) SdfReadError.[Symbol․dispose]() (SdfReadError method) SdfReadError.cause (SdfReadError attribute) SdfReadError.context (SdfReadError attribute) SdfReadError.domain (SdfReadError attribute) SdfReadError.free() (SdfReadError method) SdfReadError.kind (SdfReadError attribute) SdfReadError.message (SdfReadError attribute) SdfReadParams (class in cosmolkit) SdfReadParams() (class) SdfReadParams.[Symbol․dispose]() (SdfReadParams method) SdfReadParams.coordinateMode (SdfReadParams attribute) SdfReadParams.expandAttachmentPoints (SdfReadParams attribute) SdfReadParams.free() (SdfReadParams method) SdfReadParams.processPropertyLists (SdfReadParams attribute) SdfReadParams.removeHs (SdfReadParams attribute) SdfReadParams.sanitize (SdfReadParams attribute) SdfReadParams.strictParsing (SdfReadParams attribute) SdfReadParamsOptions() (interface) SdfReadParamsOptions.coordinateMode? (SdfReadParamsOptions attribute) SdfReadParamsOptions.expandAttachmentPoints? (SdfReadParamsOptions attribute) SdfReadParamsOptions.processPropertyLists? (SdfReadParamsOptions attribute) SdfReadParamsOptions.removeHs? (SdfReadParamsOptions attribute) SdfReadParamsOptions.sanitize? (SdfReadParamsOptions attribute) SdfReadParamsOptions.strictParsing? (SdfReadParamsOptions attribute) SdfRecord (class in cosmolkit) SdfRecord() (class) SdfRecord.[Symbol․dispose]() (SdfRecord method) SdfRecord.dataField() (SdfRecord method) SdfRecord.dataFields() (SdfRecord method) SdfRecord.free() (SdfRecord method) SdfRecord.fromQueryGraph() (SdfRecord method) SdfRecord.fromSdf() (SdfRecord method) SdfRecord.fromSdfWithParams() (SdfRecord method) SdfRecord.graph() (SdfRecord method) SdfRecord.index() (SdfRecord method) SdfRecord.molecule() (SdfRecord method) SdfRecord.properties() (SdfRecord method) SdfRecord.queryGraph() (SdfRecord method) SdfRecord.sourceCoordinateDim() (SdfRecord method) SdfRecord.substanceGroups() (SdfRecord method) SdfRecord.title() (SdfRecord method) SdfRecord.toMol() (SdfRecord method) SdfRecord.toMolWithParams() (SdfRecord method) SdfRecord.toSdf() (SdfRecord method) SdfRecord.toSdfWithParams() (SdfRecord method) SdfRecordMetadata (class in cosmolkit) SdfRecordMetadata() (class) SdfRecordMetadata.[Symbol․dispose]() (SdfRecordMetadata method) SdfRecordMetadata.byteLen() (SdfRecordMetadata method) SdfRecordMetadata.byteOffset() (SdfRecordMetadata method) SdfRecordMetadata.byteRange() (SdfRecordMetadata method) SdfRecordMetadata.free() (SdfRecordMetadata method) SdfRecordMetadata.index() (SdfRecordMetadata method) SdfRecordMetadata.lineRange() (SdfRecordMetadata method) SdfRecordMetadata.title() (SdfRecordMetadata method) SdfRecordStream (class in cosmolkit) SdfRecordStream() (class) SdfRecordStream.[Symbol․dispose]() (SdfRecordStream method) SdfRecordStream.batches() (SdfRecordStream method) SdfRecordStream.bytesConsumed() (SdfRecordStream method) SdfRecordStream.free() (SdfRecordStream method) SdfRecordStream.isEnd() (SdfRecordStream method) SdfRecordStream.linesConsumed() (SdfRecordStream method) SdfRecordStream.nextRecord() (SdfRecordStream method) SdfRecordStream.open() (SdfRecordStream method) SdfRecordStream.openWithParams() (SdfRecordStream method) SdfRecordStream.recordsConsumed() (SdfRecordStream method) SDS (cosmolkit.ResidueCode attribute) SE (cosmolkit.Element attribute) SEC (cosmolkit.ResidueCode attribute) segment (cosmolkit.ResidueAddress attribute) selected_atom_ids() (cosmolkit.BioStructure method) (cosmolkit.Protein method) selection_summary() (cosmolkit.Protein method) selections (cosmolkit.BioTlsGroup attribute) semantic_preconditions (cosmolkit.MoleculeOpSpec attribute) sense (cosmolkit.BioStrand attribute) SEP (cosmolkit.ResidueCode attribute) seq_begin (cosmolkit.BioEntityDbRef attribute) seq_end (cosmolkit.BioEntityDbRef attribute) seq_id() (cosmolkit.ResidueSourceIds method) seq_num() (cosmolkit.PdbSeqId method) sequence_number (cosmolkit.ResidueAddress attribute) SER (cosmolkit.ResidueCode attribute) serial() (cosmolkit.AtomSourceIds method) set_2d_coordinates() (cosmolkit.MoleculeBuilder method) set_2d_coordinates_() (cosmolkit.Molecule method) set_2d_coordinates_with_params_() (cosmolkit.Molecule method) set_3d_coordinates_() (cosmolkit.Molecule method) set_3d_coordinates_with_params_() (cosmolkit.Molecule method) SET_AROMATICITY (cosmolkit.SanitizeOperations attribute) set_atom_formal_charge() (cosmolkit.MoleculeBuilder method) set_atom_position_() (cosmolkit.Molecule method) set_atom_position_with_params_() (cosmolkit.Molecule method) set_atom_property_() (cosmolkit.Molecule method) set_bits_per_feature() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_bond_order() (cosmolkit.MoleculeBuilder method) set_callback() (cosmolkit.TautomerParams method) SET_CONJUGATION (cosmolkit.SanitizeOperations attribute) set_count_bounds() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_count_simulation() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_fixed_atoms_() (cosmolkit.MolecularForceField method) set_fp_size() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) SET_HYBRIDIZATION (cosmolkit.SanitizeOperations attribute) set_include_chirality() (cosmolkit.MorganSettings method) (cosmolkit.TopologicalTorsionSettings method) set_include_redundant_environments() (cosmolkit.MorganSettings method) set_max_tautomers() (cosmolkit.TautomerParams method) set_max_transforms() (cosmolkit.TautomerParams method) set_only_3d_conformer_() (cosmolkit.Molecule method) set_only_3d_conformer_with_params_() (cosmolkit.Molecule method) set_only_bits (cosmolkit.LayeredFingerprintParams property) set_only_nonzero_invariants() (cosmolkit.MorganSettings method) set_only_shortest_paths() (cosmolkit.TopologicalTorsionSettings method) set_position_() (cosmolkit.MolecularForceField method) set_positions_() (cosmolkit.MolecularForceField method) set_radius() (cosmolkit.MorganSettings method) set_reassign_stereo() (cosmolkit.TautomerParams method) set_remove_bond_stereo() (cosmolkit.TautomerParams method) set_remove_isotopic_hydrogens() (cosmolkit.TautomerParams method) set_remove_sp3_stereo() (cosmolkit.TautomerParams method) set_scorer() (cosmolkit.TautomerParams method) set_torsion_atom_count() (cosmolkit.TopologicalTorsionSettings method) set_value() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) SetAromaticity (cosmolkit.SanitizeStage attribute) SetConjugation (cosmolkit.SanitizeStage attribute) SetHybridization (cosmolkit.SanitizeStage attribute) settings() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) severity (cosmolkit.ReactionValidationIssue attribute) SF4 (cosmolkit.ResidueCode attribute) SG (cosmolkit.Element attribute) SGroupBracket (class in cosmolkit) SGroupBracket() (class) SGroupBracket.[Symbol․dispose]() (SGroupBracket method) SGroupBracket.free() (SGroupBracket method) SGroupBracket.new() (SGroupBracket method) SGroupBracket.points() (SGroupBracket method) SGroupCState (class in cosmolkit) SGroupCState() (class) SGroupCState.[Symbol․dispose]() (SGroupCState method) SGroupCState.bond() (SGroupCState method) SGroupCState.free() (SGroupCState method) SGroupCState.new() (SGroupCState method) SGroupCState.vector() (SGroupCState method) SGroupDisplay (class in cosmolkit) SGroupDisplay() (class) SGroupDisplay.[Symbol․dispose]() (SGroupDisplay method) SGroupDisplay.brackets() (SGroupDisplay method) SGroupDisplay.free() (SGroupDisplay method) SGROUPS (cosmolkit.CxSmilesFields attribute) Sheets (cosmolkit.BioMmcifReadStage attribute) sheets() (cosmolkit.BioStructure method) shells (cosmolkit.BioExperimentInfo attribute) show_warnings (cosmolkit.RemoveHsParams property) SI (cosmolkit.Element attribute) SIA (cosmolkit.ResidueCode attribute) sifts_unp() (cosmolkit.BioResidueRow method) SiftsUnp (cosmolkit.BioMmcifReadStage attribute) silent (cosmolkit.ReactionValidationParams property) Simple (cosmolkit.AromaticityModel attribute) SINGLE (cosmolkit.BondOrder attribute) skip_cleanup (cosmolkit.SmartsParseParams property) (cosmolkit.SmilesParseParams property) skip_queries (cosmolkit.AddHsParams property) skip_remarks (cosmolkit.BioPdbReadParams property) slogp_vsa() (cosmolkit.Molecule method) slogp_vsa_1() (cosmolkit.Molecule method) slogp_vsa_10() (cosmolkit.Molecule method) slogp_vsa_11() (cosmolkit.Molecule method) slogp_vsa_12() (cosmolkit.Molecule method) slogp_vsa_2() (cosmolkit.Molecule method) slogp_vsa_3() (cosmolkit.Molecule method) slogp_vsa_4() (cosmolkit.Molecule method) slogp_vsa_5() (cosmolkit.Molecule method) slogp_vsa_6() (cosmolkit.Molecule method) slogp_vsa_7() (cosmolkit.Molecule method) slogp_vsa_8() (cosmolkit.Molecule method) slogp_vsa_9() (cosmolkit.Molecule method) slogp_vsa_with_params() (cosmolkit.Molecule method) SM (cosmolkit.Element attribute) smarts (cosmolkit.McsResult attribute) smarts() (cosmolkit.TautomerScoreTerm method) SmartsParseError SmartsParseError() (class) SmartsParseError.[Symbol․dispose]() (SmartsParseError method) SmartsParseError.atom (SmartsParseError attribute) SmartsParseError.beginAtom (SmartsParseError attribute) SmartsParseError.carrier (SmartsParseError attribute) SmartsParseError.cause (SmartsParseError attribute) SmartsParseError.character (SmartsParseError attribute) SmartsParseError.context (SmartsParseError attribute) SmartsParseError.domain (SmartsParseError attribute) SmartsParseError.endAtom (SmartsParseError attribute) SmartsParseError.feature (SmartsParseError attribute) SmartsParseError.free() (SmartsParseError method) SmartsParseError.kind (SmartsParseError attribute) SmartsParseError.message (SmartsParseError attribute) SmartsParseError.position (SmartsParseError attribute) SmartsParseError.primitiveDetail (SmartsParseError attribute) SmartsParseError.ring (SmartsParseError attribute) SmartsParseParams (class in cosmolkit) SmartsParseParams() (class) SmartsParseParams.[Symbol․dispose]() (SmartsParseParams method) SmartsParseParams.allowCxsmiles (SmartsParseParams attribute) SmartsParseParams.debugParse (SmartsParseParams attribute) SmartsParseParams.free() (SmartsParseParams method) SmartsParseParams.mergeHs (SmartsParseParams attribute) SmartsParseParams.parseName (SmartsParseParams attribute) SmartsParseParams.replacements (SmartsParseParams attribute) SmartsParseParams.skipCleanup (SmartsParseParams attribute) SmartsParseParams.strictCxsmiles (SmartsParseParams attribute) SmartsParseParamsOptions() (interface) SmartsParseParamsOptions.allowCxsmiles? (SmartsParseParamsOptions attribute) SmartsParseParamsOptions.debugParse? (SmartsParseParamsOptions attribute) SmartsParseParamsOptions.mergeHs? (SmartsParseParamsOptions attribute) SmartsParseParamsOptions.parseName? (SmartsParseParamsOptions attribute) SmartsParseParamsOptions.replacements? (SmartsParseParamsOptions attribute) SmartsParseParamsOptions.skipCleanup? (SmartsParseParamsOptions attribute) SmartsParseParamsOptions.strictCxsmiles? (SmartsParseParamsOptions attribute) SmartsWriteError SmartsWriteError() (class) SmartsWriteError.[Symbol․dispose]() (SmartsWriteError method) SmartsWriteError.cause (SmartsWriteError attribute) SmartsWriteError.domain (SmartsWriteError attribute) SmartsWriteError.free() (SmartsWriteError method) SmartsWriteError.kind (SmartsWriteError attribute) SmartsWriteError.message (SmartsWriteError attribute) SmartsWriteParams (class in cosmolkit) SmartsWriteParams() (class) SmartsWriteParams.[Symbol․dispose]() (SmartsWriteParams method) SmartsWriteParams.free() (SmartsWriteParams method) SmartsWriteParams.includeAtomMaps (SmartsWriteParams attribute) SmartsWriteParams.includeDativeBonds (SmartsWriteParams attribute) SmartsWriteParams.isomericSmiles (SmartsWriteParams attribute) SmartsWriteParams.rootedAtAtom (SmartsWriteParams attribute) SmartsWriteParamsOptions() (interface) SmartsWriteParamsOptions.includeAtomMaps? (SmartsWriteParamsOptions attribute) SmartsWriteParamsOptions.includeDativeBonds? (SmartsWriteParamsOptions attribute) SmartsWriteParamsOptions.isomericSmiles? (SmartsWriteParamsOptions attribute) SmartsWriteParamsOptions.rootedAtAtom? (SmartsWriteParamsOptions attribute) SMC (cosmolkit.ResidueCode attribute) SME (cosmolkit.ResidueCode attribute) smiles (cosmolkit.CxSmilesWriteParams property) (cosmolkit.FragmentSmilesWriteParams property) SmilesError SmilesError() (class) SmilesError.[Symbol․dispose]() (SmilesError method) SmilesError.cause (SmilesError attribute) SmilesError.domain (SmilesError attribute) SmilesError.free() (SmilesError method) SmilesError.kind (SmilesError attribute) SmilesError.message (SmilesError attribute) SmilesParseParams (class in cosmolkit) SmilesParseParams() (class) SmilesParseParams.[Symbol․dispose]() (SmilesParseParams method) SmilesParseParams.allowCxsmiles (SmilesParseParams attribute) SmilesParseParams.debugParse (SmilesParseParams attribute) SmilesParseParams.free() (SmilesParseParams method) SmilesParseParams.parseName (SmilesParseParams attribute) SmilesParseParams.removeHs (SmilesParseParams attribute) SmilesParseParams.replacements (SmilesParseParams attribute) SmilesParseParams.sanitize (SmilesParseParams attribute) SmilesParseParams.skipCleanup (SmilesParseParams attribute) SmilesParseParams.strictCxsmiles (SmilesParseParams attribute) SmilesParseParamsOptions() (interface) SmilesParseParamsOptions.allowCxsmiles? (SmilesParseParamsOptions attribute) SmilesParseParamsOptions.debugParse? (SmilesParseParamsOptions attribute) SmilesParseParamsOptions.parseName? (SmilesParseParamsOptions attribute) SmilesParseParamsOptions.removeHs? (SmilesParseParamsOptions attribute) SmilesParseParamsOptions.replacements? (SmilesParseParamsOptions attribute) SmilesParseParamsOptions.sanitize? (SmilesParseParamsOptions attribute) SmilesParseParamsOptions.skipCleanup? (SmilesParseParamsOptions attribute) SmilesParseParamsOptions.strictCxsmiles? (SmilesParseParamsOptions attribute) SmilesStereoError SmilesStereoError() (class) SmilesStereoError.[Symbol․dispose]() (SmilesStereoError method) SmilesStereoError.actual (SmilesStereoError attribute) SmilesStereoError.cause (SmilesStereoError attribute) SmilesStereoError.dimension (SmilesStereoError attribute) SmilesStereoError.domain (SmilesStereoError attribute) SmilesStereoError.expected (SmilesStereoError attribute) SmilesStereoError.field (SmilesStereoError attribute) SmilesStereoError.free() (SmilesStereoError method) SmilesStereoError.id (SmilesStereoError attribute) SmilesStereoError.kind (SmilesStereoError attribute) SmilesStereoError.message (SmilesStereoError attribute) SmilesWriteError SmilesWriteError() (class) SmilesWriteError.[Symbol․dispose]() (SmilesWriteError method) SmilesWriteError.cause (SmilesWriteError attribute) SmilesWriteError.domain (SmilesWriteError attribute) SmilesWriteError.free() (SmilesWriteError method) SmilesWriteError.kind (SmilesWriteError attribute) SmilesWriteError.message (SmilesWriteError attribute) SmilesWriteParams (class in cosmolkit) SmilesWriteParams() (class) SmilesWriteParams.[Symbol․dispose]() (SmilesWriteParams method) SmilesWriteParams.allBondsExplicit (SmilesWriteParams attribute) SmilesWriteParams.allHydrogensExplicit (SmilesWriteParams attribute) SmilesWriteParams.canonical (SmilesWriteParams attribute) SmilesWriteParams.cleanStereo (SmilesWriteParams attribute) SmilesWriteParams.free() (SmilesWriteParams method) SmilesWriteParams.ignoreAtomMapNumbers (SmilesWriteParams attribute) SmilesWriteParams.includeDativeBonds (SmilesWriteParams attribute) SmilesWriteParams.isomericSmiles (SmilesWriteParams attribute) SmilesWriteParams.kekule (SmilesWriteParams attribute) SmilesWriteParams.rootedAtAtom (SmilesWriteParams attribute) SmilesWriteParamsOptions() (interface) SmilesWriteParamsOptions.allBondsExplicit? (SmilesWriteParamsOptions attribute) SmilesWriteParamsOptions.allHydrogensExplicit? (SmilesWriteParamsOptions attribute) SmilesWriteParamsOptions.canonical? (SmilesWriteParamsOptions attribute) SmilesWriteParamsOptions.cleanStereo? (SmilesWriteParamsOptions attribute) SmilesWriteParamsOptions.ignoreAtomMapNumbers? (SmilesWriteParamsOptions attribute) SmilesWriteParamsOptions.includeDativeBonds? (SmilesWriteParamsOptions attribute) SmilesWriteParamsOptions.isomericSmiles? (SmilesWriteParamsOptions attribute) SmilesWriteParamsOptions.kekule? (SmilesWriteParamsOptions attribute) SmilesWriteParamsOptions.rootedAtAtom? (SmilesWriteParamsOptions attribute) smr_vsa() (cosmolkit.Molecule method) smr_vsa_1() (cosmolkit.Molecule method) smr_vsa_10() (cosmolkit.Molecule method) smr_vsa_2() (cosmolkit.Molecule method) smr_vsa_3() (cosmolkit.Molecule method) smr_vsa_4() (cosmolkit.Molecule method) smr_vsa_5() (cosmolkit.Molecule method) smr_vsa_6() (cosmolkit.Molecule method) smr_vsa_7() (cosmolkit.Molecule method) smr_vsa_8() (cosmolkit.Molecule method) smr_vsa_9() (cosmolkit.Molecule method) smr_vsa_with_params() (cosmolkit.Molecule method) SN (cosmolkit.Element attribute) SNC (cosmolkit.ResidueCode attribute) SNN (cosmolkit.ResidueCode attribute) SO4 (cosmolkit.ResidueCode attribute) software (cosmolkit.BioMetadata attribute) Software (cosmolkit.BioMmcifReadStage attribute) software (cosmolkit.BioMmcifWriteParams property) software_determined (cosmolkit.BioAssembly attribute) software_name (cosmolkit.BioAssembly attribute) solved_by (cosmolkit.BioMetadata attribute) solvent_free_energy_change (cosmolkit.BioAssembly attribute) SOR (cosmolkit.ResidueCode attribute) source (cosmolkit.BioDiffractionInfo attribute) source() (cosmolkit.BioAtomRow method) (cosmolkit.BioChainRow method) (cosmolkit.BioEntityRow method) (cosmolkit.BioResidueRow method) (cosmolkit.ProteinChainRef method) source_conformer_order (cosmolkit.CoordinateBlock attribute) source_coordinate_dim (cosmolkit.CoordinateBlock attribute) source_coordinate_dim() (cosmolkit.SdfRecord method) source_entity_id() (cosmolkit.EntitySourceIds method) source_model_number() (cosmolkit.BioModelRow method) source_name (cosmolkit.BioReadParams property) source_state() (cosmolkit.BioStructure method) source_type (cosmolkit.BioDiffractionInfo attribute) SourcePort (cosmolkit.InchiErrorKind attribute) SP (cosmolkit.Hybridization attribute) SP2 (cosmolkit.Hybridization attribute) SP2D (cosmolkit.Hybridization attribute) SP3 (cosmolkit.Hybridization attribute) SP3D (cosmolkit.Hybridization attribute) SP3D2 (cosmolkit.Hybridization attribute) space_group_number() (cosmolkit.BioCrystalInfo method) sparse_counts() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) sparse_fingerprints() (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) SparseBitFingerprint (class in cosmolkit) SparseBitFingerprint() (class) SparseBitFingerprint.[Symbol․dispose]() (SparseBitFingerprint method) SparseBitFingerprint.free() (SparseBitFingerprint method) SparseBitFingerprint.nBits() (SparseBitFingerprint method) SparseBitFingerprint.onBits() (SparseBitFingerprint method) SparseCountFingerprint (class in cosmolkit) SparseCountFingerprint() (class) SparseCountFingerprint.[Symbol․dispose]() (SparseCountFingerprint method) SparseCountFingerprint.free() (SparseCountFingerprint method) SparseCountFingerprint.fuzzyAnd() (SparseCountFingerprint method) SparseCountFingerprint.fuzzyOr() (SparseCountFingerprint method) SparseCountFingerprint.length() (SparseCountFingerprint method) SparseCountFingerprint.new() (SparseCountFingerprint method) SparseCountFingerprint.nonzeroElements() (SparseCountFingerprint method) SparseCountFingerprint.setValue() (SparseCountFingerprint method) SparseCountFingerprint.totalValue() (SparseCountFingerprint method) SparseCountFingerprint.value() (SparseCountFingerprint method) SparseCountFingerprint.withAdded() (SparseCountFingerprint method) SparseCountFingerprint.withAddedScalar() (SparseCountFingerprint method) SparseCountFingerprint.withDividedScalar() (SparseCountFingerprint method) SparseCountFingerprint.withMultipliedScalar() (SparseCountFingerprint method) SparseCountFingerprint.withSubtracted() (SparseCountFingerprint method) SparseCountFingerprint.withSubtractedScalar() (SparseCountFingerprint method) SparseCountFingerprint32 (class in cosmolkit) SparseCountFingerprint32() (class) SparseCountFingerprint32.[Symbol․dispose]() (SparseCountFingerprint32 method) SparseCountFingerprint32.free() (SparseCountFingerprint32 method) SparseCountFingerprint32.fuzzyAnd() (SparseCountFingerprint32 method) SparseCountFingerprint32.fuzzyOr() (SparseCountFingerprint32 method) SparseCountFingerprint32.length() (SparseCountFingerprint32 method) SparseCountFingerprint32.new() (SparseCountFingerprint32 method) SparseCountFingerprint32.nonzeroElements() (SparseCountFingerprint32 method) SparseCountFingerprint32.setValue() (SparseCountFingerprint32 method) SparseCountFingerprint32.totalValue() (SparseCountFingerprint32 method) SparseCountFingerprint32.value() (SparseCountFingerprint32 method) SparseCountFingerprint32.withAdded() (SparseCountFingerprint32 method) SparseCountFingerprint32.withAddedScalar() (SparseCountFingerprint32 method) SparseCountFingerprint32.withDividedScalar() (SparseCountFingerprint32 method) SparseCountFingerprint32.withMultipliedScalar() (SparseCountFingerprint32 method) SparseCountFingerprint32.withSubtracted() (SparseCountFingerprint32 method) SparseCountFingerprint32.withSubtractedScalar() (SparseCountFingerprint32 method) SPD (cosmolkit.ResidueCode attribute) special_kind (cosmolkit.BioAssembly attribute) specified (cosmolkit.PotentialStereoInfo attribute) SPECIFIED (cosmolkit.PotentialStereoSpecified attribute) specified_stereo_query_matches_unspecified (cosmolkit.SubstructMatchParams property) SPK (cosmolkit.ResidueCode attribute) split_chain_on_ter (cosmolkit.BioPdbReadParams property) SPM (cosmolkit.ResidueCode attribute) SR (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) sr_etkdg_v3() (cosmolkit.EmbedParams static method) stage() (cosmolkit.BioMmcifReadError method) (cosmolkit.BioPdbReadError method) start (cosmolkit.BioHelix attribute) (cosmolkit.BioStrand attribute) start() (cosmolkit.BioRowSpan method) starting_model (cosmolkit.BioMetadata attribute) status (cosmolkit.MoleculeOpSpec attribute) status() (cosmolkit.TautomerEnumeration method) (cosmolkit.TautomerProgress method) status_code() (cosmolkit.MmffOptimizeMoleculeConfResult method) (cosmolkit.MmffOptimizeMoleculeResult method) (cosmolkit.UffConformerResult method) (cosmolkit.UffOptimizationResult method) stereo (cosmolkit.PotentialStereoResult attribute) stereo() (cosmolkit.Bond method) stereo_atoms() (cosmolkit.Bond method) stereo_code() (cosmolkit.Bond method) stereo_groups (cosmolkit.TopologyBlock attribute) stereo_groups() (cosmolkit.MoleculeBuilder method) stereo_name() (cosmolkit.Bond method) stereo_type (cosmolkit.PotentialStereoInfo attribute) STEREOANY (cosmolkit.BondStereo attribute) STEREOATROPCCW (cosmolkit.BondStereo attribute) STEREOATROPCW (cosmolkit.BondStereo attribute) STEREOCIS (cosmolkit.BondStereo attribute) STEREOE (cosmolkit.BondStereo attribute) StereoError StereoError() (class) StereoError.[Symbol․dispose]() (StereoError method) StereoError.cause (StereoError attribute) StereoError.domain (StereoError attribute) StereoError.free() (StereoError method) StereoError.kind (StereoError attribute) StereoError.message (StereoError attribute) StereoGroup (class in cosmolkit) StereoGroup() (class) StereoGroup.[Symbol․dispose]() (StereoGroup method) StereoGroup.atoms() (StereoGroup method) StereoGroup.bonds() (StereoGroup method) StereoGroup.free() (StereoGroup method) StereoGroup.kind() (StereoGroup method) StereoGroupKind (None attribute) StereoGroupKind.Absolute (StereoGroupKind attribute) StereoGroupKind.And (StereoGroupKind attribute) StereoGroupKind.Or (StereoGroupKind attribute) stereoisomer_count() (cosmolkit.Molecule method) stereoisomer_count_with_options() (cosmolkit.Molecule method) StereoisomerIterator (class in cosmolkit) StereoisomerIterator() (class) StereoisomerIterator.[Symbol․dispose]() (StereoisomerIterator method) StereoisomerIterator.free() (StereoisomerIterator method) StereoisomerIterator.next() (StereoisomerIterator method) StereoisomerIterator.yieldedCount (StereoisomerIterator attribute) StereoisomerOptions (class in cosmolkit) StereoisomerOptions() (class) StereoisomerOptions.[Symbol․dispose]() (StereoisomerOptions method) StereoisomerOptions.default() (StereoisomerOptions method) StereoisomerOptions.free() (StereoisomerOptions method) StereoisomerOptions.maxIsomers (StereoisomerOptions attribute) StereoisomerOptions.onlyStereoGroups (StereoisomerOptions attribute) StereoisomerOptions.onlyUnassigned (StereoisomerOptions attribute) StereoisomerOptions.randomSource (StereoisomerOptions attribute) StereoisomerOptions.setMaxIsomers() (StereoisomerOptions method) StereoisomerOptions.setOnlyStereoGroups() (StereoisomerOptions method) StereoisomerOptions.setOnlyUnassigned() (StereoisomerOptions method) StereoisomerOptions.setRandomSource() (StereoisomerOptions method) StereoisomerOptions.setTryEmbedding() (StereoisomerOptions method) StereoisomerOptions.setUnique() (StereoisomerOptions method) StereoisomerOptions.tryEmbedding (StereoisomerOptions attribute) StereoisomerOptions.unique (StereoisomerOptions attribute) StereoisomerOptionsConfiguration() (interface) StereoisomerOptionsConfiguration.maxIsomers? (StereoisomerOptionsConfiguration attribute) StereoisomerOptionsConfiguration.onlyStereoGroups? (StereoisomerOptionsConfiguration attribute) StereoisomerOptionsConfiguration.onlyUnassigned? (StereoisomerOptionsConfiguration attribute) StereoisomerOptionsConfiguration.randomSource? (StereoisomerOptionsConfiguration attribute) StereoisomerOptionsConfiguration.tryEmbedding? (StereoisomerOptionsConfiguration attribute) StereoisomerOptionsConfiguration.unique? (StereoisomerOptionsConfiguration attribute) StereoisomerRandomSource (class in cosmolkit) StereoisomerRandomSource() (class) StereoisomerRandomSource.[Symbol․dispose]() (StereoisomerRandomSource method) StereoisomerRandomSource.free() (StereoisomerRandomSource method) StereoisomerRandomSource.fromIntegerSeed() (StereoisomerRandomSource method) StereoisomerRandomSource.fromRandomBits() (StereoisomerRandomSource method) STEREONONE (cosmolkit.BondStereo attribute) StereoReadError StereoReadError() (class) StereoReadError.[Symbol․dispose]() (StereoReadError method) StereoReadError.cause (StereoReadError attribute) StereoReadError.domain (StereoReadError attribute) StereoReadError.free() (StereoReadError method) StereoReadError.kind (StereoReadError attribute) StereoReadError.message (StereoReadError attribute) STEREOTRANS (cosmolkit.BondStereo attribute) STEREOZ (cosmolkit.BondStereo attribute) store_all (cosmolkit.McsParameters property) strands (cosmolkit.BioSheet attribute) Stream (cosmolkit.BioPdbReadStage attribute) Strict (cosmolkit.RotatableBondsOptions attribute) strict (cosmolkit.ValenceParams property) strict_cxsmiles (cosmolkit.ReactionParseParams property) (cosmolkit.SmartsParseParams property) (cosmolkit.SmilesParseParams property) strict_parsing (cosmolkit.SdfReadParams property) StrictLinkages (cosmolkit.RotatableBondsOptions attribute) String (cosmolkit.PropertyValueKind attribute) StringVector (cosmolkit.PropertyValueKind attribute) struct_asym (cosmolkit.BioMmcifWriteParams property) struct_biol (cosmolkit.BioMmcifWriteParams property) struct_conf (cosmolkit.BioMmcifWriteParams property) struct_ref (cosmolkit.BioMmcifWriteParams property) struct_sheet (cosmolkit.BioMmcifWriteParams property) StructuralRepeatUnit (cosmolkit.SubstanceGroupKind attribute) StructureTagParams (class in cosmolkit) StructureTagParams() (class) StructureTagParams.[Symbol․dispose]() (StructureTagParams method) StructureTagParams.conformerId (StructureTagParams attribute) StructureTagParams.free() (StructureTagParams method) StructureTagParams.replaceExistingTags (StructureTagParams attribute) StructureTagParamsOptions() (interface) StructureTagParamsOptions.conformerId? (StructureTagParamsOptions attribute) StructureTagParamsOptions.replaceExistingTags? (StructureTagParamsOptions attribute) StructureValidation (cosmolkit.BioMmcifReadStage attribute) subchain_id() (cosmolkit.ResidueSourceIds method) subchains (cosmolkit.BioAssemblyGenerator attribute) subchains() (cosmolkit.BioEntityRow method) substance_groups (cosmolkit.TopologyBlock attribute) substance_groups() (cosmolkit.MoleculeBuilder method) (cosmolkit.SdfRecord method) SubstanceGroup (class in cosmolkit) SubstanceGroup() (class) SubstanceGroup.[Symbol․dispose]() (SubstanceGroup method) SubstanceGroup.crossingBondCorrespondence() (SubstanceGroup method) SubstanceGroup.cstates() (SubstanceGroup method) SubstanceGroup.display() (SubstanceGroup method) SubstanceGroup.free() (SubstanceGroup method) SubstanceGroup.headCrossingBonds() (SubstanceGroup method) SubstanceGroup.id() (SubstanceGroup method) SubstanceGroup.kind() (SubstanceGroup method) SubstanceGroup.new() (SubstanceGroup method) SubstanceGroupId (class in cosmolkit) SubstanceGroupId() (class) SubstanceGroupId.[Symbol․dispose]() (SubstanceGroupId method) SubstanceGroupId.free() (SubstanceGroupId method) SubstanceGroupId.index() (SubstanceGroupId method) SubstanceGroupId.new() (SubstanceGroupId method) SubstanceGroupKind (class in cosmolkit) SubstanceGroupKind() (class) SubstanceGroupKind.[Symbol․dispose]() (SubstanceGroupKind method) SubstanceGroupKind.AnyPolymer (SubstanceGroupKind attribute) SubstanceGroupKind.Copolymer (SubstanceGroupKind attribute) SubstanceGroupKind.Crosslink (SubstanceGroupKind attribute) SubstanceGroupKind.Data (SubstanceGroupKind attribute) SubstanceGroupKind.equals() (SubstanceGroupKind method) SubstanceGroupKind.Formulation (SubstanceGroupKind attribute) SubstanceGroupKind.free() (SubstanceGroupKind method) SubstanceGroupKind.Generic() (SubstanceGroupKind method) SubstanceGroupKind.genericValue (SubstanceGroupKind attribute) SubstanceGroupKind.Graft (SubstanceGroupKind attribute) SubstanceGroupKind.Mer (SubstanceGroupKind attribute) SubstanceGroupKind.Mixture (SubstanceGroupKind attribute) SubstanceGroupKind.MixtureComponent (SubstanceGroupKind attribute) SubstanceGroupKind.Modification (SubstanceGroupKind attribute) SubstanceGroupKind.Monomer (SubstanceGroupKind attribute) SubstanceGroupKind.MultipleGroup (SubstanceGroupKind attribute) SubstanceGroupKind.StructuralRepeatUnit (SubstanceGroupKind attribute) SubstanceGroupKind.Superatom (SubstanceGroupKind attribute) substruct_match() (cosmolkit.Molecule method) substruct_match_with_params() (cosmolkit.Molecule method) substruct_matches() (cosmolkit.Molecule method) substruct_matches_compiled() (cosmolkit.Molecule method) substruct_matches_with_params() (cosmolkit.Molecule method) SubstructMatchError SubstructMatchError() (class) SubstructMatchError.[Symbol․dispose]() (SubstructMatchError method) SubstructMatchError.branch (SubstructMatchError attribute) SubstructMatchError.cause (SubstructMatchError attribute) SubstructMatchError.domain (SubstructMatchError attribute) SubstructMatchError.free() (SubstructMatchError method) SubstructMatchError.kind (SubstructMatchError attribute) SubstructMatchError.message (SubstructMatchError attribute) SubstructMatchError.rdkitFunction (SubstructMatchError attribute) SubstructMatchOptions() (interface) SubstructMatchOptions.aromaticMatchesConjugated? (SubstructMatchOptions attribute) SubstructMatchOptions.aromaticMatchesSingleOrDouble? (SubstructMatchOptions attribute) SubstructMatchOptions.atomMatch? (SubstructMatchOptions attribute) SubstructMatchOptions.atomProperties? (SubstructMatchOptions attribute) SubstructMatchOptions.bondMatch? (SubstructMatchOptions attribute) SubstructMatchOptions.bondProperties? (SubstructMatchOptions attribute) SubstructMatchOptions.extraAtomCheckOverridesDefaultCheck? (SubstructMatchOptions attribute) SubstructMatchOptions.extraBondCheckOverridesDefaultCheck? (SubstructMatchOptions attribute) SubstructMatchOptions.finalMatch? (SubstructMatchOptions attribute) SubstructMatchOptions.maxMatches? (SubstructMatchOptions attribute) SubstructMatchOptions.maxRecursiveMatches? (SubstructMatchOptions attribute) SubstructMatchOptions.numThreads? (SubstructMatchOptions attribute) SubstructMatchOptions.recursionPossible? (SubstructMatchOptions attribute) SubstructMatchOptions.specifiedStereoQueryMatchesUnspecified? (SubstructMatchOptions attribute) SubstructMatchOptions.uniquify? (SubstructMatchOptions attribute) SubstructMatchOptions.useChirality? (SubstructMatchOptions attribute) SubstructMatchOptions.useEnhancedStereo? (SubstructMatchOptions attribute) SubstructMatchOptions.useGenericMatchers? (SubstructMatchOptions attribute) SubstructMatchOptions.useQueryQueryMatches? (SubstructMatchOptions attribute) SubstructMatchParams (class in cosmolkit) SubstructMatchParams() (class) SubstructMatchParams.[Symbol․dispose]() (SubstructMatchParams method) SubstructMatchParams.aromaticMatchesConjugated (SubstructMatchParams attribute) SubstructMatchParams.aromaticMatchesSingleOrDouble (SubstructMatchParams attribute) SubstructMatchParams.atomMatch (SubstructMatchParams attribute) SubstructMatchParams.atomProperties (SubstructMatchParams attribute) SubstructMatchParams.bondMatch (SubstructMatchParams attribute) SubstructMatchParams.bondProperties (SubstructMatchParams attribute) SubstructMatchParams.extraAtomCheckOverridesDefaultCheck (SubstructMatchParams attribute) SubstructMatchParams.extraBondCheckOverridesDefaultCheck (SubstructMatchParams attribute) SubstructMatchParams.finalMatch (SubstructMatchParams attribute) SubstructMatchParams.free() (SubstructMatchParams method) SubstructMatchParams.maxMatches (SubstructMatchParams attribute) SubstructMatchParams.maxRecursiveMatches (SubstructMatchParams attribute) SubstructMatchParams.numThreads (SubstructMatchParams attribute) SubstructMatchParams.recursionPossible (SubstructMatchParams attribute) SubstructMatchParams.specifiedStereoQueryMatchesUnspecified (SubstructMatchParams attribute) SubstructMatchParams.uniquify (SubstructMatchParams attribute) SubstructMatchParams.useChirality (SubstructMatchParams attribute) SubstructMatchParams.useEnhancedStereo (SubstructMatchParams attribute) SubstructMatchParams.useGenericMatchers (SubstructMatchParams attribute) SubstructMatchParams.useQueryQueryMatches (SubstructMatchParams attribute) substructure() (cosmolkit.TautomerScore method) SUC (cosmolkit.ResidueCode attribute) success() (cosmolkit.BatchExportReport method) Superatom (cosmolkit.SubstanceGroupKind attribute) support_matrix() (in module cosmolkit) supportMatrix() (built-in function) SupportMatrixEntry (class in cosmolkit) SupportMatrixEntry() (class) SupportMatrixEntry.[Symbol․dispose]() (SupportMatrixEntry method) SupportMatrixEntry.feature (SupportMatrixEntry attribute) SupportMatrixEntry.free() (SupportMatrixEntry method) SupportMatrixEntry.operation (SupportMatrixEntry attribute) surface_area (cosmolkit.BioAssembly attribute) symbol() (cosmolkit.AtomCodeExplanation method) (cosmolkit.Element method) (cosmolkit.ElementInfo method) SYMM_RINGS (cosmolkit.SanitizeOperations attribute) symmetrize_conjugated_terminal_groups (cosmolkit.AllConformerRmsdParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.CoordinateRmsdParameters property) symmetrize_conjugated_terminal_groups_for_pruning (cosmolkit.EmbedParams property) symmetry (cosmolkit.BioMmcifWriteParams property) SymmRings (cosmolkit.SanitizeStage attribute) synchrotron (cosmolkit.BioDiffractionInfo attribute) T t (cosmolkit.BioTlsGroup attribute) TA (cosmolkit.Element attribute) tanimoto() (cosmolkit.Fingerprint method) TAR (cosmolkit.ResidueCode attribute) target() (cosmolkit.SdfPropertyList method) (cosmolkit.TemplateAttachment method) target_density (cosmolkit.TopologicalFingerprintParams property) TAU (cosmolkit.ResidueCode attribute) tautomer_score() (cosmolkit.Molecule method) (cosmolkit.TautomerMoleculeView method) tautomer_score_with_params() (cosmolkit.Molecule method) TautomerCatalogError TautomerCatalogError() (class) TautomerCatalogError.[Symbol․dispose]() (TautomerCatalogError method) TautomerCatalogError.cause (TautomerCatalogError attribute) TautomerCatalogError.domain (TautomerCatalogError attribute) TautomerCatalogError.free() (TautomerCatalogError method) TautomerCatalogError.kind (TautomerCatalogError attribute) TautomerCatalogError.message (TautomerCatalogError attribute) TautomerEnumeration (class in cosmolkit) TautomerEnumeration() (class) TautomerEnumeration.[Symbol․dispose]() (TautomerEnumeration method) TautomerEnumeration.canonicalSmiles() (TautomerEnumeration method) TautomerEnumeration.canonicalTautomer() (TautomerEnumeration method) TautomerEnumeration.canonicalTautomerWithParams() (TautomerEnumeration method) TautomerEnumeration.entries() (TautomerEnumeration method) TautomerEnumeration.free() (TautomerEnumeration method) TautomerEnumeration.get() (TautomerEnumeration method) TautomerEnumeration.isEmpty() (TautomerEnumeration method) TautomerEnumeration.iter() (TautomerEnumeration method) TautomerEnumeration.len() (TautomerEnumeration method) TautomerEnumeration.modifiedAtoms (TautomerEnumeration attribute) TautomerEnumeration.modifiedBonds (TautomerEnumeration attribute) TautomerEnumeration.status (TautomerEnumeration attribute) TautomerEnumerationStatus (class in cosmolkit) (None attribute) TautomerEnumerationStatus.Canceled (TautomerEnumerationStatus attribute) TautomerEnumerationStatus.Completed (TautomerEnumerationStatus attribute) TautomerEnumerationStatus.MaxTautomersReached (TautomerEnumerationStatus attribute) TautomerEnumerationStatus.MaxTransformsReached (TautomerEnumerationStatus attribute) tautomeric (cosmolkit.PatternFingerprintParams property) TautomerMoleculeView (class in cosmolkit) TautomerMoleculeView() (class) TautomerMoleculeView.[Symbol․dispose]() (TautomerMoleculeView method) TautomerMoleculeView.atom() (TautomerMoleculeView method) TautomerMoleculeView.atomDegree() (TautomerMoleculeView method) TautomerMoleculeView.atomMetadata() (TautomerMoleculeView method) TautomerMoleculeView.atoms() (TautomerMoleculeView method) TautomerMoleculeView.bond() (TautomerMoleculeView method) TautomerMoleculeView.bonds() (TautomerMoleculeView method) TautomerMoleculeView.free() (TautomerMoleculeView method) TautomerMoleculeView.numAtoms() (TautomerMoleculeView method) TautomerMoleculeView.numBonds() (TautomerMoleculeView method) TautomerMoleculeView.properties() (TautomerMoleculeView method) TautomerMoleculeView.tautomerScore() (TautomerMoleculeView method) TautomerMoleculeView.toOwned() (TautomerMoleculeView method) TautomerMoleculeView.toSmiles() (TautomerMoleculeView method) TautomerParams (class in cosmolkit) TautomerParams() (class) TautomerParams.[Symbol․dispose]() (TautomerParams method) TautomerParams.callback (TautomerParams attribute) TautomerParams.free() (TautomerParams method) TautomerParams.fromTransformData() (TautomerParams method) TautomerParams.fromTransformFile() (TautomerParams method) TautomerParams.maxTautomers (TautomerParams attribute) TautomerParams.maxTransforms (TautomerParams attribute) TautomerParams.reassignStereo (TautomerParams attribute) TautomerParams.removeBondStereo (TautomerParams attribute) TautomerParams.removeIsotopicHydrogens (TautomerParams attribute) TautomerParams.removeSp3Stereo (TautomerParams attribute) TautomerParams.scoreParams (TautomerParams attribute) TautomerParams.scorer (TautomerParams attribute) TautomerParams.setCallback() (TautomerParams method) TautomerParams.setMaxTautomers() (TautomerParams method) TautomerParams.setMaxTransforms() (TautomerParams method) TautomerParams.setReassignStereo() (TautomerParams method) TautomerParams.setRemoveBondStereo() (TautomerParams method) TautomerParams.setRemoveIsotopicHydrogens() (TautomerParams method) TautomerParams.setRemoveSp3Stereo() (TautomerParams method) TautomerParams.setScorer() (TautomerParams method) TautomerParams.transformCount (TautomerParams attribute) TautomerParams.v1() (TautomerParams method) TautomerParams.withMaxTautomers() (TautomerParams method) TautomerParams.withMaxTransforms() (TautomerParams method) TautomerParams.withReassignStereo() (TautomerParams method) TautomerParams.withRemoveBondStereo() (TautomerParams method) TautomerParams.withRemoveIsotopicHydrogens() (TautomerParams method) TautomerParams.withRemoveSp3Stereo() (TautomerParams method) TautomerParamsOptions() (interface) TautomerParamsOptions.callback? (TautomerParamsOptions attribute) TautomerParamsOptions.maxTautomers? (TautomerParamsOptions attribute) TautomerParamsOptions.maxTransforms? (TautomerParamsOptions attribute) TautomerParamsOptions.reassignStereo? (TautomerParamsOptions attribute) TautomerParamsOptions.removeBondStereo? (TautomerParamsOptions attribute) TautomerParamsOptions.removeIsotopicHydrogens? (TautomerParamsOptions attribute) TautomerParamsOptions.removeSp3Stereo? (TautomerParamsOptions attribute) TautomerParamsOptions.scoreParams? (TautomerParamsOptions attribute) TautomerParamsOptions.scorer? (TautomerParamsOptions attribute) TautomerProgress (class in cosmolkit) TautomerProgress() (class) TautomerProgress.[Symbol․dispose]() (TautomerProgress method) TautomerProgress.entries() (TautomerProgress method) TautomerProgress.free() (TautomerProgress method) TautomerProgress.isEmpty() (TautomerProgress method) TautomerProgress.len() (TautomerProgress method) TautomerProgress.modifiedAtoms (TautomerProgress attribute) TautomerProgress.modifiedBonds (TautomerProgress attribute) TautomerProgress.numTransforms (TautomerProgress attribute) TautomerProgress.status (TautomerProgress attribute) TautomerProgress.toOwned() (TautomerProgress method) TautomerRunError TautomerRunError() (class) TautomerRunError.[Symbol․dispose]() (TautomerRunError method) TautomerRunError.cause (TautomerRunError attribute) TautomerRunError.domain (TautomerRunError attribute) TautomerRunError.free() (TautomerRunError method) TautomerRunError.kind (TautomerRunError attribute) TautomerRunError.message (TautomerRunError attribute) TautomerScore (class in cosmolkit) TautomerScore() (class) TautomerScore.[Symbol․dispose]() (TautomerScore method) TautomerScore.free() (TautomerScore method) TautomerScore.heteroHydrogen (TautomerScore attribute) TautomerScore.ring (TautomerScore attribute) TautomerScore.substructure (TautomerScore attribute) TautomerScore.total (TautomerScore attribute) TautomerScoreParams (class in cosmolkit) TautomerScoreParams() (class) TautomerScoreParams.[Symbol․dispose]() (TautomerScoreParams method) TautomerScoreParams.free() (TautomerScoreParams method) TautomerScoreParams.terms (TautomerScoreParams attribute) TautomerScoreParamsOptions() (interface) TautomerScoreParamsOptions.terms? (TautomerScoreParamsOptions attribute) TautomerScoreTerm (class in cosmolkit) TautomerScoreTerm() (class) TautomerScoreTerm.[Symbol․dispose]() (TautomerScoreTerm method) TautomerScoreTerm.free() (TautomerScoreTerm method) TautomerScoreTerm.name (TautomerScoreTerm attribute) TautomerScoreTerm.score (TautomerScoreTerm attribute) TautomerScoreTerm.smarts (TautomerScoreTerm attribute) TB (cosmolkit.Element attribute) TBU (cosmolkit.ResidueCode attribute) TC (cosmolkit.Element attribute) TE (cosmolkit.Element attribute) temperature (cosmolkit.BioDiffractionInfo attribute) template (cosmolkit.ReactionValidationIssue attribute) template_attachment_order() (cosmolkit.Atom method) TemplateAttachment (class in cosmolkit) TemplateAttachment() (class) TemplateAttachment.[Symbol․dispose]() (TemplateAttachment method) TemplateAttachment.free() (TemplateAttachment method) TemplateAttachment.label() (TemplateAttachment method) TemplateAttachment.target() (TemplateAttachment method) TemplateAttachmentOrder (class in cosmolkit) TemplateAttachmentOrder() (class) TemplateAttachmentOrder.[Symbol․dispose]() (TemplateAttachmentOrder method) TemplateAttachmentOrder.entries() (TemplateAttachmentOrder method) TemplateAttachmentOrder.free() (TemplateAttachmentOrder method) TemplateAttachmentOrderError TemplateAttachmentOrderError() (class) TemplateAttachmentOrderError.[Symbol․dispose]() (TemplateAttachmentOrderError method) TemplateAttachmentOrderError.atomCount (TemplateAttachmentOrderError attribute) TemplateAttachmentOrderError.duplicatePosition (TemplateAttachmentOrderError attribute) TemplateAttachmentOrderError.firstPosition (TemplateAttachmentOrderError attribute) TemplateAttachmentOrderError.free() (TemplateAttachmentOrderError method) TemplateAttachmentOrderError.kind (TemplateAttachmentOrderError attribute) TemplateAttachmentOrderError.label (TemplateAttachmentOrderError attribute) TemplateAttachmentOrderError.mappingLen (TemplateAttachmentOrderError attribute) TemplateAttachmentOrderError.message (TemplateAttachmentOrderError attribute) TemplateAttachmentOrderError.position (TemplateAttachmentOrderError attribute) TemplateAttachmentOrderError.target (TemplateAttachmentOrderError attribute) TEP (cosmolkit.ResidueCode attribute) ter_ignores_type (cosmolkit.BioPdbWriteParams property) ter_records (cosmolkit.BioPdbWriteParams property) ter_status (cosmolkit.BioStructureSourceState attribute) ter_status() (cosmolkit.BioStructure method) terms (cosmolkit.TautomerScoreParams property) TETRAHEDRAL_CLOCKWISE (cosmolkit.PotentialStereoDescriptor attribute) TETRAHEDRAL_COUNTERCLOCKWISE (cosmolkit.PotentialStereoDescriptor attribute) tetrahedral_stereo() (cosmolkit.Molecule method) TetrahedralStereo (class in cosmolkit) TetrahedralStereo() (class) TetrahedralStereo.[Symbol․dispose]() (TetrahedralStereo method) TetrahedralStereo.center (TetrahedralStereo attribute) TetrahedralStereo.free() (TetrahedralStereo method) TetrahedralStereo.ligands (TetrahedralStereo attribute) TFP (cosmolkit.ResidueCode attribute) TH (cosmolkit.Element attribute) THR (cosmolkit.ResidueCode attribute) three_d() (cosmolkit.CxCoordinateSelection static method) (cosmolkit.MolCoordinateSelection static method) (cosmolkit.ReactionCoordinateSelection static method) THREEANDAHALF (cosmolkit.BondOrder attribute) THREECENTER (cosmolkit.BondOrder attribute) ThreeD (cosmolkit.CoordinateDimension attribute) threshold (cosmolkit.McsParameters property) threshold_unmapped_atoms (cosmolkit.ReactionTemplateRemovalParams property) TI (cosmolkit.Element attribute) timeout (cosmolkit.EmbedParams property) (cosmolkit.McsParameters property) title() (cosmolkit.SdfRecord method) (cosmolkit.SdfRecordMetadata method) title_keywords (cosmolkit.BioMmcifWriteParams property) TL (cosmolkit.Element attribute) TLA (cosmolkit.ResidueCode attribute) Tls (cosmolkit.BioMmcifReadStage attribute) tls (cosmolkit.BioMmcifWriteParams property) tls_groups (cosmolkit.BioRefinementInfo attribute) TM (cosmolkit.Element attribute) TMA (cosmolkit.ResidueCode attribute) to_binary() (cosmolkit.Molecule method) to_builder() (cosmolkit.Molecule method) to_cid() (cosmolkit.BioSelection method) to_cx_smarts() (cosmolkit.Molecule method) to_cx_smarts_with_params() (cosmolkit.Molecule method) to_cx_smiles() (cosmolkit.Molecule method) to_cx_smiles_with_params() (cosmolkit.Molecule method) to_cx_smirks() (cosmolkit.Reaction method) to_cx_smirks_with_params() (cosmolkit.Reaction method) to_fragment_cx_smiles() (cosmolkit.Molecule method) to_fragment_cx_smiles_with_params() (cosmolkit.Molecule method) to_fragment_smiles() (cosmolkit.Molecule method) to_fragment_smiles_with_params() (cosmolkit.Molecule method) to_inchi() (cosmolkit.Molecule method) to_inchi_key() (cosmolkit.Molecule method) to_inchi_key_with_params() (cosmolkit.Molecule method) to_inchi_with_params() (cosmolkit.Molecule method) to_json() (cosmolkit.AtomPairAtomInvariantsGenerator method) (cosmolkit.AtomPairParams method) (cosmolkit.EmbedParams method) (cosmolkit.MorganFingerprintGenerator method) (cosmolkit.MorganParams method) (cosmolkit.TopologicalTorsionFingerprintGenerator method) (cosmolkit.TopologicalTorsionParams method) to_list() (cosmolkit.MoleculeBatch method) to_mmcif() (cosmolkit.BioStructure method) to_mmcif_with_params() (cosmolkit.BioStructure method) to_mol() (cosmolkit.Molecule method) (cosmolkit.SdfRecord method) to_mol_with_params() (cosmolkit.Molecule method) (cosmolkit.SdfRecord method) to_molecule() (cosmolkit.BioStructure method) (cosmolkit.Protein method) to_molecule_with_params() (cosmolkit.BioStructure method) (cosmolkit.Protein method) to_numpy() (cosmolkit.Fingerprint method) (cosmolkit.FingerprintBatch method) to_owned() (cosmolkit.TautomerMoleculeView method) (cosmolkit.TautomerProgress method) to_pdb() (cosmolkit.BioStructure method) to_pdb_with_params() (cosmolkit.BioStructure method) to_png() (cosmolkit.Molecule method) to_random_smiles() (cosmolkit.Molecule method) to_random_smiles_with_params() (cosmolkit.Molecule method) to_sdf() (cosmolkit.Molecule method) (cosmolkit.SdfRecord method) to_sdf_2d() (cosmolkit.Molecule method) to_sdf_2d_with_params() (cosmolkit.Molecule method) to_sdf_3d() (cosmolkit.Molecule method) to_sdf_3d_with_params() (cosmolkit.Molecule method) to_sdf_with_params() (cosmolkit.Molecule method) (cosmolkit.SdfRecord method) to_smarts() (cosmolkit.Molecule method) to_smarts_with_params() (cosmolkit.Molecule method) to_smiles() (cosmolkit.Molecule method) (cosmolkit.TautomerMoleculeView method) to_smiles_list() (cosmolkit.MoleculeBatch method) to_smiles_list_with_params() (cosmolkit.MoleculeBatch method) to_smiles_with_params() (cosmolkit.Molecule method) to_smirks() (cosmolkit.Reaction method) to_smirks_with_params() (cosmolkit.Reaction method) to_svg() (cosmolkit.Molecule method) to_svg_list() (cosmolkit.MoleculeBatch method) to_svg_list_with_params() (cosmolkit.MoleculeBatch method) to_xyz() (cosmolkit.Molecule method) to_xyz_with_params() (cosmolkit.Molecule method) Toolkit (cosmolkit.InchiErrorKind attribute) topological_torsion_correction (cosmolkit.AtomPairAtomInvariantsGenerator property) topological_torsion_ids() (cosmolkit.Molecule method) topological_torsion_ids_with_params() (cosmolkit.Molecule method) topological_torsion_path_score() (cosmolkit.Molecule method) TopologicalFingerprintError TopologicalFingerprintError() (class) TopologicalFingerprintError.[Symbol․dispose]() (TopologicalFingerprintError method) TopologicalFingerprintError.cause (TopologicalFingerprintError attribute) TopologicalFingerprintError.domain (TopologicalFingerprintError attribute) TopologicalFingerprintError.field (TopologicalFingerprintError attribute) TopologicalFingerprintError.free() (TopologicalFingerprintError method) TopologicalFingerprintError.kind (TopologicalFingerprintError attribute) TopologicalFingerprintError.message (TopologicalFingerprintError attribute) TopologicalFingerprintError.reason (TopologicalFingerprintError attribute) TopologicalFingerprintOutput (class in cosmolkit) TopologicalFingerprintOutput() (class) TopologicalFingerprintOutput.[Symbol․dispose]() (TopologicalFingerprintOutput method) TopologicalFingerprintOutput.atomBits (TopologicalFingerprintOutput attribute) TopologicalFingerprintOutput.bitInfo (TopologicalFingerprintOutput attribute) TopologicalFingerprintOutput.free() (TopologicalFingerprintOutput method) TopologicalFingerprintOutputRequest (class in cosmolkit) TopologicalFingerprintOutputRequest() (class) TopologicalFingerprintOutputRequest.[Symbol․dispose]() (TopologicalFingerprintOutputRequest method) TopologicalFingerprintOutputRequest.atomBits (TopologicalFingerprintOutputRequest attribute) TopologicalFingerprintOutputRequest.bitInfo (TopologicalFingerprintOutputRequest attribute) TopologicalFingerprintOutputRequest.free() (TopologicalFingerprintOutputRequest method) TopologicalFingerprintOutputRequestOptions() (interface) TopologicalFingerprintOutputRequestOptions.atomBits? (TopologicalFingerprintOutputRequestOptions attribute) TopologicalFingerprintOutputRequestOptions.bitInfo? (TopologicalFingerprintOutputRequestOptions attribute) TopologicalFingerprintParams (class in cosmolkit) TopologicalFingerprintParams() (class) TopologicalFingerprintParams.[Symbol․dispose]() (TopologicalFingerprintParams method) TopologicalFingerprintParams.atomInvariants (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.branchedPaths (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.fpSize (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.free() (TopologicalFingerprintParams method) TopologicalFingerprintParams.fromAtoms (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.maxPath (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.minPath (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.minSize (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.numBitsPerFeature (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.targetDensity (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.useBondOrder (TopologicalFingerprintParams attribute) TopologicalFingerprintParams.useHs (TopologicalFingerprintParams attribute) TopologicalFingerprintParamsOptions() (interface) TopologicalFingerprintParamsOptions.atomInvariants? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.branchedPaths? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.fpSize? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.fromAtoms? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.maxPath? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.minPath? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.minSize? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.numBitsPerFeature? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.targetDensity? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.useBondOrder? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintParamsOptions.useHs? (TopologicalFingerprintParamsOptions attribute) TopologicalFingerprintResult (class in cosmolkit) TopologicalFingerprintResult() (class) TopologicalFingerprintResult.[Symbol․dispose]() (TopologicalFingerprintResult method) TopologicalFingerprintResult.atomBits() (TopologicalFingerprintResult method) TopologicalFingerprintResult.bitInfo() (TopologicalFingerprintResult method) TopologicalFingerprintResult.fingerprint() (TopologicalFingerprintResult method) TopologicalFingerprintResult.free() (TopologicalFingerprintResult method) TopologicalTorsionCallParams (class in cosmolkit) TopologicalTorsionCallParams() (class) TopologicalTorsionCallParams.[Symbol․dispose]() (TopologicalTorsionCallParams method) TopologicalTorsionCallParams.conformerId (TopologicalTorsionCallParams attribute) TopologicalTorsionCallParams.customAtomInvariants (TopologicalTorsionCallParams attribute) TopologicalTorsionCallParams.customBondInvariants (TopologicalTorsionCallParams attribute) TopologicalTorsionCallParams.free() (TopologicalTorsionCallParams method) TopologicalTorsionCallParams.fromAtoms (TopologicalTorsionCallParams attribute) TopologicalTorsionCallParams.ignoreAtoms (TopologicalTorsionCallParams attribute) TopologicalTorsionCallParams.useLegacyStereoPerception (TopologicalTorsionCallParams attribute) TopologicalTorsionCallParamsOptions() (interface) TopologicalTorsionCallParamsOptions.conformerId? (TopologicalTorsionCallParamsOptions attribute) TopologicalTorsionCallParamsOptions.customAtomInvariants? (TopologicalTorsionCallParamsOptions attribute) TopologicalTorsionCallParamsOptions.customBondInvariants? (TopologicalTorsionCallParamsOptions attribute) TopologicalTorsionCallParamsOptions.fromAtoms? (TopologicalTorsionCallParamsOptions attribute) TopologicalTorsionCallParamsOptions.ignoreAtoms? (TopologicalTorsionCallParamsOptions attribute) TopologicalTorsionCallParamsOptions.useLegacyStereoPerception? (TopologicalTorsionCallParamsOptions attribute) TopologicalTorsionFingerprintGenerator (class in cosmolkit) TopologicalTorsionFingerprintGenerator() (class) TopologicalTorsionFingerprintGenerator.[Symbol․dispose]() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.counts() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.fingerprints() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.free() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.fromJson() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.infoString() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.new() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.settings() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.sparseCounts() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.sparseFingerprints() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintGenerator.toJson() (TopologicalTorsionFingerprintGenerator method) TopologicalTorsionFingerprintParams (class in cosmolkit) TopologicalTorsionFingerprintParams() (class) TopologicalTorsionFingerprintParams.[Symbol․dispose]() (TopologicalTorsionFingerprintParams method) TopologicalTorsionFingerprintParams.atomInvariantsGenerator (TopologicalTorsionFingerprintParams attribute) TopologicalTorsionFingerprintParams.conformerId (TopologicalTorsionFingerprintParams attribute) TopologicalTorsionFingerprintParams.customAtomInvariants (TopologicalTorsionFingerprintParams attribute) TopologicalTorsionFingerprintParams.customBondInvariants (TopologicalTorsionFingerprintParams attribute) TopologicalTorsionFingerprintParams.free() (TopologicalTorsionFingerprintParams method) TopologicalTorsionFingerprintParams.fromAtoms (TopologicalTorsionFingerprintParams attribute) TopologicalTorsionFingerprintParams.generator (TopologicalTorsionFingerprintParams attribute) TopologicalTorsionFingerprintParams.ignoreAtoms (TopologicalTorsionFingerprintParams attribute) TopologicalTorsionFingerprintParams.useLegacyStereoPerception (TopologicalTorsionFingerprintParams attribute) TopologicalTorsionFingerprintParamsOptions() (interface) TopologicalTorsionFingerprintParamsOptions.atomInvariantsGenerator? (TopologicalTorsionFingerprintParamsOptions attribute) TopologicalTorsionFingerprintParamsOptions.conformerId? (TopologicalTorsionFingerprintParamsOptions attribute) TopologicalTorsionFingerprintParamsOptions.customAtomInvariants? (TopologicalTorsionFingerprintParamsOptions attribute) TopologicalTorsionFingerprintParamsOptions.customBondInvariants? (TopologicalTorsionFingerprintParamsOptions attribute) TopologicalTorsionFingerprintParamsOptions.fromAtoms? (TopologicalTorsionFingerprintParamsOptions attribute) TopologicalTorsionFingerprintParamsOptions.generator? (TopologicalTorsionFingerprintParamsOptions attribute) TopologicalTorsionFingerprintParamsOptions.ignoreAtoms? (TopologicalTorsionFingerprintParamsOptions attribute) TopologicalTorsionFingerprintParamsOptions.useLegacyStereoPerception? (TopologicalTorsionFingerprintParamsOptions attribute) TopologicalTorsionParams (class in cosmolkit) TopologicalTorsionParams() (class) TopologicalTorsionParams.[Symbol․dispose]() (TopologicalTorsionParams method) TopologicalTorsionParams.bitsPerFeature (TopologicalTorsionParams attribute) TopologicalTorsionParams.countBounds (TopologicalTorsionParams attribute) TopologicalTorsionParams.countSimulation (TopologicalTorsionParams attribute) TopologicalTorsionParams.fpSize (TopologicalTorsionParams attribute) TopologicalTorsionParams.free() (TopologicalTorsionParams method) TopologicalTorsionParams.includeChirality (TopologicalTorsionParams attribute) TopologicalTorsionParams.infoString() (TopologicalTorsionParams method) TopologicalTorsionParams.onlyShortestPaths (TopologicalTorsionParams attribute) TopologicalTorsionParams.toJson() (TopologicalTorsionParams method) TopologicalTorsionParams.torsionAtomCount (TopologicalTorsionParams attribute) TopologicalTorsionParams.withJson() (TopologicalTorsionParams method) TopologicalTorsionParamsOptions() (interface) TopologicalTorsionParamsOptions.bitsPerFeature? (TopologicalTorsionParamsOptions attribute) TopologicalTorsionParamsOptions.countBounds? (TopologicalTorsionParamsOptions attribute) TopologicalTorsionParamsOptions.countSimulation? (TopologicalTorsionParamsOptions attribute) TopologicalTorsionParamsOptions.fpSize? (TopologicalTorsionParamsOptions attribute) TopologicalTorsionParamsOptions.includeChirality? (TopologicalTorsionParamsOptions attribute) TopologicalTorsionParamsOptions.onlyShortestPaths? (TopologicalTorsionParamsOptions attribute) TopologicalTorsionParamsOptions.torsionAtomCount? (TopologicalTorsionParamsOptions attribute) TopologicalTorsionPathScoreError TopologicalTorsionPathScoreError() (class) TopologicalTorsionPathScoreError.[Symbol․dispose]() (TopologicalTorsionPathScoreError method) TopologicalTorsionPathScoreError.actual (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.atomCount (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.cause (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.code (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.domain (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.free() (TopologicalTorsionPathScoreError method) TopologicalTorsionPathScoreError.index (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.kind (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.message (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.required (TopologicalTorsionPathScoreError attribute) TopologicalTorsionPathScoreError.subtract (TopologicalTorsionPathScoreError attribute) TopologicalTorsionReadError TopologicalTorsionReadError() (class) TopologicalTorsionReadError.[Symbol․dispose]() (TopologicalTorsionReadError method) TopologicalTorsionReadError.cause (TopologicalTorsionReadError attribute) TopologicalTorsionReadError.domain (TopologicalTorsionReadError attribute) TopologicalTorsionReadError.free() (TopologicalTorsionReadError method) TopologicalTorsionReadError.kind (TopologicalTorsionReadError attribute) TopologicalTorsionReadError.message (TopologicalTorsionReadError attribute) TopologicalTorsionSettings (class in cosmolkit) TopologicalTorsionSettings() (class) TopologicalTorsionSettings.[Symbol․dispose]() (TopologicalTorsionSettings method) TopologicalTorsionSettings.bitsPerFeature (TopologicalTorsionSettings attribute) TopologicalTorsionSettings.countBounds (TopologicalTorsionSettings attribute) TopologicalTorsionSettings.countSimulation (TopologicalTorsionSettings attribute) TopologicalTorsionSettings.fpSize (TopologicalTorsionSettings attribute) TopologicalTorsionSettings.free() (TopologicalTorsionSettings method) TopologicalTorsionSettings.includeChirality (TopologicalTorsionSettings attribute) TopologicalTorsionSettings.onlyShortestPaths (TopologicalTorsionSettings attribute) TopologicalTorsionSettings.params() (TopologicalTorsionSettings method) TopologicalTorsionSettings.setBitsPerFeature() (TopologicalTorsionSettings method) TopologicalTorsionSettings.setCountBounds() (TopologicalTorsionSettings method) TopologicalTorsionSettings.setCountSimulation() (TopologicalTorsionSettings method) TopologicalTorsionSettings.setFpSize() (TopologicalTorsionSettings method) TopologicalTorsionSettings.setIncludeChirality() (TopologicalTorsionSettings method) TopologicalTorsionSettings.setOnlyShortestPaths() (TopologicalTorsionSettings method) TopologicalTorsionSettings.setTorsionAtomCount() (TopologicalTorsionSettings method) TopologicalTorsionSettings.torsionAtomCount (TopologicalTorsionSettings attribute) topology() (cosmolkit.Molecule method) topology_edit (cosmolkit.MoleculeOpSpec attribute) TopologyBlock (class in cosmolkit) TopologyBlock() (class) TopologyBlock.[Symbol․dispose]() (TopologyBlock method) TopologyBlock.atoms (TopologyBlock attribute) TopologyBlock.bonds (TopologyBlock attribute) TopologyBlock.free() (TopologyBlock method) TopologyBlock.stereoGroups (TopologyBlock attribute) TopologyBlock.substanceGroups (TopologyBlock attribute) torsion_atom_count (cosmolkit.LegacyTopologicalTorsionParams property) (cosmolkit.TopologicalTorsionParams property) (cosmolkit.TopologicalTorsionSettings attribute) total() (cosmolkit.BatchExportReport method) (cosmolkit.TautomerScore method) total_atom_count() (cosmolkit.Molecule method) total_hydrogens() (cosmolkit.Atom method) (cosmolkit.AtomMetadata method) total_valence() (cosmolkit.Atom method) (cosmolkit.AtomMetadata method) total_value() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) TOX (cosmolkit.ResidueCode attribute) TPO (cosmolkit.ResidueCode attribute) TPQ (cosmolkit.ResidueCode attribute) tpsa() (cosmolkit.Molecule method) tpsa_with_params() (cosmolkit.Molecule method) track_failures (cosmolkit.EmbedParams property) transform (cosmolkit.BioAssemblyOperator attribute) (cosmolkit.BioNcsOperator attribute) transform() (cosmolkit.AlignmentResult method) transform_count() (cosmolkit.TautomerParams method) TransformError TransformError() (class) TransformError.[Symbol․dispose]() (TransformError method) TransformError.cause (TransformError attribute) TransformError.domain (TransformError attribute) TransformError.free() (TransformError method) TransformError.kind (TransformError attribute) TransformError.message (TransformError attribute) translate_() (cosmolkit.BioStructure method) (cosmolkit.Protein method) translation (cosmolkit.BioTransform attribute) TRE (cosmolkit.ResidueCode attribute) TRIPLE (cosmolkit.BondOrder attribute) TRP (cosmolkit.ResidueCode attribute) TRQ (cosmolkit.ResidueCode attribute) TRS (cosmolkit.ResidueCode attribute) TRT (cosmolkit.ResidueCode attribute) try_embedding (cosmolkit.StereoisomerOptions property) TS (cosmolkit.Element attribute) two_d() (cosmolkit.CxCoordinateSelection static method) (cosmolkit.MolCoordinateSelection static method) (cosmolkit.ReactionCoordinateSelection static method) TWOANDAHALF (cosmolkit.BondOrder attribute) TwoD (cosmolkit.CoordinateDimension attribute) Typing (cosmolkit.UffParameterErrorKind attribute) TYR (cosmolkit.ResidueCode attribute) TYS (cosmolkit.ResidueCode attribute) U U (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) uff_energy_gradient() (cosmolkit.Molecule method) uff_energy_gradient_with_params() (cosmolkit.Molecule method) uff_force_field() (cosmolkit.Molecule method) uff_force_field_with_params() (cosmolkit.Molecule method) uff_has_all_molecule_params() (cosmolkit.Molecule method) UffConformerOptimizationParams (class in cosmolkit) UffConformerOptimizationParams() (class) UffConformerOptimizationParams.[Symbol․dispose]() (UffConformerOptimizationParams method) UffConformerOptimizationParams.free() (UffConformerOptimizationParams method) UffConformerOptimizationParams.ignoreInterfragmentInteractions (UffConformerOptimizationParams attribute) UffConformerOptimizationParams.maxIterations (UffConformerOptimizationParams attribute) UffConformerOptimizationParams.numThreads (UffConformerOptimizationParams attribute) UffConformerOptimizationParams.vdwThreshold (UffConformerOptimizationParams attribute) UffConformerOptimizationParamsOptions() (interface) UffConformerOptimizationParamsOptions.ignoreInterfragmentInteractions? (UffConformerOptimizationParamsOptions attribute) UffConformerOptimizationParamsOptions.maxIterations? (UffConformerOptimizationParamsOptions attribute) UffConformerOptimizationParamsOptions.numThreads? (UffConformerOptimizationParamsOptions attribute) UffConformerOptimizationParamsOptions.vdwThreshold? (UffConformerOptimizationParamsOptions attribute) UffConformerOptimizationResult (class in cosmolkit) UffConformerOptimizationResult() (class) UffConformerOptimizationResult.[Symbol․dispose]() (UffConformerOptimizationResult method) UffConformerOptimizationResult.conformerResults() (UffConformerOptimizationResult method) UffConformerOptimizationResult.free() (UffConformerOptimizationResult method) UffConformerOptimizationResult.molecule() (UffConformerOptimizationResult method) UffConformerResult (class in cosmolkit) UffConformerResult() (class) UffConformerResult.[Symbol․dispose]() (UffConformerResult method) UffConformerResult.conformerId() (UffConformerResult method) UffConformerResult.energy() (UffConformerResult method) UffConformerResult.free() (UffConformerResult method) UffConformerResult.needsMore() (UffConformerResult method) UffConformerResult.statusCode() (UffConformerResult method) UffEnergyGradient (class in cosmolkit) UffEnergyGradient() (class) UffEnergyGradient.[Symbol․dispose]() (UffEnergyGradient method) UffEnergyGradient.energy() (UffEnergyGradient method) UffEnergyGradient.free() (UffEnergyGradient method) UffEnergyGradient.gradient() (UffEnergyGradient method) UffEvaluationParams (class in cosmolkit) UffEvaluationParams() (class) UffEvaluationParams.[Symbol․dispose]() (UffEvaluationParams method) UffEvaluationParams.conformerId (UffEvaluationParams attribute) UffEvaluationParams.free() (UffEvaluationParams method) UffEvaluationParams.ignoreInterfragmentInteractions (UffEvaluationParams attribute) UffEvaluationParams.vdwThreshold (UffEvaluationParams attribute) UffEvaluationParamsOptions() (interface) UffEvaluationParamsOptions.conformerId? (UffEvaluationParamsOptions attribute) UffEvaluationParamsOptions.ignoreInterfragmentInteractions? (UffEvaluationParamsOptions attribute) UffEvaluationParamsOptions.vdwThreshold? (UffEvaluationParamsOptions attribute) UffForceFieldError UffForceFieldError() (class) UffForceFieldError.[Symbol․dispose]() (UffForceFieldError method) UffForceFieldError.cause (UffForceFieldError attribute) UffForceFieldError.free() (UffForceFieldError method) UffForceFieldError.kind() (UffForceFieldError method) UffForceFieldError.message (UffForceFieldError attribute) UffForceFieldError.requested() (UffForceFieldError method) UffForceFieldParams (class in cosmolkit) UffForceFieldParams() (class) UffForceFieldParams.[Symbol․dispose]() (UffForceFieldParams method) UffForceFieldParams.conformerId (UffForceFieldParams attribute) UffForceFieldParams.free() (UffForceFieldParams method) UffForceFieldParams.ignoreInterfragmentInteractions (UffForceFieldParams attribute) UffForceFieldParams.vdwThreshold (UffForceFieldParams attribute) UffForceFieldParamsOptions() (interface) UffForceFieldParamsOptions.conformerId? (UffForceFieldParamsOptions attribute) UffForceFieldParamsOptions.ignoreInterfragmentInteractions? (UffForceFieldParamsOptions attribute) UffForceFieldParamsOptions.vdwThreshold? (UffForceFieldParamsOptions attribute) UffOptimizationError UffOptimizationError() (class) UffOptimizationError.[Symbol․dispose]() (UffOptimizationError method) UffOptimizationError.cause (UffOptimizationError attribute) UffOptimizationError.free() (UffOptimizationError method) UffOptimizationError.kind() (UffOptimizationError method) UffOptimizationError.message (UffOptimizationError attribute) UffOptimizationErrorKind (class in cosmolkit) UffOptimizationErrorKind() (class) UffOptimizationErrorKind.[Symbol․dispose]() (UffOptimizationErrorKind method) UffOptimizationErrorKind.equals() (UffOptimizationErrorKind method) UffOptimizationErrorKind.free() (UffOptimizationErrorKind method) UffOptimizationErrorKind.requested (UffOptimizationErrorKind attribute) UffOptimizationErrorKind.variant (UffOptimizationErrorKind attribute) UffOptimizationParams (class in cosmolkit) UffOptimizationParams() (class) UffOptimizationParams.[Symbol․dispose]() (UffOptimizationParams method) UffOptimizationParams.conformerId (UffOptimizationParams attribute) UffOptimizationParams.free() (UffOptimizationParams method) UffOptimizationParams.ignoreInterfragmentInteractions (UffOptimizationParams attribute) UffOptimizationParams.maxIterations (UffOptimizationParams attribute) UffOptimizationParams.vdwThreshold (UffOptimizationParams attribute) UffOptimizationParamsOptions() (interface) UffOptimizationParamsOptions.conformerId? (UffOptimizationParamsOptions attribute) UffOptimizationParamsOptions.ignoreInterfragmentInteractions? (UffOptimizationParamsOptions attribute) UffOptimizationParamsOptions.maxIterations? (UffOptimizationParamsOptions attribute) UffOptimizationParamsOptions.vdwThreshold? (UffOptimizationParamsOptions attribute) UffOptimizationResult (class in cosmolkit) UffOptimizationResult() (class) UffOptimizationResult.[Symbol․dispose]() (UffOptimizationResult method) UffOptimizationResult.energy() (UffOptimizationResult method) UffOptimizationResult.free() (UffOptimizationResult method) UffOptimizationResult.molecule() (UffOptimizationResult method) UffOptimizationResult.needsMore() (UffOptimizationResult method) UffOptimizationResult.statusCode() (UffOptimizationResult method) UffParameterError UffParameterError() (class) UffParameterError.[Symbol․dispose]() (UffParameterError method) UffParameterError.cause (UffParameterError attribute) UffParameterError.free() (UffParameterError method) UffParameterError.kind() (UffParameterError method) UffParameterError.message (UffParameterError attribute) UffParameterErrorKind (class in cosmolkit) (None attribute) UffParameterErrorKind.ParameterTable (UffParameterErrorKind attribute) UffParameterErrorKind.Preparation (UffParameterErrorKind attribute) UffParameterErrorKind.Typing (UffParameterErrorKind attribute) UffParameterQueryError UffParameterQueryError() (class) UffParameterQueryError.[Symbol․dispose]() (UffParameterQueryError method) UffParameterQueryError.cause (UffParameterQueryError attribute) UffParameterQueryError.domain (UffParameterQueryError attribute) UffParameterQueryError.free() (UffParameterQueryError method) UffParameterQueryError.kind (UffParameterQueryError attribute) UffParameterQueryError.message (UffParameterQueryError attribute) UInt (cosmolkit.PropertyValueKind attribute) UMQ (cosmolkit.ResidueCode attribute) unique (cosmolkit.StereoisomerOptions property) unique_reflections (cosmolkit.BioExperimentInfo attribute) uniquify (cosmolkit.SubstructMatchParams property) UNK (cosmolkit.ResidueCode attribute) Unknown (cosmolkit.BioConnectionKind attribute) (cosmolkit.BioCoordinateFormat attribute) UNKNOWN (cosmolkit.BondDirection attribute) Unknown (cosmolkit.ChainKind attribute) (cosmolkit.EntityKind attribute) (cosmolkit.PolymerKind attribute) UNKNOWN (cosmolkit.PotentialStereoSpecified attribute) (cosmolkit.ResidueCode attribute) (cosmolkit.ResidueInfoKind attribute) Unknown (cosmolkit.ResidueKind attribute) UnknownHelix (cosmolkit.BioHelixClass attribute) UnmappedProduct (cosmolkit.ReactionValidationIssueKind attribute) UnmappedReactant (cosmolkit.ReactionValidationIssueKind attribute) UnmappedReactantMaps (cosmolkit.ReactionValidationIssueKind attribute) Unspecified (cosmolkit.BioSoftwareClassification attribute) UNSPECIFIED (cosmolkit.BondOrder attribute) (cosmolkit.Hybridization attribute) (cosmolkit.PotentialStereoSpecified attribute) UnsupportedState (cosmolkit.InchiErrorKind attribute) update_explicit_count (cosmolkit.RemoveHsParams property) UR3 (cosmolkit.ResidueCode attribute) URE (cosmolkit.ResidueCode attribute) use_2d (cosmolkit.AtomPairParams property) use_atom_weights (cosmolkit.DistanceMatrix3dParams property) (cosmolkit.DistanceMatrixParams property) use_basic_knowledge (cosmolkit.EmbedParams property) use_bond_order (cosmolkit.DistanceMatrixParams property) (cosmolkit.TopologicalFingerprintParams property) use_bond_types (cosmolkit.MorganBondInvariantsGenerator property) (cosmolkit.MorganParams property) use_chirality (cosmolkit.SubstructMatchParams property) use_enhanced_stereo (cosmolkit.SubstructMatchParams property) use_exp_torsion_angle_prefs (cosmolkit.EmbedParams property) use_generic_matchers (cosmolkit.SubstructMatchParams property) use_hs (cosmolkit.TopologicalFingerprintParams property) use_legacy_stereo_perception (cosmolkit.AtomPairFingerprintParams property) (cosmolkit.TopologicalTorsionCallParams property) (cosmolkit.TopologicalTorsionFingerprintParams property) use_macrocycle14config (cosmolkit.EmbedParams property) use_macrocycle_torsions (cosmolkit.EmbedParams property) use_query_query_matches (cosmolkit.SubstructMatchParams property) use_random_coords (cosmolkit.EmbedParams property) use_ring_templates (cosmolkit.Coordinate2DParams property) use_small_ring_torsions (cosmolkit.EmbedParams property) use_smiles (cosmolkit.ReactionParseParams property) use_symmetry_for_pruning (cosmolkit.EmbedParams property) V V (cosmolkit.Element attribute) v1() (cosmolkit.TautomerParams static method) V2000 (cosmolkit.SdfFormat attribute) V3000 (cosmolkit.SdfFormat attribute) VAL (cosmolkit.ResidueCode attribute) ValenceError ValenceError() (class) ValenceError.[Symbol․dispose]() (ValenceError method) ValenceError.atom (ValenceError attribute) ValenceError.atomCount (ValenceError attribute) ValenceError.atomicNumber (ValenceError attribute) ValenceError.begin (ValenceError attribute) ValenceError.bond (ValenceError attribute) ValenceError.bondCount (ValenceError attribute) ValenceError.calculated (ValenceError attribute) ValenceError.cause (ValenceError attribute) ValenceError.domain (ValenceError attribute) ValenceError.end (ValenceError attribute) ValenceError.explicit (ValenceError attribute) ValenceError.explicitValence (ValenceError attribute) ValenceError.field (ValenceError attribute) ValenceError.formalCharge (ValenceError attribute) ValenceError.free() (ValenceError method) ValenceError.implicit (ValenceError attribute) ValenceError.kind (ValenceError attribute) ValenceError.message (ValenceError attribute) ValenceError.neighborAtom (ValenceError attribute) ValenceError.neighborHydrogens (ValenceError attribute) ValenceError.order (ValenceError attribute) ValenceError.phase (ValenceError attribute) ValenceError.physicalBonds (ValenceError attribute) ValenceError.reason (ValenceError attribute) ValenceError.value (ValenceError attribute) ValenceModel (class in cosmolkit) (None attribute) ValenceModel.RdkitLike (ValenceModel attribute) ValenceParams (class in cosmolkit) ValenceParams() (class) ValenceParams.[Symbol․dispose]() (ValenceParams method) ValenceParams.free() (ValenceParams method) ValenceParams.model (ValenceParams attribute) ValenceParams.strict (ValenceParams attribute) ValenceParamsOptions() (interface) ValenceParamsOptions.model? (ValenceParamsOptions attribute) ValenceParamsOptions.strict? (ValenceParamsOptions attribute) valences() (cosmolkit.ElementInfo method) valid_count() (cosmolkit.MoleculeBatch method) valid_mask() (cosmolkit.MoleculeBatch method) validate() (cosmolkit.BioStructure method) (cosmolkit.Reaction method) validate_parts() (cosmolkit.BioStructure static method) validate_with_params() (cosmolkit.Reaction method) value() (cosmolkit.AltLocLabel method) (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) values() (cosmolkit.DenseMatrix method) (cosmolkit.SdfPropertyList method) variant (cosmolkit.Mol2ReadParams property) (cosmolkit.UffOptimizationErrorKind attribute) variant() (cosmolkit.MmffProperties method) vdw_threshold (cosmolkit.UffConformerOptimizationParams property) (cosmolkit.UffEvaluationParams property) (cosmolkit.UffForceFieldParams property) (cosmolkit.UffOptimizationParams property) vector() (cosmolkit.SGroupCState method) verbose (cosmolkit.EmbedParams property) (cosmolkit.McsParameters property) version (cosmolkit.BioSoftwareItem attribute) version() (built-in function) (cosmolkit.AtomPairsParameters static method) (in module cosmolkit) W W (cosmolkit.Element attribute) Warning (cosmolkit.ReactionValidationSeverity attribute) warnings (cosmolkit.ReactionValidationReport attribute) wasm_wasm.d (module) Water (cosmolkit.EntityKind attribute) (cosmolkit.ResidueKind attribute) WaterOnly (cosmolkit.ChainKind attribute) wavelengths (cosmolkit.BioDiffractionInfo attribute) weight (cosmolkit.BioRefinementRestraint attribute) weight() (cosmolkit.ResidueInfo method) weights (cosmolkit.AlignmentParameters property) (cosmolkit.AllConformerRmsdParameters property) (cosmolkit.BestAlignmentParameters property) (cosmolkit.ConformerAlignmentParameters property) (cosmolkit.CoordinateRmsdParameters property) width (cosmolkit.BatchImageParams property) with_2d_coordinate_block() (cosmolkit.Molecule method) with_2d_coordinate_block_with_params() (cosmolkit.Molecule method) with_2d_coordinates() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_2d_coordinates_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_3d_conformer() (cosmolkit.Molecule method) with_3d_conformer_result() (cosmolkit.Molecule method) with_3d_conformer_result_with_params() (cosmolkit.Molecule method) with_3d_conformer_with_params() (cosmolkit.Molecule method) with_3d_conformers() (cosmolkit.Molecule method) with_3d_conformers_result() (cosmolkit.Molecule method) with_3d_conformers_result_with_params() (cosmolkit.Molecule method) with_3d_conformers_with_params() (cosmolkit.Molecule method) with_3d_coordinates() (cosmolkit.Molecule method) with_3d_coordinates_with_params() (cosmolkit.Molecule method) with_added() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_added_3d_conformer() (cosmolkit.Molecule method) with_added_3d_conformer_with_params() (cosmolkit.Molecule method) with_added_scalar() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_agent_template() (cosmolkit.Reaction method) with_aligned_conformers() (cosmolkit.Molecule method) with_aligned_conformers_with_params() (cosmolkit.Molecule method) with_alignment_to() (cosmolkit.Molecule method) with_alignment_to_with_params() (cosmolkit.Molecule method) with_assigned_aromaticity() (cosmolkit.Molecule method) with_assigned_aromaticity_with_params() (cosmolkit.Molecule method) with_assigned_radicals() (cosmolkit.Molecule method) with_assigned_ring_families() (cosmolkit.Molecule method) with_assigned_ring_families_with_params() (cosmolkit.Molecule method) with_assigned_rings() (cosmolkit.Molecule method) with_assigned_valence() (cosmolkit.Molecule method) with_assigned_valence_with_params() (cosmolkit.Molecule method) with_atom_map() (cosmolkit.AtomSpec method) with_atom_pair_atom_code() (cosmolkit.Molecule method) with_atom_position() (cosmolkit.Molecule method) with_atom_position_with_params() (cosmolkit.Molecule method) with_atom_property() (cosmolkit.Molecule method) with_chiral_tags_from_structure() (cosmolkit.Molecule method) with_chiral_tags_from_structure_with_params() (cosmolkit.Molecule method) with_cip_labels() (cosmolkit.Molecule method) with_cip_labels_with_options() (cosmolkit.Molecule method) with_cleared_3d_conformers() (cosmolkit.Molecule method) with_divided_scalar() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_explicit_hydrogens() (cosmolkit.AtomSpec method) with_formal_charge() (cosmolkit.AtomSpec method) with_hydrogens() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_hydrogens_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_implicit_properties() (cosmolkit.Reaction method) with_initialized() (cosmolkit.Reaction method) with_initialized_with_params() (cosmolkit.Reaction method) with_isotope() (cosmolkit.AtomSpec method) with_json() (cosmolkit.AtomPairParams method) (cosmolkit.EmbedParams method) (cosmolkit.MorganParams method) (cosmolkit.TopologicalTorsionParams method) with_kekulized_bonds() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_kekulized_bonds_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) with_match_params() (cosmolkit.Reaction method) with_max_tautomers() (cosmolkit.TautomerParams method) with_max_transforms() (cosmolkit.TautomerParams method) with_mmff_optimized() (cosmolkit.Molecule method) with_mmff_optimized_conformers() (cosmolkit.Molecule method) with_mmff_optimized_conformers_with_params() (cosmolkit.Molecule method) with_mmff_optimized_with_params() (cosmolkit.Molecule method) with_multiplied_scalar() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_name() (cosmolkit.MoleculeBuilder method) with_no_implicit() (cosmolkit.AtomSpec method) with_only_3d_conformer() (cosmolkit.Molecule method) with_only_3d_conformer_with_params() (cosmolkit.Molecule method) with_parallel_jobs() (cosmolkit.MoleculeBatch method) with_product_template() (cosmolkit.Reaction method) with_progress_bar() (cosmolkit.MoleculeBatch method) with_properties() (cosmolkit.MoleculeBuilder method) with_property() (cosmolkit.MoleculeBuilder method) with_reactant_template() (cosmolkit.Reaction method) with_reassign_stereo() (cosmolkit.TautomerParams method) with_remove_bond_stereo() (cosmolkit.TautomerParams method) with_remove_isotopic_hydrogens() (cosmolkit.TautomerParams method) with_remove_sp3_stereo() (cosmolkit.TautomerParams method) with_sdf_data_field() (cosmolkit.MoleculeBuilder method) with_selection() (cosmolkit.BioStructure method) (cosmolkit.Protein method) with_subtracted() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_subtracted_scalar() (cosmolkit.SparseCountFingerprint method) (cosmolkit.SparseCountFingerprint32 method) with_translated_coordinates() (cosmolkit.BioStructure method) (cosmolkit.Protein method) with_uff_optimized() (cosmolkit.Molecule method) with_uff_optimized_conformers() (cosmolkit.Molecule method) with_uff_optimized_conformers_with_params() (cosmolkit.Molecule method) with_uff_optimized_with_params() (cosmolkit.Molecule method) with_valid_records() (cosmolkit.MoleculeBatch method) without_agents() (cosmolkit.Reaction method) without_hydrogens() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) without_hydrogens_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) without_unmapped_products() (cosmolkit.Reaction method) without_unmapped_products_with_params() (cosmolkit.Reaction method) without_unmapped_reactants() (cosmolkit.Reaction method) without_unmapped_reactants_with_params() (cosmolkit.Reaction method) work_set_count (cosmolkit.BioBasicRefinementInfo attribute) write_cx_smarts() (in module cosmolkit) write_images() (cosmolkit.MoleculeBatch method) write_images_with_params() (cosmolkit.MoleculeBatch method) write_mmcif() (cosmolkit.BioStructure method) write_mmcif_with_params() (cosmolkit.BioStructure method) write_mol() (cosmolkit.Molecule method) write_mol_with_params() (cosmolkit.Molecule method) write_pdb() (cosmolkit.BioStructure method) write_pdb_with_params() (cosmolkit.BioStructure method) write_png() (cosmolkit.Molecule method) write_report() (cosmolkit.BatchExportReport method) write_sdf() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_sdf_files() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_sdf_files_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_sdf_with_params() (cosmolkit.Molecule method) (cosmolkit.MoleculeBatch method) write_smarts() (in module cosmolkit) write_svg() (cosmolkit.Molecule method) write_xyz() (cosmolkit.Molecule method) write_xyz_with_params() (cosmolkit.Molecule method) writeCxSmarts() (built-in function) writeSmarts() (built-in function) X XE (cosmolkit.Element attribute) XPE (cosmolkit.ResidueCode attribute) XYP (cosmolkit.ResidueCode attribute) XyzReadError XyzReadError() (class) XyzReadError.[Symbol․dispose]() (XyzReadError method) XyzReadError.cause (XyzReadError attribute) XyzReadError.domain (XyzReadError attribute) XyzReadError.free() (XyzReadError method) XyzReadError.kind (XyzReadError attribute) XyzReadError.line (XyzReadError attribute) XyzReadError.message (XyzReadError attribute) XyzReadError.value (XyzReadError attribute) XyzWriteError XyzWriteError() (class) XyzWriteError.[Symbol․dispose]() (XyzWriteError method) XyzWriteError.cause (XyzWriteError attribute) XyzWriteError.domain (XyzWriteError attribute) XyzWriteError.free() (XyzWriteError method) XyzWriteError.id (XyzWriteError attribute) XyzWriteError.kind (XyzWriteError attribute) XyzWriteError.message (XyzWriteError attribute) XyzWriteParams (class in cosmolkit) XyzWriteParams() (class) XyzWriteParams.[Symbol․dispose]() (XyzWriteParams method) XyzWriteParams.conformerId (XyzWriteParams attribute) XyzWriteParams.free() (XyzWriteParams method) XyzWriteParams.precision (XyzWriteParams attribute) XyzWriteParamsOptions() (interface) XyzWriteParamsOptions.conformerId? (XyzWriteParamsOptions attribute) XyzWriteParamsOptions.precision? (XyzWriteParamsOptions attribute) Y Y (cosmolkit.Element attribute) Y1 (cosmolkit.ResidueCode attribute) YB (cosmolkit.Element attribute) YCM (cosmolkit.ResidueCode attribute) yielded_count (cosmolkit.StereoisomerIterator attribute) YT3 (cosmolkit.ResidueCode attribute) Z Z (cosmolkit.CipDescriptor attribute) z (cosmolkit.CipDescriptor attribute) z_policy (cosmolkit.Coordinate2DInputParams property) ZERO (cosmolkit.BondOrder attribute) ZERO_BONDS (cosmolkit.CxSmilesFields attribute) ZN (cosmolkit.Element attribute) (cosmolkit.ResidueCode attribute) ZN2 (cosmolkit.ResidueCode attribute) ZR (cosmolkit.Element attribute)