Index

A

add() (moleculekit.representations.Representations method) add_lalr_lookaheads() (moleculekit.ply.yacc.LRTable method) add_lookaheads() (moleculekit.ply.yacc.LRTable method) add_production() (moleculekit.ply.yacc.Grammar method) addBond() (moleculekit.molecule.Molecule method) addHs() (moleculekit.smallmol.smallmol.SmallMol method) align() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) align_to_opm() (in module moleculekit.opm) alignBySequence() (moleculekit.molecule.Molecule method) ALPHAFOLDread() (in module moleculekit.readers) altloc (moleculekit.molecule.Molecule attribute) analyze() (in module moleculekit.atomselect.analyze) analyze_molecule() (in module moleculekit.atomselect_utils) anchor_atom (moleculekit.tools.nonstandard_residues.ChainResidueSpec attribute) angles (moleculekit.molecule.Molecule attribute) append() (moleculekit.molecule.Molecule method) (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) (moleculekit.representations.Representations method)

appendAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) appendAttributeExtendRows() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) appendFrames() (moleculekit.molecule.Molecule method) appendSmallLib() (moleculekit.smallmol.smallmollib.SmallMolLib method) appendSmallMol() (moleculekit.smallmol.smallmollib.SmallMolLib method) areLigandsDocked() (in module moleculekit.tools.moleculechecks) areLigandsOptimized() (in module moleculekit.tools.moleculechecks) assertSameAsReferenceDir() (in module moleculekit.util) assignStereoChemistry() (moleculekit.smallmol.smallmol.SmallMol method) assignValue() (moleculekit.fileformats.netcdf.netcdf_variable method) atominfo (moleculekit.readers.Topology property) AtomNotFoundException atomselect() (in module moleculekit.atomselect.atomselect) (moleculekit.molecule.Molecule method) atomtype (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) atomtypingValidityChecks() (in module moleculekit.tools.atomtyper) attributePart() (moleculekit.pdbx.reader.PdbxContainers.CifName static method) autoSegment() (in module moleculekit.tools.autosegment) autoSegment2() (in module moleculekit.tools.autosegment)

B

bCifCodeTypeD (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders attribute) BCIFread() (in module moleculekit.readers) bCifTypeD (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders attribute) BCIFwrite() (in module moleculekit.writers) begin() (moleculekit.ply.lex.Lexer method) beta (moleculekit.molecule.Molecule attribute) BinaryCifDecoders (class in moleculekit.pdbx.reader.BinaryCifReader) BinaryCifEncoders (class in moleculekit.pdbx.writer.BinaryCifWriter) BinaryCifReader (class in moleculekit.pdbx.reader.BinaryCifReader) BinaryCifWriter (class in moleculekit.pdbx.writer.BinaryCifWriter) BINCOORread() (in module moleculekit.readers) BINCOORwrite() (in module moleculekit.writers) bind() (moleculekit.ply.yacc.Production method) bind_callables() (moleculekit.ply.yacc.LRTable method) BINPOSread() (in module moleculekit.readers) BINPOSTrajectoryFile (class in moleculekit.binpos)

BINPOSwrite() (in module moleculekit.writers) blast_search_opm() (in module moleculekit.opm) bond_grid_search() (in module moleculekit.bondguesser) bonds (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) bondtype (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) boundingBox() (in module moleculekit.util) box (moleculekit.molecule.Molecule attribute) box_vectors_to_lengths_and_angles() (in module moleculekit.unitcell) boxangles (moleculekit.molecule.Molecule attribute) boxsize (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree attribute) boxvectors (moleculekit.molecule.Molecule property) build_lritems() (moleculekit.ply.yacc.Grammar method) byteArrayDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) byteArrayEncoderTyped() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method)

C

calculate() (in module moleculekit.interactions.cationpi) (in module moleculekit.interactions.hbonds) (in module moleculekit.interactions.pipi) (in module moleculekit.interactions.sigmahole) calculate_contacts() (in module moleculekit.distance) calculate_occupancy() (in module moleculekit.occupancy_utils) calculateAnglesAndDihedrals() (in module moleculekit.cython_utils) (in module moleculekit.util) calculateUniqueBonds() (in module moleculekit.molecule) cast_indices() (in module moleculekit.fileformats.utils) categoryPart() (moleculekit.pdbx.reader.PdbxContainers.CifName static method) cationpi_calculate() (in module moleculekit.interactions.interactions) cdist() (in module moleculekit.distance) (in module moleculekit.distance_utils) center() (moleculekit.molecule.Molecule method) chain (moleculekit.molecule.Molecule attribute) ChainResidueSpec (class in moleculekit.tools.nonstandard_residues) charge (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) check_backbone() (in module moleculekit.tools.backbone) check_port() (in module moleculekit.util) checkTruncations() (in module moleculekit.writers) chi1() (moleculekit.projections.metricdihedral.Dihedral static method) chi2() (moleculekit.projections.metricdihedral.Dihedral static method) chi3() (moleculekit.projections.metricdihedral.Dihedral static method) chi4() (moleculekit.projections.metricdihedral.Dihedral static method) chi5() (moleculekit.projections.metricdihedral.Dihedral static method) children (moleculekit.kdtree.cKDTreeNode attribute), [1] (moleculekit.kdtree.KDTree.innernode property) (moleculekit.kdtree.KDTree.leafnode property) CifName (class in moleculekit.pdbx.reader.PdbxContainers) CIFread() (in module moleculekit.readers) CIFwrite() (in module moleculekit.writers) cKDTree (class in moleculekit.kdtree) cKDTreeNode (class in moleculekit.kdtree) clone() (moleculekit.ply.lex.Lexer method) close() (moleculekit.binpos.BINPOSTrajectoryFile method) (moleculekit.dcd.DCDTrajectoryFile method) (moleculekit.fileformats.netcdf.netcdf_file method) (moleculekit.trr.TRRTrajectoryFile method) (moleculekit.vmdviewer.VMD method)

closestDistance() (in module moleculekit.tools.moleculechecks) compareGraphs() (in module moleculekit.tools.graphalignment) completed() (moleculekit.vmdviewer.VMD method) compute_first() (moleculekit.ply.yacc.Grammar method) compute_follow() (moleculekit.ply.yacc.Grammar method) compute_follow_sets() (moleculekit.ply.yacc.LRTable method) compute_lookback_includes() (moleculekit.ply.yacc.LRTable method) compute_nullable_nonterminals() (moleculekit.ply.yacc.LRTable method) compute_read_sets() (moleculekit.ply.yacc.LRTable method) config() (in module moleculekit.config) connected_component_subgraphs() (in module moleculekit.tools.detect) construct() (moleculekit.readers.MolFactory static method) contacts_trajectory() (in module moleculekit.distance_utils) contactVecToMatrix() (in module moleculekit.projections.metricdistance) ContainerBase (class in moleculekit.pdbx.reader.PdbxContainers) containsMetals() (moleculekit.smallmol.smallmol.SmallMol method) convertToString() (in module moleculekit.smallmol.util) coords (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) coords_to_bytes() (in module moleculekit.viewer.molstar.registry) copy() (moleculekit.molecule.Molecule method) (moleculekit.projections.projection.Projection method) (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmollib.SmallMolLib method) (moleculekit.vmdviewer.VMD method) count (moleculekit.vmdgraphics.VMDLabels attribute) count_neighbors() (moleculekit.kdtree.cKDTree method) (moleculekit.kdtree.KDTree method) counter (moleculekit.vmdgraphics.VMDGraphicObject attribute) CovalentLigandSpec (class in moleculekit.tools.nonstandard_residues) CRDCARDread() (in module moleculekit.readers) CRDread() (in module moleculekit.readers) createDimension() (moleculekit.fileformats.netcdf.netcdf_file method) createProductGraph() (in module moleculekit.tools.graphalignment) createVariable() (moleculekit.fileformats.netcdf.netcdf_file method) critical() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) crystalinfo (moleculekit.molecule.Molecule attribute) csvReader() (in module moleculekit.smallmol.smallmollib) current_state() (moleculekit.ply.lex.Lexer method) CustomResidue (class in moleculekit.tools.preparation_customres)

D

data (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree attribute) (moleculekit.pdbx.writer.BinaryCifWriter.TypedArray attribute) data_points (moleculekit.kdtree.cKDTreeNode attribute), [1] DataCategory (class in moleculekit.pdbx.reader.PdbxContainers) DataCategoryBase (class in moleculekit.pdbx.reader.PdbxContainers) DataContainer (class in moleculekit.pdbx.reader.PdbxContainers) DCDread() (in module moleculekit.readers) DCDTrajectoryFile (class in moleculekit.dcd) DCDwrite() (in module moleculekit.writers) debug() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) decode() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) DefinitionContainer (class in moleculekit.pdbx.reader.PdbxContainers) delete() (moleculekit.vmdgraphics.VMDGraphicObject method) (moleculekit.vmdgraphics.VMDIsosurface method) (moleculekit.vmdgraphics.VMDLabels method) deleteBonds() (moleculekit.molecule.Molecule method) deltaDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) deltaEncoderTyped() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) depict() (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmollib.SmallMolLib method) depictMultipleMols() (in module moleculekit.smallmol.util) deserialize() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifReader method) detectEquivalentAtoms() (in module moleculekit.tools.detect)

detectNonStandardResidues() (in module moleculekit.tools.nonstandard_residues) detectParameterizableCores() (in module moleculekit.tools.detect) detectParameterizableDihedrals() (in module moleculekit.tools.detect) diff_and_snapshot() (moleculekit.viewer.molstar.registry.Registry method) digraph() (in module moleculekit.ply.yacc) Dihedral (class in moleculekit.projections.metricdihedral) dihedralAngle() (in module moleculekit.dihedral) dihedrals (moleculekit.molecule.Molecule attribute) dihedralsToIndexes() (moleculekit.projections.metricdihedral.Dihedral static method) dimensions (moleculekit.fileformats.netcdf.netcdf_variable attribute) disable_defaulted_states() (moleculekit.ply.yacc.LRParser method) disjoint_set_find() (in module moleculekit.wrapping) disjoint_set_merge() (in module moleculekit.wrapping) dist_trajectory() (in module moleculekit.distance_utils) dist_trajectory_reduction() (in module moleculekit.distance_utils) dist_trajectory_reduction_pairs() (in module moleculekit.distance_utils) distance_unit (moleculekit.binpos.BINPOSTrajectoryFile attribute) (moleculekit.dcd.DCDTrajectoryFile attribute) (moleculekit.trr.TRRTrajectoryFile attribute) dock() (in module moleculekit.tools.docking) dr_relation() (moleculekit.ply.yacc.LRTable method) draw_cylinder() (in module moleculekit.pymolgraphics) dropFrames() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) dtype (moleculekit.pdbx.writer.BinaryCifWriter.TypedArray attribute) dumpIt() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)

E

element (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) elements_from_masses() (in module moleculekit.periodictable) empty() (moleculekit.molecule.Molecule method) encode() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) encodeWithMask() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) end_idx (moleculekit.kdtree.cKDTreeNode attribute) ensure_type() (in module moleculekit.fileformats.utils)

ensurelist() (in module moleculekit.util) errok() (moleculekit.ply.yacc.LRParser method) error() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) (moleculekit.ply.yacc.YaccProduction method) exists() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) extend_residue_from_smiles() (in module moleculekit.rdkittools) extendResidueFromSmiles() (moleculekit.molecule.Molecule method)

F

file_diff() (in module moleculekit.util) fileloc (moleculekit.molecule.Molecule attribute) filter() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) filter_props() (in module moleculekit.interactions.interactions) find_backbone() (in module moleculekit.atomselect.analyze) find_clashes() (in module moleculekit.distance) find_executable() (in module moleculekit.util) find_nonterminal_transitions() (moleculekit.ply.yacc.LRTable method) find_unreachable() (moleculekit.ply.yacc.Grammar method) fixedPointDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) floatArrayMaskedEncoder() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) flush() (moleculekit.fileformats.netcdf.netcdf_file method) folder_diff() (in module moleculekit.util)

formalcharge (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) format_result() (in module moleculekit.ply.yacc) format_stack_entry() (in module moleculekit.ply.yacc) FormatError foundBondBetween() (moleculekit.smallmol.smallmol.SmallMol method) frame (moleculekit.molecule.Molecule property) (moleculekit.smallmol.smallmol.SmallMol property) fromDict() (moleculekit.molecule.Molecule static method) fromMolecule() (moleculekit.molecule.UniqueAtomID static method) (moleculekit.molecule.UniqueResidueID static method) (moleculekit.readers.Topology method) fromOpenMMTopology() (moleculekit.molecule.Molecule static method) fromRDKitMol() (moleculekit.molecule.Molecule static method) fstep (moleculekit.molecule.Molecule property)

G

generate_opm_sequences() (in module moleculekit.opm) generateConformers() (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmolcdp.SmallMolCDP method) generateCrystalPacking() (in module moleculekit.tools.crystalpacking) genTemplate() (in module moleculekit.projections.metricplumed2) (moleculekit.projections.metricplumed2.PlumedCV method) get() (moleculekit.molecule.Molecule method) (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) (moleculekit.smallmol.smallmol.SmallMol method) get_all() (moleculekit.ply.lex.LexerReflect method) (moleculekit.ply.yacc.ParserReflect method) get_bonded_groups() (in module moleculekit.wrapping) get_caller_module_dict() (in module moleculekit.ply.lex) (in module moleculekit.ply.yacc) get_collisions() (in module moleculekit.distance_utils) get_donors_acceptors() (in module moleculekit.interactions.interactions) get_error_func() (moleculekit.ply.yacc.ParserReflect method) get_ligand_aryl_halides() (in module moleculekit.interactions.interactions) get_ligand_charged() (in module moleculekit.interactions.interactions) get_ligand_donors_acceptors() (in module moleculekit.interactions.interactions) get_ligand_props() (in module moleculekit.interactions.interactions) get_ligand_rings() (in module moleculekit.interactions.interactions) get_literals() (moleculekit.ply.lex.LexerReflect method) get_metal_charged() (in module moleculekit.interactions.interactions) get_molprop() (in module moleculekit.atomselect.atomselect) get_nucleic_charged() (in module moleculekit.interactions.interactions) get_nucleic_rings() (in module moleculekit.interactions.interactions) get_opm_pdb() (in module moleculekit.opm) get_or_start_server() (in module moleculekit.viewer.molstar.server) get_pfunctions() (moleculekit.ply.yacc.ParserReflect method) get_precedence() (moleculekit.ply.yacc.ParserReflect method) get_protein_aryl_halides() (in module moleculekit.interactions.interactions) get_protein_charged() (in module moleculekit.interactions.interactions) get_protein_rings() (in module moleculekit.interactions.interactions) get_raw_data_from_url() (in module moleculekit.readers) get_receptor_props() (in module moleculekit.interactions.interactions) get_receptor_rings() (in module moleculekit.interactions.interactions) get_reduced_distances() (in module moleculekit.projections.util) get_registry() (in module moleculekit.viewer.molstar.server) get_rules() (moleculekit.ply.lex.LexerReflect method) get_start() (moleculekit.ply.yacc.ParserReflect method) get_states() (moleculekit.ply.lex.LexerReflect method) get_tokens() (moleculekit.ply.lex.LexerReflect method) (moleculekit.ply.yacc.ParserReflect method) getAtoms() (moleculekit.smallmol.smallmol.SmallMol method) getAttributeCount() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeLengthMaximumList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeListWithOrder() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeValueMaxLengthList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getBondedGroups() (in module moleculekit.molecule) getCenter() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) getCenters() (in module moleculekit.tools.voxeldescriptors) getChannels() (in module moleculekit.tools.voxeldescriptors) getChemblLigandByDrugName() (in module moleculekit.smallmol.util) getChemblSimilarLigandsBySmile() (in module moleculekit.smallmol.util) getCurrentAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getCurrentPymolViewer() (in module moleculekit.viewer) getCurrentViewer() (in module moleculekit.viewer) (in module moleculekit.vmdviewer)

getDescriptors() (moleculekit.smallmol.smallmol.SmallMol method) getDihedral() (moleculekit.molecule.Molecule method) getFeatures() (in module moleculekit.tools.atomtyper) getFingerprint() (moleculekit.smallmol.smallmol.SmallMol method) getFormatTypeList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getFormatTypeListX() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getFullRow() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getGlobal() (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) getIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getItemNameList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getMapping() (moleculekit.projections.metriccoordinate.MetricCoordinate method) (moleculekit.projections.metricdihedral.MetricDihedral method) (moleculekit.projections.metricdistance.MetricDistance method) (moleculekit.projections.metricfluctuation.MetricFluctuation method) (moleculekit.projections.metricgyration.MetricGyration method) (moleculekit.projections.metricplumed2.MetricPlumed2 method) (moleculekit.projections.metricrmsd.MetricRmsd method) (moleculekit.projections.metricsasa.MetricSasa method) (moleculekit.projections.metricsecondarystructure.MetricSecondaryStructure method) (moleculekit.projections.metricshell.MetricShell method) (moleculekit.projections.metricsphericalcoordinate.MetricSphericalCoordinate method) (moleculekit.projections.metrictmscore.MetricTMscore method) (moleculekit.projections.projection.Projection method) getMask() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) getMols() (moleculekit.smallmol.smallmollib.SmallMolLib method) getName() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getNeighbors() (moleculekit.molecule.Molecule method) getObj() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) getObjNameList() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) getOpenBabelProperties() (in module moleculekit.tools.obabel_tools) (in module moleculekit.tools.obabel_tools.obabel_cli) getPDBQTAtomType() (in module moleculekit.tools.atomtyper) getPDBQTAtomTypesAndCharges() (in module moleculekit.tools.atomtyper) getProp() (moleculekit.smallmol.smallmol.SmallMol method) getRCSBLigandByLigname() (in module moleculekit.smallmol.util) getResidues() (moleculekit.molecule.Molecule method) getRow() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getRowCount() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getRowIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getRowList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getSequence() (moleculekit.molecule.Molecule method) getSequenceProfile() (in module moleculekit.tools.hhblitsprofile) getTautomers() (moleculekit.smallmol.smallmol.SmallMol method) getType() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) getValue() (moleculekit.fileformats.netcdf.netcdf_variable method) (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getValueFormatted() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getValueFormattedByIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getVMDpath() (in module moleculekit.vmdviewer) getVoxelDescriptors() (in module moleculekit.tools.voxeldescriptors) GJFread() (in module moleculekit.readers) Grammar (class in moleculekit.ply.yacc) GrammarError greater (moleculekit.kdtree.cKDTreeNode attribute), [1] grid_bonds() (in module moleculekit.bondguesser_utils) GROTOPread() (in module moleculekit.readers) group_objects() (in module moleculekit.pymolgraphics) GROwrite() (in module moleculekit.writers) guess_bonds() (in module moleculekit.bondguesser) guess_bonds_rdkit() (in module moleculekit.bondguesser) guessAnglesAndDihedrals() (in module moleculekit.util) guessBonds() (moleculekit.molecule.Molecule method)

H

hasAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) hasBond() (moleculekit.molecule.Molecule method)

hbonds_calculate() (in module moleculekit.interactions.interactions) httpd (moleculekit.viewer.molstar.server.ServerState attribute) hydrophobic_calculate() (in module moleculekit.interactions.interactions)

I

idx (moleculekit.kdtree.KDTree.leafnode property) impropers (moleculekit.molecule.Molecule attribute) indices (moleculekit.kdtree.cKDTree attribute) (moleculekit.kdtree.cKDTreeNode attribute), [1] infinite_cycles() (moleculekit.ply.yacc.Grammar method) info() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) INPCRDread() (in module moleculekit.readers) INPCRDwrite() (in module moleculekit.writers) input() (in module moleculekit.ply.lex) (moleculekit.ply.lex.Lexer method) insert() (moleculekit.molecule.Molecule method) insertion (moleculekit.molecule.Molecule attribute) intArrayMaskedEncoder() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) integerPackingDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method)

integerPackingEncoderTyped() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) intervalQuantizationDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) invokeAttributeMethod() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) invokeCategoryMethod() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) invokeDataBlockMethod() (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) is_c_term (moleculekit.tools.nonstandard_residues.ChainResidueSpec attribute) is_n_term (moleculekit.tools.nonstandard_residues.ChainResidueSpec attribute) isAttribute() (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) isCategory() (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) isChiral() (moleculekit.smallmol.smallmol.SmallMol method) isLigandDocked() (in module moleculekit.tools.moleculechecks) isLigandOptimized() (in module moleculekit.tools.moleculechecks) isProteinProtonated() (in module moleculekit.tools.moleculechecks) isrec (moleculekit.fileformats.netcdf.netcdf_variable property) itemsize() (moleculekit.fileformats.netcdf.netcdf_variable method)

J

JSONread() (in module moleculekit.readers)

JSONwrite() (in module moleculekit.writers)

K

KDTree (class in moleculekit.kdtree) KDTree.innernode (class in moleculekit.kdtree)

KDTree.leafnode (class in moleculekit.kdtree) KDTree.node (class in moleculekit.kdtree)

L

label (moleculekit.viewer.molstar.registry.Slot attribute) LALRError leafsize (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree attribute) lengths_and_angles_to_box_vectors() (in module moleculekit.unitcell) lengths_and_angles_to_tilt_factors() (in module moleculekit.unitcell) lesser (moleculekit.kdtree.cKDTreeNode attribute), [1] letter_code() (moleculekit.tools.preparation_customres.CustomResidue method) level (moleculekit.kdtree.cKDTreeNode attribute), [1] lex() (in module moleculekit.ply.lex) Lexer (class in moleculekit.ply.lex) LexerReflect (class in moleculekit.ply.lex) LexError lexpos() (moleculekit.ply.yacc.YaccProduction method) lexspan() (moleculekit.ply.yacc.YaccProduction method) LexToken (class in moleculekit.ply.lex) LigandSpec (class in moleculekit.tools.nonstandard_residues)

ligname (moleculekit.smallmol.smallmol.SmallMol property) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) lineno() (moleculekit.ply.yacc.YaccProduction method) linespan() (moleculekit.ply.yacc.YaccProduction method) list() (moleculekit.representations.Representations method) load_binpos() (in module moleculekit.binpos) load_dcd() (in module moleculekit.dcd) load_trr() (in module moleculekit.trr) loadMol() (moleculekit.vmdviewer.VMD method) lr0_closure() (moleculekit.ply.yacc.LRTable method) lr0_goto() (moleculekit.ply.yacc.LRTable method) lr0_items() (moleculekit.ply.yacc.LRTable method) lr_item() (moleculekit.ply.yacc.Production method) lr_parse_table() (moleculekit.ply.yacc.LRTable method) LRItem (class in moleculekit.ply.yacc) LRParser (class in moleculekit.ply.yacc) LRTable (class in moleculekit.ply.yacc)

M

m (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree attribute) MAEread() (in module moleculekit.readers) make_grid_neighborlist_nonperiodic() (in module moleculekit.bondguesser_utils) makeMolGraph() (in module moleculekit.tools.graphalignment) manual() (in module moleculekit.projections.metricplumed2) masses (moleculekit.molecule.Molecule attribute) maxDistance() (in module moleculekit.util) maxes (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree attribute) maximalSubstructureAlignment() (in module moleculekit.tools.graphalignment) mcsAtomMatching() (in module moleculekit.tools.graphalignment) MDTRAJread() (in module moleculekit.readers) MDTRAJTOPOread() (in module moleculekit.readers) MDTRAJwrite() (in module moleculekit.writers) metal_coordination_calculate() (in module moleculekit.interactions.interactions) MetricCoordinate (class in moleculekit.projections.metriccoordinate) MetricDihedral (class in moleculekit.projections.metricdihedral) MetricDistance (class in moleculekit.projections.metricdistance) MetricFluctuation (class in moleculekit.projections.metricfluctuation) MetricGyration (class in moleculekit.projections.metricgyration) MetricPlumed2 (class in moleculekit.projections.metricplumed2) MetricRmsd (class in moleculekit.projections.metricrmsd) MetricSasa (class in moleculekit.projections.metricsasa) MetricSecondaryStructure (class in moleculekit.projections.metricsecondarystructure) MetricSelfDistance (class in moleculekit.projections.metricdistance) MetricShell (class in moleculekit.projections.metricshell) MetricSphericalCoordinate (class in moleculekit.projections.metricsphericalcoordinate) MetricTMscore (class in moleculekit.projections.metrictmscore) minimize_soft_potential() (in module moleculekit.openmmtools) minkowski_distance() (in module moleculekit.kdtree) minkowski_distance_p() (in module moleculekit.kdtree) mins (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree attribute) MissingBackboneError MissingTopologyError MMTFread() (in module moleculekit.readers) MMTFwrite() (in module moleculekit.writers) model_gaps() (in module moleculekit.tools.modelling) module moleculekit moleculekit.align moleculekit.atomselect moleculekit.atomselect.analyze moleculekit.atomselect.atomselect moleculekit.atomselect_utils moleculekit.binpos moleculekit.bondguesser moleculekit.bondguesser_utils moleculekit.config moleculekit.cython_utils moleculekit.dcd moleculekit.dihedral moleculekit.distance moleculekit.distance_utils moleculekit.fileformats moleculekit.fileformats.netcdf moleculekit.fileformats.utils moleculekit.interactions moleculekit.interactions.cationpi moleculekit.interactions.hbonds moleculekit.interactions.interactions moleculekit.interactions.pipi moleculekit.interactions.sigmahole moleculekit.kdtree moleculekit.molecule moleculekit.occupancy_utils moleculekit.openmmtools moleculekit.opm moleculekit.pdbx moleculekit.pdbx.reader moleculekit.pdbx.reader.BinaryCifReader moleculekit.pdbx.reader.PdbxContainers moleculekit.pdbx.reader.PdbxParser moleculekit.pdbx.reader.PdbxReader moleculekit.pdbx.writer moleculekit.pdbx.writer.BinaryCifWriter moleculekit.pdbx.writer.PdbxWriter moleculekit.periodictable moleculekit.ply moleculekit.ply.lex moleculekit.ply.yacc moleculekit.projections moleculekit.projections.metriccoordinate moleculekit.projections.metricdihedral moleculekit.projections.metricdistance moleculekit.projections.metricfluctuation moleculekit.projections.metricgyration moleculekit.projections.metricplumed2 moleculekit.projections.metricrmsd moleculekit.projections.metricsasa moleculekit.projections.metricsecondarystructure moleculekit.projections.metricshell moleculekit.projections.metricsphericalcoordinate moleculekit.projections.metrictmscore moleculekit.projections.projection moleculekit.projections.util moleculekit.pymolgraphics moleculekit.rcsb moleculekit.rdkittools moleculekit.readers moleculekit.representations moleculekit.residues moleculekit.smallmol moleculekit.smallmol.smallmol moleculekit.smallmol.smallmolcdp moleculekit.smallmol.smallmollib moleculekit.smallmol.util moleculekit.tmalign moleculekit.tools moleculekit.tools.atomtyper moleculekit.tools.autosegment moleculekit.tools.backbone moleculekit.tools.crystalpacking moleculekit.tools.detect moleculekit.tools.docking moleculekit.tools.graphalignment moleculekit.tools.hhblitsprofile moleculekit.tools.modelling moleculekit.tools.moleculechecks moleculekit.tools.mutate moleculekit.tools.nonstandard_residues moleculekit.tools.obabel_tools moleculekit.tools.obabel_tools.obabel_cli moleculekit.tools.preparation moleculekit.tools.preparation_customres moleculekit.tools.sequencestructuralalignment moleculekit.tools.voxeldescriptors moleculekit.trr moleculekit.unitcell moleculekit.util moleculekit.viewer moleculekit.viewer.molstar moleculekit.viewer.molstar.registry moleculekit.viewer.molstar.serialize moleculekit.viewer.molstar.server moleculekit.vmdgraphics moleculekit.vmdviewer moleculekit.wrapping moleculekit.writers moleculekit.xtc MOL2read() (in module moleculekit.readers) MOL2write() (in module moleculekit.writers) mol_equal() (in module moleculekit.molecule) mol_ref (moleculekit.viewer.molstar.registry.Slot attribute) Molecule (class in moleculekit.molecule) molecule_to_dict() (in module moleculekit.viewer.molstar.serialize) molecule_to_rdkitmol() (in module moleculekit.rdkittools) moleculekit module moleculekit.align module moleculekit.atomselect module moleculekit.atomselect.analyze module moleculekit.atomselect.atomselect module moleculekit.atomselect_utils module moleculekit.binpos module moleculekit.bondguesser module moleculekit.bondguesser_utils module moleculekit.config module moleculekit.cython_utils module moleculekit.dcd module moleculekit.dihedral module moleculekit.distance module moleculekit.distance_utils module moleculekit.fileformats module

moleculekit.fileformats.netcdf module moleculekit.fileformats.utils module moleculekit.interactions module moleculekit.interactions.cationpi module moleculekit.interactions.hbonds module moleculekit.interactions.interactions module moleculekit.interactions.pipi module moleculekit.interactions.sigmahole module moleculekit.kdtree module moleculekit.molecule module moleculekit.occupancy_utils module moleculekit.openmmtools module moleculekit.opm module moleculekit.pdbx module moleculekit.pdbx.reader module moleculekit.pdbx.reader.BinaryCifReader module moleculekit.pdbx.reader.PdbxContainers module moleculekit.pdbx.reader.PdbxParser module moleculekit.pdbx.reader.PdbxReader module moleculekit.pdbx.writer module moleculekit.pdbx.writer.BinaryCifWriter module moleculekit.pdbx.writer.PdbxWriter module moleculekit.periodictable module moleculekit.ply module moleculekit.ply.lex module moleculekit.ply.yacc module moleculekit.projections module moleculekit.projections.metriccoordinate module moleculekit.projections.metricdihedral module moleculekit.projections.metricdistance module moleculekit.projections.metricfluctuation module moleculekit.projections.metricgyration module moleculekit.projections.metricplumed2 module moleculekit.projections.metricrmsd module moleculekit.projections.metricsasa module moleculekit.projections.metricsecondarystructure module moleculekit.projections.metricshell module moleculekit.projections.metricsphericalcoordinate module moleculekit.projections.metrictmscore module moleculekit.projections.projection module moleculekit.projections.util module moleculekit.pymolgraphics module moleculekit.rcsb module moleculekit.rdkittools module moleculekit.readers module moleculekit.representations module moleculekit.residues module moleculekit.smallmol module moleculekit.smallmol.smallmol module moleculekit.smallmol.smallmolcdp module moleculekit.smallmol.smallmollib module moleculekit.smallmol.util module moleculekit.tmalign module moleculekit.tools module moleculekit.tools.atomtyper module moleculekit.tools.autosegment module moleculekit.tools.backbone module moleculekit.tools.crystalpacking module moleculekit.tools.detect module moleculekit.tools.docking module moleculekit.tools.graphalignment module moleculekit.tools.hhblitsprofile module moleculekit.tools.modelling module moleculekit.tools.moleculechecks module moleculekit.tools.mutate module moleculekit.tools.nonstandard_residues module moleculekit.tools.obabel_tools module moleculekit.tools.obabel_tools.obabel_cli module moleculekit.tools.preparation module moleculekit.tools.preparation_customres module moleculekit.tools.sequencestructuralalignment module moleculekit.tools.voxeldescriptors module moleculekit.trr module moleculekit.unitcell module moleculekit.util module moleculekit.viewer module moleculekit.viewer.molstar module moleculekit.viewer.molstar.registry module moleculekit.viewer.molstar.serialize module moleculekit.viewer.molstar.server module moleculekit.vmdgraphics module moleculekit.vmdviewer module moleculekit.wrapping module moleculekit.writers module moleculekit.xtc module MolFactory (class in moleculekit.readers) molRMSD() (in module moleculekit.util) molTMalign() (in module moleculekit.align) molTMscore() (in module moleculekit.align) monitor_thread (moleculekit.viewer.molstar.server.ServerState attribute) moveBy() (moleculekit.molecule.Molecule method) movie_reps() (moleculekit.vmdviewer.VMD method) mutate_residue() (in module moleculekit.tools.mutate) mutateResidue() (moleculekit.molecule.Molecule method)

N

n (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree attribute) name (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) natsorted() (in module moleculekit.util) netcdf_file (class in moleculekit.fileformats.netcdf) netcdf_variable (class in moleculekit.fileformats.netcdf) NETCDFread() (in module moleculekit.readers) NETCDFwrite() (in module moleculekit.writers) new_resname (moleculekit.tools.nonstandard_residues.ChainResidueSpec attribute)

NullLogger (class in moleculekit.ply.yacc) numAtoms (moleculekit.molecule.Molecule property) (moleculekit.smallmol.smallmol.SmallMol property) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) numBonds (moleculekit.molecule.Molecule property) numFrames (moleculekit.molecule.Molecule property) (moleculekit.readers.Trajectory property) (moleculekit.smallmol.smallmol.SmallMol property) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) numMols (moleculekit.smallmol.smallmollib.SmallMolLib property) numResidues (moleculekit.molecule.Molecule property)

O

occupancy (moleculekit.molecule.Molecule attribute) offset_ligand_props() (in module moleculekit.interactions.interactions) offsets (moleculekit.trr.TRRTrajectoryFile attribute) omega() (moleculekit.projections.metricdihedral.Dihedral static method)

openbabelConvert() (in module moleculekit.tools.obabel_tools) openFileOrStringIO() (in module moleculekit.readers) openmm_to_molecule() (in module moleculekit.openmmtools) opm() (in module moleculekit.util) orientOnAxes() (in module moleculekit.util)

P

parallel() (in module moleculekit.tools.atomtyper) parse() (in module moleculekit.ply.yacc) (moleculekit.ply.yacc.LRParser method) parse_grammar() (in module moleculekit.ply.yacc) ParserReflect (class in moleculekit.ply.yacc) parseV3000SDF() (in module moleculekit.readers) pdbGuessElementByName() (in module moleculekit.readers) PDBQTread() (in module moleculekit.readers) PDBQTwrite() (in module moleculekit.writers) PDBread() (in module moleculekit.readers) PDBwrite() (in module moleculekit.writers) PdbxError, [1], [2] PdbxReader (class in moleculekit.pdbx.reader.PdbxParser) (class in moleculekit.pdbx.reader.PdbxReader) PdbxWriter (class in moleculekit.pdbx.reader.PdbxParser) (class in moleculekit.pdbx.writer.PdbxWriter) pdist() (in module moleculekit.distance) (in module moleculekit.distance_utils) phi() (moleculekit.projections.metricdihedral.Dihedral static method) pipi_calculate() (in module moleculekit.interactions.interactions) PlumedCOM (class in moleculekit.projections.metricplumed2) PlumedCV (class in moleculekit.projections.metricplumed2) PlumedGenericGroup (class in moleculekit.projections.metricplumed2) PlumedGroup (class in moleculekit.projections.metricplumed2) PlumedMolinfo (class in moleculekit.projections.metricplumed2) PlumedStatement (class in moleculekit.projections.metricplumed2) PlumedVerbatim (class in moleculekit.projections.metricplumed2) PlyLogger (class in moleculekit.ply.lex) (class in moleculekit.ply.yacc) pop_state() (moleculekit.ply.lex.Lexer method)

port (moleculekit.viewer.molstar.server.ServerState attribute) pp_calcDistances() (in module moleculekit.projections.util) pp_calcMinDistances() (in module moleculekit.projections.util) prepareProteinForAtomtyping() (in module moleculekit.tools.atomtyper) PREPIread() (in module moleculekit.readers) printIt() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) PRMTOPread() (in module moleculekit.readers) Production (class in moleculekit.ply.yacc) project() (moleculekit.projections.metriccoordinate.MetricCoordinate method) (moleculekit.projections.metricdihedral.MetricDihedral method) (moleculekit.projections.metricdistance.MetricDistance method) (moleculekit.projections.metricfluctuation.MetricFluctuation method) (moleculekit.projections.metricgyration.MetricGyration method) (moleculekit.projections.metricplumed2.MetricPlumed2 method) (moleculekit.projections.metricrmsd.MetricRmsd method) (moleculekit.projections.metricsasa.MetricSasa method) (moleculekit.projections.metricsecondarystructure.MetricSecondaryStructure method) (moleculekit.projections.metricshell.MetricShell method) (moleculekit.projections.metricsphericalcoordinate.MetricSphericalCoordinate method) (moleculekit.projections.metrictmscore.MetricTMscore method) (moleculekit.projections.projection.Projection method) Projection (class in moleculekit.projections.projection) proteinDihedrals() (moleculekit.projections.metricdihedral.Dihedral static method) proteinHasBonds() (in module moleculekit.tools.moleculechecks) PSFread() (in module moleculekit.readers) PSFwrite() (in module moleculekit.writers) psi() (moleculekit.projections.metricdihedral.Dihedral static method) push_state() (moleculekit.ply.lex.Lexer method)

Q

query() (moleculekit.kdtree.cKDTree method) (moleculekit.kdtree.KDTree method) query_ball_point() (moleculekit.kdtree.cKDTree method) (moleculekit.kdtree.KDTree method)

query_ball_tree() (moleculekit.kdtree.cKDTree method) (moleculekit.kdtree.KDTree method) query_pairs() (moleculekit.kdtree.cKDTree method) (moleculekit.kdtree.KDTree method)

R

rcsbFindLigands() (in module moleculekit.rcsb) rcsbFindMutatedResidues() (in module moleculekit.rcsb) rdkitmol_to_molecule() (in module moleculekit.rdkittools) read() (moleculekit.binpos.BINPOSTrajectoryFile method) (moleculekit.dcd.DCDTrajectoryFile method) (moleculekit.molecule.Molecule method) (moleculekit.pdbx.reader.PdbxParser.PdbxReader method) (moleculekit.pdbx.reader.PdbxReader.PdbxReader method) (moleculekit.trr.TRRTrajectoryFile method) read_header() (moleculekit.dcd.DCDTrajectoryFile method) read_xtc() (in module moleculekit.xtc) read_xtc_frames() (in module moleculekit.xtc) readCube() (in module moleculekit.util) reads_relation() (moleculekit.ply.yacc.LRTable method) reconstructContactMap() (in module moleculekit.projections.metricdistance) record (moleculekit.molecule.Molecule attribute) reduced (moleculekit.ply.yacc.Production attribute) register() (in module moleculekit.viewer.molstar.server) (moleculekit.viewer.molstar.registry.Registry method) Registry (class in moleculekit.viewer.molstar.registry) registry (moleculekit.viewer.molstar.server.ServerState attribute) remove() (moleculekit.molecule.Molecule method) (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.representations.Representations method) (moleculekit.viewer.molstar.registry.Registry method) removeBond() (moleculekit.molecule.Molecule method) removeHs() (moleculekit.smallmol.smallmol.SmallMol method) removeMols() (moleculekit.smallmol.smallmollib.SmallMolLib method) removeRow() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) rename() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)

renameAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) render() (moleculekit.vmdviewer.VMD method) renumberResidues() (moleculekit.molecule.Molecule method) reorderAtoms() (moleculekit.molecule.Molecule method) rep() (moleculekit.vmdviewer.VMD method) replace() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) replaceSubstring() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) replaceValue() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) Representations (class in moleculekit.representations) reps (moleculekit.molecule.Molecule attribute) resid (moleculekit.molecule.Molecule attribute) residue (moleculekit.tools.nonstandard_residues.ChainResidueSpec attribute) (moleculekit.tools.nonstandard_residues.CovalentLigandSpec attribute) (moleculekit.tools.nonstandard_residues.LigandSpec attribute) (moleculekit.tools.nonstandard_residues.ScaffoldSpec attribute) resname (moleculekit.molecule.Molecule attribute) (moleculekit.tools.nonstandard_residues.ChainResidueSpec attribute) (moleculekit.tools.nonstandard_residues.CovalentLigandSpec attribute) (moleculekit.tools.nonstandard_residues.LigandSpec attribute) (moleculekit.tools.nonstandard_residues.ScaffoldSpec attribute) restart() (moleculekit.ply.yacc.LRParser method) rightmost_terminal() (in module moleculekit.ply.yacc) rooted_tree_isomorphism() (in module moleculekit.tools.detect) rotateBy() (moleculekit.molecule.Molecule method) rotateCoordinates() (in module moleculekit.tools.voxeldescriptors) rotation_matrix_from_vectors() (in module moleculekit.util) rotationMatrix() (in module moleculekit.util) RTFread() (in module moleculekit.readers) runLengthDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) runLengthEncoderTyped() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) runmain() (in module moleculekit.ply.lex)

S

saltbridge_calculate() (in module moleculekit.interactions.interactions) sanitize() (moleculekit.smallmol.smallmol.SmallMol method) ScaffoldSpec (class in moleculekit.tools.nonstandard_residues) sdf_generator() (in module moleculekit.readers) SDFread() (in module moleculekit.readers) sdfReader() (in module moleculekit.smallmol.smallmollib) SDFwrite() (in module moleculekit.writers) seek() (moleculekit.binpos.BINPOSTrajectoryFile method) (moleculekit.dcd.DCDTrajectoryFile method) (moleculekit.trr.TRRTrajectoryFile method) segid (moleculekit.molecule.Molecule attribute) selectAtom() (moleculekit.molecule.UniqueAtomID method) selectAtoms() (moleculekit.molecule.UniqueResidueID method) send() (moleculekit.vmdviewer.VMD method) sequence() (moleculekit.molecule.Molecule method) sequenceID() (in module moleculekit.util) sequenceStructureAlignment() (in module moleculekit.tools.sequencestructuralalignment) serial (moleculekit.molecule.Molecule attribute) serialize() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifWriter method) server_thread (moleculekit.viewer.molstar.server.ServerState attribute) ServerState (class in moleculekit.viewer.molstar.server) session (moleculekit.viewer.molstar.server.ServerState attribute) set() (moleculekit.molecule.Molecule method) set_defaulted_states() (moleculekit.ply.yacc.LRParser method) set_lexpos() (moleculekit.ply.yacc.YaccProduction method) set_lineno() (moleculekit.ply.yacc.YaccProduction method) set_precedence() (moleculekit.ply.yacc.Grammar method) set_start() (moleculekit.ply.yacc.Grammar method) setAttributeNameList() (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) setDihedral() (moleculekit.molecule.Molecule method) setGlobal() (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) setName() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) setProp() (moleculekit.smallmol.smallmol.SmallMol method) setRowList() (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) setRowPartition() (moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method)

setType() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) setValue() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) shape (moleculekit.fileformats.netcdf.netcdf_variable property) shutdown_for_tests() (in module moleculekit.viewer.molstar.server) sigmahole_calculate() (in module moleculekit.interactions.interactions) signature() (moleculekit.ply.yacc.ParserReflect method) size (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree attribute) skip() (moleculekit.ply.lex.Lexer method) Slot (class in moleculekit.viewer.molstar.registry) SmallMol (class in moleculekit.smallmol.smallmol) SmallMolCDP (class in moleculekit.smallmol.smallmolcdp) SmallMolLib (class in moleculekit.smallmol.smallmollib) SmallMolStack (in module moleculekit.smallmol.smallmollib) smiReader() (in module moleculekit.smallmol.smallmollib) snapshot (moleculekit.viewer.molstar.registry.Slot attribute) sparse_distance_matrix() (moleculekit.kdtree.cKDTree method) (moleculekit.kdtree.KDTree method) split (moleculekit.kdtree.cKDTreeNode attribute), [1] (moleculekit.kdtree.KDTree.innernode property) split_dim (moleculekit.kdtree.cKDTreeNode attribute), [1] (moleculekit.kdtree.KDTree.innernode property) squareform() (in module moleculekit.distance) (in module moleculekit.distance_utils) start_for_tests() (in module moleculekit.viewer.molstar.server) start_idx (moleculekit.kdtree.cKDTreeNode attribute) step (moleculekit.molecule.Molecule attribute) stop_event (moleculekit.viewer.molstar.server.ServerState attribute) string_to_tempfile() (in module moleculekit.util) stringArrayDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) stringArrayMaskedEncoder() (moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders method) stripSalts() (moleculekit.smallmol.smallmol.SmallMol method) subscribers (moleculekit.viewer.molstar.server.ServerState attribute) subscribers_lock (moleculekit.viewer.molstar.server.ServerState attribute) sync() (moleculekit.fileformats.netcdf.netcdf_file method) SyntaxError, [1] systemPrepare() (in module moleculekit.tools.preparation)

T

tell() (moleculekit.binpos.BINPOSTrajectoryFile method) (moleculekit.dcd.DCDTrajectoryFile method) (moleculekit.trr.TRRTrajectoryFile method) template_residue_from_smiles() (in module moleculekit.rdkittools) templateResidueFromSmiles() (moleculekit.molecule.Molecule method) tempname() (in module moleculekit.util) time (moleculekit.molecule.Molecule attribute) tmalign() (in module moleculekit.tmalign) toDataFrame() (moleculekit.smallmol.smallmollib.SmallMolLib method) toDict() (moleculekit.molecule.Molecule method) toGraph() (moleculekit.molecule.Molecule method) TOKEN() (in module moleculekit.ply.lex) token() (in module moleculekit.ply.lex) (moleculekit.ply.lex.Lexer method) toMolecule() (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmolcdp.SmallMolCDP method) toOpenFFMolecule() (moleculekit.molecule.Molecule method) topo_hash (moleculekit.viewer.molstar.registry.Slot attribute)

topo_hash() (in module moleculekit.viewer.molstar.registry) Topology (class in moleculekit.readers) TopologyInconsistencyError, [1] toRDKitMol() (moleculekit.molecule.Molecule method) toSMARTS() (moleculekit.smallmol.smallmol.SmallMol method) toSMILES() (moleculekit.smallmol.smallmol.SmallMol method) tq() (moleculekit.vmdgraphics.VMDGraphicObject static method) Trajectory (class in moleculekit.readers) translateBy() (moleculekit.molecule.Molecule method) traverse() (in module moleculekit.ply.yacc) traverse_ast() (in module moleculekit.atomselect.atomselect) tree (moleculekit.kdtree.cKDTree attribute), [1] (moleculekit.kdtree.KDTree property) TRRread() (in module moleculekit.readers) TRRTrajectoryFile (class in moleculekit.trr) TRRwrite() (in module moleculekit.writers) TypeCastPerformanceWarning typecode() (moleculekit.fileformats.netcdf.netcdf_variable method) TypedArray (class in moleculekit.pdbx.writer.BinaryCifWriter)

U

undefined_symbols() (moleculekit.ply.yacc.Grammar method) uniformRandomRotation() (in module moleculekit.util) UniqueAtomID (class in moleculekit.molecule) UniqueResidueID (class in moleculekit.molecule)

unused_precedence() (moleculekit.ply.yacc.Grammar method) unused_rules() (moleculekit.ply.yacc.Grammar method) unused_terminals() (moleculekit.ply.yacc.Grammar method) uuid (moleculekit.viewer.molstar.registry.Slot attribute)

V

validate_all() (moleculekit.ply.lex.LexerReflect method) (moleculekit.ply.yacc.ParserReflect method) validate_error_func() (moleculekit.ply.yacc.ParserReflect method) validate_literals() (moleculekit.ply.lex.LexerReflect method) validate_module() (moleculekit.ply.lex.LexerReflect method) validate_modules() (moleculekit.ply.yacc.ParserReflect method) validate_pfunctions() (moleculekit.ply.yacc.ParserReflect method) validate_precedence() (moleculekit.ply.yacc.ParserReflect method) validate_rules() (moleculekit.ply.lex.LexerReflect method) validate_start() (moleculekit.ply.yacc.ParserReflect method) validate_tokens() (moleculekit.ply.lex.LexerReflect method) (moleculekit.ply.yacc.ParserReflect method) view() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmolcdp.SmallMolCDP method)

view_hbonds() (in module moleculekit.interactions.interactions) viewer() (in module moleculekit.vmdviewer) viewname (moleculekit.molecule.Molecule attribute) viewVoxelFeatures() (in module moleculekit.tools.voxeldescriptors) virtualsite (moleculekit.molecule.Molecule attribute) visible (moleculekit.viewer.molstar.registry.Slot attribute) VMD (class in moleculekit.vmdviewer) VMDBox (class in moleculekit.vmdgraphics) VMDConvexHull (class in moleculekit.vmdgraphics) VMDCylinder (class in moleculekit.vmdgraphics) VMDGraphicObject (class in moleculekit.vmdgraphics) VMDIsosurface (class in moleculekit.vmdgraphics) VMDLabels (class in moleculekit.vmdgraphics) VMDSphere (class in moleculekit.vmdgraphics) VMDText (class in moleculekit.vmdgraphics)

W

wait_for_port() (in module moleculekit.util) warning() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) waterbridge_calculate() (in module moleculekit.interactions.interactions) within_distance() (in module moleculekit.atomselect_utils) wrap() (moleculekit.molecule.Molecule method) wrap_box() (in module moleculekit.wrapping) wrap_compact_unitcell() (in module moleculekit.wrapping) wrap_triclinic_unitcell() (in module moleculekit.wrapping) write() (moleculekit.binpos.BINPOSTrajectoryFile method) (moleculekit.dcd.DCDTrajectoryFile method) (moleculekit.molecule.Molecule method) (moleculekit.pdbx.reader.PdbxParser.PdbxWriter method) (moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method) (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.trr.TRRTrajectoryFile method)

write_xtc() (in module moleculekit.xtc) writeContainer() (moleculekit.pdbx.reader.PdbxParser.PdbxWriter method) (moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method) writeCube() (in module moleculekit.util) writeSdf() (moleculekit.smallmol.smallmollib.SmallMolLib method) writeSmiles() (moleculekit.smallmol.smallmollib.SmallMolLib method) writeVoxels() (in module moleculekit.util)

X

x (moleculekit.molecule.Molecule property) XSCread() (in module moleculekit.readers) XSCwrite() (in module moleculekit.writers)

XTCread() (in module moleculekit.readers) XTCwrite() (in module moleculekit.writers) XYZread() (in module moleculekit.readers) XYZwrite() (in module moleculekit.writers)

Y

y (moleculekit.molecule.Molecule property) yacc() (in module moleculekit.ply.yacc)

YaccError YaccProduction (class in moleculekit.ply.yacc) YaccSymbol (class in moleculekit.ply.yacc)

Z

z (moleculekit.molecule.Molecule property)