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 _ __del__() (moleculekit.fileformats.netcdf.netcdf_file method) __getitem__() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) A abs2rel() (htmd.metricdata.MetricData method) (in module htmd.metricdatagenerator) abs2sim() (htmd.metricdata.MetricData method) acemd module Acemd (class in htmd.mdengine.acemd.acemd) acemd() (in module acemd.acemd) acemd.acemd module acemd.charmm module acemd.licensing module acemd.minimizer module acemd.protocols module acemd.reporters module acemd.restraints module acemd.utils module acemd.versionwarnings module acemd_register() (in module acemd.licensing) AdaptiveBandit (class in htmd.adaptive.adaptivebandit) AdaptiveBase (class in htmd.adaptive.adaptive) AdaptiveGoal (class in htmd.adaptive.adaptivegoal) AdaptiveGoalEG (class in htmd.adaptive.adaptivegoaleg) AdaptiveMD (class in htmd.adaptive.adaptiverun) add() (moleculekit.molecule.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) addConstraint() (htmd.protocols.production_v6.Production method) addHs() (moleculekit.smallmol.smallmol.SmallMol method) addPoint() (htmd.pathplanning.Tree method) aggregateTime (htmd.metricdata.MetricData property) aliases (acemd.reporters.LoggingReporter attribute) aliases2 (acemd.reporters.LoggingReporter attribute) 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) ANGLES (acemd.acemd.FGROUPS attribute) angles (moleculekit.molecule.Molecule attribute) append() (htmd.metricdata.MetricData method) (moleculekit.molecule.Molecule method) (moleculekit.molecule.Representations method) (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategory 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 htmd.util) (in module moleculekit.util) assignStereoChemistry() (moleculekit.smallmol.smallmol.SmallMol method) assignValue() (moleculekit.fileformats.netcdf.netcdf_variable method) atominfo (moleculekit.readers.Topology property) AtomNotFoundException AtomRestraint (class in htmd.mdengine.acemd.acemd) 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 BAROSTAT (acemd.acemd.FGROUPS attribute) 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) BinaryCifReader (class in moleculekit.pdbx.reader.BinaryCifReader) 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) BINPOSwrite() (in module moleculekit.writers) blast_search_opm() (in module moleculekit.opm) bond_grid_search() (in module moleculekit.bondguesser) BONDS (acemd.acemd.FGROUPS attribute) bonds (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) bondtype (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) bootstrap() (htmd.metricdata.MetricData method) 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) boxvectors (moleculekit.molecule.Molecule property) bracket_and_golden_section_search() (in module acemd.minimizer) build() (in module htmd.builder.amber) (in module htmd.builder.charmm) build_lritems() (moleculekit.ply.yacc.Grammar method) BuildError buildMembrane() (in module htmd.membranebuilder.build_membrane) byteArrayDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) C calculate() (htmd.mutualinformation.MutualInformation method) calculate_contacts() (in module moleculekit.distance) calculateAnglesAndDihedrals() (in module moleculekit.util) calculateUniqueBonds() (in module moleculekit.molecule) CANCELLED (jobqueues.simqueue.QueueJobStatus attribute) 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) CeleryQueue (class in jobqueues.celeryqueue) center() (moleculekit.molecule.Molecule method) centerFrames (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) Centers (htmd.metricdata.MetricData attribute) cgmin_compute() (in module acemd.minimizer) chain (moleculekit.molecule.Molecule attribute) charge (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) check_for_license() (in module htmd.license) 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) CifName (class in moleculekit.pdbx.reader.PdbxContainers) CIFread() (in module moleculekit.readers) CIFwrite() (in module moleculekit.writers) cktest() (htmd.model.Model method) cleanup_charmm_prm() (in module acemd.charmm) (in module htmd.builder.charmm) clone() (moleculekit.ply.lex.Lexer method) close() (moleculekit.fileformats.netcdf.netcdf_file method) (moleculekit.vmdviewer.VMD method) closestDistance() (in module moleculekit.tools.moleculechecks) cluster (htmd.metricdata.Trajectory property) cluster() (htmd.metricdata.MetricData method) cluster_centers (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) cluster_centers_ (htmd.clustering.regular.RegCluster property) cluster_ofmicro (htmd.model.Model property) clusterSize (htmd.clustering.regular.RegCluster property) clusterSize_ (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) CMAP (acemd.acemd.FGROUPS attribute) combine() (htmd.metricdata.MetricData method) (in module htmd.builder.charmm) compareGraphs() (in module moleculekit.tools.graphalignment) compareVersions() (in module htmd.latest) COMPLETED (jobqueues.simqueue.QueueJobStatus attribute) (playmolecule.apps.JobStatus attribute) 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 htmd.config) (in module jobqueues.config) (in module moleculekit.config) conformationStationaryDistribution() (htmd.adaptive.adaptivebandit.AdaptiveBandit method) connected_component_subgraphs() (in module moleculekit.tools.detect) construct() (moleculekit.readers.MolFactory static method) contactVecToMatrix() (in module moleculekit.projections.metricdistance) ContainerBase (class in moleculekit.pdbx.reader.PdbxContainers) containsMetals() (moleculekit.smallmol.smallmol.SmallMol method) convert() (in module htmd.units) convertDisulfide() (in module htmd.builder.builder) convertToString() (in module moleculekit.smallmol.util) coords (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) copy() (htmd.metricdata.MetricData method) (htmd.metricdata.Trajectory method) (htmd.model.Model method) (htmd.simlist.Sim method) (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_pucb() (htmd.adaptive.adaptivebandit.AdaptiveBandit method) count_ucb() (htmd.adaptive.adaptivebandit.AdaptiveBandit method) counter (moleculekit.vmdgraphics.VMDGraphicObject attribute) CRDCARDread() (in module moleculekit.readers) CRDread() (in module moleculekit.readers) createCoreSetModel() (htmd.model.Model method) createDimension() (moleculekit.fileformats.netcdf.netcdf_file method) createProductGraph() (in module moleculekit.tools.graphalignment) createState() (htmd.model.Model method) 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) CustomReporter (class in acemd.reporters) CustomResidue (class in moleculekit.tools.preparation_customres) D dat (htmd.metricdata.MetricData property) 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) DCDwrite() (in module moleculekit.writers) DEBUG (acemd.acemd.FGROUPS attribute) debug() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) decode() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) deconcatenate() (htmd.metricdata.MetricData method) defaultAmberHome() (in module htmd.builder.amber) defaultEquilRestraints() (htmd.protocols.equilibration_v3.Equilibration method) defaultFf() (in module htmd.builder.amber) defaultParam() (in module htmd.builder.amber) (in module htmd.builder.charmm) defaultStream() (in module htmd.builder.charmm) defaultTopo() (in module htmd.builder.amber) (in module htmd.builder.charmm) 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) depict() (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmollib.SmallMolLib method) depictMultipleMols() (in module moleculekit.smallmol.util) describe() (jobqueues.simqueue.QueueJobStatus method) (playmolecule.apps.JobStatus method) describe_apps() (in module playmolecule), [1] describeNextReport() (acemd.reporters.CustomReporter method) (acemd.reporters.LoggingReporter method) description (htmd.metricdata.MetricData attribute) deserialize() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifReader method) detect_input_file() (in module acemd.acemd) detectCisPeptideBonds() (in module htmd.builder.builder) detectDisulfideBonds() (in module htmd.builder.builder) detectEquivalentAtoms() (in module moleculekit.tools.detect) detectParameterizableCores() (in module moleculekit.tools.detect) detectParameterizableDihedrals() (in module moleculekit.tools.detect) diffMolecules() (in module htmd.util) digraph() (in module moleculekit.ply.yacc) Dihedral (class in moleculekit.projections.metricdihedral) dihedralAngle() (in module moleculekit.dihedral) DIHEDRALS (acemd.acemd.FGROUPS attribute) 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) distance (htmd.clustering.kcenters.KCenter attribute) distributeLipids() (in module htmd.membranebuilder.ljfluid) dock() (in module htmd.dock) (in module moleculekit.tools.docking) dr_relation() (moleculekit.ply.yacc.LRTable method) draw_cylinder() (in module moleculekit.pymolgraphics) dropDimensions() (htmd.metricdata.MetricData method) dropFrames() (htmd.metricdata.MetricData method) (htmd.metricdata.Trajectory method) (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) dropTraj() (htmd.metricdata.MetricData method) 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) embed() (in module htmd.builder.builder) empty() (moleculekit.molecule.Molecule method) ensure_type() (in module moleculekit.fileformats.utils) ensurelist() (in module htmd.util) (in module jobqueues.util) (in module moleculekit.util) epochSimIndexes() (in module htmd.adaptive.adaptive) eqDistribution() (htmd.model.Model method) Equilibration (class in htmd.protocols.equilibration_v3) errok() (moleculekit.ply.yacc.LRParser method) ERROR (playmolecule.apps.JobStatus attribute) error() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) (moleculekit.ply.yacc.YaccProduction method) ExecutableDirectory (class in playmolecule.apps) execute_cpu_job() (in module jobqueues.celeryfiles.tasks) execute_gpu_job() (in module jobqueues.celeryfiles.tasks) exists() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) EXTERNAL (acemd.acemd.FGROUPS attribute) F FAILED (jobqueues.simqueue.QueueJobStatus attribute) FGROUPS (class in acemd.acemd) field_widths (acemd.reporters.LoggingReporter attribute) 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_executable() (in module moleculekit.util) find_file() (in module acemd.acemd) find_nonterminal_transitions() (moleculekit.ply.yacc.LRTable method) find_unreachable() (moleculekit.ply.yacc.Grammar method) fit() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) fixedPointDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders 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 (class in htmd.simlist) frame (htmd.simlist.Frame attribute) (moleculekit.molecule.Molecule attribute) (moleculekit.molecule.Molecule property) (moleculekit.smallmol.smallmol.SmallMol property) from_restraint_dict() (acemd.restraints.PositionalRestraint static method) from_restraint_str() (acemd.restraints.PositionalRestraint static method) fromDict() (moleculekit.molecule.Molecule static method) fromHDF5() (htmd.metricdata.MetricData static method) (htmd.metricdata.Trajectory static method) (htmd.simlist.Sim static method) fromMolecule() (moleculekit.molecule.UniqueAtomID static method) (moleculekit.molecule.UniqueResidueID static method) (moleculekit.readers.Topology method) fstep (htmd.metricdata.MetricData attribute) (moleculekit.molecule.Molecule attribute) (moleculekit.molecule.Molecule property) G g0eq (htmd.kinetics.Rates attribute) 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_acemd_system() (in module acemd.acemd) get_all() (moleculekit.ply.lex.LexerReflect method) (moleculekit.ply.yacc.ParserReflect method) get_caller_module_dict() (in module moleculekit.ply.lex) (in module moleculekit.ply.yacc) get_donors_acceptors() (in module moleculekit.interactions.interactions) get_energy_decomposition() (in module acemd.acemd) get_energy_forces() (in module acemd.minimizer) get_error_func() (moleculekit.ply.yacc.ParserReflect method) get_force_str() (in module acemd.restraints) 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_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_rules() (moleculekit.ply.lex.LexerReflect method) get_sim_properties() (in module acemd.acemd) 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) getAllNeighbours() (in module htmd.membranebuilder.ringpenetration) 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) getCurrentPMViewer() (in module moleculekit.viewer) 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) getEpochFromName() (in module htmd.adaptive.adaptive) getEpochSimIdx() (in module htmd.adaptive.util) getEpochTrajectoryDictionary() (in module htmd.adaptive.util) 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() (htmd.projections.metric.Metric method) (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) 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) getParentSimIdxFrame() (in module htmd.adaptive.util) getPDBQTAtomType() (in module moleculekit.tools.atomtyper) getPDBQTAtomTypesAndCharges() (in module moleculekit.tools.atomtyper) getPdbStrings() (in module htmd.util) getProp() (moleculekit.smallmol.smallmol.SmallMol method) getRates() (htmd.kinetics.Kinetics method) getRCSBLigandByLigname() (in module moleculekit.smallmol.util) getRewards() (htmd.adaptive.adaptivebandit.AdaptiveBandit 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) getSequenceProfile() (in module moleculekit.tools.hhblitsprofile) getStates() (htmd.model.Model method) getStateStatistic() (in module htmd.model) 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 GROTOPread() (in module moleculekit.readers) group_objects() (in module moleculekit.pymolgraphics) GroupRestraint (class in htmd.mdengine.acemd.acemd) 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) GWPCA (class in htmd.projections.gwpca) H hasAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) hasBond() (moleculekit.molecule.Molecule method) hbonds_calculate() (in module moleculekit.interactions.interactions) home() (in module htmd.home) (in module jobqueues.home) htmd module htmd.adaptive module htmd.adaptive.adaptive module htmd.adaptive.adaptivebandit module htmd.adaptive.adaptivegoal module htmd.adaptive.adaptivegoaleg module htmd.adaptive.adaptiverun module htmd.adaptive.util module htmd.builder module htmd.builder.amber module htmd.builder.builder module htmd.builder.charmm module htmd.builder.ionize module htmd.builder.loopmodeler module htmd.builder.noncanonical module htmd.builder.solvate module htmd.clustering module htmd.clustering.kcenters module htmd.clustering.regular module htmd.config module htmd.decorators module htmd.dock module htmd.home module htmd.kinetics module htmd.latest module htmd.license module htmd.mdengine module htmd.mdengine.acemd module htmd.mdengine.acemd.acemd module htmd.membranebuilder module htmd.membranebuilder.build_membrane module htmd.membranebuilder.globalminimization module htmd.membranebuilder.ljfluid module htmd.membranebuilder.ringpenetration module htmd.metricdata module htmd.metricdatagenerator module htmd.model module htmd.mutualinformation module htmd.parallelprogress module htmd.pathplanning module htmd.projections module htmd.projections.gwpca module htmd.projections.kmeanstri module htmd.projections.metric module htmd.projections.tica module htmd.protocols module htmd.protocols.equilibration_v3 module htmd.protocols.production_v6 module htmd.session module htmd.simlist module htmd.ui module htmd.units module htmd.util module htmd.versionwarnings module htmd_register() (in module htmd.license) htmd_registration() (in module htmd.license) htmd_show_news() (in module htmd.license) htmdAmberHome() (in module htmd.builder.amber) htmdCharmmHome() (in module htmd.builder.charmm) htmdload() (in module htmd.session) htmdsave() (in module htmd.session) hydrophobic_calculate() (in module moleculekit.interactions.interactions) I IMPLICIT (acemd.acemd.FGROUPS attribute) IMPROPER (acemd.acemd.FGROUPS attribute) impropers (moleculekit.molecule.Molecule attribute) 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) inprogress() (jobqueues.celeryqueue.CeleryQueue method) (jobqueues.lsfqueue.LsfQueue method) (jobqueues.pbsqueue.PBSQueue method) (jobqueues.playqueue.PlayQueue method) (jobqueues.sgequeue.SgeQueue method) (jobqueues.simqueue.SimQueue method) (jobqueues.slurmqueue.SlurmQueue method) InProgressError input() (in module moleculekit.ply.lex) (moleculekit.ply.lex.Lexer method) insert() (moleculekit.molecule.Molecule method) insertion (moleculekit.molecule.Molecule attribute) integerPackingDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders 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) ionize() (in module htmd.builder.ionize) ionizePlace() (in module htmd.builder.ionize) 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 jobInfo() (jobqueues.slurmqueue.SlurmQueue method) jobqueues module jobqueues.celeryfiles module jobqueues.celeryfiles.celery module jobqueues.celeryfiles.tasks module jobqueues.celeryqueue module jobqueues.config module jobqueues.home module jobqueues.localqueue module jobqueues.lsfqueue module jobqueues.pbsqueue module jobqueues.playqueue module jobqueues.sgequeue module jobqueues.simqueue module jobqueues.slurmqueue module jobqueues.util module JobStatus (class in playmolecule.apps) JSONread() (in module moleculekit.readers) JSONwrite() (in module moleculekit.writers) K K (htmd.metricdata.MetricData attribute) KCenter (class in htmd.clustering.kcenters) kdeq (htmd.kinetics.Rates attribute) kill() (in module jobqueues.celeryfiles.tasks) Kinetics (class in htmd.kinetics) KMeansTri (class in htmd.projections.kmeanstri) koff (htmd.kinetics.Rates attribute) kon (htmd.kinetics.Rates attribute) KWARGS (class in playmolecule.apps) L labels_ (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) LALRError least_square_fit_plane() (in module htmd.membranebuilder.ringpenetration) lengths_and_angles_to_box_vectors() (in module moleculekit.unitcell) lengths_and_angles_to_tilt_factors() (in module moleculekit.unitcell) letter_code() (moleculekit.tools.preparation_customres.CustomResidue method) 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) 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.molecule.Representations method) listFiles() (in module htmd.builder.amber) (in module htmd.builder.charmm) listLipids() (in module htmd.membranebuilder.build_membrane) load() (htmd.metricdata.MetricData method) (htmd.model.Model method) load_molecule() (in module acemd.acemd) loadConfig() (in module jobqueues.config) loadMI() (htmd.mutualinformation.MutualInformation method) loadMol() (moleculekit.vmdviewer.VMD method) LocalCPUQueue (class in jobqueues.localqueue) LocalGPUQueue (class in jobqueues.localqueue) LoggingReporter (class in acemd.reporters) loopModeller() (in module htmd.builder.loopmodeler) 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) LsfQueue (class in jobqueues.lsfqueue) M macro_ofcluster (htmd.model.Model property) macro_ofmicro (htmd.model.Model property) macroAccumulate() (in module htmd.model) macronum (htmd.model.Model property) MAEread() (in module moleculekit.readers) makeMolGraph() (in module moleculekit.tools.graphalignment) manual() (in module moleculekit.projections.metricplumed2) map (htmd.metricdata.MetricData property) markovModel() (htmd.model.Model method) masses (moleculekit.molecule.Molecule attribute) maxConnectedLag() (htmd.model.Model method) maxDistance() (in module moleculekit.util) 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) memory (jobqueues.celeryqueue.CeleryQueue property) (jobqueues.localqueue.LocalCPUQueue property) (jobqueues.localqueue.LocalGPUQueue property) (jobqueues.lsfqueue.LsfQueue property) (jobqueues.pbsqueue.PBSQueue property) (jobqueues.playqueue.PlayQueue property) (jobqueues.sgequeue.SgeQueue property) (jobqueues.simqueue.SimQueue property) (jobqueues.slurmqueue.SlurmQueue property) metal_coordination_calculate() (in module moleculekit.interactions.interactions) Metric (class in htmd.projections.metric) MetricCoordinate (class in moleculekit.projections.metriccoordinate) MetricData (class in htmd.metricdata) MetricDataGenerator (class in htmd.metricdatagenerator) 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) mfptoff (htmd.kinetics.Rates attribute) mfpton (htmd.kinetics.Rates attribute) micro_ofcluster (htmd.model.Model property) micronum (htmd.model.Model property) minimalRotation() (in module htmd.builder.builder) minimize() (in module acemd.minimizer) (in module htmd.membranebuilder.globalminimization) MissingAngleError MissingAtomTypeError MissingBondError MissingParameterError MissingResidueError MissingTorsionError MixedSegmentError MMTFread() (in module moleculekit.readers) MMTFwrite() (in module moleculekit.writers) Model (class in htmd.model) model_gaps() (in module moleculekit.tools.modelling) module acemd acemd.acemd acemd.charmm acemd.licensing acemd.minimizer acemd.protocols acemd.reporters acemd.restraints acemd.utils acemd.versionwarnings htmd htmd.adaptive htmd.adaptive.adaptive htmd.adaptive.adaptivebandit htmd.adaptive.adaptivegoal htmd.adaptive.adaptivegoaleg htmd.adaptive.adaptiverun htmd.adaptive.util htmd.builder htmd.builder.amber htmd.builder.builder htmd.builder.charmm htmd.builder.ionize htmd.builder.loopmodeler htmd.builder.noncanonical htmd.builder.solvate htmd.clustering htmd.clustering.kcenters htmd.clustering.regular htmd.config htmd.decorators htmd.dock htmd.home htmd.kinetics htmd.latest htmd.license htmd.mdengine htmd.mdengine.acemd htmd.mdengine.acemd.acemd htmd.membranebuilder htmd.membranebuilder.build_membrane htmd.membranebuilder.globalminimization htmd.membranebuilder.ljfluid htmd.membranebuilder.ringpenetration htmd.metricdata htmd.metricdatagenerator htmd.model htmd.mutualinformation htmd.parallelprogress htmd.pathplanning htmd.projections htmd.projections.gwpca htmd.projections.kmeanstri htmd.projections.metric htmd.projections.tica htmd.protocols htmd.protocols.equilibration_v3 htmd.protocols.production_v6 htmd.session htmd.simlist htmd.ui htmd.units htmd.util htmd.versionwarnings jobqueues jobqueues.celeryfiles jobqueues.celeryfiles.celery jobqueues.celeryfiles.tasks jobqueues.celeryqueue jobqueues.config jobqueues.home jobqueues.localqueue jobqueues.lsfqueue jobqueues.pbsqueue jobqueues.playqueue jobqueues.sgequeue jobqueues.simqueue jobqueues.slurmqueue jobqueues.util moleculekit moleculekit.align moleculekit.atomselect moleculekit.atomselect.analyze moleculekit.atomselect.atomselect moleculekit.atomselect.languageparser moleculekit.bondguesser moleculekit.config moleculekit.dihedral moleculekit.distance moleculekit.fileformats moleculekit.fileformats.netcdf moleculekit.fileformats.utils moleculekit.interactions moleculekit.interactions.interactions moleculekit.molecule 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.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.rdkitintegration moleculekit.readers moleculekit.smallmol moleculekit.smallmol.smallmol moleculekit.smallmol.smallmolcdp moleculekit.smallmol.smallmollib moleculekit.smallmol.util moleculekit.tools moleculekit.tools.atomtyper moleculekit.tools.autosegment moleculekit.tools.crystalpacking moleculekit.tools.detect moleculekit.tools.docking moleculekit.tools.graphalignment moleculekit.tools.hhblitsprofile moleculekit.tools.modelling moleculekit.tools.moleculechecks moleculekit.tools.obabel_tools moleculekit.tools.obabel_tools.obabel_cli moleculekit.tools.preparation moleculekit.tools.preparation_customres moleculekit.tools.sequencestructuralalignment moleculekit.tools.voxeldescriptors moleculekit.unitcell moleculekit.util moleculekit.viewer moleculekit.vmdgraphics moleculekit.vmdviewer moleculekit.writers playmolecule, [1] playmolecule.apps MOL2read() (in module moleculekit.readers) MOL2write() (in module moleculekit.writers) mol_equal() (in module moleculekit.molecule) Molecule (class in moleculekit.molecule) moleculekit module moleculekit.align module moleculekit.atomselect module moleculekit.atomselect.analyze module moleculekit.atomselect.atomselect module moleculekit.atomselect.languageparser module moleculekit.bondguesser module moleculekit.config module moleculekit.dihedral module moleculekit.distance module moleculekit.fileformats module moleculekit.fileformats.netcdf module moleculekit.fileformats.utils module moleculekit.interactions module moleculekit.interactions.interactions module moleculekit.molecule 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.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.rdkitintegration module moleculekit.readers module moleculekit.smallmol module moleculekit.smallmol.smallmol module moleculekit.smallmol.smallmolcdp module moleculekit.smallmol.smallmollib module moleculekit.smallmol.util module moleculekit.tools module moleculekit.tools.atomtyper module moleculekit.tools.autosegment 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.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.unitcell module moleculekit.util module moleculekit.viewer module moleculekit.vmdgraphics module moleculekit.vmdviewer module moleculekit.writers module MolFactory (class in moleculekit.readers) molRMSD() (in module moleculekit.util) molTMalign() (in module moleculekit.align) molTMscore() (in module moleculekit.align) moveBy() (moleculekit.molecule.Molecule method) moveLipidToPos() (in module htmd.membranebuilder.ringpenetration) movie_reps() (moleculekit.vmdviewer.VMD method) mutateResidue() (moleculekit.molecule.Molecule method) MutualInformation (class in htmd.mutualinformation) N N (htmd.metricdata.MetricData attribute) name (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) natsorted() (in module moleculekit.util) ncpu (jobqueues.celeryqueue.CeleryQueue property) (jobqueues.localqueue.LocalCPUQueue property) (jobqueues.localqueue.LocalGPUQueue property) (jobqueues.lsfqueue.LsfQueue property) (jobqueues.pbsqueue.PBSQueue property) (jobqueues.playqueue.PlayQueue property) (jobqueues.sgequeue.SgeQueue property) (jobqueues.simqueue.SimQueue property) (jobqueues.slurmqueue.SlurmQueue property) netcdf_file (class in moleculekit.fileformats.netcdf) netcdf_variable (class in moleculekit.fileformats.netcdf) NETCDFread() (in module moleculekit.readers) NETCDFwrite() (in module moleculekit.writers) newMetricData() (htmd.metricdatagenerator.MetricDataGenerator method) newTrajectoriesClusterJumping() (htmd.metricdatagenerator.MetricDataGenerator method) newTrajectoriesFiller() (htmd.metricdatagenerator.MetricDataGenerator method) newTrajectoriesMSM() (htmd.metricdatagenerator.MetricDataGenerator method) newTrajectoriesSimple() (htmd.metricdatagenerator.MetricDataGenerator method) ngpu (jobqueues.celeryqueue.CeleryQueue property) (jobqueues.localqueue.LocalCPUQueue property) (jobqueues.localqueue.LocalGPUQueue property) (jobqueues.lsfqueue.LsfQueue property) (jobqueues.pbsqueue.PBSQueue property) (jobqueues.playqueue.PlayQueue property) (jobqueues.sgequeue.SgeQueue property) (jobqueues.simqueue.SimQueue property) (jobqueues.slurmqueue.SlurmQueue property) NNP (acemd.acemd.FGROUPS attribute) NONBONDED (acemd.acemd.FGROUPS attribute) notcompleted() (jobqueues.simqueue.SimQueue method) NullLogger (class in moleculekit.ply.yacc) numAtoms (moleculekit.molecule.Molecule attribute) (moleculekit.molecule.Molecule property) (moleculekit.smallmol.smallmol.SmallMol property) (moleculekit.smallmol.smallmolcdp.SmallMolCDP property) numBonds (moleculekit.molecule.Molecule property) numDimensions (htmd.metricdata.MetricData property) (htmd.metricdata.Trajectory property) numFrames (htmd.metricdata.MetricData property) (htmd.metricdata.Trajectory property) (moleculekit.molecule.Molecule attribute) (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 attribute) (moleculekit.molecule.Molecule property) numTrajectories (htmd.metricdata.MetricData property) O occupancy (moleculekit.molecule.Molecule attribute) offset_ligand_props() (in module moleculekit.interactions.interactions) omega() (moleculekit.projections.metricdihedral.Dihedral static method) openbabelConvert() (in module moleculekit.tools.obabel_tools) openFileOrStringIO() (in module moleculekit.readers) opm() (in module moleculekit.util) orientOnAxes() (in module moleculekit.util) OUT_OF_MEMORY (jobqueues.simqueue.QueueJobStatus attribute) P P (htmd.model.Model property) p_compop() (in module moleculekit.atomselect.languageparser) p_error() (in module moleculekit.atomselect.languageparser) p_expression_backbonetype() (in module moleculekit.atomselect.languageparser) p_expression_comp() (in module moleculekit.atomselect.languageparser) p_expression_exwithin() (in module moleculekit.atomselect.languageparser) p_expression_grouped() (in module moleculekit.atomselect.languageparser) p_expression_logop() (in module moleculekit.atomselect.languageparser) p_expression_molprop() (in module moleculekit.atomselect.languageparser) p_expression_numprop() (in module moleculekit.atomselect.languageparser) p_expression_sameas() (in module moleculekit.atomselect.languageparser) p_expression_unary_not() (in module moleculekit.atomselect.languageparser) p_expression_within() (in module moleculekit.atomselect.languageparser) p_float() (in module moleculekit.atomselect.languageparser) p_float_unary_minus() (in module moleculekit.atomselect.languageparser) p_func_number() (in module moleculekit.atomselect.languageparser) p_integer() (in module moleculekit.atomselect.languageparser) p_integer_range() (in module moleculekit.atomselect.languageparser) p_integer_unary_minus() (in module moleculekit.atomselect.languageparser) p_literal_list() (in module moleculekit.atomselect.languageparser) p_logop() (in module moleculekit.atomselect.languageparser) p_mathop() (in module moleculekit.atomselect.languageparser) p_molecule() (in module moleculekit.atomselect.languageparser) p_molprop_int() (in module moleculekit.atomselect.languageparser) p_molprop_int_comp() (in module moleculekit.atomselect.languageparser) p_molprop_int_eq() (in module moleculekit.atomselect.languageparser) p_molprop_int_modulo() (in module moleculekit.atomselect.languageparser) p_molprop_string() (in module moleculekit.atomselect.languageparser) p_molprop_string_eq() (in module moleculekit.atomselect.languageparser) p_num_funcs() (in module moleculekit.atomselect.languageparser) p_number() (in module moleculekit.atomselect.languageparser) p_number_expression() (in module moleculekit.atomselect.languageparser) p_number_mathop() (in module moleculekit.atomselect.languageparser) p_number_unary_minus() (in module moleculekit.atomselect.languageparser) p_numprop_as_str() (in module moleculekit.atomselect.languageparser) p_numprop_eq_list() (in module moleculekit.atomselect.languageparser) p_numprop_eq_number() (in module moleculekit.atomselect.languageparser) p_numprop_mathop() (in module moleculekit.atomselect.languageparser) p_numprop_number() (in module moleculekit.atomselect.languageparser) p_prop_funcs() (in module moleculekit.atomselect.languageparser) p_string() (in module moleculekit.atomselect.languageparser) parallel() (in module moleculekit.tools.atomtyper) ParallelExecutor() (in module htmd.parallelprogress) parallelfunc() (in module htmd.pathplanning) parallelTest() (htmd.metricdatagenerator.MetricDataGenerator method) parameterizeNonCanonicalResidues() (in module htmd.builder.noncanonical) parse() (in module moleculekit.ply.yacc) (moleculekit.ply.yacc.LRParser method) parse_grammar() (in module moleculekit.ply.yacc) parse_input_file() (in module acemd.acemd) parse_restraint() (acemd.restraints.PositionalRestraint static method) parse_setpoint() (in module acemd.restraints) parse_setpoints() (in module acemd.restraints) ParserReflect (class in moleculekit.ply.yacc) parseV3000SDF() (in module moleculekit.readers) PBSQueue (class in jobqueues.pbsqueue) 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) PENDING (jobqueues.simqueue.QueueJobStatus attribute) phi() (moleculekit.projections.metricdihedral.Dihedral static method) piece (htmd.simlist.Frame attribute) pipi_calculate() (in module moleculekit.interactions.interactions) playmolecule module, [1] playmolecule.apps module PlayQueue (class in jobqueues.playqueue) plotClusters() (htmd.metricdata.MetricData method) plotCounts() (htmd.metricdata.MetricData method) plotFES() (htmd.model.Model method) plotFluxPathways() (htmd.kinetics.Kinetics method) plotMarkovModel() (htmd.kinetics.Kinetics method) plotRates() (htmd.kinetics.Kinetics method) plotTimescales() (htmd.model.Model method) plotTrajSizes() (htmd.metricdata.MetricData method) PLUMED (acemd.acemd.FGROUPS attribute) plumed_parser() (in module acemd.utils) 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) pmws() (playmolecule.apps.ExecutableDirectory method) pop_state() (moleculekit.ply.lex.Lexer method) PositionalRestraint (class in acemd.restraints) 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) print_energy_decomposition() (in module acemd.acemd) 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 htmd.protocols.production_v6) (class in moleculekit.ply.yacc) project() (htmd.projections.gwpca.GWPCA method) (htmd.projections.kmeanstri.KMeansTri method) (htmd.projections.metric.Metric method) (htmd.projections.tica.TICA method) (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) projection (htmd.metricdata.Trajectory property) ProjectNotExistError proteinDihedrals() (moleculekit.projections.metricdihedral.Dihedral static method) proteinHasBonds() (in module moleculekit.tools.moleculechecks) proteinPrepare() (in module moleculekit.tools.preparation) 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 QueueJobStatus (class in jobqueues.simqueue) R Rates (class in htmd.kinetics) raytracing() (in module htmd.pathplanning) rcsbFindLigands() (in module moleculekit.rcsb) rcsbFindMutatedResidues() (in module moleculekit.rcsb) read() (moleculekit.molecule.Molecule method) (moleculekit.pdbx.reader.PdbxParser.PdbxReader method) (moleculekit.pdbx.reader.PdbxReader.PdbxReader method) readConfig() (htmd.mdengine.acemd.acemd.Acemd method) readCube() (in module moleculekit.util) reads_relation() (moleculekit.ply.yacc.LRTable method) reconstructAdaptiveTraj() (in module htmd.adaptive.adaptive) reconstructContactMap() (in module moleculekit.projections.metricdistance) record (moleculekit.molecule.Molecule attribute) reduced (moleculekit.ply.yacc.Production attribute) ref (htmd.metricdata.MetricData property) reference (htmd.metricdata.Trajectory property) RegCluster (class in htmd.clustering.regular) rel2sim() (htmd.metricdata.MetricData method) remove() (moleculekit.molecule.Molecule method) (moleculekit.molecule.Representations method) (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) removeAtomsInHull() (in module htmd.builder.builder) removeBond() (moleculekit.molecule.Molecule method) removeHET() (in module htmd.builder.builder) removeHs() (moleculekit.smallmol.smallmol.SmallMol method) removeLipidsInProtein() (in module htmd.builder.builder) 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) report() (acemd.reporters.CustomReporter method) (acemd.reporters.LoggingReporter method) Representations (class in moleculekit.molecule) reps (moleculekit.molecule.Molecule attribute) resid (moleculekit.molecule.Molecule attribute) ResidueInsertionError resname (moleculekit.molecule.Molecule attribute) resolveRingPenetrations() (in module htmd.membranebuilder.ringpenetration) restart() (moleculekit.ply.yacc.LRParser method) retrieve() (jobqueues.celeryqueue.CeleryQueue method) (jobqueues.lsfqueue.LsfQueue method) (jobqueues.pbsqueue.PBSQueue method) (jobqueues.playqueue.PlayQueue method) (jobqueues.sgequeue.SgeQueue method) (jobqueues.simqueue.SimQueue method) (jobqueues.slurmqueue.SlurmQueue method) RetrieveError 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) rrt() (in module htmd.pathplanning) rrtstarsmart() (in module htmd.pathplanning) RTFread() (in module moleculekit.readers) run() (htmd.adaptive.adaptive.AdaptiveBase method) (in module acemd.acemd) (playmolecule.apps.ExecutableDirectory method) runLengthDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) runmain() (in module moleculekit.ply.lex) RUNNING (jobqueues.simqueue.QueueJobStatus attribute) (playmolecule.apps.JobStatus attribute) S saltbridge_calculate() (in module moleculekit.interactions.interactions) sampleClusters() (htmd.metricdata.MetricData method) sampleRegion() (htmd.metricdata.MetricData method) sampleStates() (htmd.model.Model method) sanitize() (moleculekit.smallmol.smallmol.SmallMol method) save() (htmd.metricdata.MetricData method) (htmd.model.Model method) save_graphml() (htmd.mutualinformation.MutualInformation method) saveMI() (htmd.mutualinformation.MutualInformation method) sdf_generator() (in module moleculekit.readers) SDFread() (in module moleculekit.readers) sdfReader() (in module moleculekit.smallmol.smallmollib) SDFwrite() (in module moleculekit.writers) search() (in module htmd.builder.charmm) 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) set() (htmd.projections.metric.Metric method) (moleculekit.molecule.Molecule method) set_defaulted_states() (moleculekit.ply.yacc.LRParser method) set_fit_request() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster 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) setup_acemd() (in module acemd.acemd) setup_barostat() (in module acemd.acemd) setup_equilibration() (in module acemd.protocols) setup_extforces() (in module acemd.restraints) setup_production() (in module acemd.protocols) setup_reporters() (in module acemd.reporters) setupForce() (acemd.restraints.PositionalRestraint method) setValue() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) SgeQueue (class in jobqueues.sgequeue) shape (moleculekit.fileformats.netcdf.netcdf_variable property) sigmahole_calculate() (in module moleculekit.interactions.interactions) signature() (moleculekit.ply.yacc.ParserReflect method) Sim (class in htmd.simlist) sim (htmd.simlist.Frame attribute) simfilter() (in module htmd.simlist) simlist (htmd.metricdata.MetricData property) simlist() (in module htmd.simlist) simmerge() (in module htmd.simlist) SimQueue (class in jobqueues.simqueue) skip() (moleculekit.ply.lex.Lexer method) slurm() (playmolecule.apps.ExecutableDirectory method) slurm_mps() (in module playmolecule.apps) SlurmQueue (class in jobqueues.slurmqueue) 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) solvate() (in module htmd.builder.solvate) SpeedLogger (class in acemd.reporters) split() (in module htmd.builder.charmm) splitCols() (htmd.metricdata.MetricData method) squareform() (in module moleculekit.distance) St (htmd.metricdata.MetricData property) StandardPDBChiralAtom() (in module moleculekit.rdkitintegration) StandardPDBResidueChirality() (in module moleculekit.rdkitintegration) status (playmolecule.apps.ExecutableDirectory property) step() (acemd.reporters.SpeedLogger method) stop() (jobqueues.celeryqueue.CeleryQueue method) (jobqueues.lsfqueue.LsfQueue method) (jobqueues.pbsqueue.PBSQueue method) (jobqueues.playqueue.PlayQueue method) (jobqueues.sgequeue.SgeQueue method) (jobqueues.simqueue.SimQueue method) (jobqueues.slurmqueue.SlurmQueue method) string_to_tempfile() (in module moleculekit.util) stringArrayDecoder() (moleculekit.pdbx.reader.BinaryCifReader.BinaryCifDecoders method) stripSalts() (moleculekit.smallmol.smallmol.SmallMol method) submit() (jobqueues.celeryqueue.CeleryQueue method) (jobqueues.lsfqueue.LsfQueue method) (jobqueues.pbsqueue.PBSQueue method) (jobqueues.playqueue.PlayQueue method) (jobqueues.sgequeue.SgeQueue method) (jobqueues.simqueue.SimQueue method) (jobqueues.slurmqueue.SlurmQueue method) SubmitError sync() (moleculekit.fileformats.netcdf.netcdf_file method) SyntaxError, [1] systemPrepare() (in module moleculekit.tools.preparation) T t_error() (in module moleculekit.atomselect.languageparser) t_FLOAT() (in module moleculekit.atomselect.languageparser) t_INTEGER() (in module moleculekit.atomselect.languageparser) t_QUOTEDFLOAT() (in module moleculekit.atomselect.languageparser) t_QUOTEDINT() (in module moleculekit.atomselect.languageparser) t_QUOTEDSTRING() (in module moleculekit.atomselect.languageparser) t_QUOTEDSTRINGSINGLE() (in module moleculekit.atomselect.languageparser) t_STRING() (in module moleculekit.atomselect.languageparser) t_XCOOR() (in module moleculekit.atomselect.languageparser) t_YCOOR() (in module moleculekit.atomselect.languageparser) t_ZCOOR() (in module moleculekit.atomselect.languageparser) tempname() (in module htmd.util) (in module moleculekit.util) testDHFR() (in module htmd.util) TICA (class in htmd.projections.tica) tileMembrane() (in module htmd.builder.builder) time (moleculekit.molecule.Molecule attribute) TIMEOUT (jobqueues.simqueue.QueueJobStatus attribute) to_dict() (acemd.restraints.PositionalRestraint method) toDataFrame() (moleculekit.smallmol.smallmollib.SmallMolLib method) toDict() (moleculekit.molecule.Molecule method) toGraph() (moleculekit.molecule.Molecule method) toHDF5() (htmd.metricdata.MetricData method) (htmd.metricdata.Trajectory method) (htmd.simlist.Sim 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) Topology (class in moleculekit.readers) TopologyInconsistencyError, [1] toRDKITmol() (in module moleculekit.rdkitintegration) toSMARTS() (moleculekit.smallmol.smallmol.SmallMol method) toSMILES() (moleculekit.smallmol.smallmol.SmallMol method) tq() (moleculekit.vmdgraphics.VMDGraphicObject static method) trajectories (htmd.metricdata.MetricData attribute) Trajectory (class in htmd.metricdata) (class in moleculekit.readers) trajLengths (htmd.metricdata.MetricData property) translateBy() (moleculekit.molecule.Molecule method) traverse() (in module moleculekit.ply.yacc) traverse_ast() (in module moleculekit.atomselect.atomselect) Tree (class in htmd.pathplanning) TRRread() (in module moleculekit.readers) TRRwrite() (in module moleculekit.writers) TypeCastPerformanceWarning typecode() (moleculekit.fileformats.netcdf.netcdf_variable method) 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) update_restraints() (in module acemd.restraints) updatingMean() (in module htmd.adaptive.util) UREYBRADLEY (acemd.acemd.FGROUPS 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() (htmd.mdengine.acemd.acemd.GroupRestraint method) (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) viewStates() (htmd.model.Model method) viewVoxelFeatures() (in module moleculekit.tools.voxeldescriptors) 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() (jobqueues.simqueue.SimQueue method) wait_for_port() (in module moleculekit.util) WAITING_INFO (playmolecule.apps.JobStatus attribute) warning() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) waterbridge_calculate() (in module moleculekit.interactions.interactions) weightGraph() (htmd.mutualinformation.MutualInformation method) wrap() (in module htmd.membranebuilder.ringpenetration) (moleculekit.molecule.Molecule method) wrapping_dist_python() (in module htmd.membranebuilder.build_membrane) write() (htmd.mdengine.acemd.acemd.Acemd method) (htmd.protocols.equilibration_v3.Equilibration method) (htmd.protocols.production_v6.Production method) (moleculekit.molecule.Molecule method) (moleculekit.pdbx.reader.PdbxParser.PdbxWriter method) (moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method) (moleculekit.smallmol.smallmol.SmallMol method) 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)
