Index

_

__getitem__() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method)

A

abs2rel() (htmd.metricdata.MetricData method) (in module htmd.metricdatagenerator) abs2sim() (htmd.metricdata.MetricData method) Acemd (class in htmd.mdengine.acemd.acemd) 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_fields() (playmolecule.jsonlogger.JsonFormatter 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) addsubcommands() (playmolecule.plac.ArgumentParser method) aggregateTime (htmd.metricdata.MetricData property) alias() (playmolecule.plac.ArgumentParser method) align() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) alignBySequence() (moleculekit.molecule.Molecule method) ALPHAFOLDread() (in module moleculekit.readers) altloc (moleculekit.molecule.Molecule attribute) analyze() (in module moleculekit.atomselect.analyze) angles (moleculekit.molecule.Molecule attribute) Annotation (class in playmolecule.plac)

annotations() (in module playmolecule.plac) app_arg_parser() (in module playmolecule.devutils) app_arg_parser2() (in module playmolecule.devutils) app_wrapper() (in module playmolecule.devutils) app_wrapper2() (in module playmolecule.devutils) 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) ArgumentParser (class in playmolecule.plac) assertSameAsReferenceDir() (in module htmd.util) (in module moleculekit.util) 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) 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

basenameInputs() (in module playmolecule.devutils) begin() (moleculekit.ply.lex.Lexer method) beta (moleculekit.molecule.Molecule attribute) BINCOORread() (in module moleculekit.readers) BINCOORwrite() (in module moleculekit.writers) bind() (moleculekit.ply.yacc.Production method) bind_callables() (moleculekit.ply.yacc.LRTable method) bond_grid_search() (in module moleculekit.bondguesser) bonds (moleculekit.molecule.Molecule attribute)

bondtype (moleculekit.molecule.Molecule attribute) bootstrap() (htmd.metricdata.MetricData method) boundingBox() (in module moleculekit.util) box (moleculekit.molecule.Molecule attribute) boxangles (moleculekit.molecule.Molecule attribute) 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)

C

calculate() (htmd.mutualinformation.MutualInformation method) calculateUniqueBonds() (in module moleculekit.molecule) call() (in module playmolecule.plac) cancel() (playmolecule.job.Job method) cancel_job() (playmolecule.session.Session method) CANCELLED (jobqueues.simqueue.QueueJobStatus attribute) case_sensitive (playmolecule.plac.ArgumentParser attribute) categoryPart() (moleculekit.pdbx.reader.PdbxContainers.CifName static method) cationpi_calculate() (in module moleculekit.interactions.interactions) 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) chain (moleculekit.molecule.Molecule attribute) change_password() (playmolecule.session.Session method) charge (moleculekit.molecule.Molecule attribute) 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) clone() (moleculekit.ply.lex.Lexer method) close() (moleculekit.vmdviewer.VMD method) closestDistance() (in module moleculekit.tools.moleculechecks) cluster (htmd.metricdata.Trajectory property) cluster() (htmd.metricdata.MetricData method) (in module moleculekit.smallmol.tools.clustering) 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) 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.job.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) consume() (playmolecule.plac.ArgumentParser 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) 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) createProductGraph() (in module moleculekit.tools.graphalignment) createState() (htmd.model.Model method) critical() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) crystalinfo (moleculekit.molecule.Molecule attribute) current_state() (moleculekit.ply.lex.Lexer method) CustomResidue (class in moleculekit.tools.preparation_customres)

D

dat (htmd.metricdata.MetricData attribute) (htmd.metricdata.MetricData property) DataCategory (class in moleculekit.pdbx.reader.PdbxContainers) DataCategoryBase (class in moleculekit.pdbx.reader.PdbxContainers) DataCenter (class in playmolecule.datacenter) DataCenterError DataContainer (class in moleculekit.pdbx.reader.PdbxContainers) Dataset (class in playmolecule.datacenter) debug() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) deconcatenate() (htmd.metricdata.MetricData method) default() (playmolecule.jsonlogger.JsonEncoder 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) delete_job() (playmolecule.session.Session method) deleteBonds() (moleculekit.molecule.Molecule method) depict() (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmollib.SmallMolLib method) depictMultipleMols() (in module moleculekit.smallmol.util) describe() (jobqueues.simqueue.QueueJobStatus method) (playmolecule.job.Job method) (playmolecule.job.JobStatus method)

describe_app() (playmolecule.session.Session method) describeNextReport() (htmd.membranebuilder.pdbreporter.PDBReporter method) 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) DiceDistances() (in module moleculekit.smallmol.tools.clustering) diffMolecules() (in module htmd.util) 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) 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) download() (playmolecule.datacenter.Dataset method) download_dataset() (in module playmolecule.datacenter) (playmolecule.datacenter.DataCenter method) 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) elements_from_masses() (in module moleculekit.periodictable) embed() (in module htmd.builder.builder) empty() (moleculekit.molecule.Molecule method) enable_json_logger() (in module playmolecule.jsonlogger) ensurelist() (in module htmd.util) (in module jobqueues.util) (in module moleculekit.util) (in module playmolecule.utils)

epochSimIndexes() (in module htmd.adaptive.adaptive) eqDistribution() (htmd.model.Model method) equilibrateSystem() (in module htmd.membranebuilder.simulate_openmm) Equilibration (class in htmd.protocols.equilibration_v3) errok() (moleculekit.ply.yacc.LRParser method) ERROR (playmolecule.job.JobStatus attribute) error() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) (moleculekit.ply.yacc.YaccProduction method) exists() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)

F

FAILED (jobqueues.simqueue.QueueJobStatus attribute) file_diff() (in module moleculekit.util) fileloc (moleculekit.molecule.Molecule attribute) filter() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) find_backbone() (in module moleculekit.atomselect.analyze) find_executable() (in module moleculekit.util) 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) flg() (in module playmolecule.plac) folder_diff() (in module moleculekit.util) formalcharge (moleculekit.molecule.Molecule attribute) format() (playmolecule.jsonlogger.JsonFormatter method) format_datetime_obj() (playmolecule.jsonlogger.JsonEncoder method) format_filesize() (in module playmolecule.utils) 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_() (playmolecule.plac.Annotation class 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) generateConformers() (moleculekit.smallmol.smallmol.SmallMol 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_apps() (playmolecule.session.Session method) get_caller_module_dict() (in module moleculekit.ply.lex) (in module moleculekit.ply.yacc) get_children() (playmolecule.job.Job method) get_dataset_tags() (playmolecule.datacenter.DataCenter method) get_datasets() (in module playmolecule.datacenter) (playmolecule.datacenter.DataCenter method) get_destination_folder() (in module playmolecule.utils) get_donors_acceptors() (in module moleculekit.interactions.interactions) get_error_func() (moleculekit.ply.yacc.ParserReflect method) get_error_info() (playmolecule.job.Job method) get_job() (playmolecule.session.Session method) get_jobs() (playmolecule.session.Session method) get_ligand_aryl_halides() (in module moleculekit.interactions.interactions) get_ligand_charged() (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_pfunctions() (moleculekit.ply.yacc.ParserReflect method) get_precedence() (moleculekit.ply.yacc.ParserReflect method) get_progress() (playmolecule.job.Job 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_rules() (moleculekit.ply.lex.LexerReflect method) get_service_status() (playmolecule.session.Session method) get_start() (moleculekit.ply.yacc.ParserReflect method) get_states() (moleculekit.ply.lex.LexerReflect method) get_status() (playmolecule.job.Job method) get_tokens() (moleculekit.ply.lex.LexerReflect method) (moleculekit.ply.yacc.ParserReflect method) getAllNeighbours() (in module htmd.membranebuilder.ringpenetration) getargspec() (in module playmolecule.plac) 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.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) getCurrentMolstarViewer() (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) getJobId() (in module playmolecule.devutils) 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) getMaximumCommonSubstructure() (in module moleculekit.smallmol.tools.clustering) 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) 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.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) guessAnglesAndDihedrals() (in module moleculekit.util) 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) (in module moleculekit.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.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.pdbreporter module htmd.membranebuilder.ringpenetration module htmd.membranebuilder.simulate_openmm module htmd.metricdata module htmd.metricdatagenerator module htmd.model module

htmd.molecule module htmd.molecule.molecule module htmd.molecule.util 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.metriccoordinate module htmd.projections.metricdihedral module htmd.projections.metricdistance module htmd.projections.metricfluctuation module htmd.projections.metricplumed2 module htmd.projections.metricrmsd module htmd.projections.metricsasa module htmd.projections.metricsecondarystructure module htmd.projections.metricshell module htmd.projections.metricsphericalcoordinate module htmd.projections.metrictmscore module htmd.projections.tica module htmd.protocols module htmd.protocols.equilibration_v3 module htmd.protocols.production_v6 module htmd.queues module htmd.queues.localqueue module htmd.queues.lsfqueue module htmd.queues.pbsqueue module htmd.queues.playqueue module htmd.queues.simqueue module htmd.queues.slurmqueue module htmd.session module htmd.simlist module htmd.ui module htmd.units module htmd.util module htmd.version module htmd.versionwarnings module htmdAmberHome() (in module htmd.builder.amber) htmdCharmmHome() (in module htmd.builder.charmm) htmdload() (in module htmd.session) htmdsave() (in module htmd.session)

I

identifier (playmolecule.datacenter.Dataset property) impropers (moleculekit.molecule.Molecule attribute) infinite_cycles() (moleculekit.ply.yacc.Grammar method) info() (moleculekit.ply.lex.PlyLogger method) (moleculekit.ply.yacc.PlyLogger method) 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) (playmolecule.playqueue.PlayQueue method) InProgressError input (htmd.simlist.Sim attribute) input() (in module moleculekit.ply.lex) (moleculekit.ply.lex.Lexer method)

insert() (moleculekit.molecule.Molecule method) insertion (moleculekit.molecule.Molecule attribute) 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) is_annotation() (in module playmolecule.plac) 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) iterable() (in module playmolecule.plac)

J

Job (class in playmolecule.job) JobBucketNotFoundError JobConfigNotLoadedError JobError 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.job) JsonEncoder (class in playmolecule.jsonlogger) JsonFormatter (class in playmolecule.jsonlogger) jsonify_log_record() (playmolecule.jsonlogger.JsonFormatter method)

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)

L

labels_ (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) LALRError least_square_fit_plane() (in module htmd.membranebuilder.ringpenetration) 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) lineno() (moleculekit.ply.yacc.YaccProduction method) linespan() (moleculekit.ply.yacc.YaccProduction method) list() (moleculekit.molecule.Representations method) list_files() (playmolecule.datacenter.Dataset 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) loadConfig() (in module jobqueues.config) (in module playmolecule.config) loadMI() (htmd.mutualinformation.MutualInformation method) loadMol() (moleculekit.vmdviewer.VMD method) LocalCPUQueue (class in jobqueues.localqueue) LocalGPUQueue (class in jobqueues.localqueue) login() (playmolecule.session.Session method) 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 attribute) (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) (playmolecule.playqueue.PlayQueue property) merge_record_extra() (in module playmolecule.jsonlogger) 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 htmd.membranebuilder.globalminimization) missing() (playmolecule.plac.ArgumentParser method) MissingAngleError MissingAtomTypeError MissingBondError MissingParameterError MissingTorsionError MixedSegmentError MMTFread() (in module moleculekit.readers) MMTFwrite() (in module moleculekit.writers) Model (class in htmd.model) module 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.mdengine htmd.mdengine.acemd htmd.mdengine.acemd.acemd htmd.membranebuilder htmd.membranebuilder.build_membrane htmd.membranebuilder.globalminimization htmd.membranebuilder.ljfluid htmd.membranebuilder.pdbreporter htmd.membranebuilder.ringpenetration htmd.membranebuilder.simulate_openmm htmd.metricdata htmd.metricdatagenerator htmd.model htmd.molecule htmd.molecule.molecule htmd.molecule.util htmd.mutualinformation htmd.parallelprogress htmd.pathplanning htmd.projections htmd.projections.gwpca htmd.projections.kmeanstri htmd.projections.metric htmd.projections.metriccoordinate htmd.projections.metricdihedral htmd.projections.metricdistance htmd.projections.metricfluctuation htmd.projections.metricplumed2 htmd.projections.metricrmsd htmd.projections.metricsasa htmd.projections.metricsecondarystructure htmd.projections.metricshell htmd.projections.metricsphericalcoordinate htmd.projections.metrictmscore htmd.projections.tica htmd.protocols htmd.protocols.equilibration_v3 htmd.protocols.production_v6 htmd.queues htmd.queues.localqueue htmd.queues.lsfqueue htmd.queues.pbsqueue htmd.queues.playqueue htmd.queues.simqueue htmd.queues.slurmqueue htmd.session htmd.simlist htmd.ui htmd.units htmd.util htmd.version 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.home moleculekit.interactions moleculekit.interactions.interactions moleculekit.molecule moleculekit.pdbx moleculekit.pdbx.reader 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.smallmollib moleculekit.smallmol.test_smallmol moleculekit.smallmol.test_smallmollib moleculekit.smallmol.tools moleculekit.smallmol.tools.clustering moleculekit.smallmol.tools.restrainedembed moleculekit.smallmol.tools.test_tools 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.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.util moleculekit.version moleculekit.viewer moleculekit.vmdgraphics moleculekit.vmdviewer moleculekit.writers playmolecule playmolecule.config playmolecule.datacenter playmolecule.devutils playmolecule.job playmolecule.jsonlogger playmolecule.plac playmolecule.playqueue playmolecule.session playmolecule.utils

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.home module moleculekit.interactions module moleculekit.interactions.interactions module moleculekit.molecule module moleculekit.pdbx module moleculekit.pdbx.reader 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.smallmollib module moleculekit.smallmol.test_smallmol module moleculekit.smallmol.test_smallmollib module moleculekit.smallmol.tools module moleculekit.smallmol.tools.clustering module moleculekit.smallmol.tools.restrainedembed module moleculekit.smallmol.tools.test_tools 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.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.util module moleculekit.version module moleculekit.viewer module moleculekit.vmdgraphics module moleculekit.vmdviewer module moleculekit.writers module MolFactory (class in moleculekit.readers) molfile (htmd.simlist.Sim attribute) molRMSD() (in module moleculekit.util) molTMscore() (in module moleculekit.util) move() (playmolecule.datacenter.Dataset method) move_dataset() (in module playmolecule.datacenter) 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) 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) (playmolecule.playqueue.PlayQueue property) 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) (playmolecule.playqueue.PlayQueue property)

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) numBonds (moleculekit.molecule.Molecule property) numDimensions (htmd.metricdata.MetricData property) (htmd.metricdata.Trajectory property) numFrames (htmd.metricdata.MetricData property) (htmd.metricdata.Trajectory property) numframes (htmd.simlist.Sim attribute) numFrames (moleculekit.molecule.Molecule attribute) (moleculekit.molecule.Molecule property) (moleculekit.readers.Trajectory property) (moleculekit.smallmol.smallmol.SmallMol property) numMols (moleculekit.smallmol.smallmollib.SmallMolLib attribute) (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) omega() (moleculekit.projections.metricdihedral.Dihedral static method) openbabelConvert() (in module moleculekit.tools.obabel_tools) openFileOrStringIO() (in module moleculekit.readers)

opm() (in module moleculekit.util) opt() (in module playmolecule.plac) 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_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_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_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) (in module moleculekit.smallmol.tools.clustering) parallelfunc() (in module htmd.pathplanning) parallelTest() (htmd.metricdatagenerator.MetricDataGenerator method) parameterizeNonCanonicalResidues() (in module htmd.builder.noncanonical) parent (htmd.metricdata.MetricData attribute) (htmd.simlist.Sim attribute) parse() (in module moleculekit.ply.yacc) (moleculekit.ply.yacc.LRParser method) (playmolecule.jsonlogger.JsonFormatter method) parse_grammar() (in module moleculekit.ply.yacc) parse_timestamp_utc() (in module playmolecule.utils) parser_from() (in module playmolecule.plac) ParserReflect (class in moleculekit.ply.yacc) PBSQueue (class in jobqueues.pbsqueue) pconf() (in module playmolecule.plac) pdbGuessElementByName() (in module moleculekit.readers) PDBQTread() (in module moleculekit.readers) PDBQTwrite() (in module moleculekit.writers) PDBread() (in module moleculekit.readers) PDBReporter (class in htmd.membranebuilder.pdbreporter) PDBwrite() (in module moleculekit.writers) PdbxError, [1], [2] PdbxReader (class in moleculekit.pdbx.reader.PdbxParser) (class in moleculekit.pdbx.reader.PdbxReader) PDBxReporter (class in htmd.membranebuilder.pdbreporter) PdbxWriter (class in moleculekit.pdbx.reader.PdbxParser) (class in moleculekit.pdbx.writer.PdbxWriter) 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 playmolecule.config module playmolecule.datacenter module

playmolecule.devutils module playmolecule.job module playmolecule.jsonlogger module playmolecule.plac module playmolecule.playqueue module playmolecule.session module playmolecule.utils module PlayQueue (class in jobqueues.playqueue) (class in playmolecule.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) 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) pmtryexcept() (in module playmolecule.devutils) pmws_wrapper() (in module playmolecule.devutils) pop_state() (moleculekit.ply.lex.Lexer method) populate_from() (playmolecule.plac.ArgumentParser method) 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_actions() (playmolecule.plac.ArgumentParser method) printIt() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) PRMTOPread() (in module moleculekit.readers) process_log_record() (playmolecule.jsonlogger.JsonFormatter method) 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

QUEUED (playmolecule.job.JobStatus attribute)

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) read_arguments() (playmolecule.job.Job method) readConfig() (htmd.mdengine.acemd.acemd.Acemd method) 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 attribute) (htmd.metricdata.MetricData property) reference (htmd.metricdata.Trajectory property) RegCluster (class in htmd.clustering.regular) register() (playmolecule.session.Session method) rel2sim() (htmd.metricdata.MetricData method) remove() (moleculekit.molecule.Molecule method) (moleculekit.molecule.Representations method) (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (playmolecule.datacenter.Dataset method) remove_dataset() (in module playmolecule.datacenter) (playmolecule.datacenter.DataCenter method) remove_dataset_tag() (playmolecule.datacenter.DataCenter method) remove_tags() (playmolecule.datacenter.Dataset 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() (htmd.membranebuilder.pdbreporter.PDBReporter method) (htmd.membranebuilder.pdbreporter.PDBxReporter 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) restrainedEmbed() (in module moleculekit.smallmol.tools.restrainedembed) 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) (playmolecule.job.Job method) (playmolecule.playqueue.PlayQueue method) retrieve_jobs() (playmolecule.session.Session method) RetrieveError rightmost_terminal() (in module moleculekit.ply.yacc) rotateBy() (moleculekit.molecule.Molecule method) rotateCoordinates() (in module moleculekit.tools.voxeldescriptors) 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) runmain() (in module moleculekit.ply.lex) RUNNING (jobqueues.simqueue.QueueJobStatus attribute) (playmolecule.job.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) save() (htmd.metricdata.MetricData method) (htmd.model.Model method) save_graphml() (htmd.mutualinformation.MutualInformation method) saveMI() (htmd.mutualinformation.MutualInformation method) 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) Session (class in playmolecule.session) SessionError set() (htmd.projections.metric.Metric method) (moleculekit.molecule.Molecule method) set_defaulted_states() (moleculekit.ply.yacc.LRParser method) set_job_status() (playmolecule.session.Session 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) setAsCompleted() (in module playmolecule.devutils) setAsError() (in module playmolecule.devutils) setAsSleep() (in module playmolecule.devutils) 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) 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) SgeQueue (class in jobqueues.sgequeue) short_execid() (in module playmolecule.job) 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) simid (htmd.simlist.Sim attribute) simlist (htmd.metricdata.MetricData attribute) (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) SLEEPING (playmolecule.job.JobStatus attribute) SlurmQueue (class in jobqueues.slurmqueue) SmallMol (class in moleculekit.smallmol.smallmol) SmallMolLib (class in moleculekit.smallmol.smallmollib) SmallMolStack (in module moleculekit.smallmol.smallmollib) smiReader() (in module moleculekit.smallmol.smallmollib) solvate() (in module htmd.builder.solvate) split() (in module htmd.builder.charmm) splitCols() (htmd.metricdata.MetricData method) St (htmd.metricdata.MetricData attribute) (htmd.metricdata.MetricData property) StandardPDBChiralAtom() (in module moleculekit.rdkitintegration) StandardPDBResidueChirality() (in module moleculekit.rdkitintegration) start_app() (playmolecule.session.Session 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) (playmolecule.playqueue.PlayQueue method) string_to_tempfile() (in module moleculekit.util) StringOrDataset (class in playmolecule.job) 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) (playmolecule.job.Job method) (playmolecule.playqueue.PlayQueue method) SubmitError subset() (playmolecule.datacenter.Dataset 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) TanimotoDistances() (in module moleculekit.smallmol.tools.clustering) tarFolder() (in module playmolecule.devutils) tempname() (in module htmd.util) (in module moleculekit.util) (in module playmolecule.utils) 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_date() (in module playmolecule.plac)

to_datetime() (in module playmolecule.plac) toDataFrame() (moleculekit.smallmol.smallmollib.SmallMolLib 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) 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) Trajectory (class in htmd.metricdata) (class in moleculekit.readers) trajectory (htmd.simlist.Sim attribute) trajLengths (htmd.metricdata.MetricData property) traverse() (in module moleculekit.ply.yacc) traverse_ast() (in module moleculekit.atomselect.atomselect) Tree (class in htmd.pathplanning)

U

undefined_symbols() (moleculekit.ply.yacc.Grammar method) uniformRandomRotation() (in module moleculekit.util) UniqueAtomID (class in moleculekit.molecule) UniqueResidueID (class in moleculekit.molecule) UnknownResidueError unused_precedence() (moleculekit.ply.yacc.Grammar method) unused_rules() (moleculekit.ply.yacc.Grammar method) unused_terminals() (moleculekit.ply.yacc.Grammar method) unzipit() (in module playmolecule.devutils)

update() (playmolecule.datacenter.Dataset method) update_comments() (playmolecule.datacenter.Dataset method) update_dataset_comments() (in module playmolecule.datacenter) updatingMean() (in module htmd.adaptive.util) upload_dataset() (playmolecule.datacenter.DataCenter method) UserFailedRegistrationError UserNotFoundError UserUpdateError utc_timestamp_to_local() (in module playmolecule.utils)

V

validate() (playmolecule.job.StringOrDataset method) 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) VALIDATING (playmolecule.job.JobStatus attribute) version() (in module htmd.version) (in module moleculekit.version)

view() (htmd.mdengine.acemd.acemd.GroupRestraint method) (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol 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) (playmolecule.job.Job method) wait_children() (playmolecule.job.Job method) wait_for_backend() (playmolecule.session.Session method) wait_for_port() (in module moleculekit.util) WAITING_APPROVAL (playmolecule.job.JobStatus attribute) WAITING_DATA (playmolecule.job.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)

write_arguments() (playmolecule.job.Job method) writeContainer() (moleculekit.pdbx.reader.PdbxParser.PdbxWriter method) (moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method) writeInputsOptionsLog() (in module playmolecule.devutils) writeInputsOptionsLog2() (in module playmolecule.devutils) writeSdf() (moleculekit.smallmol.smallmollib.SmallMolLib method) writeSentinel() (in module playmolecule.devutils) 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)

zipdir() (in module playmolecule.devutils) zipit() (in module playmolecule.devutils)