Index

_

__call__() (moleculekit.smallmol.tools.molvstautomer.TautomerEnumerator method) (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method)

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

A

abs2rel() (htmd.metricdata.MetricData method) abs2sim() (htmd.metricdata.MetricData method) Acemd (class in htmd.apps.acemd) add() (moleculekit.molecule.Representations method) add_fields() (playmolecule.jsonlogger.JsonFormatter method) addConstraint() (htmd.protocols.equilibration_v1.Equilibration method) (htmd.protocols.equilibration_v2.Equilibration method) (htmd.protocols.production_v5.Production method) (htmd.protocols.production_v6.Production method) addPoint() (htmd.pathplanning.Tree method) aggregateTime (htmd.metricdata.MetricData attribute) align() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) alignBySequence() (moleculekit.molecule.Molecule method) altloc (moleculekit.molecule.Molecule 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) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer 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) apply_bounds (htmd.charge.esp.ESP attribute) args (htmd.builder.builder.BuildError attribute) (htmd.builder.builder.MissingAngleError attribute) (htmd.builder.builder.MissingAtomTypeError attribute) (htmd.builder.builder.MissingBondError attribute) (htmd.builder.builder.MissingParameterError attribute) (htmd.builder.builder.MissingTorsionError attribute) (htmd.builder.builder.MixedSegmentError attribute) (htmd.builder.builder.ResidueInsertionError attribute) (htmd.builder.builder.UnknownResidueError attribute) (moleculekit.molecule.TopologyInconsistencyError attribute) (moleculekit.pdbx.reader.PdbxParser.PdbxError attribute) (moleculekit.pdbx.reader.PdbxParser.SyntaxError attribute) (moleculekit.pdbx.reader.PdbxReader.PdbxError attribute) (moleculekit.pdbx.reader.PdbxReader.SyntaxError attribute) (moleculekit.pdbx.writer.PdbxWriter.PdbxError attribute) (moleculekit.projections.metricdihedral.AtomNotFoundException attribute) (moleculekit.readers.FormatError attribute) (moleculekit.readers.TopologyInconsistencyError attribute) (playmolecule.job.JobError attribute) (playmolecule.session.SessionError attribute)

args() (htmd.protocols.oldprotocolinterface.BinaryValidator method) (htmd.protocols.oldprotocolinterface.BooleanValidator method) (htmd.protocols.oldprotocolinterface.ClassValidator method) (htmd.protocols.oldprotocolinterface.DictionaryValidator method) (htmd.protocols.oldprotocolinterface.FileValidator method) (htmd.protocols.oldprotocolinterface.FunctionValidator method) (htmd.protocols.oldprotocolinterface.ListListValidator method) (htmd.protocols.oldprotocolinterface.ListValidator method) (htmd.protocols.oldprotocolinterface.ObjectValidator method) (htmd.protocols.oldprotocolinterface.StringValidator method) (htmd.protocols.oldprotocolinterface.TimestepValidator method) assertSameAsReferenceDir() (in module htmd.util) atominfo (moleculekit.readers.Topology attribute) AtomNotFoundException atoms (moleculekit.smallmol.tools.tautomers.Fragment attribute) 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) beta (moleculekit.molecule.Molecule attribute) BinaryValidator (class in htmd.protocols.oldprotocolinterface) BINCOORread() (in module moleculekit.readers) BINCOORwrite() (in module moleculekit.writers) BONDMAP (moleculekit.smallmol.tools.molvstautomer.TautomerTransform attribute) bonds (moleculekit.molecule.Molecule attribute) bondtype (moleculekit.molecule.Molecule attribute)

BooleanValidator (class in htmd.protocols.oldprotocolinterface) 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) BuildError buildMembrane() (in module htmd.membranebuilder.build_membrane)

C

calculate() (htmd.ffevaluation.ffevaluate.FFEvaluate method) (htmd.mutualinformation.MutualInformation method) calculateEnergies() (htmd.ffevaluation.ffevaluate.FFEvaluate method) calculateSets() (in module htmd.ffevaluation.ffevaluate) calculateUniqueBonds() (in module moleculekit.molecule) canonicalize() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method) categoryPart() (moleculekit.pdbx.reader.PdbxContainers.CifName static method) center() (moleculekit.molecule.Molecule method) centerFrames (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) Centers (htmd.metricdata.MetricData attribute) centreOfMass() (in module htmd.parameterization.util) chain (moleculekit.molecule.Molecule attribute) charge (moleculekit.molecule.Molecule attribute) CHARGEMAP (moleculekit.smallmol.tools.molvstautomer.TautomerTransform attribute) 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) cktest() (htmd.model.Model method) ClassValidator (class in htmd.protocols.oldprotocolinterface) close() (moleculekit.vmdviewer.VMD method) cluster (htmd.metricdata.Trajectory attribute) 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 attribute) cluster_ofmicro (htmd.model.Model attribute) clusterSize (htmd.clustering.regular.RegCluster attribute) clusterSize_ (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) combine() (htmd.metricdata.MetricData method) (in module htmd.builder.charmm) compareEnergies() (in module htmd.ffevaluation.test_ffevaluate) compareForces() (in module htmd.ffevaluation.test_ffevaluate) compareGraphs() (in module moleculekit.tools.graphalignment) compareVersions() (in module htmd.latest) COMPLETED (playmolecule.job.JobStatus attribute) completed() (moleculekit.vmdviewer.VMD method) compute_paths() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) compute_score() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method) config() (in module htmd.config) (in module moleculekit.config)

connected_component_subgraphs() (in module htmd.parameterization.detect) connection (moleculekit.smallmol.tools.tautomers.Fragment attribute) construct() (moleculekit.readers.MolFactory static method) contactVecToMatrix() (in module moleculekit.projections.metricdistance) ContainerBase (class in moleculekit.pdbx.reader.PdbxContainers) convert() (in module htmd.units) convertDisulfide() (in module htmd.builder.builder) converter() (playmolecule.jsonlogger.JsonFormatter method) 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.metriccoordinate.MetricCoordinate method) (moleculekit.projections.metricdihedral.MetricDihedral method) (moleculekit.projections.metricdistance.MetricDistance method) (moleculekit.projections.metricdistance.MetricSelfDistance method) (moleculekit.projections.metricfluctuation.MetricFluctuation 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) (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmollib.SmallMolLib method) (moleculekit.vmdviewer.VMD method) count (moleculekit.vmdgraphics.VMDLabels attribute) counter (moleculekit.vmdgraphics.VMDBox attribute) (moleculekit.vmdgraphics.VMDConvexHull attribute) (moleculekit.vmdgraphics.VMDCylinder attribute) (moleculekit.vmdgraphics.VMDGraphicObject attribute) (moleculekit.vmdgraphics.VMDIsosurface attribute) (moleculekit.vmdgraphics.VMDLabels attribute) (moleculekit.vmdgraphics.VMDSphere attribute) (moleculekit.vmdgraphics.VMDText attribute) CRDCARDread() (in module moleculekit.readers) CRDread() (in module moleculekit.readers) createCoreSetModel() (htmd.model.Model method) createMultitermDihedralTypes() (in module htmd.parameterization.parameterset) createProductGraph() (in module moleculekit.tools.graphalignment) createState() (htmd.model.Model method) cross (in module htmd.numbautil) crystalinfo (moleculekit.molecule.Molecule attribute)

D

dat (htmd.metricdata.MetricData attribute), [1] data (moleculekit.tools.preparationdata.PreparationData attribute) DataCategory (class in moleculekit.pdbx.reader.PdbxContainers) DataCategoryBase (class in moleculekit.pdbx.reader.PdbxContainers) DataContainer (class in moleculekit.pdbx.reader.PdbxContainers) deconcatenate() (htmd.metricdata.MetricData method) default() (playmolecule.jsonlogger.JsonEncoder method) default_msec_format (playmolecule.jsonlogger.JsonFormatter attribute) default_time_format (playmolecule.jsonlogger.JsonFormatter attribute) defaultAmberHome() (in module htmd.builder.amber) 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.VMDBox method) (moleculekit.vmdgraphics.VMDConvexHull method) (moleculekit.vmdgraphics.VMDCylinder method) (moleculekit.vmdgraphics.VMDGraphicObject method) (moleculekit.vmdgraphics.VMDIsosurface method) (moleculekit.vmdgraphics.VMDLabels method) (moleculekit.vmdgraphics.VMDSphere method) (moleculekit.vmdgraphics.VMDText method) deleteBonds() (moleculekit.molecule.Molecule method) depict() (moleculekit.smallmol.smallmol.SmallMol method) (moleculekit.smallmol.smallmollib.SmallMolLib method) depict_tautomers() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method) depictMultipleMols() (in module moleculekit.smallmol.util) describe() (playmolecule.job.Job method) describeApp() (playmolecule.session.Session method) describeNextReport() (htmd.membranebuilder.pdbreporter.PDBReporter method) (htmd.membranebuilder.pdbreporter.PDBxReporter method) detectChiralCenters() (in module htmd.parameterization.util) detectCisPeptideBonds() (in module htmd.builder.builder) detectDisulfideBonds() (in module htmd.builder.builder) detectEquivalentAtoms() (in module htmd.parameterization.detect) detectImproperCenter() (in module htmd.ffevaluation.ffevaluate)

detectParameterizableCores() (in module htmd.parameterization.detect) detectParameterizableDihedrals() (in module htmd.parameterization.detect) DiceDistances() (in module moleculekit.smallmol.tools.clustering) DictionaryValidator (class in htmd.protocols.oldprotocolinterface) diffMolecules() (in module htmd.util) Dihedral (class in moleculekit.projections.metricdihedral) dihedralAngle() (in module moleculekit.dihedral) dihedralAngleFrames (in module moleculekit.dihedral) dihedralAngleFull (in module moleculekit.dihedral) DihedralFitting (class in htmd.parameterization.dihedral) dihedrals (htmd.parameterization.dihedral.DihedralFitting attribute) (moleculekit.molecule.Molecule attribute) dihedralsToIndexes() (moleculekit.projections.metricdihedral.Dihedral static method) disableDispersionCorrection() (in module htmd.ffevaluation.test_ffevaluate) distance (htmd.clustering.kcenters.KCenter attribute) distributeLipids() (in module htmd.membranebuilder.ljfluid) DisulfideBridge (class in htmd.builder.builder) dock() (in module htmd.dock) docString() (htmd.protocols.oldprotocolinterface.BinaryValidator method) (htmd.protocols.oldprotocolinterface.BooleanValidator method) (htmd.protocols.oldprotocolinterface.ClassValidator method) (htmd.protocols.oldprotocolinterface.DictionaryValidator method) (htmd.protocols.oldprotocolinterface.FileValidator method) (htmd.protocols.oldprotocolinterface.FunctionValidator method) (htmd.protocols.oldprotocolinterface.ListListValidator method) (htmd.protocols.oldprotocolinterface.ListValidator method) (htmd.protocols.oldprotocolinterface.ObjectValidator method) (htmd.protocols.oldprotocolinterface.StringValidator method) (htmd.protocols.oldprotocolinterface.TimestepValidator method) (htmd.protocols.oldprotocolinterface.Validator method) (htmd.protocols.oldprotocolinterface.ValueValidator method) dot (in module htmd.numbautil) 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) encode() (playmolecule.jsonlogger.JsonEncoder method) ensurelist() (in module htmd.util) (in module moleculekit.util) (in module playmolecule.utils) enumerate() (moleculekit.smallmol.tools.molvstautomer.TautomerEnumerator method)

eqDistribution() (htmd.model.Model method) (htmd.modelhmm.ModelHMM method) equilibrateSystem() (in module htmd.membranebuilder.simulate_openmm) Equilibration (class in htmd.protocols.equilibration_v1) (class in htmd.protocols.equilibration_v2) (class in htmd.protocols.pmemdequilibration) ERROR (playmolecule.job.JobStatus attribute) ESP (class in htmd.charge.esp) exists() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method)

F

FFEvaluate (class in htmd.ffevaluation.ffevaluate) fftype() (in module htmd.parameterization.fftype) fileloc (moleculekit.molecule.Molecule attribute) FileValidator (class in htmd.protocols.oldprotocolinterface) filter() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) filter_tautomers() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer static method) filterQMResults() (in module htmd.parameterization.util) findDihedralType() (in module htmd.parameterization.parameterset) findHbonds() (moleculekit.tools.preparationdata.PreparationData method) findImproperType() (in module htmd.parameterization.parameterset) fit() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) fit_predict() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) fit_transform() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) fitChargesWithAntechamber() (in module htmd.charge.charge) fitESPCharges() (in module htmd.charge.charge) fitGasteigerCharges() (in module htmd.charge.charge) fixed (htmd.charge.esp.ESP attribute) fixParameters() (in module htmd.ffevaluation.test_ffevaluate) fixPhosphateTypes() (in module htmd.parameterization.fixes)

format() (playmolecule.jsonlogger.JsonFormatter method) format_datetime_obj() (playmolecule.jsonlogger.JsonEncoder method) formatEnergies() (htmd.ffevaluation.ffevaluate.FFEvaluate static method) FormatError formatException() (playmolecule.jsonlogger.JsonFormatter method) formatMessage() (playmolecule.jsonlogger.JsonFormatter method) formatStack() (playmolecule.jsonlogger.JsonFormatter method) formatTime() (playmolecule.jsonlogger.JsonFormatter method) foundBondBetween() (moleculekit.smallmol.smallmol.SmallMol method) Fragment (class in moleculekit.smallmol.tools.tautomers) fragment() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) fragments (moleculekit.smallmol.tools.tautomers.MolFragmenter attribute) Frame (class in htmd.simlist) frame (htmd.simlist.Frame attribute) (moleculekit.molecule.Molecule attribute), [1] (moleculekit.smallmol.smallmol.SmallMol attribute) fromMolecule() (moleculekit.molecule.UniqueAtomID static method) (moleculekit.molecule.UniqueResidueID static method) (moleculekit.readers.Topology method) fstep (htmd.metricdata.MetricData attribute) (moleculekit.molecule.Molecule attribute), [1] ftype (moleculekit.smallmol.tools.tautomers.Fragment attribute) FunctionValidator (class in htmd.protocols.oldprotocolinterface)

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.DataCategory method) (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) (moleculekit.smallmol.smallmol.SmallMol method) get_conjugate() (moleculekit.smallmol.tools.tautomers.TautomerCanonicalizer method) get_conjugate_length() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) get_connection() (moleculekit.smallmol.tools.tautomers.Fragment method) get_depiction_atoms() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) get_fragment() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) get_graphs() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) get_longest_path() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) get_num_fragments() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) get_params() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) getAllNeighbours() (in module htmd.membranebuilder.ringpenetration) getArgumentParser() (in module htmd.parameterization.cli) getAtoms() (moleculekit.smallmol.smallmol.SmallMol method) getAtomTypeMapping() (in module htmd.parameterization.writers) 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) 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) getChildren() (playmolecule.job.Job method) getConfig() (playmolecule.job.Job method) getCurrentAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getCurrentViewer() (in module moleculekit.vmdviewer) getDestinationFile() (in module playmolecule.utils) getDestinationFolder() (in module playmolecule.utils) getDihedral() (moleculekit.molecule.Molecule method) getDipole() (in module htmd.parameterization.util) getEpochSimIdx() (in module htmd.adaptive.util) getEpochTrajectoryDictionary() (in module htmd.adaptive.util) getFeatures() (in module moleculekit.tools.atomtyper) getFixedChargeAtomIndices() (in module htmd.parameterization.util) 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) getImproperParameter() (in module htmd.ffevaluation.ffevaluate) getIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getItemNameList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getJob() (playmolecule.session.Session 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.metricdistance.MetricSelfDistance method) (moleculekit.projections.metricfluctuation.MetricFluctuation 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) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) getObj() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) getObjNameList() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) getParameter() (in module htmd.parameterization.parameterset) getParentSimIdxFrame() (in module htmd.adaptive.util) getPDBQTAtomType() (in module moleculekit.tools.atomtyper) getPDBQTAtomTypesAndCharges() (in module moleculekit.tools.atomtyper) getPdbStrings() (in module htmd.util) getPoints() (htmd.charge.esp.MoleculeGrid method) getProgress() (playmolecule.job.Job method) getProperties() (in module moleculekit.tools.atomtyper) getRates() (htmd.kinetics.Kinetics method) (htmd.kineticshmm.KineticsHMM method) getRCSBLigandByLigname() (in module moleculekit.smallmol.util) getRequest() (in module playmolecule.utils) 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) getSortedAndUniqueTypes() (in module htmd.parameterization.writers) getStates() (htmd.model.Model method) getStateStatistic() (in module htmd.model) getStatus() (playmolecule.job.Job method) getTerminiBuriedness() (moleculekit.tools.preparationdata.PreparationData method) getTerminiHbonds() (moleculekit.tools.preparationdata.PreparationData method) getType() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) getURLs() (playmolecule.job.Job 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) graphs (moleculekit.smallmol.tools.tautomers.Fragment attribute) GROTOPread() (in module moleculekit.readers) GROwrite() (in module moleculekit.writers) guessAnglesAndDihedrals() (in module moleculekit.util) guessbonds() (in module moleculekit.vmdparser) guessBondType() (in module htmd.parameterization.util) guessElements() (in module htmd.parameterization.util) GWPCA (class in htmd.projections.gwpca)

H

hasAttribute() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) header (moleculekit.tools.preparationdata.PreparationData attribute) home() (in module htmd.home) (in module moleculekit.home) htmd (module) htmd.adaptive (module) htmd.adaptive.util (module) htmd.apps (module) htmd.apps.acemd (module) htmd.apps.pmemd (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.preparation (module) htmd.builder.solvate (module) htmd.charge (module) htmd.charge.charge (module) htmd.charge.esp (module) htmd.clustering (module) htmd.clustering.kcenters (module) htmd.clustering.regular (module) htmd.config (module) htmd.decorators (module) htmd.dock (module) htmd.ffevaluation (module) htmd.ffevaluation.ffevaluate (module) htmd.ffevaluation.test_ffevaluate (module) htmd.home (module) htmd.kinetics (module) htmd.kineticshmm (module) htmd.latest (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.model (module) htmd.modelhmm (module) htmd.molecule (module) htmd.molecule.molecule (module) htmd.molecule.util (module) htmd.mutualinformation (module) htmd.numbautil (module) htmd.parallelprogress (module)

htmd.parameterization (module) htmd.parameterization.cli (module) htmd.parameterization.detect (module) htmd.parameterization.dihedral (module) htmd.parameterization.fftype (module) htmd.parameterization.fixes (module) htmd.parameterization.parameterset (module) htmd.parameterization.readers (module) htmd.parameterization.test (module) htmd.parameterization.util (module) htmd.parameterization.writers (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_v1 (module) htmd.protocols.equilibration_v2 (module) htmd.protocols.oldprotocolinterface (module) htmd.protocols.pmemdequilibration (module) htmd.protocols.pmemdproduction (module) htmd.protocols.production_v1 (module) htmd.protocols.production_v2 (module) htmd.protocols.production_v3 (module) htmd.protocols.production_v4 (module) htmd.protocols.production_v5 (module) htmd.protocols.production_v6 (module) htmd.queues (module) htmd.session (module) htmd.simlist (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

improperGraph() (in module htmd.ffevaluation.ffevaluate) impropers (moleculekit.molecule.Molecule attribute) init() (in module htmd.ffevaluation.ffevaluate) input (htmd.simlist.Sim attribute) insert() (moleculekit.molecule.Molecule method) insertion (moleculekit.molecule.Molecule attribute) inventAtomTypes() (in module htmd.parameterization.parameterset) 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) item_separator (playmolecule.jsonlogger.JsonEncoder attribute) iterencode() (playmolecule.jsonlogger.JsonEncoder method)

J

Job (class in playmolecule.job) JobError 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) keepForces() (in module htmd.ffevaluation.test_ffevaluate) keepForcesAmber() (in module htmd.ffevaluation.test_ffevaluate)

key_separator (playmolecule.jsonlogger.JsonEncoder attribute) Kinetics (class in htmd.kinetics) KineticsHMM (class in htmd.kineticshmm) 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) least_square_fit_plane() (in module htmd.membranebuilder.ringpenetration) ligname (moleculekit.smallmol.smallmol.SmallMol attribute) list() (moleculekit.molecule.Representations method) listApps() (playmolecule.session.Session method) listAppsClient() (playmolecule.session.Session method) listFiles() (in module htmd.builder.amber) (in module htmd.builder.charmm) listJobs() (playmolecule.session.Session method) listLipids() (in module htmd.membranebuilder.build_membrane)

ListListValidator (class in htmd.protocols.oldprotocolinterface) ListValidator (class in htmd.protocols.oldprotocolinterface) load() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) (htmd.metricdata.MetricData method) (htmd.model.Model method) load_tests() (in module htmd.charge.esp) loadConfig() (in module playmolecule.config) loadMI() (htmd.mutualinformation.MutualInformation method) loadMol() (moleculekit.vmdviewer.VMD method) loadParameters() (in module htmd.ffevaluation.ffevaluate) loopModeller() (in module htmd.builder.loopmodeler)

M

macro_ofcluster (htmd.model.Model attribute) macro_ofmicro (htmd.model.Model attribute) macroAccumulate() (in module htmd.model) macronum (htmd.model.Model attribute) (htmd.modelhmm.ModelHMM attribute) MAEread() (in module moleculekit.readers) main_parameterize() (in module htmd.parameterization.cli) makeAtomNamesUnique() (in module htmd.parameterization.util) makeMolGraph() (in module moleculekit.tools.graphalignment) manual() (in module moleculekit.projections.metricplumed2) map (htmd.metricdata.MetricData attribute), [1] mapAtomTypesParameterSet() (in module htmd.parameterization.writers) markovModel() (htmd.model.Model method) (htmd.modelhmm.ModelHMM method) masses (moleculekit.molecule.Molecule attribute) MAX_DIHEDRAL_MULTIPLICITY (htmd.parameterization.dihedral.DihedralFitting attribute) MAX_TAUTOMERS (in module moleculekit.smallmol.tools.molvstautomer) maxConnectedLag() (htmd.model.Model method) maxDistance() (in module moleculekit.util) maximalSubstructureAlignment() (in module moleculekit.tools.graphalignment) MDTRAJread() (in module moleculekit.readers) MDTRAJTOPOread() (in module moleculekit.readers) MDTRAJwrite() (in module moleculekit.writers) memoized_property() (in module moleculekit.smallmol.tools.molvstautomer) merge_record_extra() (in module playmolecule.jsonlogger) Metric (class in htmd.projections.metric) MetricCoordinate (class in moleculekit.projections.metriccoordinate) MetricData (class in htmd.metricdata) MetricDihedral (class in moleculekit.projections.metricdihedral) MetricDistance (class in moleculekit.projections.metricdistance) MetricFluctuation (class in moleculekit.projections.metricfluctuation) 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) mfptGraph() (htmd.kinetics.Kinetics method) mfptoff (htmd.kinetics.Rates attribute) mfpton (htmd.kinetics.Rates attribute) micro_ofcluster (htmd.model.Model attribute) micronum (htmd.model.Model attribute) minimalRotation() (in module htmd.builder.builder) minimize() (in module htmd.membranebuilder.globalminimization) (in module htmd.parameterization.util) missedLigands (moleculekit.tools.preparationdata.PreparationData attribute) MissingAngleError MissingAtomTypeError MissingBondError MissingParameterError MissingTorsionError MixedSegmentError Model (class in htmd.model) ModelHMM (class in htmd.modelhmm) mol (moleculekit.smallmol.tools.tautomers.MolFragmenter attribute) MOL2read() (in module moleculekit.readers) MOL2write() (in module moleculekit.writers) mol_equal() (in module moleculekit.molecule) Molecule (class in moleculekit.molecule) molecule (htmd.charge.esp.ESP attribute) (htmd.parameterization.dihedral.DihedralFitting attribute) MoleculeGrid (class in htmd.charge.esp) moleculekit (module) moleculekit.align (module) moleculekit.config (module) moleculekit.dihedral (module) moleculekit.home (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.tests (module) moleculekit.pdbx.tests.PdbxReaderTests (module) moleculekit.pdbx.tests.PdbxReadWriteTests (module) moleculekit.pdbx.tests.PdbxWriterTests (module) moleculekit.pdbx.writer (module) moleculekit.pdbx.writer.PdbxWriter (module) moleculekit.periodictable (module) moleculekit.projections (module) moleculekit.projections.metriccoordinate (module) moleculekit.projections.metricdihedral (module) moleculekit.projections.metricdistance (module) moleculekit.projections.metricfluctuation (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.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.molvstautomer (module) moleculekit.smallmol.tools.restrainedembed (module) moleculekit.smallmol.tools.tautomers (module) moleculekit.smallmol.tools.test_tools (module) moleculekit.smallmol.util (module) moleculekit.support (module) moleculekit.tools (module) moleculekit.tools.atomtyper (module) moleculekit.tools.autosegment (module) moleculekit.tools.crystalpacking (module) moleculekit.tools.graphalignment (module) moleculekit.tools.hhblitsprofile (module) moleculekit.tools.pka (module) moleculekit.tools.preparation (module) moleculekit.tools.preparationdata (module) moleculekit.tools.sequencestructuralalignment (module) moleculekit.tools.voxeldescriptors (module) moleculekit.util (module) moleculekit.version (module) moleculekit.vmdgraphics (module) moleculekit.vmdparser (module) moleculekit.vmdviewer (module) moleculekit.wrap (module) moleculekit.writers (module) MolFactory (class in moleculekit.readers) molfile (htmd.simlist.Sim attribute) MolFragmenter (class in moleculekit.smallmol.tools.tautomers) molRMSD() (in module moleculekit.util) molTMscore() (in module moleculekit.util) moveBy() (moleculekit.molecule.Molecule method) moveLipidToPos() (in module htmd.membranebuilder.ringpenetration) mutateResidue() (moleculekit.molecule.Molecule method) MutualInformation (class in htmd.mutualinformation)

N

N (htmd.metricdata.MetricData attribute) name (moleculekit.molecule.Molecule attribute) (moleculekit.smallmol.tools.tautomers.Fragment attribute) nestedListToArray() (in module htmd.ffevaluation.ffevaluate) ngroups (htmd.charge.esp.ESP attribute) norm (in module htmd.numbautil) numAtoms (moleculekit.molecule.Molecule attribute), [1] (moleculekit.smallmol.smallmol.SmallMol attribute) numDihedrals (htmd.parameterization.dihedral.DihedralFitting attribute) numDimensions (htmd.metricdata.MetricData attribute) (htmd.metricdata.Trajectory attribute)

numFrames (htmd.metricdata.MetricData attribute) (htmd.metricdata.Trajectory attribute) numframes (htmd.simlist.Sim attribute) numFrames (moleculekit.molecule.Molecule attribute), [1] (moleculekit.readers.Trajectory attribute) (moleculekit.smallmol.smallmol.SmallMol attribute) numMols (moleculekit.smallmol.smallmollib.SmallMolLib attribute), [1] numResidues (moleculekit.molecule.Molecule attribute), [1] numTrajectories (htmd.metricdata.MetricData attribute)

O

ObjectValidator (class in htmd.protocols.oldprotocolinterface) occupancy (moleculekit.molecule.Molecule attribute) omega() (moleculekit.projections.metricdihedral.Dihedral static method)

openbabelConvert() (in module moleculekit.smallmol.util) openmm_energy() (in module htmd.ffevaluation.test_ffevaluate) opm() (in module moleculekit.util) orientOnAxes() (in module moleculekit.util)

P

P (htmd.model.Model attribute) pack_double_buffer() (in module moleculekit.support) pack_int_buffer() (in module moleculekit.support) pack_string_buffer() (in module moleculekit.support) pack_ulong_buffer() (in module moleculekit.support) pairwise() (in module moleculekit.smallmol.tools.molvstautomer) pairwiseRMSD (in module htmd.numbautil) parallel() (in module moleculekit.tools.atomtyper) ParallelExecutor() (in module htmd.parallelprogress) (in module moleculekit.smallmol.tools.clustering) parallelfunc() (in module htmd.pathplanning) parent (htmd.metricdata.MetricData attribute) (htmd.simlist.Sim attribute) parse() (playmolecule.jsonlogger.JsonFormatter method) paths (moleculekit.smallmol.tools.tautomers.MolFragmenter attribute) 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] PDBXMMCIFread() (in module moleculekit.readers) 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) phi() (moleculekit.projections.metricdihedral.Dihedral static method) piece (htmd.simlist.Frame attribute) playmolecule (module) playmolecule.config (module) playmolecule.devutils (module) playmolecule.job (module) playmolecule.jsonlogger (module) playmolecule.session (module) playmolecule.utils (module) plotClusters() (htmd.metricdata.MetricData method) plotConformerEnergies() (htmd.parameterization.dihedral.DihedralFitting method) plotCounts() (htmd.metricdata.MetricData method) plotDihedralEnergies() (htmd.parameterization.dihedral.DihedralFitting method) plotFES() (htmd.model.Model method) plotFluxPathways() (htmd.kinetics.Kinetics method) plotRates() (htmd.kinetics.Kinetics method) plotTimescales() (htmd.model.Model method) (htmd.modelhmm.ModelHMM 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) Pmemd (class in htmd.apps.pmemd) pmtryexcept() (in module playmolecule.devutils) postRequest() (in module playmolecule.utils) pp_calcDistances() (in module moleculekit.projections.util) pp_calcMinDistances() (in module moleculekit.projections.util) PreparationData (class in moleculekit.tools.preparationdata) prepareProteinForAtomtyping() (in module moleculekit.tools.atomtyper) PREPIread() (in module moleculekit.readers) prettyPrintResidue() (in module moleculekit.tools.preparationdata) printIt() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) PRMTOPread() (in module moleculekit.readers) process_log_record() (playmolecule.jsonlogger.JsonFormatter method) Production (class in htmd.protocols.pmemdproduction) (class in htmd.protocols.production_v1) (class in htmd.protocols.production_v2) (class in htmd.protocols.production_v3) (class in htmd.protocols.production_v4) (class in htmd.protocols.production_v5) (class in htmd.protocols.production_v6) 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.metricdistance.MetricSelfDistance method) (moleculekit.projections.metricfluctuation.MetricFluctuation 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 attribute) propkaContainer (moleculekit.tools.preparationdata.PreparationData attribute) proteinDihedrals() (moleculekit.projections.metricdihedral.Dihedral static method) proteinPrepare() (in module moleculekit.tools.preparation) ProtocolInterface (class in htmd.protocols.oldprotocolinterface) PSFread() (in module moleculekit.readers) PSFwrite() (in module moleculekit.writers) psi() (moleculekit.projections.metricdihedral.Dihedral static method)

Q

qm_results (htmd.charge.esp.ESP attribute) (htmd.parameterization.dihedral.DihedralFitting attribute)

QUEUED (playmolecule.job.JobStatus attribute)

R

randomPointsOnSphere() (in module htmd.charge.esp) 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) readFRCMOD() (in module htmd.parameterization.readers) readPREPI() (in module htmd.parameterization.readers) readRTF() (in module htmd.parameterization.readers) reconstructContactMap() (in module moleculekit.projections.metricdistance) record (moleculekit.molecule.Molecule attribute) recreateParameters() (in module htmd.parameterization.parameterset) ref (htmd.metricdata.MetricData attribute), [1] reference (htmd.metricdata.Trajectory attribute) 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) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) removeAtomsInHull() (in module htmd.builder.builder) removeHET() (in module htmd.builder.builder) 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) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer 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) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer 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) reprepare() (moleculekit.tools.preparationdata.PreparationData 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) restrainedEmbed() (in module moleculekit.smallmol.tools.restrainedembed) restraint_factor (htmd.charge.esp.ESP attribute) result_directory (htmd.parameterization.dihedral.DihedralFitting attribute) retrieve() (playmolecule.job.Job method) retrieveJobs() (playmolecule.session.Session method) 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.charge.esp.ESP method) (htmd.ffevaluation.ffevaluate.FFEvaluate method) (htmd.parameterization.dihedral.DihedralFitting method) RUNNING (playmolecule.job.JobStatus attribute)

S

sampleClusters() (htmd.metricdata.MetricData method) sampleRegion() (htmd.metricdata.MetricData method) sampleStates() (htmd.model.Model method) save() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) (htmd.metricdata.MetricData method) (htmd.model.Model method) save_graphml() (htmd.mutualinformation.MutualInformation method) saveMI() (htmd.mutualinformation.MutualInformation method) scanDihedrals() (in module htmd.parameterization.util) SCORE_dict (moleculekit.smallmol.tools.tautomers.MolFragmenter attribute) sdfReader() (in module moleculekit.smallmol.smallmollib) SDFwrite() (in module moleculekit.writers) search() (in module htmd.builder.charmm) search_fragment_by_atom() (moleculekit.smallmol.tools.tautomers.MolFragmenter method) segid (moleculekit.molecule.Molecule attribute) selectAtom() (moleculekit.molecule.UniqueAtomID method) selectAtoms() (moleculekit.molecule.UniqueResidueID method) send() (moleculekit.vmdviewer.VMD method) sequence() (moleculekit.molecule.Molecule method) sequenceID() (in module moleculekit.util) sequenceStructureAlignment() (in module moleculekit.tools.sequencestructuralalignment) serial (moleculekit.molecule.Molecule attribute) Session (class in playmolecule.session) SessionError set() (htmd.projections.metric.Metric method) (moleculekit.molecule.Molecule method) set_params() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) setAsCompleted() (in module playmolecule.devutils) setAsError() (in module playmolecule.devutils) setAttributeNameList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) setComplete() (playmolecule.job.Job method) setDihedral() (moleculekit.molecule.Molecule method) setError() (playmolecule.job.Job method) setGlobal() (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) setName() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method)

setProgress() (playmolecule.job.Job method) setRowList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) setRowPartition() (moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method) setSleep() (playmolecule.job.Job method) setStart() (playmolecule.job.Job method) setType() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataContainer method) (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) setup() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) setValue() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) show() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd 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), [1] simlist() (in module htmd.simlist) simmerge() (in module htmd.simlist) simpleSuite() (in module moleculekit.pdbx.tests.PdbxReaderTests) (in module moleculekit.pdbx.tests.PdbxReadWriteTests) SLEEPING (playmolecule.job.JobStatus attribute) SmallMol (class in moleculekit.smallmol.smallmol) SmallMolLib (class in moleculekit.smallmol.smallmollib) SmallMolStack (in module moleculekit.smallmol.smallmollib) smarts (moleculekit.smallmol.tools.molvstautomer.TautomerScore attribute) 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), [1] StandardPDBChiralAtom() (in module moleculekit.rdkitintegration) StandardPDBResidueChirality() (in module moleculekit.rdkitintegration) startApp() (playmolecule.session.Session method) string_to_tempfile() (in module moleculekit.support) StringValidator (class in htmd.protocols.oldprotocolinterface) submit() (playmolecule.job.Job method) suite() (in module moleculekit.pdbx.tests.PdbxWriterTests) symmetrizeCharges() (in module htmd.charge.charge) SyntaxError, [1]

T

TanimotoDistances() (in module moleculekit.smallmol.tools.clustering) tarFolder() (in module playmolecule.devutils) tautomer (moleculekit.smallmol.tools.molvstautomer.TautomerTransform attribute) TAUTOMER_SCORES (in module moleculekit.smallmol.tools.molvstautomer) TAUTOMER_TRANSFORMS (in module moleculekit.smallmol.tools.molvstautomer) TautomerCanonicalizer (class in moleculekit.smallmol.tools.tautomers) TautomerEnumerator (class in moleculekit.smallmol.tools.molvstautomer) TautomerScore (class in moleculekit.smallmol.tools.molvstautomer) TautomerTransform (class in moleculekit.smallmol.tools.molvstautomer) 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) TimestepValidator (class in htmd.protocols.oldprotocolinterface) toDataFrame() (moleculekit.smallmol.smallmollib.SmallMolLib 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.VMDBox static method) (moleculekit.vmdgraphics.VMDConvexHull static method) (moleculekit.vmdgraphics.VMDCylinder static method) (moleculekit.vmdgraphics.VMDGraphicObject static method) (moleculekit.vmdgraphics.VMDIsosurface static method) (moleculekit.vmdgraphics.VMDLabels static method) (moleculekit.vmdgraphics.VMDSphere static method) (moleculekit.vmdgraphics.VMDText static method) Trajectory (class in htmd.metricdata) (class in moleculekit.readers) trajectory (htmd.simlist.Sim attribute) trajLengths (htmd.metricdata.MetricData attribute) Tree (class in htmd.pathplanning)

U

uniformRandomRotation() (in module moleculekit.util) UniqueAtomID (class in moleculekit.molecule) UniqueResidueID (class in moleculekit.molecule) UnknownResidueError

unzipit() (in module playmolecule.devutils) updatingMean() (in module htmd.adaptive.util) uploadFolder() (in module playmolecule.devutils) usesTime() (playmolecule.jsonlogger.JsonFormatter method)

V

validate() (htmd.protocols.oldprotocolinterface.BinaryValidator method) (htmd.protocols.oldprotocolinterface.BooleanValidator method) (htmd.protocols.oldprotocolinterface.ClassValidator method) (htmd.protocols.oldprotocolinterface.DictionaryValidator method) (htmd.protocols.oldprotocolinterface.FileValidator method) (htmd.protocols.oldprotocolinterface.FunctionValidator method) (htmd.protocols.oldprotocolinterface.ListListValidator method) (htmd.protocols.oldprotocolinterface.ListValidator method) (htmd.protocols.oldprotocolinterface.ObjectValidator method) (htmd.protocols.oldprotocolinterface.StringValidator method) (htmd.protocols.oldprotocolinterface.TimestepValidator method) (htmd.protocols.oldprotocolinterface.ValueValidator method) VALIDATING (playmolecule.job.JobStatus attribute) Validator (class in htmd.protocols.oldprotocolinterface) ValueValidator (class in htmd.protocols.oldprotocolinterface) version() (in module htmd.version) (in module moleculekit.version)

view() (moleculekit.molecule.Molecule method) (moleculekit.smallmol.smallmol.SmallMol method) viewer() (in module moleculekit.vmdviewer) viewForces() (in module htmd.ffevaluation.ffevaluate) viewname (moleculekit.molecule.Molecule attribute) viewStates() (htmd.model.Model method) (htmd.modelhmm.ModelHMM 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) vmdselection() (in module moleculekit.vmdparser) VMDSphere (class in moleculekit.vmdgraphics) VMDText (class in moleculekit.vmdgraphics)

W

wait() (playmolecule.job.Job method) waitChildren() (playmolecule.job.Job method) WAITING_APPROVAL (playmolecule.job.JobStatus attribute) WAITING_DATA (playmolecule.job.JobStatus attribute) warnIfTerminiSuspect() (moleculekit.tools.preparationdata.PreparationData method) weightGraph() (htmd.mutualinformation.MutualInformation method) with_traceback() (htmd.builder.builder.BuildError method) (htmd.builder.builder.MissingAngleError method) (htmd.builder.builder.MissingAtomTypeError method) (htmd.builder.builder.MissingBondError method) (htmd.builder.builder.MissingParameterError method) (htmd.builder.builder.MissingTorsionError method) (htmd.builder.builder.MixedSegmentError method) (htmd.builder.builder.ResidueInsertionError method) (htmd.builder.builder.UnknownResidueError method) (moleculekit.molecule.TopologyInconsistencyError method) (moleculekit.pdbx.reader.PdbxParser.PdbxError method) (moleculekit.pdbx.reader.PdbxParser.SyntaxError method) (moleculekit.pdbx.reader.PdbxReader.PdbxError method) (moleculekit.pdbx.reader.PdbxReader.SyntaxError method) (moleculekit.pdbx.writer.PdbxWriter.PdbxError method) (moleculekit.projections.metricdihedral.AtomNotFoundException method) (moleculekit.readers.FormatError method) (moleculekit.readers.TopologyInconsistencyError method) (playmolecule.job.JobError method) (playmolecule.session.SessionError method) wrap() (in module htmd.membranebuilder.ringpenetration) (in module moleculekit.wrap) (moleculekit.molecule.Molecule method) wrapBondedDistance (in module moleculekit.dihedral)

wrapDistance (in module moleculekit.dihedral) wrapping_dist_python() (in module htmd.membranebuilder.build_membrane) write() (htmd.protocols.equilibration_v1.Equilibration method) (htmd.protocols.equilibration_v2.Equilibration method) (htmd.protocols.pmemdequilibration.Equilibration method) (htmd.protocols.pmemdproduction.Production method) (htmd.protocols.production_v1.Production method) (htmd.protocols.production_v2.Production method) (htmd.protocols.production_v3.Production method) (htmd.protocols.production_v4.Production method) (htmd.protocols.production_v5.Production 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) writeConf() (htmd.apps.acemd.Acemd method) (htmd.apps.pmemd.Pmemd method) writeContainer() (moleculekit.pdbx.reader.PdbxParser.PdbxWriter method) (moleculekit.pdbx.writer.PdbxWriter.PdbxWriter method) writeFRCMOD() (in module htmd.parameterization.writers) writeInputsOptionsLog() (in module playmolecule.devutils) writeParameters() (in module htmd.parameterization.writers) writePRM() (in module htmd.parameterization.writers) writeRTF() (in module htmd.parameterization.writers) writeSdf() (moleculekit.smallmol.smallmollib.SmallMolLib method) writeSentinel() (in module playmolecule.devutils) writeSmiles() (moleculekit.smallmol.smallmollib.SmallMolLib method) writeVoxels() (in module moleculekit.util) writeXYZ() (htmd.charge.esp.MoleculeGrid method)

X

x (moleculekit.molecule.Molecule attribute) xtc_lib() (in module moleculekit.support) 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 attribute)

Z

z (moleculekit.molecule.Molecule attribute)

zerod_parameters (htmd.parameterization.dihedral.DihedralFitting attribute)