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) (class in htmd.mdengine.acemd.acemd) Acemd2 (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) 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) addHs() (moleculekit.smallmol.smallmol.SmallMol method) addPoint() (htmd.pathplanning.Tree method) aggregateTime() (htmd.metricdata.MetricData property) 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)

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) 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) (in module moleculekit.util) atominfo() (moleculekit.readers.Topology property) AtomNotFoundException AtomRestraint (class in htmd.mdengine.acemd.acemd) 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.mutualinformation.MutualInformation method) calculateUniqueBonds() (in module moleculekit.molecule) cancel() (playmolecule.job.Job method) cancelJob() (playmolecule.session.Session method) 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) 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.MetricData method) (htmd.metricdata.Trajectory property) (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 (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) conformationStationaryDistribution() (htmd.adaptive.adaptivebandit.AdaptiveBandit method) 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) 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) cross() (in module htmd.numbautil) crystalinfo (moleculekit.molecule.Molecule attribute)

D

dat (htmd.metricdata.MetricData attribute) dat() (htmd.metricdata.MetricData property) 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) defaultAmberHome() (in module htmd.builder.amber) defaultEquilRestraints() (htmd.protocols.equilibration_v3.Equilibration method) defaultFf() (in module htmd.builder.amber) defaultParam() (in module htmd.builder.amber) (in module htmd.builder.charmm) defaultStream() (in module htmd.builder.charmm) defaultTopo() (in module htmd.builder.amber) (in module htmd.builder.charmm) DefinitionContainer (class in moleculekit.pdbx.reader.PdbxContainers) delete() (moleculekit.vmdgraphics.VMDGraphicObject method) (moleculekit.vmdgraphics.VMDIsosurface method) (moleculekit.vmdgraphics.VMDLabels method) deleteBonds() (moleculekit.molecule.Molecule method) 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) (playmolecule.job.JobStatus method)

describeApp() (playmolecule.session.Session method) describeNextReport() (htmd.membranebuilder.pdbreporter.PDBReporter method) detectCisPeptideBonds() (in module htmd.builder.builder) detectDisulfideBonds() (in module htmd.builder.builder) 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) dihedrals (moleculekit.molecule.Molecule attribute) dihedralsToIndexes() (moleculekit.projections.metricdihedral.Dihedral static method) distance (htmd.clustering.kcenters.KCenter attribute) distributeLipids() (in module htmd.membranebuilder.ljfluid) DisulfideBridge (class in htmd.builder.builder) dock() (in module htmd.dock) (in module moleculekit.tools.docking) docString() (htmd.protocols.oldprotocolinterface.Validator 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) ensurelist() (in module htmd.util) (in module moleculekit.util) (in module playmolecule.utils) enumerate() (moleculekit.smallmol.tools.molvstautomer.TautomerEnumerator method)

epochSimIndexes() (in module htmd.adaptive.adaptive) 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.equilibration_v3) (class in htmd.protocols.pmemdequilibration) ERROR (playmolecule.job.JobStatus attribute) exists() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method)

F

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) findHbonds() (moleculekit.tools.preparationdata.PreparationData method) fit() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) format() (playmolecule.jsonlogger.JsonFormatter method) format_datetime_obj() (playmolecule.jsonlogger.JsonEncoder method) FormatError 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) frame() (moleculekit.molecule.Molecule property) (moleculekit.smallmol.smallmol.SmallMol property) fromMolecule() (moleculekit.molecule.UniqueAtomID static method) (moleculekit.molecule.UniqueResidueID static method) (moleculekit.readers.Topology method) fstep (htmd.metricdata.MetricData attribute) (moleculekit.molecule.Molecule attribute) fstep() (moleculekit.molecule.Molecule property) 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.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) getAllNeighbours() (in module htmd.membranebuilder.ringpenetration) getAtoms() (moleculekit.smallmol.smallmol.SmallMol method) getAttributeCount() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeIndex() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeLengthMaximumList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeListWithOrder() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) getAttributeValueMaxLengthList() (moleculekit.pdbx.reader.PdbxContainers.DataCategory method) 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) getEpochFromName() (in module htmd.adaptive.adaptive) getEpochSimIdx() (in module htmd.adaptive.util) getEpochTrajectoryDictionary() (in module htmd.adaptive.util) getErrorInfo() (playmolecule.job.Job method) getFeatures() (in module moleculekit.tools.atomtyper) 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) getJob() (playmolecule.session.Session method) getJobId() (in module playmolecule.devutils) getJobsByGroup() (playmolecule.session.Session method) getMapping() (htmd.projections.metric.Metric method) (moleculekit.projections.metriccoordinate.MetricCoordinate method) (moleculekit.projections.metricdihedral.MetricDihedral method) (moleculekit.projections.metricdistance.MetricDistance method) (moleculekit.projections.metricfluctuation.MetricFluctuation method) (moleculekit.projections.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) getObj() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) getObjNameList() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) getParentSimIdxFrame() (in module htmd.adaptive.util) getPDBQTAtomType() (in module moleculekit.tools.atomtyper) getPDBQTAtomTypesAndCharges() (in module moleculekit.tools.atomtyper) getPdbStrings() (in module htmd.util) 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) 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) getServiceStatus() (playmolecule.session.Session method) 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) 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) GroupRestraint (class in htmd.mdengine.acemd.acemd) GROwrite() (in module moleculekit.writers) guessAnglesAndDihedrals() (in module moleculekit.util) guessbonds() (in module moleculekit.vmdparser) 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.adaptive module htmd.adaptive.adaptivebandit module htmd.adaptive.adaptivegoal module htmd.adaptive.adaptivegoaleg module htmd.adaptive.adaptiverun 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.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.kineticshmm 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.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.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.equilibration_v3 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.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

impropers (moleculekit.molecule.Molecule attribute) inprogress() (htmd.queues.playqueue.PlayQueue method) input (htmd.simlist.Sim attribute) 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) isAttribute() (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) isCategory() (moleculekit.pdbx.reader.PdbxContainers.DefinitionContainer method) isChiral() (moleculekit.smallmol.smallmol.SmallMol method)

J

Job (class in playmolecule.job) JobBucketNotFoundError JobConfigNotLoadedError 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) 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 property) list() (moleculekit.molecule.Representations method) listApps() (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) loadConfig() (in module playmolecule.config) loadMI() (htmd.mutualinformation.MutualInformation method) loadMol() (moleculekit.vmdviewer.VMD method) login() (playmolecule.session.Session method) loopModeller() (in module htmd.builder.loopmodeler)

M

macro_ofcluster() (htmd.model.Model property) macro_ofmicro() (htmd.model.Model property) macroAccumulate() (in module htmd.model) macronum() (htmd.model.Model property) (htmd.modelhmm.ModelHMM property) MAEread() (in module moleculekit.readers) makeMolGraph() (in module moleculekit.tools.graphalignment) manual() (in module moleculekit.projections.metricplumed2) map (htmd.metricdata.MetricData attribute) map() (htmd.metricdata.MetricData property) markovModel() (htmd.model.Model method) (htmd.modelhmm.ModelHMM method) masses (moleculekit.molecule.Molecule 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) memory() (htmd.queues.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) 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 property) micronum() (htmd.model.Model property) minimalRotation() (in module htmd.builder.builder) minimize() (in module htmd.membranebuilder.globalminimization) missedLigands (moleculekit.tools.preparationdata.PreparationData attribute) MissingAngleError MissingAtomTypeError MissingBondError MissingParameterError MissingTorsionError MixedSegmentError Model (class in htmd.model) ModelHMM (class in htmd.modelhmm) module htmd htmd.adaptive htmd.adaptive.adaptive htmd.adaptive.adaptivebandit htmd.adaptive.adaptivegoal htmd.adaptive.adaptivegoaleg htmd.adaptive.adaptiverun htmd.adaptive.util htmd.apps htmd.apps.acemd htmd.apps.pmemd htmd.builder htmd.builder.amber htmd.builder.builder htmd.builder.charmm htmd.builder.ionize htmd.builder.loopmodeler htmd.builder.preparation htmd.builder.solvate htmd.clustering htmd.clustering.kcenters htmd.clustering.regular htmd.config htmd.decorators htmd.dock htmd.home htmd.kinetics htmd.kineticshmm 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.model htmd.modelhmm htmd.molecule htmd.molecule.molecule htmd.molecule.util htmd.mutualinformation htmd.numbautil 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_v1 htmd.protocols.equilibration_v2 htmd.protocols.equilibration_v3 htmd.protocols.oldprotocolinterface htmd.protocols.pmemdequilibration htmd.protocols.pmemdproduction htmd.protocols.production_v1 htmd.protocols.production_v2 htmd.protocols.production_v3 htmd.protocols.production_v4 htmd.protocols.production_v5 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 moleculekit moleculekit.align moleculekit.config moleculekit.dihedral moleculekit.home moleculekit.molecule moleculekit.pdbx moleculekit.pdbx.reader moleculekit.pdbx.reader.PdbxContainers moleculekit.pdbx.reader.PdbxParser moleculekit.pdbx.reader.PdbxReader moleculekit.pdbx.tests moleculekit.pdbx.tests.PdbxReaderTests moleculekit.pdbx.tests.PdbxReadWriteTests moleculekit.pdbx.tests.PdbxWriterTests moleculekit.pdbx.writer moleculekit.pdbx.writer.PdbxWriter moleculekit.periodictable moleculekit.projections moleculekit.projections.metriccoordinate moleculekit.projections.metricdihedral moleculekit.projections.metricdistance moleculekit.projections.metricfluctuation 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.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.molvstautomer moleculekit.smallmol.tools.restrainedembed moleculekit.smallmol.tools.tautomers moleculekit.smallmol.tools.test_tools moleculekit.smallmol.util moleculekit.support moleculekit.tools moleculekit.tools.atomtyper moleculekit.tools.autosegment moleculekit.tools.crystalpacking moleculekit.tools.docking moleculekit.tools.graphalignment moleculekit.tools.hhblitsprofile moleculekit.tools.pka moleculekit.tools.preparation moleculekit.tools.preparationdata moleculekit.tools.sequencestructuralalignment moleculekit.tools.voxeldescriptors moleculekit.util moleculekit.version moleculekit.vmdgraphics moleculekit.vmdparser moleculekit.vmdviewer moleculekit.wrap moleculekit.writers playmolecule playmolecule.config playmolecule.devutils playmolecule.job playmolecule.jsonlogger playmolecule.session playmolecule.utils

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) 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.docking 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) natsorted() (in module moleculekit.util) ncpu() (htmd.queues.playqueue.PlayQueue property) ngpu() (htmd.queues.playqueue.PlayQueue property) norm() (in module htmd.numbautil) numAtoms (moleculekit.molecule.Molecule attribute) numAtoms() (moleculekit.molecule.Molecule property) (moleculekit.smallmol.smallmol.SmallMol property) numDimensions() (htmd.metricdata.MetricData property) (htmd.metricdata.Trajectory property)

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

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) opm() (in module moleculekit.util) orientOnAxes() (in module moleculekit.util)

P

P() (htmd.model.Model property) 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 PlayQueue (class in htmd.queues.playqueue) plotClusters() (htmd.metricdata.MetricData method) plotCounts() (htmd.metricdata.MetricData 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) 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.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.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 property) 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

QUEUED (playmolecule.job.JobStatus attribute)

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) readArguments() (playmolecule.job.Job method) readConfig() (htmd.mdengine.acemd.acemd.Acemd method) reconstructAdaptiveTraj() (in module htmd.adaptive.adaptive) reconstructContactMap() (in module moleculekit.projections.metricdistance) record (moleculekit.molecule.Molecule attribute) ref (htmd.metricdata.MetricData attribute) ref() (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) removeAtomsInHull() (in module htmd.builder.builder) 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) 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) retrieve() (htmd.queues.playqueue.PlayQueue method) (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.adaptive.adaptive.AdaptiveBase 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) 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) setAsCompleted() (in module playmolecule.devutils) setAsError() (in module playmolecule.devutils) setAsSleep() (in module playmolecule.devutils) setAttributeNameList() (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) setJobStatus() (playmolecule.session.Session method) setName() (moleculekit.pdbx.reader.PdbxContainers.ContainerBase method) (moleculekit.pdbx.reader.PdbxContainers.DataCategoryBase method) setProgress() (playmolecule.job.Job method) setRowList() (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) 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) simlist() (htmd.metricdata.MetricData property) (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 property) 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) St() (htmd.metricdata.MetricData property) StandardPDBChiralAtom() (in module moleculekit.rdkitintegration) StandardPDBResidueChirality() (in module moleculekit.rdkitintegration) startApp() (playmolecule.session.Session method) stop() (htmd.queues.playqueue.PlayQueue method) string_to_tempfile() (in module moleculekit.support) StringValidator (class in htmd.protocols.oldprotocolinterface) submit() (htmd.queues.playqueue.PlayQueue method) (playmolecule.job.Job method) suite() (in module moleculekit.pdbx.tests.PdbxWriterTests) SyntaxError, [1]

T

TanimotoDistances() (in module moleculekit.smallmol.tools.clustering) tarFolder() (in module playmolecule.devutils) tautomer() (moleculekit.smallmol.tools.molvstautomer.TautomerTransform property) 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.VMDGraphicObject static method) Trajectory (class in htmd.metricdata) (class in moleculekit.readers) trajectory (htmd.simlist.Sim attribute) trajLengths() (htmd.metricdata.MetricData property) 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)

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) 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) 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.mdengine.acemd.acemd.Acemd method) (htmd.protocols.equilibration_v1.Equilibration method) (htmd.protocols.equilibration_v2.Equilibration method) (htmd.protocols.equilibration_v3.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)

writeArguments() (playmolecule.job.Job 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) writeInputsOptionsLog() (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) 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 property)

Z

z() (moleculekit.molecule.Molecule property)

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