Index

A

abs2rel() (htmd.metricdata.MetricData method) (in module htmd.metricdatagenerator) abs2sim() (htmd.metricdata.MetricData method) 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)

addPoint() (htmd.pathplanning.Tree method) aggregateTime (htmd.metricdata.MetricData property) append() (htmd.metricdata.MetricData method) assertSameAsReferenceDir() (in module htmd.util) atom_a (htmd.builder.nonstandard.ClusterBond attribute) atom_b (htmd.builder.nonstandard.ClusterBond attribute) atom_map (htmd.builder.nonstandard.ClusterModel attribute) atom_to_orig_name (htmd.builder.nonstandard.ClusterModel attribute) atom_to_residue (htmd.builder.nonstandard.ClusterModel attribute)

B

bonds (htmd.builder.nonstandard.ClusterSpec attribute) bootstrap() (htmd.metricdata.MetricData method) build() (in module htmd.builder.amber) (in module htmd.builder.charmm) (in module htmd.builder.openmm)

buildClusterModel() (in module htmd.builder.nonstandard) BuildError buildMembrane() (in module htmd.membranebuilder.build_membrane)

C

calculate() (htmd.mutualinformation.MutualInformation method) canonical_renames (htmd.builder.nonstandard.ClusterModel attribute) canonical_resnames (htmd.builder.nonstandard.ClusterSpec attribute) canonical_terminus (htmd.builder.nonstandard.ClusterSpec attribute) centerFrames (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) Centers (htmd.metricdata.MetricData attribute) check_for_license() (in module htmd.license) cif_path (htmd.builder.nonstandard.ClusterModel attribute) cktest() (htmd.model.Model method) cluster (htmd.metricdata.Trajectory property) cluster() (htmd.metricdata.MetricData method) cluster_centers (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) cluster_centers_ (htmd.clustering.regular.RegCluster property) cluster_ofmicro (htmd.model.Model property) ClusterBond (class in htmd.builder.nonstandard) ClusterModel (class in htmd.builder.nonstandard) ClusterOutputs (class in htmd.builder.nonstandard)

clusterSize (htmd.clustering.regular.RegCluster property) clusterSize_ (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) ClusterSpec (class in htmd.builder.nonstandard) combine() (htmd.metricdata.MetricData method) compareVersions() (in module htmd.latest) config() (in module htmd.config) conformationStationaryDistribution() (htmd.adaptive.adaptivebandit.AdaptiveBandit method) convert() (in module htmd.units) convertDisulfide() (in module htmd.builder.builder) copy() (htmd.metricdata.MetricData method) (htmd.metricdata.Trajectory method) (htmd.model.Model method) (htmd.simlist.Sim method) count_pucb() (htmd.adaptive.adaptivebandit.AdaptiveBandit method) count_ucb() (htmd.adaptive.adaptivebandit.AdaptiveBandit method) createCoreSetModel() (htmd.model.Model method) createState() (htmd.model.Model method) custombonds (htmd.builder.nonstandard.ClusterOutputs attribute)

D

dat (htmd.metricdata.MetricData property) deconcatenate() (htmd.metricdata.MetricData method) defaultAmberHome() (in module htmd.builder.amber) defaultFf() (in module htmd.builder.amber) (in module htmd.builder.openmm) defaultParam() (in module htmd.builder.amber) defaultTopo() (in module htmd.builder.amber) (in module htmd.builder.charmm) description (htmd.metricdata.MetricData attribute)

detectCisPeptideBonds() (in module htmd.builder.builder) detectDisulfideBonds() (in module htmd.builder.builder) diffMolecules() (in module htmd.util) distance (htmd.clustering.kcenters.KCenter attribute) distributeLipids() (in module htmd.membranebuilder.ljfluid) dock() (in module htmd.dock) dropDimensions() (htmd.metricdata.MetricData method) dropFrames() (htmd.metricdata.MetricData method) (htmd.metricdata.Trajectory method) dropTraj() (htmd.metricdata.MetricData method)

E

embed() (in module htmd.builder.builder) ensurelist() (in module htmd.util)

epochSimIndexes() (in module htmd.adaptive.adaptive) eqDistribution() (htmd.model.Model method) equilibrateMembrane() (in module htmd.membranebuilder.build_membrane)

F

ff_type (htmd.builder.nonstandard.ModelAtom attribute) fit() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method) Frame (class in htmd.simlist) frame (htmd.simlist.Frame attribute)

frcmod_paths (htmd.builder.nonstandard.ClusterOutputs attribute) fromHDF5() (htmd.metricdata.MetricData static method) (htmd.metricdata.Trajectory static method) (htmd.simlist.Sim static method) fstep (htmd.metricdata.MetricData attribute)

G

g0eq (htmd.kinetics.Rates attribute) getAllNeighbours() (in module htmd.membranebuilder.ringpenetration) getEpochFromName() (in module htmd.adaptive.adaptive) getEpochSimIdx() (in module htmd.adaptive.util) getEpochTrajectoryDictionary() (in module htmd.adaptive.util) getMapping() (htmd.projections.metric.Metric method)

getParentSimIdxFrame() (in module htmd.adaptive.util) getPdbStrings() (in module htmd.util) getRates() (htmd.kinetics.Kinetics method) getRewards() (htmd.adaptive.adaptivebandit.AdaptiveBandit method) getStates() (htmd.model.Model method) getStateStatistic() (in module htmd.model) GWPCA (class in htmd.projections.gwpca)

H

home() (in module htmd.home) htmd module htmd.adaptive module htmd.adaptive.adaptive module htmd.adaptive.adaptivebandit module htmd.adaptive.adaptivegoal module htmd.adaptive.adaptivegoaleg module htmd.adaptive.adaptiverun module htmd.adaptive.util module htmd.builder module htmd.builder.amber module htmd.builder.builder module htmd.builder.charmm module htmd.builder.ionize module htmd.builder.loopmodeler module htmd.builder.nonstandard module htmd.builder.openmm module htmd.builder.solvate module htmd.clustering module htmd.clustering.kcenters module htmd.clustering.regular module htmd.config module htmd.decorators module htmd.dock module htmd.home module htmd.kinetics module htmd.latest module

htmd.license module htmd.membranebuilder module htmd.membranebuilder.build_membrane module htmd.membranebuilder.globalminimization module htmd.membranebuilder.ljfluid module htmd.membranebuilder.ringpenetration module htmd.metricdata module htmd.metricdatagenerator module htmd.model module htmd.mutualinformation module htmd.parallelprogress module htmd.pathplanning module htmd.projections module htmd.projections.gwpca module htmd.projections.kmeanstri module htmd.projections.metric module htmd.projections.tica module htmd.session module htmd.simlist module htmd.ui module htmd.units module htmd.util module htmd.versionwarnings module htmd_register() (in module htmd.license) htmd_registration() (in module htmd.license) htmd_show_news() (in module htmd.license) htmdAmberHome() (in module htmd.builder.amber) htmdCharmmHome() (in module htmd.builder.charmm) htmdload() (in module htmd.session) htmdsave() (in module htmd.session)

I

ionize() (in module htmd.builder.ionize) ionizePlace() (in module htmd.builder.ionize) is_c_term (htmd.builder.nonstandard.ClusterSpec attribute)

is_canonical (htmd.builder.nonstandard.ClusterSpec attribute) is_chain_resident (htmd.builder.nonstandard.ClusterSpec attribute) is_n_term (htmd.builder.nonstandard.ClusterSpec attribute)

K

K (htmd.metricdata.MetricData attribute) KCenter (class in htmd.clustering.kcenters) kdeq (htmd.kinetics.Rates attribute)

Kinetics (class in htmd.kinetics) KMeansTri (class in htmd.projections.kmeanstri) koff (htmd.kinetics.Rates attribute) kon (htmd.kinetics.Rates attribute)

L

labels_ (htmd.clustering.kcenters.KCenter attribute) (htmd.clustering.regular.RegCluster attribute) least_square_fit_plane() (in module htmd.membranebuilder.ringpenetration) listFiles() (in module htmd.builder.amber) (in module htmd.builder.charmm)

listLipids() (in module htmd.membranebuilder.build_membrane) load() (htmd.metricdata.MetricData method) (htmd.model.Model method) loadMI() (htmd.mutualinformation.MutualInformation 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) map (htmd.metricdata.MetricData property) markovModel() (htmd.model.Model method) maxConnectedLag() (htmd.model.Model method) Metric (class in htmd.projections.metric) MetricData (class in htmd.metricdata) MetricDataGenerator (class in htmd.metricdatagenerator) 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) MissingAngleError MissingAtomTypeError MissingBondError MissingParameterError MissingResidueError MissingTorsionError MixedSegmentError Model (class in htmd.model) ModelAtom (class in htmd.builder.nonstandard) module htmd htmd.adaptive htmd.adaptive.adaptive htmd.adaptive.adaptivebandit htmd.adaptive.adaptivegoal htmd.adaptive.adaptivegoaleg htmd.adaptive.adaptiverun htmd.adaptive.util htmd.builder htmd.builder.amber htmd.builder.builder htmd.builder.charmm htmd.builder.ionize htmd.builder.loopmodeler htmd.builder.nonstandard htmd.builder.openmm htmd.builder.solvate htmd.clustering htmd.clustering.kcenters htmd.clustering.regular htmd.config htmd.decorators htmd.dock htmd.home htmd.kinetics htmd.latest htmd.license htmd.membranebuilder htmd.membranebuilder.build_membrane htmd.membranebuilder.globalminimization htmd.membranebuilder.ljfluid htmd.membranebuilder.ringpenetration htmd.metricdata htmd.metricdatagenerator htmd.model htmd.mutualinformation htmd.parallelprogress htmd.pathplanning htmd.projections htmd.projections.gwpca htmd.projections.kmeanstri htmd.projections.metric htmd.projections.tica htmd.session htmd.simlist htmd.ui htmd.units htmd.util htmd.versionwarnings

moveLipidToPos() (in module htmd.membranebuilder.ringpenetration) MutualInformation (class in htmd.mutualinformation)

N

N (htmd.metricdata.MetricData attribute) newMetricData() (htmd.metricdatagenerator.MetricDataGenerator method) newTrajectoriesClusterJumping() (htmd.metricdatagenerator.MetricDataGenerator method) newTrajectoriesFiller() (htmd.metricdatagenerator.MetricDataGenerator method) newTrajectoriesMSM() (htmd.metricdatagenerator.MetricDataGenerator method)

newTrajectoriesSimple() (htmd.metricdatagenerator.MetricDataGenerator method) numDimensions (htmd.metricdata.MetricData property) (htmd.metricdata.Trajectory property) numFrames (htmd.metricdata.MetricData property) (htmd.metricdata.Trajectory property) numTrajectories (htmd.metricdata.MetricData property)

P

P (htmd.model.Model property) ParallelExecutor() (in module htmd.parallelprogress) parallelfunc() (in module htmd.pathplanning) parallelTest() (htmd.metricdatagenerator.MetricDataGenerator method) parameterizeFromSpecs() (in module htmd.builder.nonstandard) parameterizeLigandsOpenFF() (in module htmd.builder.openmm) piece (htmd.simlist.Frame attribute) plotClusters() (htmd.metricdata.MetricData method) plotCounts() (htmd.metricdata.MetricData method) plotFES() (htmd.model.Model method)

plotFluxPathways() (htmd.kinetics.Kinetics method) plotMarkovModel() (htmd.kinetics.Kinetics method) plotRates() (htmd.kinetics.Kinetics method) plotTimescales() (htmd.model.Model method) plotTrajSizes() (htmd.metricdata.MetricData method) prepareClusterResidues() (in module htmd.builder.nonstandard) project() (htmd.projections.gwpca.GWPCA method) (htmd.projections.kmeanstri.KMeansTri method) (htmd.projections.metric.Metric method) (htmd.projections.tica.TICA method) projection (htmd.metricdata.Trajectory property)

R

Rates (class in htmd.kinetics) raytracing() (in module htmd.pathplanning) reconstructAdaptiveTraj() (in module htmd.adaptive.adaptive) ref (htmd.metricdata.MetricData property) reference (htmd.metricdata.Trajectory property) RegCluster (class in htmd.clustering.regular) rel2sim() (htmd.metricdata.MetricData method) removeAtomsInHull() (in module htmd.builder.builder) removeHET() (in module htmd.builder.builder)

removeLipidsInProtein() (in module htmd.builder.builder) ResidueInsertionError residues (htmd.builder.nonstandard.ClusterSpec attribute) resolveRingPenetrations() (in module htmd.membranebuilder.ringpenetration) role (htmd.builder.nonstandard.ModelAtom attribute) roles (htmd.builder.nonstandard.ClusterSpec attribute) rrt() (in module htmd.pathplanning) rrtstarsmart() (in module htmd.pathplanning) run() (htmd.adaptive.adaptive.AdaptiveBase method)

S

sampleClusters() (htmd.metricdata.MetricData method) sampleRegion() (htmd.metricdata.MetricData method) sampleStates() (htmd.model.Model method) save() (htmd.metricdata.MetricData method) (htmd.model.Model method) save_graphml() (htmd.mutualinformation.MutualInformation method) saveMI() (htmd.mutualinformation.MutualInformation method) search() (in module htmd.builder.charmm) set() (htmd.projections.metric.Metric method) set_fit_request() (htmd.clustering.kcenters.KCenter method) (htmd.clustering.regular.RegCluster method)

Sim (class in htmd.simlist) sim (htmd.simlist.Frame attribute) simfilter() (in module htmd.simlist) simlist (htmd.metricdata.MetricData property) simlist() (in module htmd.simlist) simmerge() (in module htmd.simlist) solvate() (in module htmd.builder.solvate) spec (htmd.builder.nonstandard.ClusterModel attribute) splitCols() (htmd.metricdata.MetricData method) St (htmd.metricdata.MetricData property) subtype (htmd.builder.nonstandard.ClusterSpec attribute)

T

tempname() (in module htmd.util) testDHFR() (in module htmd.util) TICA (class in htmd.projections.tica) tileMembrane() (in module htmd.builder.builder) toHDF5() (htmd.metricdata.MetricData method) (htmd.metricdata.Trajectory method) (htmd.simlist.Sim method)

topo_paths (htmd.builder.nonstandard.ClusterOutputs attribute) trajectories (htmd.metricdata.MetricData attribute) Trajectory (class in htmd.metricdata) trajLengths (htmd.metricdata.MetricData property) Tree (class in htmd.pathplanning)

U

updatingMean() (in module htmd.adaptive.util)

V

viewStates() (htmd.model.Model method)

W

weightGraph() (htmd.mutualinformation.MutualInformation method)

wrap() (in module htmd.membranebuilder.ringpenetration) wrapping_dist_python() (in module htmd.membranebuilder.build_membrane)

X

xml_paths (htmd.builder.nonstandard.ClusterOutputs attribute)