Index

_

__init__() (openpathsampling.analysis.ChannelAnalysis method) (openpathsampling.analysis.PathDensityHistogram method) (openpathsampling.analysis.PathHistogram method) (openpathsampling.analysis.ReplicaNetwork method) (openpathsampling.analysis.ReplicaNetworkGraph method) (openpathsampling.analysis.ShootingPointAnalysis method) (openpathsampling.analysis.tis.ConditionalTransitionProbability method) (openpathsampling.analysis.tis.DictFlux method) (openpathsampling.analysis.tis.EnsembleHistogrammer method) (openpathsampling.analysis.tis.FullHistogramMaxLambdas method) (openpathsampling.analysis.tis.MinusMoveFlux method) (openpathsampling.analysis.tis.MultiEnsembleSamplingAnalyzer method) (openpathsampling.analysis.tis.PathLengthHistogrammer method) (openpathsampling.analysis.tis.StandardTISAnalysis method) (openpathsampling.analysis.tis.StandardTransitionProbability method) (openpathsampling.analysis.tis.TISAnalysis method) (openpathsampling.analysis.tis.TotalCrossingProbability method) (openpathsampling.analysis.tis.TransitionDictResults method) (openpathsampling.collectivevariables.CollectiveVariable method) (openpathsampling.collectivevariables.CoordinateFunctionCV method) (openpathsampling.collectivevariables.CoordinateGeneratorCV method) (openpathsampling.collectivevariables.FunctionCV method) (openpathsampling.collectivevariables.GeneratorCV method) (openpathsampling.collectivevariables.InVolumeCV method) (openpathsampling.collectivevariables.MDTrajFunctionCV method) (openpathsampling.collectivevariables.MSMBFeaturizerCV method) (openpathsampling.collectivevariables.PLUMEDCV method) (openpathsampling.collectivevariables.PLUMEDInterface method) (openpathsampling.collectivevariables.PyEMMAFeaturizerCV method) (openpathsampling.CommittorSimulation method) (openpathsampling.Details method) (openpathsampling.DirectSimulation method) (openpathsampling.engines.BaseSnapshot method) (openpathsampling.engines.DynamicsEngine method) (openpathsampling.engines.gromacs.engine.GromacsEngine method) (openpathsampling.engines.gromacs.ExternalMDSnapshot method) (openpathsampling.engines.openmm.engine.OpenMMEngine method) (openpathsampling.engines.openmm.MDSnapshot method) (openpathsampling.engines.openmm.Snapshot method) (openpathsampling.engines.openmm.topology.MDTrajTopology method) (openpathsampling.engines.SnapshotDescriptor method) (openpathsampling.engines.Topology method) (openpathsampling.engines.toy.Gaussian method) (openpathsampling.engines.toy.HarmonicOscillator method) (openpathsampling.engines.toy.integrators.ToyIntegrator method) (openpathsampling.engines.toy.LangevinBAOABIntegrator method) (openpathsampling.engines.toy.LeapfrogVerletIntegrator method) (openpathsampling.engines.toy.LinearSlope method) (openpathsampling.engines.toy.OuterWalls method) (openpathsampling.engines.toy.PES method) (openpathsampling.engines.toy.PES_Add method) (openpathsampling.engines.toy.PES_Sub method) (openpathsampling.engines.toy.ToyEngine method) (openpathsampling.engines.toy.ToySnapshot method) (openpathsampling.engines.Trajectory method) (openpathsampling.ensemble.AllInXEnsemble method) (openpathsampling.ensemble.AllOutXEnsemble method) (openpathsampling.ensemble.EmptyEnsemble method) (openpathsampling.ensemble.Ensemble method) (openpathsampling.ensemble.EnsembleCombination method) (openpathsampling.ensemble.FullEnsemble method) (openpathsampling.ensemble.IntersectionEnsemble method) (openpathsampling.ensemble.LengthEnsemble method) (openpathsampling.ensemble.MinusInterfaceEnsemble method) (openpathsampling.ensemble.OptionalEnsemble method) (openpathsampling.ensemble.PartInXEnsemble method) (openpathsampling.ensemble.PartOutXEnsemble method) (openpathsampling.ensemble.PrefixTrajectoryEnsemble method) (openpathsampling.ensemble.ReversedTrajectoryEnsemble method) (openpathsampling.ensemble.SequentialEnsemble method) (openpathsampling.ensemble.SingleFrameEnsemble method) (openpathsampling.ensemble.SuffixTrajectoryEnsemble method) (openpathsampling.ensemble.TISEnsemble method) (openpathsampling.ensemble.UnionEnsemble method) (openpathsampling.ensemble.VolumeEnsemble method) (openpathsampling.ensemble.WrappedEnsemble method) (openpathsampling.FullBootstrapping method) (openpathsampling.high_level.interface_set.GenericVolumeInterfaceSet method) (openpathsampling.high_level.interface_set.InterfaceSet method) (openpathsampling.high_level.interface_set.PeriodicVolumeInterfaceSet method) (openpathsampling.high_level.interface_set.VolumeInterfaceSet method) (openpathsampling.high_level.move_strategy.AllSetRepExStrategy method) (openpathsampling.high_level.move_strategy.EnsembleHopStrategy method) (openpathsampling.high_level.move_strategy.ForwardShootingStrategy method) (openpathsampling.high_level.move_strategy.MinusMoveStrategy method) (openpathsampling.high_level.move_strategy.MoveStrategy method) (openpathsampling.high_level.move_strategy.NearestNeighborRepExStrategy method) (openpathsampling.high_level.move_strategy.OneWayShootingStrategy method) (openpathsampling.high_level.move_strategy.OrganizeByEnsembleStrategy method) (openpathsampling.high_level.move_strategy.OrganizeByMoveGroupStrategy method) (openpathsampling.high_level.move_strategy.PathReversalStrategy method) (openpathsampling.high_level.move_strategy.PoorSingleReplicaStrategy method) (openpathsampling.high_level.move_strategy.ReplicaExchangeStrategy method) (openpathsampling.high_level.move_strategy.SelectedPairsRepExStrategy method) (openpathsampling.high_level.move_strategy.SingleReplicaMinusMoveStrategy method) (openpathsampling.high_level.move_strategy.TwoWayShootingStrategy method) (openpathsampling.high_level.network.FixedLengthTPSNetwork method) (openpathsampling.high_level.network.MISTISNetwork method) (openpathsampling.high_level.network.MSTISNetwork method) (openpathsampling.high_level.network.TPSNetwork method) (openpathsampling.high_level.network.TransitionNetwork method) (openpathsampling.high_level.transition.FixedLengthTPSTransition method) (openpathsampling.high_level.transition.TISTransition method) (openpathsampling.high_level.transition.TPSTransition method) (openpathsampling.high_level.transition.Transition method) (openpathsampling.MCStep method) (openpathsampling.MoveChange method) (openpathsampling.MoveDetails method) (openpathsampling.netcdfplus.base.StorableNamedObject method) (openpathsampling.netcdfplus.base.StorableObject method) (openpathsampling.netcdfplus.cache.Cache method) (openpathsampling.netcdfplus.cache.LRUCache method) (openpathsampling.netcdfplus.cache.MaxCache method) (openpathsampling.netcdfplus.cache.NoCache method) (openpathsampling.netcdfplus.cache.WeakKeyCache method) (openpathsampling.netcdfplus.cache.WeakLRUCache method) (openpathsampling.netcdfplus.cache.WeakValueCache method) (openpathsampling.netcdfplus.dictify.ObjectJSON method) (openpathsampling.netcdfplus.dictify.StorableObjectJSON method) (openpathsampling.netcdfplus.netcdfplus.NetCDFPlus method) (openpathsampling.netcdfplus.proxy.DelayedLoader method) (openpathsampling.netcdfplus.proxy.LoaderProxy method) (openpathsampling.netcdfplus.stores.DictStore method) (openpathsampling.netcdfplus.stores.ImmutableDictStore method) (openpathsampling.netcdfplus.stores.NamedObjectStore method) (openpathsampling.netcdfplus.stores.ObjectStore method) (openpathsampling.netcdfplus.stores.UniqueNamedObjectStore method) (openpathsampling.netcdfplus.stores.VariableStore method) (openpathsampling.numerics.BlockResampling method) (openpathsampling.numerics.Histogram method) (openpathsampling.numerics.Histogrammer method) (openpathsampling.numerics.HistogramPlotter2D method) (openpathsampling.numerics.LookupFunction method) (openpathsampling.numerics.LookupFunctionGroup method) (openpathsampling.numerics.ResamplingStatistics method) (openpathsampling.numerics.SparseHistogram method) (openpathsampling.numerics.VoxelLookupFunction method) (openpathsampling.numerics.WHAM method) (openpathsampling.pathmover.BackwardExtendMover method) (openpathsampling.pathmover.BackwardShootMover method) (openpathsampling.pathmover.ConditionalSequentialMover method) (openpathsampling.pathmover.EngineMover method) (openpathsampling.pathmover.EnsembleFilterMover method) (openpathsampling.pathmover.EnsembleHopMover method) (openpathsampling.pathmover.FinalSubtrajectorySelectMover method) (openpathsampling.pathmover.FirstAllowedMover method) (openpathsampling.pathmover.FirstSubtrajectorySelectMover method) (openpathsampling.pathmover.ForwardShootMover method) (openpathsampling.pathmover.LastAllowedMover method) (openpathsampling.pathmover.MinusMover method) (openpathsampling.pathmover.OneWayExtendMover method) (openpathsampling.pathmover.OneWayShootingMover method) (openpathsampling.pathmover.PartialAcceptanceSequentialMover method) (openpathsampling.pathmover.PathMover method) (openpathsampling.pathmover.PathReversalMover method) (openpathsampling.pathmover.RandomChoiceMover method) (openpathsampling.pathmover.RandomSubtrajectorySelectMover method) (openpathsampling.pathmover.ReplicaExchangeMover method) (openpathsampling.pathmover.SampleMover method) (openpathsampling.pathmover.SelectionMover method) (openpathsampling.pathmover.SequentialMover method) (openpathsampling.pathmover.SingleReplicaMinusMover method) (openpathsampling.pathmover.StateSwapMover method) (openpathsampling.pathmover.SubPathMover method) (openpathsampling.pathmover.SubtrajectorySelectMover method) (openpathsampling.pathmover.TwoWayShootingMover method) (openpathsampling.PathSampling method) (openpathsampling.PathSimulator method) (openpathsampling.ReactiveFluxSimulation method) (openpathsampling.Sample method) (openpathsampling.SampleDetails method) (openpathsampling.SampleSet method) (openpathsampling.shooting.BiasedSelector method) (openpathsampling.shooting.FinalFrameSelector method) (openpathsampling.shooting.FirstFrameSelector method) (openpathsampling.shooting.GaussianBiasSelector method) (openpathsampling.shooting.InterfaceConstrainedSelector method) (openpathsampling.shooting.ShootingPointSelector method) (openpathsampling.shooting.UniformSelector method) (openpathsampling.snapshot_modifier.GeneralizedDirectionModifier method) (openpathsampling.snapshot_modifier.NoModification method) (openpathsampling.snapshot_modifier.RandomVelocities method) (openpathsampling.snapshot_modifier.SingleAtomVelocityDirectionModifier method) (openpathsampling.snapshot_modifier.SnapshotModifier method) (openpathsampling.snapshot_modifier.VelocityDirectionModifier method) (openpathsampling.storage.AnalysisStorage method) (openpathsampling.storage.Storage method) (openpathsampling.storage.stores.CVStore method) (openpathsampling.storage.stores.MCStepStore method) (openpathsampling.storage.stores.MoveChangeStore method) (openpathsampling.storage.stores.PathSimulatorStore method) (openpathsampling.storage.stores.SampleSetStore method) (openpathsampling.storage.stores.SampleStore method) (openpathsampling.storage.stores.SnapshotWrapperStore method) (openpathsampling.storage.stores.TrajectoryStore method) (openpathsampling.treelogic.TreeMixin method) (openpathsampling.volume.CVDefinedVolume method) (openpathsampling.volume.EmptyVolume method) (openpathsampling.volume.FullVolume method) (openpathsampling.volume.IntersectionVolume method) (openpathsampling.volume.PeriodicCVDefinedVolume method) (openpathsampling.volume.RelativeComplementVolume method) (openpathsampling.volume.SymmetricDifferenceVolume method) (openpathsampling.volume.UnionVolume method) (openpathsampling.volume.Volume method) (openpathsampling.volume.VolumeCombination method)

_cache_dict (openpathsampling.collectivevariables.CollectiveVariable attribute)

A

active (openpathsampling.MCStep attribute) all_ensembles (openpathsampling.high_level.network.TransitionNetwork attribute) AllInXEnsemble (class in openpathsampling.ensemble)

AllOutXEnsemble (class in openpathsampling.ensemble) allow_refresh (openpathsampling.PathSimulator attribute) AllSetRepExStrategy (class in openpathsampling.high_level.move_strategy) AnalysisStorage (class in openpathsampling.storage)

B

BackwardExtendMover (class in openpathsampling.pathmover) BackwardShootMover (class in openpathsampling.pathmover) BaseSnapshot (class in openpathsampling.engines)

beta (openpathsampling.engines.toy.LangevinBAOABIntegrator attribute) BiasedSelector (class in openpathsampling.shooting) BlockResampling (class in openpathsampling.numerics)

C

c1 (openpathsampling.engines.toy.LangevinBAOABIntegrator attribute) c2 (openpathsampling.engines.toy.LangevinBAOABIntegrator attribute) c3 (openpathsampling.engines.toy.LangevinBAOABIntegrator attribute) Cache (class in openpathsampling.netcdfplus.cache) cache (openpathsampling.netcdfplus.stores.ObjectStore attribute) change (openpathsampling.MCStep attribute) ChannelAnalysis (class in openpathsampling.analysis) CollectiveVariable (class in openpathsampling.collectivevariables) CommittorSimulation (class in openpathsampling) ConditionalSequentialMover (class in openpathsampling.pathmover) ConditionalTransitionProbability (class in openpathsampling.analysis.tis)

content_class (openpathsampling.netcdfplus.stores.ObjectStore attribute) CoordinateFunctionCV (class in openpathsampling.collectivevariables) CoordinateGeneratorCV (class in openpathsampling.collectivevariables) coordinates (openpathsampling.engines.openmm.MDSnapshot attribute) (openpathsampling.engines.toy.ToySnapshot attribute) current_snapshot (openpathsampling.engines.toy.ToyEngine attribute) cv_callable (openpathsampling.collectivevariables.CoordinateFunctionCV attribute) (openpathsampling.collectivevariables.FunctionCV attribute) cv_time_reversible (openpathsampling.collectivevariables.CollectiveVariable attribute) CVDefinedVolume (class in openpathsampling.volume) CVStore (class in openpathsampling.storage.stores)

D

default_group_weights (openpathsampling.high_level.move_strategy.OrganizeByMoveGroupStrategy attribute) DelayedLoader (class in openpathsampling.netcdfplus.proxy) Details (class in openpathsampling) details (openpathsampling.MoveChange attribute)

DictFlux (class in openpathsampling.analysis.tis) DictStore (class in openpathsampling.netcdfplus.stores) DirectSimulation (class in openpathsampling) DynamicsEngine (class in openpathsampling.engines)

E

empty_snapshot_from_openmm_topology() (in module openpathsampling.engines.openmm) EmptyEnsemble (class in openpathsampling.ensemble) EmptyVolume (class in openpathsampling.volume) Engine (in module openpathsampling.engines.gromacs) (in module openpathsampling.engines.openmm) (in module openpathsampling.engines.toy) engine (openpathsampling.engines.gromacs.ExternalMDSnapshot attribute) (openpathsampling.engines.openmm.MDSnapshot attribute) (openpathsampling.engines.openmm.Snapshot attribute) (openpathsampling.engines.toy.ToySnapshot attribute) EngineMover (class in openpathsampling.pathmover) Ensemble (class in openpathsampling.ensemble) ensemble (openpathsampling.ensemble.SingleFrameEnsemble attribute) (openpathsampling.pathmover.FinalSubtrajectorySelectMover attribute) (openpathsampling.pathmover.FirstSubtrajectorySelectMover attribute) (openpathsampling.pathmover.OneWayExtendMover attribute) (openpathsampling.pathmover.OneWayShootingMover attribute) (openpathsampling.pathmover.RandomSubtrajectorySelectMover attribute) (openpathsampling.pathmover.SubtrajectorySelectMover attribute) (openpathsampling.Sample attribute)

ensemble_dict (openpathsampling.SampleSet attribute) ensemble_weights (openpathsampling.high_level.move_strategy.OrganizeByEnsembleStrategy attribute) EnsembleCombination (class in openpathsampling.ensemble) EnsembleFilterMover (class in openpathsampling.pathmover) EnsembleHistogrammer (class in openpathsampling.analysis.tis) EnsembleHopMover (class in openpathsampling.pathmover) EnsembleHopStrategy (class in openpathsampling.high_level.move_strategy) ensembles (openpathsampling.ensemble.SequentialEnsemble attribute) ExternalMDSnapshot (class in openpathsampling.engines.gromacs)

F

file_name (openpathsampling.engines.gromacs.ExternalMDSnapshot attribute) file_position (openpathsampling.engines.gromacs.ExternalMDSnapshot attribute) final_states (openpathsampling.ensemble.TISEnsemble attribute) FinalFrameSelector (class in openpathsampling.shooting) FinalSubtrajectorySelectMover (class in openpathsampling.pathmover) FirstAllowedMover (class in openpathsampling.pathmover) FirstFrameSelector (class in openpathsampling.shooting) FirstSubtrajectorySelectMover (class in openpathsampling.pathmover) FixedLengthTPSNetwork (class in openpathsampling.high_level.network)

FixedLengthTPSTransition (class in openpathsampling.high_level.transition) fluxes (openpathsampling.DirectSimulation attribute) ForwardShootingStrategy (class in openpathsampling.high_level.move_strategy) ForwardShootMover (class in openpathsampling.pathmover) FullBootstrapping (class in openpathsampling) FullEnsemble (class in openpathsampling.ensemble) FullHistogramMaxLambdas (class in openpathsampling.analysis.tis) FullVolume (class in openpathsampling.volume) FunctionCV (class in openpathsampling.collectivevariables)

G

Gaussian (class in openpathsampling.engines.toy) GaussianBiasSelector (class in openpathsampling.shooting) GeneralizedDirectionModifier (class in openpathsampling.snapshot_modifier)

GeneratorCV (class in openpathsampling.collectivevariables) GenericVolumeInterfaceSet (class in openpathsampling.high_level.interface_set) GromacsEngine (class in openpathsampling.engines.gromacs.engine) group_weights (openpathsampling.high_level.move_strategy.OrganizeByMoveGroupStrategy attribute)

H

HarmonicOscillator (class in openpathsampling.engines.toy) Histogram (class in openpathsampling.numerics)

Histogrammer (class in openpathsampling.numerics) HistogramPlotter2D (class in openpathsampling.numerics) histograms_to_pandas_dataframe() (in module openpathsampling.numerics)

I

ImmutableDictStore (class in openpathsampling.netcdfplus.stores) initial_states (openpathsampling.ensemble.TISEnsemble attribute) input_transitions (openpathsampling.high_level.network.MISTISNetwork attribute) interface (openpathsampling.ensemble.TISEnsemble attribute)

InterfaceConstrainedSelector (class in openpathsampling.shooting) InterfaceSet (class in openpathsampling.high_level.interface_set) IntersectionEnsemble (class in openpathsampling.ensemble) IntersectionVolume (class in openpathsampling.volume) InVolumeCV (class in openpathsampling.collectivevariables)

J

join_ensembles() (in module openpathsampling.ensemble)

json (openpathsampling.netcdfplus.stores.ObjectStore attribute)

L

LangevinBAOABIntegrator (class in openpathsampling.engines.toy) LastAllowedMover (class in openpathsampling.pathmover) lazy_loading_attributes() (in module openpathsampling.netcdfplus.proxy) LeapfrogVerletIntegrator (class in openpathsampling.engines.toy) LengthEnsemble (class in openpathsampling.ensemble)

level (openpathsampling.high_level.move_strategy.MoveStrategy attribute) LinearSlope (class in openpathsampling.engines.toy) LoaderProxy (class in openpathsampling.netcdfplus.proxy) LookupFunction (class in openpathsampling.numerics) LookupFunctionGroup (class in openpathsampling.numerics) LRUCache (class in openpathsampling.netcdfplus.cache)

M

mass (openpathsampling.engines.toy.ToyEngine attribute) max_overlap (openpathsampling.ensemble.SequentialEnsemble attribute) MaxCache (class in openpathsampling.netcdfplus.cache) mccycle (openpathsampling.MCStep attribute) MCStep (class in openpathsampling) MCStepStore (class in openpathsampling.storage.stores) MDSnapshot (class in openpathsampling.engines.openmm) MDTrajFunctionCV (class in openpathsampling.collectivevariables) MDTrajTopology (class in openpathsampling.engines.openmm.topology) mean (openpathsampling.numerics.ResamplingStatistics attribute) min_overlap (openpathsampling.ensemble.SequentialEnsemble attribute) MinusInterfaceEnsemble (class in openpathsampling.ensemble) MinusMoveFlux (class in openpathsampling.analysis.tis) MinusMover (class in openpathsampling.pathmover) MinusMoveStrategy (class in openpathsampling.high_level.move_strategy) MISTISNetwork (class in openpathsampling.high_level.network) module openpathsampling.engines openpathsampling.engines.gromacs openpathsampling.engines.openmm openpathsampling.engines.toy openpathsampling.engines.toy.features.instantaneous_temperature

MoveChange (class in openpathsampling) MoveChangeStore (class in openpathsampling.storage.stores) MoveDetails (class in openpathsampling) mover (openpathsampling.MoveChange attribute) mover_weights (openpathsampling.high_level.move_strategy.OrganizeByEnsembleStrategy attribute) movers (openpathsampling.pathmover.FirstAllowedMover attribute) (openpathsampling.pathmover.LastAllowedMover attribute) (openpathsampling.pathmover.RandomChoiceMover attribute) (openpathsampling.pathmover.SelectionMover attribute) MoveStrategy (class in openpathsampling.high_level.move_strategy) MSMBFeaturizerCV (class in openpathsampling.collectivevariables) MSTISNetwork (class in openpathsampling.high_level.network) MultiEnsembleSamplingAnalyzer (class in openpathsampling.analysis.tis)

N

n_atoms (openpathsampling.engines.Topology attribute) n_flux_events (openpathsampling.DirectSimulation attribute) n_l (openpathsampling.pathmover.FinalSubtrajectorySelectMover attribute) (openpathsampling.pathmover.FirstSubtrajectorySelectMover attribute) (openpathsampling.pathmover.RandomSubtrajectorySelectMover attribute) (openpathsampling.pathmover.SubtrajectorySelectMover attribute) n_spatial (openpathsampling.engines.Topology attribute)

n_transitions (openpathsampling.DirectSimulation attribute) name (openpathsampling.collectivevariables.CollectiveVariable attribute) (openpathsampling.collectivevariables.InVolumeCV attribute) NamedObjectStore (class in openpathsampling.netcdfplus.stores) NearestNeighborRepExStrategy (class in openpathsampling.high_level.move_strategy) NetCDFPlus (class in openpathsampling.netcdfplus.netcdfplus) NoCache (class in openpathsampling.netcdfplus.cache) NoModification (class in openpathsampling.snapshot_modifier)

O

ObjectJSON (class in openpathsampling.netcdfplus.dictify) ObjectStore (class in openpathsampling.netcdfplus.stores) on_error (openpathsampling.engines.DynamicsEngine attribute) on_max_length (openpathsampling.engines.DynamicsEngine attribute) on_nan (openpathsampling.engines.DynamicsEngine attribute) on_retry (openpathsampling.engines.DynamicsEngine attribute) OneWayExtendMover (class in openpathsampling.pathmover) OneWayShootingMover (class in openpathsampling.pathmover) OneWayShootingStrategy (class in openpathsampling.high_level.move_strategy) OpenMMEngine (class in openpathsampling.engines.openmm.engine) openpathsampling.engines module openpathsampling.engines.gromacs module

openpathsampling.engines.openmm module openpathsampling.engines.toy module openpathsampling.engines.toy.features.instantaneous_temperature module OptionalEnsemble (class in openpathsampling.ensemble) orderparameter (openpathsampling.ensemble.TISEnsemble attribute) OrganizeByEnsembleStrategy (class in openpathsampling.high_level.move_strategy) OrganizeByMoveGroupStrategy (class in openpathsampling.high_level.move_strategy) OuterWalls (class in openpathsampling.engines.toy) output_stream (openpathsampling.PathSimulator attribute)

P

pad_end (openpathsampling.shooting.UniformSelector attribute) pad_start (openpathsampling.shooting.UniformSelector attribute) PartialAcceptanceSequentialMover (class in openpathsampling.pathmover) PartInXEnsemble (class in openpathsampling.ensemble) PartOutXEnsemble (class in openpathsampling.ensemble) PathDensityHistogram (class in openpathsampling.analysis) PathHistogram (class in openpathsampling.analysis) PathLengthHistogrammer (class in openpathsampling.analysis.tis) PathMover (class in openpathsampling.pathmover) PathReversalMover (class in openpathsampling.pathmover) PathReversalStrategy (class in openpathsampling.high_level.move_strategy) PathSampling (class in openpathsampling) PathSimulator (class in openpathsampling) PathSimulatorStore (class in openpathsampling.storage.stores)

period_max (openpathsampling.volume.PeriodicCVDefinedVolume attribute) period_min (openpathsampling.volume.PeriodicCVDefinedVolume attribute) PeriodicCVDefinedVolume (class in openpathsampling.volume) PeriodicVolumeInterfaceSet (class in openpathsampling.high_level.interface_set) PES (class in openpathsampling.engines.toy) pes (openpathsampling.engines.toy.ToyEngine attribute) PES_Add (class in openpathsampling.engines.toy) PES_Sub (class in openpathsampling.engines.toy) PLUMEDCV (class in openpathsampling.collectivevariables) PLUMEDInterface (class in openpathsampling.collectivevariables) PoorSingleReplicaStrategy (class in openpathsampling.high_level.move_strategy) PrefixTrajectoryEnsemble (class in openpathsampling.ensemble) previous (openpathsampling.MCStep attribute) PyEMMAFeaturizerCV (class in openpathsampling.collectivevariables)

R

RandomChoiceMover (class in openpathsampling.pathmover) RandomSubtrajectorySelectMover (class in openpathsampling.pathmover) RandomVelocities (class in openpathsampling.snapshot_modifier) rate_matrix (openpathsampling.DirectSimulation attribute) ReactiveFluxSimulation (class in openpathsampling) RelativeComplementVolume (class in openpathsampling.volume) replace_movers (openpathsampling.high_level.move_strategy.MoveStrategy attribute) replace_signatures (openpathsampling.high_level.move_strategy.MoveStrategy attribute) replica (openpathsampling.Sample attribute) replica_dict (openpathsampling.SampleSet attribute)

ReplicaExchangeMover (class in openpathsampling.pathmover) ReplicaExchangeStrategy (class in openpathsampling.high_level.move_strategy) ReplicaNetwork (class in openpathsampling.analysis) ReplicaNetworkGraph (class in openpathsampling.analysis) repx_network (openpathsampling.analysis.ReplicaNetworkGraph attribute) ResamplingStatistics (class in openpathsampling.numerics) results (openpathsampling.numerics.ResamplingStatistics attribute) retries_when_error (openpathsampling.engines.DynamicsEngine attribute) retries_when_max_length (openpathsampling.engines.DynamicsEngine attribute) retries_when_nan (openpathsampling.engines.DynamicsEngine attribute) ReversedTrajectoryEnsemble (class in openpathsampling.ensemble)

S

safemode (openpathsampling.netcdfplus.dictify.ObjectJSON attribute) Sample (class in openpathsampling) sample_every (openpathsampling.numerics.WHAM attribute) SampleDetails (class in openpathsampling) SampleMover (class in openpathsampling.pathmover) samples (openpathsampling.MoveChange attribute) (openpathsampling.SampleSet attribute) SampleSet (class in openpathsampling) SampleSetStore (class in openpathsampling.storage.stores) SampleStore (class in openpathsampling.storage.stores) sampling_ensembles (openpathsampling.high_level.network.TransitionNetwork attribute) sampling_transitions (openpathsampling.high_level.network.MISTISNetwork attribute) (openpathsampling.high_level.network.TransitionNetwork attribute) save_frequency (openpathsampling.PathSimulator attribute) SelectedPairsRepExStrategy (class in openpathsampling.high_level.move_strategy) SelectionMover (class in openpathsampling.pathmover) selector (openpathsampling.pathmover.OneWayShootingMover attribute) SequentialEnsemble (class in openpathsampling.ensemble) SequentialMover (class in openpathsampling.pathmover) ShootingPointAnalysis (class in openpathsampling.analysis) ShootingPointSelector (class in openpathsampling.shooting) simulation (openpathsampling.MCStep attribute) SingleAtomVelocityDirectionModifier (class in openpathsampling.snapshot_modifier) SingleFrameEnsemble (class in openpathsampling.ensemble) SingleReplicaMinusMover (class in openpathsampling.pathmover) SingleReplicaMinusMoveStrategy (class in openpathsampling.high_level.move_strategy)

Snapshot (class in openpathsampling.engines.openmm) (in module openpathsampling.engines.toy) snapshot_from_pdb() (in module openpathsampling.engines.openmm) snapshot_from_testsystem() (in module openpathsampling.engines.openmm) snapshot_timestep (openpathsampling.engines.toy.ToyEngine attribute) SnapshotDescriptor (class in openpathsampling.engines) SnapshotModifier (class in openpathsampling.snapshot_modifier) SnapshotWrapperStore (class in openpathsampling.storage.stores) SparseHistogram (class in openpathsampling.numerics) StandardTISAnalysis (class in openpathsampling.analysis.tis) StandardTransitionProbability (class in openpathsampling.analysis.tis) StateSwapMover (class in openpathsampling.pathmover) std (openpathsampling.numerics.ResamplingStatistics attribute) StorableNamedObject (class in openpathsampling.netcdfplus.base) StorableObject (class in openpathsampling.netcdfplus.base) StorableObjectJSON (class in openpathsampling.netcdfplus.dictify) Storage (class in openpathsampling.storage) sub_ensemble (openpathsampling.pathmover.FinalSubtrajectorySelectMover attribute) (openpathsampling.pathmover.FirstSubtrajectorySelectMover attribute) (openpathsampling.pathmover.RandomSubtrajectorySelectMover attribute) (openpathsampling.pathmover.SubtrajectorySelectMover attribute) subchanges (openpathsampling.MoveChange attribute) SubPathMover (class in openpathsampling.pathmover) subset_mask (openpathsampling.snapshot_modifier.SnapshotModifier attribute) SubtrajectorySelectMover (class in openpathsampling.pathmover) SuffixTrajectoryEnsemble (class in openpathsampling.ensemble) SymmetricDifferenceVolume (class in openpathsampling.volume)

T

TISAnalysis (class in openpathsampling.analysis.tis) TISEnsemble (class in openpathsampling.ensemble) TISTransition (class in openpathsampling.high_level.transition) to_openmm_topology() (in module openpathsampling.engines.openmm) Topology (class in openpathsampling.engines) (in module openpathsampling.engines.toy) TotalCrossingProbability (class in openpathsampling.analysis.tis) ToyEngine (class in openpathsampling.engines.toy) ToyIntegrator (class in openpathsampling.engines.toy.integrators) ToySnapshot (class in openpathsampling.engines.toy) TPSNetwork (class in openpathsampling.high_level.network) TPSTransition (class in openpathsampling.high_level.transition)

Trajectory (class in openpathsampling.engines) trajectory (openpathsampling.Sample attribute) trajectory_from_mdtraj() (in module openpathsampling.engines.openmm) TrajectoryStore (class in openpathsampling.storage.stores) Transition (class in openpathsampling.high_level.transition) TransitionDictResults (class in openpathsampling.analysis.tis) TransitionNetwork (class in openpathsampling.high_level.network) transitions (openpathsampling.DirectSimulation attribute) (openpathsampling.high_level.network.MISTISNetwork attribute) TreeMixin (class in openpathsampling.treelogic) TwoWayShootingMover (class in openpathsampling.pathmover) TwoWayShootingStrategy (class in openpathsampling.high_level.move_strategy)

U

UniformSelector (class in openpathsampling.shooting) UnionEnsemble (class in openpathsampling.ensemble)

UnionVolume (class in openpathsampling.volume) UniqueNamedObjectStore (class in openpathsampling.netcdfplus.stores)

V

VariableStore (class in openpathsampling.netcdfplus.stores) velocities (openpathsampling.engines.openmm.MDSnapshot attribute) (openpathsampling.engines.toy.ToySnapshot attribute) VelocityDirectionModifier (class in openpathsampling.snapshot_modifier) Volume (class in openpathsampling.volume)

volume (openpathsampling.collectivevariables.InVolumeCV attribute) VolumeCombination (class in openpathsampling.volume) VolumeEnsemble (class in openpathsampling.ensemble) VolumeInterfaceSet (class in openpathsampling.high_level.interface_set) VoxelLookupFunction (class in openpathsampling.numerics)

W

WeakKeyCache (class in openpathsampling.netcdfplus.cache) WeakLRUCache (class in openpathsampling.netcdfplus.cache) WeakValueCache (class in openpathsampling.netcdfplus.cache) weights (openpathsampling.pathmover.FirstAllowedMover attribute) (openpathsampling.pathmover.LastAllowedMover attribute) (openpathsampling.pathmover.RandomChoiceMover attribute)

WHAM (class in openpathsampling.numerics) WrappedEnsemble (class in openpathsampling.ensemble)