Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ __init__() (openff.evaluator.attributes.Attribute method) (openff.evaluator.attributes.AttributeClass method) (openff.evaluator.attributes.PlaceholderValue method) (openff.evaluator.backends.CalculationBackend method) (openff.evaluator.backends.ComputeResources method) (openff.evaluator.backends.dask.BaseDaskBackend method) (openff.evaluator.backends.dask.BaseDaskJobQueueBackend method) (openff.evaluator.backends.dask.DaskLocalCluster method) (openff.evaluator.backends.dask.DaskLSFBackend method) (openff.evaluator.backends.dask.DaskPBSBackend method) (openff.evaluator.backends.QueueWorkerResources method) (openff.evaluator.client.BatchMode method) (openff.evaluator.client.ConnectionOptions method) (openff.evaluator.client.EvaluatorClient method) (openff.evaluator.client.Request method) (openff.evaluator.client.RequestOptions method) (openff.evaluator.client.RequestResult method) (openff.evaluator.datasets.CalculationSource method) (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityData method) (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema method) (openff.evaluator.datasets.curation.components.CurationComponent method) (openff.evaluator.datasets.curation.components.CurationComponentSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByCharged method) (openff.evaluator.datasets.curation.components.filtering.FilterByChargedSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByElements method) (openff.evaluator.datasets.curation.components.filtering.FilterByElementsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByEnvironments method) (openff.evaluator.datasets.curation.components.filtering.FilterByEnvironmentsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByIonicLiquid method) (openff.evaluator.datasets.curation.components.filtering.FilterByIonicLiquidSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByMoleFraction method) (openff.evaluator.datasets.curation.components.filtering.FilterByMoleFractionSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByNComponents method) (openff.evaluator.datasets.curation.components.filtering.FilterByNComponentsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByPressure method) (openff.evaluator.datasets.curation.components.filtering.FilterByPressureSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByPropertyTypes method) (openff.evaluator.datasets.curation.components.filtering.FilterByPropertyTypesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByRacemic method) (openff.evaluator.datasets.curation.components.filtering.FilterByRacemicSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmiles method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmilesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmirks method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmirksSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByStereochemistry method) (openff.evaluator.datasets.curation.components.filtering.FilterByStereochemistrySchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySubstances method) (openff.evaluator.datasets.curation.components.filtering.FilterBySubstancesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByTemperature method) (openff.evaluator.datasets.curation.components.filtering.FilterByTemperatureSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterDuplicates method) (openff.evaluator.datasets.curation.components.filtering.FilterDuplicatesSchema method) (openff.evaluator.datasets.curation.components.freesolv.ImportFreeSolv method) (openff.evaluator.datasets.curation.components.freesolv.ImportFreeSolvSchema method) (openff.evaluator.datasets.curation.components.selection.FingerPrintType method) (openff.evaluator.datasets.curation.components.selection.SelectDataPoints method) (openff.evaluator.datasets.curation.components.selection.SelectDataPointsSchema method) (openff.evaluator.datasets.curation.components.selection.SelectSubstances method) (openff.evaluator.datasets.curation.components.selection.SelectSubstancesSchema method) (openff.evaluator.datasets.curation.components.selection.State method) (openff.evaluator.datasets.curation.components.selection.TargetState method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLData method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema method) (openff.evaluator.datasets.curation.workflow.CurationWorkflow method) (openff.evaluator.datasets.curation.workflow.CurationWorkflowSchema method) (openff.evaluator.datasets.MeasurementSource method) (openff.evaluator.datasets.PhysicalProperty method) (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.PropertyPhase method) (openff.evaluator.datasets.Source method) (openff.evaluator.datasets.taproom.TaproomDataSet method) (openff.evaluator.datasets.taproom.TaproomSource method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) (openff.evaluator.forcefield.ForceFieldSource method) (openff.evaluator.forcefield.LigParGenForceFieldSource method) (openff.evaluator.forcefield.ParameterGradient method) (openff.evaluator.forcefield.ParameterGradientKey method) (openff.evaluator.forcefield.SmirnoffForceFieldSource method) (openff.evaluator.forcefield.TLeapForceFieldSource method) (openff.evaluator.layers.CalculationLayer method) (openff.evaluator.layers.CalculationLayerResult method) (openff.evaluator.layers.CalculationLayerSchema method) (openff.evaluator.layers.reweighting.ReweightingLayer method) (openff.evaluator.layers.reweighting.ReweightingSchema method) (openff.evaluator.layers.simulation.SimulationLayer method) (openff.evaluator.layers.simulation.SimulationSchema method) (openff.evaluator.layers.workflow.WorkflowCalculationLayer method) (openff.evaluator.layers.workflow.WorkflowCalculationSchema method) (openff.evaluator.properties.Density method) (openff.evaluator.properties.DielectricConstant method) (openff.evaluator.properties.EnthalpyOfMixing method) (openff.evaluator.properties.EnthalpyOfVaporization method) (openff.evaluator.properties.ExcessMolarVolume method) (openff.evaluator.properties.HostGuestBindingAffinity method) (openff.evaluator.properties.SolvationFreeEnergy method) (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.utils.ReweightingProtocols method) (openff.evaluator.protocols.utils.SimulationProtocols method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.server.Batch method) (openff.evaluator.server.EvaluatorServer method) (openff.evaluator.storage.attributes.FilePath method) (openff.evaluator.storage.attributes.QueryAttribute method) (openff.evaluator.storage.attributes.StorageAttribute method) (openff.evaluator.storage.data.BaseSimulationData method) (openff.evaluator.storage.data.BaseStoredData method) (openff.evaluator.storage.data.ForceFieldData method) (openff.evaluator.storage.data.HashableStoredData method) (openff.evaluator.storage.data.ReplaceableData method) (openff.evaluator.storage.data.StoredFreeEnergyData method) (openff.evaluator.storage.data.StoredSimulationData method) (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.query.BaseDataQuery method) (openff.evaluator.storage.query.BaseSimulationDataQuery method) (openff.evaluator.storage.query.ForceFieldQuery method) (openff.evaluator.storage.query.FreeEnergyDataQuery method) (openff.evaluator.storage.query.SimulationDataQuery method) (openff.evaluator.storage.query.SubstanceQuery method) (openff.evaluator.storage.StorageBackend method) (openff.evaluator.substances.Amount method) (openff.evaluator.substances.Component method) (openff.evaluator.substances.ExactAmount method) (openff.evaluator.substances.MoleFraction method) (openff.evaluator.substances.Substance method) (openff.evaluator.thermodynamics.ThermodynamicState method) (openff.evaluator.utils.observables.Observable method) (openff.evaluator.utils.observables.ObservableArray method) (openff.evaluator.utils.observables.ObservableFrame method) (openff.evaluator.utils.observables.ObservableType method) (openff.evaluator.workflow.attributes.BaseMergeBehavior method) (openff.evaluator.workflow.attributes.InequalityMergeBehavior method) (openff.evaluator.workflow.attributes.InputAttribute method) (openff.evaluator.workflow.attributes.MergeBehavior method) (openff.evaluator.workflow.attributes.OutputAttribute method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGraph method) (openff.evaluator.workflow.ProtocolGroup method) (openff.evaluator.workflow.schemas.ProtocolGroupSchema method) (openff.evaluator.workflow.schemas.ProtocolReplicator method) (openff.evaluator.workflow.schemas.ProtocolSchema method) (openff.evaluator.workflow.schemas.WorkflowSchema method) (openff.evaluator.workflow.utils.ProtocolPath method) (openff.evaluator.workflow.utils.ReplicatorValue method) (openff.evaluator.workflow.Workflow method) (openff.evaluator.workflow.WorkflowGraph method) (openff.evaluator.workflow.WorkflowResult method) A absolute_tolerance (openff.evaluator.layers.CalculationLayerSchema attribute) (openff.evaluator.layers.reweighting.ReweightingSchema attribute) (openff.evaluator.layers.simulation.SimulationSchema attribute) (openff.evaluator.layers.workflow.WorkflowCalculationSchema attribute) activate_site_location (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) add_component() (openff.evaluator.substances.Substance method) add_condition() (openff.evaluator.protocols.groups.ConditionalGroup method) add_properties() (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.taproom.TaproomDataSet method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) add_protocols() (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.workflow.ProtocolGraph method) (openff.evaluator.workflow.ProtocolGroup method) add_schema() (openff.evaluator.client.RequestOptions method) add_workflows() (openff.evaluator.workflow.WorkflowGraph method) AddDummyAtoms (class in openff.evaluator.protocols.paprika.coordinates) AddValues (class in openff.evaluator.protocols.miscellaneous) allow_gpu_platforms (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) allow_merging (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.AverageFreeEnergies attribute) (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.analysis.BaseAverageObservable attribute) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol attribute) (openff.evaluator.protocols.analysis.ComputeDipoleMoments attribute) (openff.evaluator.protocols.analysis.DecorrelateObservables attribute) (openff.evaluator.protocols.analysis.DecorrelateTrajectory attribute) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) (openff.evaluator.protocols.forcefield.BaseBuildSystem attribute) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem attribute) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem attribute) (openff.evaluator.protocols.forcefield.BuildTLeapSystem attribute) (openff.evaluator.protocols.gradients.ZeroGradients attribute) (openff.evaluator.protocols.groups.ConditionalGroup attribute) (openff.evaluator.protocols.miscellaneous.AddValues attribute) (openff.evaluator.protocols.miscellaneous.DivideValue attribute) (openff.evaluator.protocols.miscellaneous.DummyProtocol attribute) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole attribute) (openff.evaluator.protocols.miscellaneous.MultiplyValue attribute) (openff.evaluator.protocols.miscellaneous.SubtractValues attribute) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction attribute) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation attribute) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase attribute) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork attribute) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection attribute) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms attribute) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates attribute) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints attribute) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ConcatenateObservables attribute) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) (openff.evaluator.workflow.Protocol attribute) (openff.evaluator.workflow.ProtocolGroup attribute) Amount (class in openff.evaluator.substances) amounts (openff.evaluator.substances.Substance attribute) AnalyzeAPRPhase (class in openff.evaluator.protocols.paprika.analysis) append_uuid() (openff.evaluator.workflow.utils.ProtocolPath method) apply() (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityData class method) (openff.evaluator.datasets.curation.components.CurationComponent class method) (openff.evaluator.datasets.curation.components.filtering.FilterByCharged class method) (openff.evaluator.datasets.curation.components.filtering.FilterByElements class method) (openff.evaluator.datasets.curation.components.filtering.FilterByEnvironments class method) (openff.evaluator.datasets.curation.components.filtering.FilterByIonicLiquid class method) (openff.evaluator.datasets.curation.components.filtering.FilterByMoleFraction class method) (openff.evaluator.datasets.curation.components.filtering.FilterByNComponents class method) (openff.evaluator.datasets.curation.components.filtering.FilterByPressure class method) (openff.evaluator.datasets.curation.components.filtering.FilterByPropertyTypes class method) (openff.evaluator.datasets.curation.components.filtering.FilterByRacemic class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmiles class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmirks class method) (openff.evaluator.datasets.curation.components.filtering.FilterByStereochemistry class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySubstances class method) (openff.evaluator.datasets.curation.components.filtering.FilterByTemperature class method) (openff.evaluator.datasets.curation.components.filtering.FilterDuplicates class method) (openff.evaluator.datasets.curation.components.freesolv.ImportFreeSolv class method) (openff.evaluator.datasets.curation.components.selection.SelectDataPoints class method) (openff.evaluator.datasets.curation.components.selection.SelectSubstances class method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLData class method) (openff.evaluator.datasets.curation.workflow.CurationWorkflow class method) (openff.evaluator.storage.query.BaseDataQuery method) (openff.evaluator.storage.query.BaseSimulationDataQuery method) (openff.evaluator.storage.query.ForceFieldQuery method) (openff.evaluator.storage.query.FreeEnergyDataQuery method) (openff.evaluator.storage.query.SimulationDataQuery method) (openff.evaluator.workflow.schemas.ProtocolReplicator method) apply_replicator() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) apply_restraints (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) ApplyRestraints (class in openff.evaluator.protocols.paprika.restraints) assigned_residue_names (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) attach_lambdas (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints attribute) Attribute (class in openff.evaluator.attributes) AttributeClass (class in openff.evaluator.attributes) AverageDielectricConstant (class in openff.evaluator.protocols.analysis) AverageFreeEnergies (class in openff.evaluator.protocols.analysis) AverageObservable (class in openff.evaluator.protocols.analysis) B BaseAverageObservable (class in openff.evaluator.protocols.analysis) BaseBuildSystem (class in openff.evaluator.protocols.forcefield) BaseDaskBackend (class in openff.evaluator.backends.dask) BaseDaskJobQueueBackend (class in openff.evaluator.backends.dask) BaseDataQuery (class in openff.evaluator.storage.query) BaseDecorrelateProtocol (class in openff.evaluator.protocols.analysis) BaseEnergyMinimisation (class in openff.evaluator.protocols.simulation) BaseEvaluateEnergies (class in openff.evaluator.protocols.reweighting) BaseMBARProtocol (class in openff.evaluator.protocols.reweighting) BaseMergeBehavior (class in openff.evaluator.workflow.attributes) BaseSimulation (class in openff.evaluator.protocols.simulation) BaseSimulationData (class in openff.evaluator.storage.data) BaseSimulationDataQuery (class in openff.evaluator.storage.query) BaseStoredData (class in openff.evaluator.storage.data) BaseYankProtocol (class in openff.evaluator.protocols.yank) Batch (class in openff.evaluator.server) batch_mode (openff.evaluator.client.RequestOptions attribute) BatchMode (class in openff.evaluator.client) beta (openff.evaluator.thermodynamics.ThermodynamicState property) bootstrap() (in module openff.evaluator.utils.observables) bootstrap_cycles (openff.evaluator.protocols.analysis.AverageFreeEnergies attribute) bootstrap_iterations (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.analysis.BaseAverageObservable attribute) (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) bootstrap_sample_size (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.analysis.BaseAverageObservable attribute) bootstrap_uncertainties (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) box_aspect_ratio (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) BuildCoordinatesPackmol (class in openff.evaluator.protocols.coordinates) BuildDockedCoordinates (class in openff.evaluator.protocols.coordinates) BuildDockedCoordinates.ActivateSiteLocation (class in openff.evaluator.protocols.coordinates) BuildLigParGenSystem (class in openff.evaluator.protocols.forcefield) BuildLigParGenSystem.WaterModel (class in openff.evaluator.protocols.forcefield) BuildSmirnoffSystem (class in openff.evaluator.protocols.forcefield) BuildTLeapSystem (class in openff.evaluator.protocols.forcefield) BuildTLeapSystem.ChargeBackend (class in openff.evaluator.protocols.forcefield) BuildTLeapSystem.WaterModel (class in openff.evaluator.protocols.forcefield) C calculate_aqueous_ionic_mole_fraction() (openff.evaluator.substances.Substance static method) calculation_layer() (in module openff.evaluator.layers) calculation_layers (openff.evaluator.client.RequestOptions attribute) calculation_schemas (openff.evaluator.client.RequestOptions attribute) CalculationBackend (class in openff.evaluator.backends) CalculationLayer (class in openff.evaluator.layers) CalculationLayerResult (class in openff.evaluator.layers) CalculationLayerSchema (class in openff.evaluator.layers) CalculationSource (class in openff.evaluator.datasets) can_merge() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) capitalize() (openff.evaluator.storage.attributes.FilePath method) casefold() (openff.evaluator.storage.attributes.FilePath method) center() (openff.evaluator.storage.attributes.FilePath method) center_solute_in_box (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) charge_backend (openff.evaluator.protocols.forcefield.BuildTLeapSystem attribute) checkpoint_frequency (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) checkpoint_interval (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) clear() (openff.evaluator.utils.observables.ObservableFrame method) clear_gradients() (openff.evaluator.utils.observables.Observable method) (openff.evaluator.utils.observables.ObservableArray method) (openff.evaluator.utils.observables.ObservableFrame method) complex_coordinate_path (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints attribute) complex_electrostatic_lambdas (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) complex_file_path (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates attribute) complex_steric_lambdas (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) Component (class in openff.evaluator.substances) component (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction attribute) Component.Role (class in openff.evaluator.substances) component_roles (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole attribute) components (openff.evaluator.substances.Substance attribute) components_only (openff.evaluator.storage.query.SubstanceQuery attribute) ComputeDipoleMoments (class in openff.evaluator.protocols.analysis) ComputeReferenceWork (class in openff.evaluator.protocols.paprika.analysis) ComputeResources (class in openff.evaluator.backends) ComputeResources.GPUPrecision (class in openff.evaluator.backends) ComputeResources.GPUToolkit (class in openff.evaluator.backends) ComputeSymmetryCorrection (class in openff.evaluator.protocols.paprika.analysis) ConcatenateObservables (class in openff.evaluator.protocols.reweighting) ConcatenateTrajectories (class in openff.evaluator.protocols.reweighting) ConditionalGroup (class in openff.evaluator.protocols.groups) ConditionalGroup.Condition (class in openff.evaluator.protocols.groups) ConditionalGroup.Condition.Type (class in openff.evaluator.protocols.groups) conditions (openff.evaluator.protocols.groups.ConditionalGroup attribute) confidence_intervals (openff.evaluator.protocols.analysis.AverageFreeEnergies attribute) connection_options (openff.evaluator.client.Request attribute) ConnectionOptions (class in openff.evaluator.client) construct() (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema class method) (openff.evaluator.datasets.curation.components.CurationComponentSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByChargedSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByElementsSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByEnvironmentsSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByIonicLiquidSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByMoleFractionSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByNComponentsSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByPressureSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByPropertyTypesSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByRacemicSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmilesSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmirksSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByStereochemistrySchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySubstancesSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByTemperatureSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterDuplicatesSchema class method) (openff.evaluator.datasets.curation.components.freesolv.ImportFreeSolvSchema class method) (openff.evaluator.datasets.curation.components.selection.SelectDataPointsSchema class method) (openff.evaluator.datasets.curation.components.selection.SelectSubstancesSchema class method) (openff.evaluator.datasets.curation.components.selection.State class method) (openff.evaluator.datasets.curation.components.selection.TargetState class method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema class method) (openff.evaluator.datasets.curation.workflow.CurationWorkflowSchema class method) ConvertExcessDensityData (class in openff.evaluator.datasets.curation.components.conversion) ConvertExcessDensityDataSchema (class in openff.evaluator.datasets.curation.components.conversion) coordinate_file_name (openff.evaluator.storage.data.StoredSimulationData attribute) coordinate_file_path (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) (openff.evaluator.protocols.forcefield.BaseBuildSystem attribute) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem attribute) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem attribute) (openff.evaluator.protocols.forcefield.BuildTLeapSystem attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) copy() (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema method) (openff.evaluator.datasets.curation.components.CurationComponentSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByChargedSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByElementsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByEnvironmentsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByIonicLiquidSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByMoleFractionSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByNComponentsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByPressureSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByPropertyTypesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByRacemicSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmilesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmirksSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByStereochemistrySchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySubstancesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByTemperatureSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterDuplicatesSchema method) (openff.evaluator.datasets.curation.components.freesolv.ImportFreeSolvSchema method) (openff.evaluator.datasets.curation.components.selection.SelectDataPointsSchema method) (openff.evaluator.datasets.curation.components.selection.SelectSubstancesSchema method) (openff.evaluator.datasets.curation.components.selection.State method) (openff.evaluator.datasets.curation.components.selection.TargetState method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema method) (openff.evaluator.datasets.curation.workflow.CurationWorkflowSchema method) (openff.evaluator.workflow.utils.ProtocolPath method) count() (openff.evaluator.storage.attributes.FilePath method) count_exact_amount (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) CurationComponent (class in openff.evaluator.datasets.curation.components) CurationComponentSchema (class in openff.evaluator.datasets.curation.components) CurationWorkflow (class in openff.evaluator.datasets.curation.workflow) CurationWorkflowSchema (class in openff.evaluator.datasets.curation.workflow) current_iteration (openff.evaluator.protocols.groups.ConditionalGroup attribute) cutoff (openff.evaluator.forcefield.LigParGenForceFieldSource property) (openff.evaluator.forcefield.TLeapForceFieldSource property) D DaskLocalCluster (class in openff.evaluator.backends.dask) DaskLSFBackend (class in openff.evaluator.backends.dask) DaskPBSBackend (class in openff.evaluator.backends.dask) data_class() (openff.evaluator.storage.query.BaseDataQuery class method) (openff.evaluator.storage.query.BaseSimulationDataQuery class method) (openff.evaluator.storage.query.ForceFieldQuery class method) (openff.evaluator.storage.query.FreeEnergyDataQuery class method) (openff.evaluator.storage.query.SimulationDataQuery class method) data_to_store (openff.evaluator.layers.CalculationLayerResult attribute) (openff.evaluator.workflow.WorkflowResult attribute) DecorrelateObservables (class in openff.evaluator.protocols.analysis) DecorrelateTrajectory (class in openff.evaluator.protocols.analysis) default_paprika_schema() (openff.evaluator.properties.HostGuestBindingAffinity class method) default_request_options() (openff.evaluator.client.EvaluatorClient static method) default_reweighting_schema() (openff.evaluator.properties.Density static method) (openff.evaluator.properties.DielectricConstant static method) (openff.evaluator.properties.EnthalpyOfMixing class method) (openff.evaluator.properties.EnthalpyOfVaporization class method) (openff.evaluator.properties.ExcessMolarVolume class method) default_simulation_schema() (openff.evaluator.properties.Density static method) (openff.evaluator.properties.DielectricConstant static method) (openff.evaluator.properties.EnthalpyOfMixing class method) (openff.evaluator.properties.EnthalpyOfVaporization static method) (openff.evaluator.properties.ExcessMolarVolume class method) (openff.evaluator.properties.SolvationFreeEnergy static method) default_storage_query() (in module openff.evaluator.layers.reweighting) default_unit() (openff.evaluator.datasets.PhysicalProperty class method) (openff.evaluator.properties.Density class method) (openff.evaluator.properties.DielectricConstant class method) (openff.evaluator.properties.EnthalpyOfMixing class method) (openff.evaluator.properties.EnthalpyOfVaporization class method) (openff.evaluator.properties.ExcessMolarVolume class method) (openff.evaluator.properties.HostGuestBindingAffinity class method) (openff.evaluator.properties.SolvationFreeEnergy class method) default_yank_schema() (openff.evaluator.properties.HostGuestBindingAffinity static method) Density (class in openff.evaluator.properties) dependencies (openff.evaluator.protocols.analysis.AverageDielectricConstant property) (openff.evaluator.protocols.analysis.AverageFreeEnergies property) (openff.evaluator.protocols.analysis.AverageObservable property) (openff.evaluator.protocols.analysis.BaseAverageObservable property) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol property) (openff.evaluator.protocols.analysis.ComputeDipoleMoments property) (openff.evaluator.protocols.analysis.DecorrelateObservables property) (openff.evaluator.protocols.analysis.DecorrelateTrajectory property) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol property) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates property) (openff.evaluator.protocols.coordinates.SolvateExistingStructure property) (openff.evaluator.protocols.forcefield.BaseBuildSystem property) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem property) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem property) (openff.evaluator.protocols.forcefield.BuildTLeapSystem property) (openff.evaluator.protocols.gradients.ZeroGradients property) (openff.evaluator.protocols.groups.ConditionalGroup property) (openff.evaluator.protocols.miscellaneous.AddValues property) (openff.evaluator.protocols.miscellaneous.DivideValue property) (openff.evaluator.protocols.miscellaneous.DummyProtocol property) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole property) (openff.evaluator.protocols.miscellaneous.MultiplyValue property) (openff.evaluator.protocols.miscellaneous.SubtractValues property) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction property) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation property) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies property) (openff.evaluator.protocols.openmm.OpenMMSimulation property) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase property) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork property) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection property) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms property) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates property) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates property) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints property) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints property) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints property) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints property) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies property) (openff.evaluator.protocols.reweighting.BaseMBARProtocol property) (openff.evaluator.protocols.reweighting.ConcatenateObservables property) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories property) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant property) (openff.evaluator.protocols.reweighting.ReweightObservable property) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation property) (openff.evaluator.protocols.simulation.BaseSimulation property) (openff.evaluator.protocols.storage.UnpackStoredSimulationData property) (openff.evaluator.protocols.yank.BaseYankProtocol property) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol property) (openff.evaluator.protocols.yank.SolvationYankProtocol property) (openff.evaluator.workflow.Protocol property) (openff.evaluator.workflow.ProtocolGroup property) dict() (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema method) (openff.evaluator.datasets.curation.components.CurationComponentSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByChargedSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByElementsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByEnvironmentsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByIonicLiquidSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByMoleFractionSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByNComponentsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByPressureSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByPropertyTypesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByRacemicSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmilesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmirksSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByStereochemistrySchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySubstancesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByTemperatureSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterDuplicatesSchema method) (openff.evaluator.datasets.curation.components.freesolv.ImportFreeSolvSchema method) (openff.evaluator.datasets.curation.components.selection.SelectDataPointsSchema method) (openff.evaluator.datasets.curation.components.selection.SelectSubstancesSchema method) (openff.evaluator.datasets.curation.components.selection.State method) (openff.evaluator.datasets.curation.components.selection.TargetState method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema method) (openff.evaluator.datasets.curation.workflow.CurationWorkflowSchema method) DielectricConstant (class in openff.evaluator.properties) dipole_moments (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.ComputeDipoleMoments attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) DivideValue (class in openff.evaluator.protocols.miscellaneous) divisor (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.miscellaneous.DivideValue attribute) docked_complex_coordinate_path (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) docked_ligand_coordinate_path (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) doi (openff.evaluator.datasets.MeasurementSource attribute) download_url (openff.evaluator.forcefield.LigParGenForceFieldSource property) DummyProtocol (class in openff.evaluator.protocols.miscellaneous) E effective_samples (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) electrostatic_lambdas_1 (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) electrostatic_lambdas_2 (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) enable_data_caching (openff.evaluator.server.Batch attribute) enable_pbc (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation attribute) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) encode() (openff.evaluator.storage.attributes.FilePath method) end_state_trajectory (openff.evaluator.storage.data.StoredFreeEnergyData attribute) endswith() (openff.evaluator.storage.attributes.FilePath method) ensemble (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) EnthalpyOfMixing (class in openff.evaluator.properties) EnthalpyOfVaporization (class in openff.evaluator.properties) estimated_properties (openff.evaluator.client.RequestResult attribute) (openff.evaluator.server.Batch attribute) EvaluatorClient (class in openff.evaluator.client) EvaluatorException EvaluatorServer (class in openff.evaluator.server) ExactAmount (class in openff.evaluator.substances) exceptions (openff.evaluator.client.RequestResult attribute) (openff.evaluator.layers.CalculationLayerResult attribute) (openff.evaluator.server.Batch attribute) (openff.evaluator.workflow.WorkflowResult attribute) ExcessMolarVolume (class in openff.evaluator.properties) execute() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGraph method) (openff.evaluator.workflow.ProtocolGroup method) (openff.evaluator.workflow.Workflow method) (openff.evaluator.workflow.WorkflowGraph method) expandtabs() (openff.evaluator.storage.attributes.FilePath method) expected_components (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole attribute) F fidelity (openff.evaluator.datasets.CalculationSource attribute) FilePath (class in openff.evaluator.storage.attributes) FilterByCharged (class in openff.evaluator.datasets.curation.components.filtering) FilterByChargedSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByElements (class in openff.evaluator.datasets.curation.components.filtering) FilterByElementsSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByEnvironments (class in openff.evaluator.datasets.curation.components.filtering) FilterByEnvironmentsSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByIonicLiquid (class in openff.evaluator.datasets.curation.components.filtering) FilterByIonicLiquidSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByMoleFraction (class in openff.evaluator.datasets.curation.components.filtering) FilterByMoleFractionSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByNComponents (class in openff.evaluator.datasets.curation.components.filtering) FilterByNComponentsSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByPressure (class in openff.evaluator.datasets.curation.components.filtering) FilterByPressureSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByPropertyTypes (class in openff.evaluator.datasets.curation.components.filtering) FilterByPropertyTypesSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByRacemic (class in openff.evaluator.datasets.curation.components.filtering) FilterByRacemicSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterBySmiles (class in openff.evaluator.datasets.curation.components.filtering) FilterBySmilesSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterBySmirks (class in openff.evaluator.datasets.curation.components.filtering) FilterBySmirksSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByStereochemistry (class in openff.evaluator.datasets.curation.components.filtering) FilterByStereochemistrySchema (class in openff.evaluator.datasets.curation.components.filtering) FilterBySubstances (class in openff.evaluator.datasets.curation.components.filtering) FilterBySubstancesSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterByTemperature (class in openff.evaluator.datasets.curation.components.filtering) FilterByTemperatureSchema (class in openff.evaluator.datasets.curation.components.filtering) FilterDuplicates (class in openff.evaluator.datasets.curation.components.filtering) FilterDuplicatesSchema (class in openff.evaluator.datasets.curation.components.filtering) filtered_substance (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole attribute) FilterSubstanceByRole (class in openff.evaluator.protocols.miscellaneous) final_value_source (openff.evaluator.workflow.schemas.WorkflowSchema attribute) (openff.evaluator.workflow.Workflow property) find() (openff.evaluator.storage.attributes.FilePath method) FingerPrintType (class in openff.evaluator.datasets.curation.components.selection) force_field_id (openff.evaluator.server.Batch attribute) (openff.evaluator.storage.data.BaseSimulationData attribute) (openff.evaluator.storage.data.StoredFreeEnergyData attribute) (openff.evaluator.storage.data.StoredSimulationData attribute) (openff.evaluator.storage.query.BaseSimulationDataQuery attribute) (openff.evaluator.storage.query.FreeEnergyDataQuery attribute) (openff.evaluator.storage.query.SimulationDataQuery attribute) force_field_path (openff.evaluator.protocols.forcefield.BaseBuildSystem attribute) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem attribute) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem attribute) (openff.evaluator.protocols.forcefield.BuildTLeapSystem attribute) (openff.evaluator.protocols.gradients.ZeroGradients attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) force_field_source (openff.evaluator.storage.data.ForceFieldData attribute) (openff.evaluator.storage.query.ForceFieldQuery attribute) ForceFieldData (class in openff.evaluator.storage.data) ForceFieldQuery (class in openff.evaluator.storage.query) ForceFieldSource (class in openff.evaluator.forcefield) format() (openff.evaluator.storage.attributes.FilePath method) format_map() (openff.evaluator.storage.attributes.FilePath method) frame_counts (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) free_energy_difference (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) (openff.evaluator.storage.data.StoredFreeEnergyData attribute) FreeEnergyDataQuery (class in openff.evaluator.storage.query) from_components() (openff.evaluator.substances.Substance class method) from_data_object() (openff.evaluator.storage.query.BaseDataQuery class method) (openff.evaluator.storage.query.BaseSimulationDataQuery class method) (openff.evaluator.storage.query.ForceFieldQuery class method) (openff.evaluator.storage.query.FreeEnergyDataQuery class method) (openff.evaluator.storage.query.SimulationDataQuery class method) from_doi() (openff.evaluator.datasets.thermoml.ThermoMLDataSet class method) from_exception() (openff.evaluator.utils.exceptions.EvaluatorException class method) (openff.evaluator.workflow.WorkflowException class method) from_file() (openff.evaluator.datasets.thermoml.ThermoMLDataSet class method) from_json() (openff.evaluator.attributes.AttributeClass class method) (openff.evaluator.client.ConnectionOptions class method) (openff.evaluator.client.Request class method) (openff.evaluator.client.RequestOptions class method) (openff.evaluator.client.RequestResult class method) (openff.evaluator.datasets.CalculationSource class method) (openff.evaluator.datasets.MeasurementSource class method) (openff.evaluator.datasets.PhysicalProperty class method) (openff.evaluator.datasets.PhysicalPropertyDataSet class method) (openff.evaluator.datasets.Source class method) (openff.evaluator.datasets.taproom.TaproomDataSet class method) (openff.evaluator.datasets.taproom.TaproomSource class method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet class method) (openff.evaluator.forcefield.ForceFieldSource class method) (openff.evaluator.forcefield.LigParGenForceFieldSource class method) (openff.evaluator.forcefield.SmirnoffForceFieldSource class method) (openff.evaluator.forcefield.TLeapForceFieldSource class method) (openff.evaluator.layers.CalculationLayerResult class method) (openff.evaluator.layers.CalculationLayerSchema class method) (openff.evaluator.layers.reweighting.ReweightingSchema class method) (openff.evaluator.layers.simulation.SimulationSchema class method) (openff.evaluator.layers.workflow.WorkflowCalculationSchema class method) (openff.evaluator.properties.Density class method) (openff.evaluator.properties.DielectricConstant class method) (openff.evaluator.properties.EnthalpyOfMixing class method) (openff.evaluator.properties.EnthalpyOfVaporization class method) (openff.evaluator.properties.ExcessMolarVolume class method) (openff.evaluator.properties.HostGuestBindingAffinity class method) (openff.evaluator.properties.SolvationFreeEnergy class method) (openff.evaluator.protocols.analysis.AverageDielectricConstant class method) (openff.evaluator.protocols.analysis.AverageFreeEnergies class method) (openff.evaluator.protocols.analysis.AverageObservable class method) (openff.evaluator.protocols.analysis.BaseAverageObservable class method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol class method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments class method) (openff.evaluator.protocols.analysis.DecorrelateObservables class method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory class method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol class method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates class method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure class method) (openff.evaluator.protocols.forcefield.BaseBuildSystem class method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem class method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem class method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem class method) (openff.evaluator.protocols.gradients.ZeroGradients class method) (openff.evaluator.protocols.groups.ConditionalGroup class method) (openff.evaluator.protocols.groups.ConditionalGroup.Condition class method) (openff.evaluator.protocols.miscellaneous.AddValues class method) (openff.evaluator.protocols.miscellaneous.DivideValue class method) (openff.evaluator.protocols.miscellaneous.DummyProtocol class method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole class method) (openff.evaluator.protocols.miscellaneous.MultiplyValue class method) (openff.evaluator.protocols.miscellaneous.SubtractValues class method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction class method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation class method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies class method) (openff.evaluator.protocols.openmm.OpenMMSimulation class method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase class method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork class method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection class method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms class method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates class method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates class method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints class method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints class method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints class method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints class method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies class method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol class method) (openff.evaluator.protocols.reweighting.ConcatenateObservables class method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories class method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant class method) (openff.evaluator.protocols.reweighting.ReweightObservable class method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation class method) (openff.evaluator.protocols.simulation.BaseSimulation class method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData class method) (openff.evaluator.protocols.yank.BaseYankProtocol class method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol class method) (openff.evaluator.protocols.yank.SolvationYankProtocol class method) (openff.evaluator.server.Batch class method) (openff.evaluator.storage.data.BaseSimulationData class method) (openff.evaluator.storage.data.BaseStoredData class method) (openff.evaluator.storage.data.ForceFieldData class method) (openff.evaluator.storage.data.HashableStoredData class method) (openff.evaluator.storage.data.ReplaceableData class method) (openff.evaluator.storage.data.StoredFreeEnergyData class method) (openff.evaluator.storage.data.StoredSimulationData class method) (openff.evaluator.storage.query.BaseDataQuery class method) (openff.evaluator.storage.query.BaseSimulationDataQuery class method) (openff.evaluator.storage.query.ForceFieldQuery class method) (openff.evaluator.storage.query.FreeEnergyDataQuery class method) (openff.evaluator.storage.query.SimulationDataQuery class method) (openff.evaluator.storage.query.SubstanceQuery class method) (openff.evaluator.substances.Amount class method) (openff.evaluator.substances.Component class method) (openff.evaluator.substances.ExactAmount class method) (openff.evaluator.substances.MoleFraction class method) (openff.evaluator.substances.Substance class method) (openff.evaluator.thermodynamics.ThermodynamicState class method) (openff.evaluator.utils.exceptions.EvaluatorException class method) (openff.evaluator.workflow.Protocol class method) (openff.evaluator.workflow.ProtocolGroup class method) (openff.evaluator.workflow.schemas.ProtocolGroupSchema class method) (openff.evaluator.workflow.schemas.ProtocolReplicator class method) (openff.evaluator.workflow.schemas.ProtocolSchema class method) (openff.evaluator.workflow.schemas.WorkflowSchema class method) (openff.evaluator.workflow.WorkflowException class method) (openff.evaluator.workflow.WorkflowResult class method) from_object() (openff.evaluator.forcefield.SmirnoffForceFieldSource class method) from_openmm() (openff.evaluator.utils.observables.ObservableFrame class method) from_pandas() (openff.evaluator.datasets.PhysicalPropertyDataSet class method) (openff.evaluator.datasets.taproom.TaproomDataSet class method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet class method) from_path() (openff.evaluator.forcefield.SmirnoffForceFieldSource class method) from_schema() (openff.evaluator.protocols.analysis.AverageDielectricConstant class method) (openff.evaluator.protocols.analysis.AverageFreeEnergies class method) (openff.evaluator.protocols.analysis.AverageObservable class method) (openff.evaluator.protocols.analysis.BaseAverageObservable class method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol class method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments class method) (openff.evaluator.protocols.analysis.DecorrelateObservables class method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory class method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol class method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates class method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure class method) (openff.evaluator.protocols.forcefield.BaseBuildSystem class method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem class method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem class method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem class method) (openff.evaluator.protocols.gradients.ZeroGradients class method) (openff.evaluator.protocols.groups.ConditionalGroup class method) (openff.evaluator.protocols.miscellaneous.AddValues class method) (openff.evaluator.protocols.miscellaneous.DivideValue class method) (openff.evaluator.protocols.miscellaneous.DummyProtocol class method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole class method) (openff.evaluator.protocols.miscellaneous.MultiplyValue class method) (openff.evaluator.protocols.miscellaneous.SubtractValues class method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction class method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation class method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies class method) (openff.evaluator.protocols.openmm.OpenMMSimulation class method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase class method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork class method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection class method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms class method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates class method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates class method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints class method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints class method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints class method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints class method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies class method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol class method) (openff.evaluator.protocols.reweighting.ConcatenateObservables class method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories class method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant class method) (openff.evaluator.protocols.reweighting.ReweightObservable class method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation class method) (openff.evaluator.protocols.simulation.BaseSimulation class method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData class method) (openff.evaluator.protocols.yank.BaseYankProtocol class method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol class method) (openff.evaluator.protocols.yank.SolvationYankProtocol class method) (openff.evaluator.workflow.Protocol class method) (openff.evaluator.workflow.ProtocolGroup class method) (openff.evaluator.workflow.Workflow class method) from_string() (openff.evaluator.datasets.PropertyPhase class method) from_url() (openff.evaluator.datasets.thermoml.ThermoMLDataSet class method) from_xml() (openff.evaluator.datasets.thermoml.ThermoMLDataSet class method) full_path (openff.evaluator.workflow.utils.ProtocolPath property) full_substance (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction attribute) G generate_base_reweighting_protocols() (in module openff.evaluator.protocols.utils) generate_default_metadata() (openff.evaluator.workflow.Workflow static method) generate_reweighting_protocols() (in module openff.evaluator.protocols.utils) generate_simulation_protocols() (in module openff.evaluator.protocols.utils) GenerateAttachRestraints (class in openff.evaluator.protocols.paprika.restraints) GeneratePullRestraints (class in openff.evaluator.protocols.paprika.restraints) GenerateReleaseRestraints (class in openff.evaluator.protocols.paprika.restraints) get() (openff.evaluator.utils.observables.ObservableFrame method) get_amounts() (openff.evaluator.substances.Substance method) get_attributes() (openff.evaluator.attributes.AttributeClass class method) (openff.evaluator.client.ConnectionOptions class method) (openff.evaluator.client.Request class method) (openff.evaluator.client.RequestOptions class method) (openff.evaluator.client.RequestResult class method) (openff.evaluator.datasets.PhysicalProperty class method) (openff.evaluator.layers.CalculationLayerResult class method) (openff.evaluator.layers.CalculationLayerSchema class method) (openff.evaluator.layers.reweighting.ReweightingSchema class method) (openff.evaluator.layers.simulation.SimulationSchema class method) (openff.evaluator.layers.workflow.WorkflowCalculationSchema class method) (openff.evaluator.properties.Density class method) (openff.evaluator.properties.DielectricConstant class method) (openff.evaluator.properties.EnthalpyOfMixing class method) (openff.evaluator.properties.EnthalpyOfVaporization class method) (openff.evaluator.properties.ExcessMolarVolume class method) (openff.evaluator.properties.HostGuestBindingAffinity class method) (openff.evaluator.properties.SolvationFreeEnergy class method) (openff.evaluator.protocols.analysis.AverageDielectricConstant class method) (openff.evaluator.protocols.analysis.AverageFreeEnergies class method) (openff.evaluator.protocols.analysis.AverageObservable class method) (openff.evaluator.protocols.analysis.BaseAverageObservable class method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol class method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments class method) (openff.evaluator.protocols.analysis.DecorrelateObservables class method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory class method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol class method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates class method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure class method) (openff.evaluator.protocols.forcefield.BaseBuildSystem class method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem class method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem class method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem class method) (openff.evaluator.protocols.gradients.ZeroGradients class method) (openff.evaluator.protocols.groups.ConditionalGroup class method) (openff.evaluator.protocols.groups.ConditionalGroup.Condition class method) (openff.evaluator.protocols.miscellaneous.AddValues class method) (openff.evaluator.protocols.miscellaneous.DivideValue class method) (openff.evaluator.protocols.miscellaneous.DummyProtocol class method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole class method) (openff.evaluator.protocols.miscellaneous.MultiplyValue class method) (openff.evaluator.protocols.miscellaneous.SubtractValues class method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction class method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation class method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies class method) (openff.evaluator.protocols.openmm.OpenMMSimulation class method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase class method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork class method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection class method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms class method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates class method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates class method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints class method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints class method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints class method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints class method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies class method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol class method) (openff.evaluator.protocols.reweighting.ConcatenateObservables class method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories class method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant class method) (openff.evaluator.protocols.reweighting.ReweightObservable class method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation class method) (openff.evaluator.protocols.simulation.BaseSimulation class method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData class method) (openff.evaluator.protocols.yank.BaseYankProtocol class method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol class method) (openff.evaluator.protocols.yank.SolvationYankProtocol class method) (openff.evaluator.server.Batch class method) (openff.evaluator.storage.data.BaseSimulationData class method) (openff.evaluator.storage.data.BaseStoredData class method) (openff.evaluator.storage.data.ForceFieldData class method) (openff.evaluator.storage.data.HashableStoredData class method) (openff.evaluator.storage.data.ReplaceableData class method) (openff.evaluator.storage.data.StoredFreeEnergyData class method) (openff.evaluator.storage.data.StoredSimulationData class method) (openff.evaluator.storage.query.BaseDataQuery class method) (openff.evaluator.storage.query.BaseSimulationDataQuery class method) (openff.evaluator.storage.query.ForceFieldQuery class method) (openff.evaluator.storage.query.FreeEnergyDataQuery class method) (openff.evaluator.storage.query.SimulationDataQuery class method) (openff.evaluator.storage.query.SubstanceQuery class method) (openff.evaluator.substances.Amount class method) (openff.evaluator.substances.Component class method) (openff.evaluator.substances.ExactAmount class method) (openff.evaluator.substances.MoleFraction class method) (openff.evaluator.substances.Substance class method) (openff.evaluator.thermodynamics.ThermodynamicState class method) (openff.evaluator.workflow.Protocol class method) (openff.evaluator.workflow.ProtocolGroup class method) (openff.evaluator.workflow.schemas.ProtocolGroupSchema class method) (openff.evaluator.workflow.schemas.ProtocolSchema class method) (openff.evaluator.workflow.schemas.WorkflowSchema class method) (openff.evaluator.workflow.WorkflowResult class method) get_class_attribute() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) get_molecules_per_component() (openff.evaluator.substances.Substance method) get_value() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) get_value_references() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) gpu_device_indices (openff.evaluator.backends.ComputeResources property) (openff.evaluator.backends.QueueWorkerResources property) gradient_parameters (openff.evaluator.protocols.analysis.ComputeDipoleMoments attribute) (openff.evaluator.protocols.gradients.ZeroGradients attribute) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) gradients (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) (openff.evaluator.workflow.WorkflowResult attribute) guest_orientation_mask (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) H has_ancillary_data() (openff.evaluator.storage.data.BaseSimulationData class method) (openff.evaluator.storage.data.BaseStoredData class method) (openff.evaluator.storage.data.ForceFieldData class method) (openff.evaluator.storage.data.HashableStoredData class method) (openff.evaluator.storage.data.ReplaceableData class method) (openff.evaluator.storage.data.StoredFreeEnergyData class method) (openff.evaluator.storage.data.StoredSimulationData class method) has_force_field() (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.StorageBackend method) has_object() (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.StorageBackend method) HashableStoredData (class in openff.evaluator.storage.data) high_precision (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) host_coordinate_path (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints attribute) HostGuestBindingAffinity (class in openff.evaluator.properties) I id (openff.evaluator.client.Request attribute) (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.AverageFreeEnergies attribute) (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.analysis.BaseAverageObservable attribute) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol attribute) (openff.evaluator.protocols.analysis.ComputeDipoleMoments attribute) (openff.evaluator.protocols.analysis.DecorrelateObservables attribute) (openff.evaluator.protocols.analysis.DecorrelateTrajectory attribute) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) (openff.evaluator.protocols.forcefield.BaseBuildSystem attribute) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem attribute) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem attribute) (openff.evaluator.protocols.forcefield.BuildTLeapSystem attribute) (openff.evaluator.protocols.gradients.ZeroGradients attribute) (openff.evaluator.protocols.groups.ConditionalGroup attribute) (openff.evaluator.protocols.miscellaneous.AddValues attribute) (openff.evaluator.protocols.miscellaneous.DivideValue attribute) (openff.evaluator.protocols.miscellaneous.DummyProtocol attribute) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole attribute) (openff.evaluator.protocols.miscellaneous.MultiplyValue attribute) (openff.evaluator.protocols.miscellaneous.SubtractValues attribute) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction attribute) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation attribute) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase attribute) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork attribute) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection attribute) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms attribute) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates attribute) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints attribute) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ConcatenateObservables attribute) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) (openff.evaluator.server.Batch attribute) (openff.evaluator.workflow.Protocol attribute) (openff.evaluator.workflow.ProtocolGroup attribute) (openff.evaluator.workflow.schemas.ProtocolGroupSchema attribute) (openff.evaluator.workflow.schemas.ProtocolSchema attribute) identifier (openff.evaluator.substances.Amount property) (openff.evaluator.substances.Component property) (openff.evaluator.substances.ExactAmount property) (openff.evaluator.substances.MoleFraction property) (openff.evaluator.substances.Substance property) ImportFreeSolv (class in openff.evaluator.datasets.curation.components.freesolv) ImportFreeSolvSchema (class in openff.evaluator.datasets.curation.components.freesolv) ImportThermoMLData (class in openff.evaluator.datasets.curation.components.thermoml) ImportThermoMLDataSchema (class in openff.evaluator.datasets.curation.components.thermoml) index() (openff.evaluator.storage.attributes.FilePath method) InequalityMergeBehavior (class in openff.evaluator.workflow.attributes) input_coordinate_file (openff.evaluator.protocols.analysis.DecorrelateTrajectory attribute) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) input_coordinate_path (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms attribute) input_coordinate_paths (openff.evaluator.protocols.reweighting.ConcatenateTrajectories attribute) input_observables (openff.evaluator.protocols.analysis.DecorrelateObservables attribute) (openff.evaluator.protocols.gradients.ZeroGradients attribute) (openff.evaluator.protocols.reweighting.ConcatenateObservables attribute) input_substance (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole attribute) input_system (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms attribute) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints attribute) input_trajectory_path (openff.evaluator.protocols.analysis.DecorrelateTrajectory attribute) input_trajectory_paths (openff.evaluator.protocols.reweighting.ConcatenateTrajectories attribute) input_value (openff.evaluator.protocols.miscellaneous.DummyProtocol attribute) InputAttribute (class in openff.evaluator.workflow.attributes) inputs (openff.evaluator.workflow.schemas.ProtocolGroupSchema attribute) (openff.evaluator.workflow.schemas.ProtocolSchema attribute) inverse_beta (openff.evaluator.thermodynamics.ThermodynamicState property) isalnum() (openff.evaluator.storage.attributes.FilePath method) isalpha() (openff.evaluator.storage.attributes.FilePath method) isascii() (openff.evaluator.storage.attributes.FilePath method) isdecimal() (openff.evaluator.storage.attributes.FilePath method) isdigit() (openff.evaluator.storage.attributes.FilePath method) isidentifier() (openff.evaluator.storage.attributes.FilePath method) islower() (openff.evaluator.storage.attributes.FilePath method) isnumeric() (openff.evaluator.storage.attributes.FilePath method) isprintable() (openff.evaluator.storage.attributes.FilePath method) isspace() (openff.evaluator.storage.attributes.FilePath method) istitle() (openff.evaluator.storage.attributes.FilePath method) isupper() (openff.evaluator.storage.attributes.FilePath method) items() (openff.evaluator.utils.observables.ObservableFrame method) J job_script() (openff.evaluator.backends.dask.BaseDaskJobQueueBackend method) (openff.evaluator.backends.dask.DaskLSFBackend method) (openff.evaluator.backends.dask.DaskPBSBackend method) join() (openff.evaluator.storage.attributes.FilePath method) (openff.evaluator.utils.observables.ObservableArray class method) (openff.evaluator.utils.observables.ObservableFrame class method) json() (openff.evaluator.attributes.AttributeClass method) (openff.evaluator.client.ConnectionOptions method) (openff.evaluator.client.Request method) (openff.evaluator.client.RequestOptions method) (openff.evaluator.client.RequestResult method) (openff.evaluator.datasets.CalculationSource method) (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema method) (openff.evaluator.datasets.curation.components.CurationComponentSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByChargedSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByElementsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByEnvironmentsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByIonicLiquidSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByMoleFractionSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByNComponentsSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByPressureSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByPropertyTypesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByRacemicSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmilesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmirksSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByStereochemistrySchema method) (openff.evaluator.datasets.curation.components.filtering.FilterBySubstancesSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterByTemperatureSchema method) (openff.evaluator.datasets.curation.components.filtering.FilterDuplicatesSchema method) (openff.evaluator.datasets.curation.components.freesolv.ImportFreeSolvSchema method) (openff.evaluator.datasets.curation.components.selection.SelectDataPointsSchema method) (openff.evaluator.datasets.curation.components.selection.SelectSubstancesSchema method) (openff.evaluator.datasets.curation.components.selection.State method) (openff.evaluator.datasets.curation.components.selection.TargetState method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema method) (openff.evaluator.datasets.curation.workflow.CurationWorkflowSchema method) (openff.evaluator.datasets.MeasurementSource method) (openff.evaluator.datasets.PhysicalProperty method) (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.Source method) (openff.evaluator.datasets.taproom.TaproomDataSet method) (openff.evaluator.datasets.taproom.TaproomSource method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) (openff.evaluator.forcefield.ForceFieldSource method) (openff.evaluator.forcefield.LigParGenForceFieldSource method) (openff.evaluator.forcefield.SmirnoffForceFieldSource method) (openff.evaluator.forcefield.TLeapForceFieldSource method) (openff.evaluator.layers.CalculationLayerResult method) (openff.evaluator.layers.CalculationLayerSchema method) (openff.evaluator.layers.reweighting.ReweightingSchema method) (openff.evaluator.layers.simulation.SimulationSchema method) (openff.evaluator.layers.workflow.WorkflowCalculationSchema method) (openff.evaluator.properties.Density method) (openff.evaluator.properties.DielectricConstant method) (openff.evaluator.properties.EnthalpyOfMixing method) (openff.evaluator.properties.EnthalpyOfVaporization method) (openff.evaluator.properties.ExcessMolarVolume method) (openff.evaluator.properties.HostGuestBindingAffinity method) (openff.evaluator.properties.SolvationFreeEnergy method) (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.groups.ConditionalGroup.Condition method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.server.Batch method) (openff.evaluator.storage.data.BaseSimulationData method) (openff.evaluator.storage.data.BaseStoredData method) (openff.evaluator.storage.data.ForceFieldData method) (openff.evaluator.storage.data.HashableStoredData method) (openff.evaluator.storage.data.ReplaceableData method) (openff.evaluator.storage.data.StoredFreeEnergyData method) (openff.evaluator.storage.data.StoredSimulationData method) (openff.evaluator.storage.query.BaseDataQuery method) (openff.evaluator.storage.query.BaseSimulationDataQuery method) (openff.evaluator.storage.query.ForceFieldQuery method) (openff.evaluator.storage.query.FreeEnergyDataQuery method) (openff.evaluator.storage.query.SimulationDataQuery method) (openff.evaluator.storage.query.SubstanceQuery method) (openff.evaluator.substances.Amount method) (openff.evaluator.substances.Component method) (openff.evaluator.substances.ExactAmount method) (openff.evaluator.substances.MoleFraction method) (openff.evaluator.substances.Substance method) (openff.evaluator.thermodynamics.ThermodynamicState method) (openff.evaluator.utils.exceptions.EvaluatorException method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) (openff.evaluator.workflow.schemas.ProtocolGroupSchema method) (openff.evaluator.workflow.schemas.ProtocolReplicator method) (openff.evaluator.workflow.schemas.ProtocolSchema method) (openff.evaluator.workflow.schemas.WorkflowSchema method) (openff.evaluator.workflow.WorkflowException method) (openff.evaluator.workflow.WorkflowResult method) K keys() (openff.evaluator.utils.observables.ObservableFrame method) L last_protocol (openff.evaluator.workflow.utils.ProtocolPath property) leap_source (openff.evaluator.forcefield.TLeapForceFieldSource property) left_hand_value (openff.evaluator.protocols.groups.ConditionalGroup.Condition attribute) ligand_electrostatic_lambdas (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) ligand_residue_name (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) ligand_steric_lambdas (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) ligand_substance (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) LigandReceptorYankProtocol (class in openff.evaluator.protocols.yank) LigandReceptorYankProtocol.RestraintType (class in openff.evaluator.protocols.yank) LigParGenForceFieldSource (class in openff.evaluator.forcefield) LigParGenForceFieldSource.ChargeModel (class in openff.evaluator.forcefield) ljust() (openff.evaluator.storage.attributes.FilePath method) load_restraints() (openff.evaluator.protocols.paprika.restraints.ApplyRestraints class method) LocalFileStorage (class in openff.evaluator.storage) lower() (openff.evaluator.storage.attributes.FilePath method) lstrip() (openff.evaluator.storage.attributes.FilePath method) M maketrans() (openff.evaluator.storage.attributes.FilePath static method) mass_density (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) max_iterations (openff.evaluator.protocols.groups.ConditionalGroup attribute) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation attribute) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation attribute) max_molecules (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) maximum_data_points (openff.evaluator.layers.reweighting.ReweightingSchema attribute) MeasurementSource (class in openff.evaluator.datasets) merge() (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.taproom.TaproomDataSet method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) MergeBehavior (class in openff.evaluator.workflow.attributes) metadata (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) MoleFraction (class in openff.evaluator.substances) most_information() (openff.evaluator.storage.data.BaseSimulationData class method) (openff.evaluator.storage.data.ReplaceableData class method) (openff.evaluator.storage.data.StoredFreeEnergyData class method) (openff.evaluator.storage.data.StoredSimulationData class method) multiplier (openff.evaluator.protocols.miscellaneous.MultiplyValue attribute) MultiplyValue (class in openff.evaluator.protocols.miscellaneous) N n_microstates (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection attribute) n_pull_windows (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints attribute) number_of_components (openff.evaluator.substances.Substance property) number_of_equilibration_iterations (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) number_of_gpus (openff.evaluator.backends.ComputeResources property) (openff.evaluator.backends.QueueWorkerResources property) number_of_iterations (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) number_of_ligand_conformers (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) number_of_molecules (openff.evaluator.storage.data.StoredSimulationData attribute) (openff.evaluator.storage.query.SimulationDataQuery attribute) number_of_threads (openff.evaluator.backends.ComputeResources property) (openff.evaluator.backends.QueueWorkerResources property) O Observable (class in openff.evaluator.utils.observables) observable (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) ObservableArray (class in openff.evaluator.utils.observables) ObservableFrame (class in openff.evaluator.utils.observables) observables (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) (openff.evaluator.storage.data.StoredSimulationData attribute) ObservableType (class in openff.evaluator.utils.observables) offset (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms attribute) OpenMMEnergyMinimisation (class in openff.evaluator.protocols.openmm) OpenMMEvaluateEnergies (class in openff.evaluator.protocols.openmm) OpenMMSimulation (class in openff.evaluator.protocols.openmm) options (openff.evaluator.server.Batch attribute) output_coordinate_file (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) output_coordinate_path (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms attribute) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates attribute) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories attribute) output_frequency (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) output_number_of_molecules (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) output_observables (openff.evaluator.protocols.analysis.DecorrelateObservables attribute) (openff.evaluator.protocols.gradients.ZeroGradients attribute) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies attribute) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.reweighting.ConcatenateObservables attribute) output_substance (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) output_system (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms attribute) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints attribute) output_trajectory_path (openff.evaluator.protocols.analysis.DecorrelateTrajectory attribute) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories attribute) output_value (openff.evaluator.protocols.miscellaneous.DummyProtocol attribute) OutputAttribute (class in openff.evaluator.workflow.attributes) outputs (openff.evaluator.protocols.analysis.AverageDielectricConstant property) (openff.evaluator.protocols.analysis.AverageFreeEnergies property) (openff.evaluator.protocols.analysis.AverageObservable property) (openff.evaluator.protocols.analysis.BaseAverageObservable property) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol property) (openff.evaluator.protocols.analysis.ComputeDipoleMoments property) (openff.evaluator.protocols.analysis.DecorrelateObservables property) (openff.evaluator.protocols.analysis.DecorrelateTrajectory property) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol property) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates property) (openff.evaluator.protocols.coordinates.SolvateExistingStructure property) (openff.evaluator.protocols.forcefield.BaseBuildSystem property) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem property) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem property) (openff.evaluator.protocols.forcefield.BuildTLeapSystem property) (openff.evaluator.protocols.gradients.ZeroGradients property) (openff.evaluator.protocols.groups.ConditionalGroup property) (openff.evaluator.protocols.miscellaneous.AddValues property) (openff.evaluator.protocols.miscellaneous.DivideValue property) (openff.evaluator.protocols.miscellaneous.DummyProtocol property) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole property) (openff.evaluator.protocols.miscellaneous.MultiplyValue property) (openff.evaluator.protocols.miscellaneous.SubtractValues property) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction property) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation property) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies property) (openff.evaluator.protocols.openmm.OpenMMSimulation property) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase property) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork property) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection property) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms property) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates property) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates property) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints property) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints property) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints property) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints property) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies property) (openff.evaluator.protocols.reweighting.BaseMBARProtocol property) (openff.evaluator.protocols.reweighting.ConcatenateObservables property) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories property) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant property) (openff.evaluator.protocols.reweighting.ReweightObservable property) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation property) (openff.evaluator.protocols.simulation.BaseSimulation property) (openff.evaluator.protocols.storage.UnpackStoredSimulationData property) (openff.evaluator.protocols.yank.BaseYankProtocol property) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol property) (openff.evaluator.protocols.yank.SolvationYankProtocol property) (openff.evaluator.workflow.Protocol property) (openff.evaluator.workflow.ProtocolGroup property) outputs_to_store (openff.evaluator.workflow.schemas.WorkflowSchema attribute) (openff.evaluator.workflow.Workflow property) P parameter_gradient_keys (openff.evaluator.server.Batch attribute) ParameterGradient (class in openff.evaluator.forcefield) ParameterGradientKey (class in openff.evaluator.forcefield) parameterized_system (openff.evaluator.protocols.analysis.ComputeDipoleMoments attribute) (openff.evaluator.protocols.forcefield.BaseBuildSystem attribute) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem attribute) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem attribute) (openff.evaluator.protocols.forcefield.BuildTLeapSystem attribute) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation attribute) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) parse_json() (openff.evaluator.attributes.AttributeClass class method) (openff.evaluator.client.ConnectionOptions class method) (openff.evaluator.client.Request class method) (openff.evaluator.client.RequestOptions class method) (openff.evaluator.client.RequestResult class method) (openff.evaluator.datasets.CalculationSource class method) (openff.evaluator.datasets.MeasurementSource class method) (openff.evaluator.datasets.PhysicalProperty class method) (openff.evaluator.datasets.PhysicalPropertyDataSet class method) (openff.evaluator.datasets.Source class method) (openff.evaluator.datasets.taproom.TaproomDataSet class method) (openff.evaluator.datasets.taproom.TaproomSource class method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet class method) (openff.evaluator.forcefield.ForceFieldSource class method) (openff.evaluator.forcefield.LigParGenForceFieldSource class method) (openff.evaluator.forcefield.SmirnoffForceFieldSource class method) (openff.evaluator.forcefield.TLeapForceFieldSource class method) (openff.evaluator.layers.CalculationLayerResult class method) (openff.evaluator.layers.CalculationLayerSchema class method) (openff.evaluator.layers.reweighting.ReweightingSchema class method) (openff.evaluator.layers.simulation.SimulationSchema class method) (openff.evaluator.layers.workflow.WorkflowCalculationSchema class method) (openff.evaluator.properties.Density class method) (openff.evaluator.properties.DielectricConstant class method) (openff.evaluator.properties.EnthalpyOfMixing class method) (openff.evaluator.properties.EnthalpyOfVaporization class method) (openff.evaluator.properties.ExcessMolarVolume class method) (openff.evaluator.properties.HostGuestBindingAffinity class method) (openff.evaluator.properties.SolvationFreeEnergy class method) (openff.evaluator.protocols.analysis.AverageDielectricConstant class method) (openff.evaluator.protocols.analysis.AverageFreeEnergies class method) (openff.evaluator.protocols.analysis.AverageObservable class method) (openff.evaluator.protocols.analysis.BaseAverageObservable class method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol class method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments class method) (openff.evaluator.protocols.analysis.DecorrelateObservables class method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory class method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol class method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates class method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure class method) (openff.evaluator.protocols.forcefield.BaseBuildSystem class method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem class method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem class method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem class method) (openff.evaluator.protocols.gradients.ZeroGradients class method) (openff.evaluator.protocols.groups.ConditionalGroup class method) (openff.evaluator.protocols.groups.ConditionalGroup.Condition class method) (openff.evaluator.protocols.miscellaneous.AddValues class method) (openff.evaluator.protocols.miscellaneous.DivideValue class method) (openff.evaluator.protocols.miscellaneous.DummyProtocol class method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole class method) (openff.evaluator.protocols.miscellaneous.MultiplyValue class method) (openff.evaluator.protocols.miscellaneous.SubtractValues class method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction class method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation class method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies class method) (openff.evaluator.protocols.openmm.OpenMMSimulation class method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase class method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork class method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection class method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms class method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates class method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates class method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints class method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints class method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints class method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints class method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies class method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol class method) (openff.evaluator.protocols.reweighting.ConcatenateObservables class method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories class method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant class method) (openff.evaluator.protocols.reweighting.ReweightObservable class method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation class method) (openff.evaluator.protocols.simulation.BaseSimulation class method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData class method) (openff.evaluator.protocols.yank.BaseYankProtocol class method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol class method) (openff.evaluator.protocols.yank.SolvationYankProtocol class method) (openff.evaluator.server.Batch class method) (openff.evaluator.storage.data.BaseSimulationData class method) (openff.evaluator.storage.data.BaseStoredData class method) (openff.evaluator.storage.data.ForceFieldData class method) (openff.evaluator.storage.data.HashableStoredData class method) (openff.evaluator.storage.data.ReplaceableData class method) (openff.evaluator.storage.data.StoredFreeEnergyData class method) (openff.evaluator.storage.data.StoredSimulationData class method) (openff.evaluator.storage.query.BaseDataQuery class method) (openff.evaluator.storage.query.BaseSimulationDataQuery class method) (openff.evaluator.storage.query.ForceFieldQuery class method) (openff.evaluator.storage.query.FreeEnergyDataQuery class method) (openff.evaluator.storage.query.SimulationDataQuery class method) (openff.evaluator.storage.query.SubstanceQuery class method) (openff.evaluator.substances.Amount class method) (openff.evaluator.substances.Component class method) (openff.evaluator.substances.ExactAmount class method) (openff.evaluator.substances.MoleFraction class method) (openff.evaluator.substances.Substance class method) (openff.evaluator.thermodynamics.ThermodynamicState class method) (openff.evaluator.utils.exceptions.EvaluatorException class method) (openff.evaluator.workflow.Protocol class method) (openff.evaluator.workflow.ProtocolGroup class method) (openff.evaluator.workflow.schemas.ProtocolGroupSchema class method) (openff.evaluator.workflow.schemas.ProtocolReplicator class method) (openff.evaluator.workflow.schemas.ProtocolSchema class method) (openff.evaluator.workflow.schemas.WorkflowSchema class method) (openff.evaluator.workflow.WorkflowException class method) (openff.evaluator.workflow.WorkflowResult class method) partition() (openff.evaluator.storage.attributes.FilePath method) per_thread_memory_limit (openff.evaluator.backends.QueueWorkerResources property) phase (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase attribute) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints attribute) physical_property (openff.evaluator.layers.CalculationLayerResult attribute) PhysicalProperty (class in openff.evaluator.datasets) PhysicalPropertyDataSet (class in openff.evaluator.datasets) placeholder_id (openff.evaluator.workflow.schemas.ProtocolReplicator property) PlaceholderValue (class in openff.evaluator.attributes) pop() (openff.evaluator.utils.observables.ObservableFrame method) pop_next_in_path() (openff.evaluator.workflow.utils.ProtocolPath method) popitem() (openff.evaluator.utils.observables.ObservableFrame method) potential_energies (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.analysis.BaseAverageObservable attribute) preferred_charge_model (openff.evaluator.forcefield.LigParGenForceFieldSource property) preferred_gpu_precision (openff.evaluator.backends.ComputeResources property) (openff.evaluator.backends.QueueWorkerResources property) preferred_gpu_toolkit (openff.evaluator.backends.ComputeResources property) (openff.evaluator.backends.QueueWorkerResources property) PreparePullCoordinates (class in openff.evaluator.protocols.paprika.coordinates) PrepareReleaseCoordinates (class in openff.evaluator.protocols.paprika.coordinates) prepend_protocol_id() (openff.evaluator.workflow.utils.ProtocolPath method) pressure (openff.evaluator.thermodynamics.ThermodynamicState attribute) properties (openff.evaluator.datasets.PhysicalPropertyDataSet property) (openff.evaluator.datasets.taproom.TaproomDataSet property) (openff.evaluator.datasets.thermoml.ThermoMLDataSet property) properties_by_substance() (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.taproom.TaproomDataSet method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) properties_by_type() (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.taproom.TaproomDataSet method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) property_name (openff.evaluator.workflow.utils.ProtocolPath property) property_phase (openff.evaluator.storage.data.BaseSimulationData attribute) (openff.evaluator.storage.data.StoredFreeEnergyData attribute) (openff.evaluator.storage.data.StoredSimulationData attribute) (openff.evaluator.storage.query.BaseSimulationDataQuery attribute) (openff.evaluator.storage.query.FreeEnergyDataQuery attribute) (openff.evaluator.storage.query.SimulationDataQuery attribute) property_types (openff.evaluator.datasets.PhysicalPropertyDataSet property) (openff.evaluator.datasets.taproom.TaproomDataSet property) (openff.evaluator.datasets.thermoml.ThermoMLDataSet property) PropertyPhase (class in openff.evaluator.datasets) Protocol (class in openff.evaluator.workflow) protocol_ids (openff.evaluator.workflow.utils.ProtocolPath property) protocol_path (openff.evaluator.workflow.utils.ProtocolPath property) protocol_replicators (openff.evaluator.workflow.schemas.WorkflowSchema attribute) protocol_schemas (openff.evaluator.workflow.schemas.ProtocolGroupSchema attribute) (openff.evaluator.workflow.schemas.WorkflowSchema attribute) ProtocolGraph (class in openff.evaluator.workflow) ProtocolGroup (class in openff.evaluator.workflow) ProtocolGroupSchema (class in openff.evaluator.workflow.schemas) ProtocolPath (class in openff.evaluator.workflow.utils) ProtocolReplicator (class in openff.evaluator.workflow.schemas) protocols (openff.evaluator.protocols.groups.ConditionalGroup property) (openff.evaluator.workflow.ProtocolGraph property) (openff.evaluator.workflow.ProtocolGroup property) (openff.evaluator.workflow.Workflow property) (openff.evaluator.workflow.WorkflowGraph property) ProtocolSchema (class in openff.evaluator.workflow.schemas) provenance (openff.evaluator.datasets.CalculationSource attribute) pull_distance (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) pull_window_index (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) Q query() (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.StorageBackend method) QueryAttribute (class in openff.evaluator.storage.attributes) queued_properties (openff.evaluator.client.RequestResult attribute) (openff.evaluator.server.Batch attribute) QueueWorkerResources (class in openff.evaluator.backends) QueueWorkerResources.GPUPrecision (class in openff.evaluator.backends) QueueWorkerResources.GPUToolkit (class in openff.evaluator.backends) R receptor_coordinate_file (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) receptor_residue_name (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) reference (openff.evaluator.datasets.MeasurementSource attribute) reference_reduced_potentials (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) register_calculation_layer() (in module openff.evaluator.layers) register_calculation_schema() (in module openff.evaluator.layers) register_default_plugins() (in module openff.evaluator.plugins) register_external_plugins() (in module openff.evaluator.plugins) register_thermoml_property() (in module openff.evaluator.datasets.thermoml) register_workflow_protocol() (in module openff.evaluator.workflow) relative_tolerance (openff.evaluator.layers.CalculationLayerSchema attribute) (openff.evaluator.layers.reweighting.ReweightingSchema attribute) (openff.evaluator.layers.simulation.SimulationSchema attribute) (openff.evaluator.layers.workflow.WorkflowCalculationSchema attribute) release_lambdas (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints attribute) removeprefix() (openff.evaluator.storage.attributes.FilePath method) removesuffix() (openff.evaluator.storage.attributes.FilePath method) replace() (openff.evaluator.storage.attributes.FilePath method) replace_protocol() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) (openff.evaluator.workflow.utils.ProtocolPath method) (openff.evaluator.workflow.Workflow method) replace_protocol_types() (openff.evaluator.workflow.schemas.WorkflowSchema method) ReplaceableData (class in openff.evaluator.storage.data) ReplicatorValue (class in openff.evaluator.workflow.utils) Request (class in openff.evaluator.client) request_estimate() (openff.evaluator.client.EvaluatorClient method) request_url (openff.evaluator.forcefield.LigParGenForceFieldSource property) RequestOptions (class in openff.evaluator.client) RequestResult (class in openff.evaluator.client) required_effective_samples (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) required_inputs (openff.evaluator.protocols.analysis.AverageDielectricConstant property) (openff.evaluator.protocols.analysis.AverageFreeEnergies property) (openff.evaluator.protocols.analysis.AverageObservable property) (openff.evaluator.protocols.analysis.BaseAverageObservable property) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol property) (openff.evaluator.protocols.analysis.ComputeDipoleMoments property) (openff.evaluator.protocols.analysis.DecorrelateObservables property) (openff.evaluator.protocols.analysis.DecorrelateTrajectory property) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol property) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates property) (openff.evaluator.protocols.coordinates.SolvateExistingStructure property) (openff.evaluator.protocols.forcefield.BaseBuildSystem property) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem property) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem property) (openff.evaluator.protocols.forcefield.BuildTLeapSystem property) (openff.evaluator.protocols.gradients.ZeroGradients property) (openff.evaluator.protocols.groups.ConditionalGroup property) (openff.evaluator.protocols.miscellaneous.AddValues property) (openff.evaluator.protocols.miscellaneous.DivideValue property) (openff.evaluator.protocols.miscellaneous.DummyProtocol property) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole property) (openff.evaluator.protocols.miscellaneous.MultiplyValue property) (openff.evaluator.protocols.miscellaneous.SubtractValues property) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction property) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation property) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies property) (openff.evaluator.protocols.openmm.OpenMMSimulation property) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase property) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork property) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection property) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms property) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates property) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates property) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints property) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints property) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints property) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints property) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies property) (openff.evaluator.protocols.reweighting.BaseMBARProtocol property) (openff.evaluator.protocols.reweighting.ConcatenateObservables property) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories property) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant property) (openff.evaluator.protocols.reweighting.ReweightObservable property) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation property) (openff.evaluator.protocols.simulation.BaseSimulation property) (openff.evaluator.protocols.storage.UnpackStoredSimulationData property) (openff.evaluator.protocols.yank.BaseYankProtocol property) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol property) (openff.evaluator.protocols.yank.SolvationYankProtocol property) (openff.evaluator.workflow.Protocol property) (openff.evaluator.workflow.ProtocolGroup property) required_schema_type() (openff.evaluator.layers.CalculationLayer class method) (openff.evaluator.layers.reweighting.ReweightingLayer class method) (openff.evaluator.layers.simulation.SimulationLayer class method) (openff.evaluator.layers.workflow.WorkflowCalculationLayer class method) restraint_schemas (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints attribute) restraint_type (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) restraints_path (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase attribute) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork attribute) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints attribute) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints attribute) result (openff.evaluator.protocols.analysis.AverageFreeEnergies attribute) (openff.evaluator.protocols.miscellaneous.AddValues attribute) (openff.evaluator.protocols.miscellaneous.DivideValue attribute) (openff.evaluator.protocols.miscellaneous.MultiplyValue attribute) (openff.evaluator.protocols.miscellaneous.SubtractValues attribute) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase attribute) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork attribute) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection attribute) results() (openff.evaluator.client.Request method) retain_packmol_files (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) retrieve_force_field() (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.StorageBackend method) retrieve_object() (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.StorageBackend method) retrieve_results() (openff.evaluator.client.EvaluatorClient method) ReweightDielectricConstant (class in openff.evaluator.protocols.reweighting) ReweightingLayer (class in openff.evaluator.layers.reweighting) ReweightingProtocols (class in openff.evaluator.protocols.utils) ReweightingSchema (class in openff.evaluator.layers.reweighting) ReweightObservable (class in openff.evaluator.protocols.reweighting) rfind() (openff.evaluator.storage.attributes.FilePath method) right_hand_value (openff.evaluator.protocols.groups.ConditionalGroup.Condition attribute) rindex() (openff.evaluator.storage.attributes.FilePath method) rjust() (openff.evaluator.storage.attributes.FilePath method) role (openff.evaluator.substances.Component attribute) root_directory (openff.evaluator.storage.LocalFileStorage property) root_protocols (openff.evaluator.workflow.ProtocolGraph property) (openff.evaluator.workflow.WorkflowGraph property) rpartition() (openff.evaluator.storage.attributes.FilePath method) rsplit() (openff.evaluator.storage.attributes.FilePath method) rstrip() (openff.evaluator.storage.attributes.FilePath method) S schedule_calculation() (openff.evaluator.layers.CalculationLayer class method) (openff.evaluator.layers.reweighting.ReweightingLayer class method) (openff.evaluator.layers.simulation.SimulationLayer class method) (openff.evaluator.layers.workflow.WorkflowCalculationLayer class method) schema (openff.evaluator.protocols.analysis.AverageDielectricConstant property) (openff.evaluator.protocols.analysis.AverageFreeEnergies property) (openff.evaluator.protocols.analysis.AverageObservable property) (openff.evaluator.protocols.analysis.BaseAverageObservable property) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol property) (openff.evaluator.protocols.analysis.ComputeDipoleMoments property) (openff.evaluator.protocols.analysis.DecorrelateObservables property) (openff.evaluator.protocols.analysis.DecorrelateTrajectory property) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol property) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates property) (openff.evaluator.protocols.coordinates.SolvateExistingStructure property) (openff.evaluator.protocols.forcefield.BaseBuildSystem property) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem property) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem property) (openff.evaluator.protocols.forcefield.BuildTLeapSystem property) (openff.evaluator.protocols.gradients.ZeroGradients property) (openff.evaluator.protocols.groups.ConditionalGroup property) (openff.evaluator.protocols.miscellaneous.AddValues property) (openff.evaluator.protocols.miscellaneous.DivideValue property) (openff.evaluator.protocols.miscellaneous.DummyProtocol property) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole property) (openff.evaluator.protocols.miscellaneous.MultiplyValue property) (openff.evaluator.protocols.miscellaneous.SubtractValues property) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction property) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation property) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies property) (openff.evaluator.protocols.openmm.OpenMMSimulation property) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase property) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork property) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection property) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms property) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates property) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates property) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints property) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints property) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints property) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints property) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies property) (openff.evaluator.protocols.reweighting.BaseMBARProtocol property) (openff.evaluator.protocols.reweighting.ConcatenateObservables property) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories property) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant property) (openff.evaluator.protocols.reweighting.ReweightObservable property) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation property) (openff.evaluator.protocols.simulation.BaseSimulation property) (openff.evaluator.protocols.storage.UnpackStoredSimulationData property) (openff.evaluator.protocols.yank.BaseYankProtocol property) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol property) (openff.evaluator.protocols.yank.SolvationYankProtocol property) (openff.evaluator.workflow.Protocol property) (openff.evaluator.workflow.ProtocolGroup property) SelectDataPoints (class in openff.evaluator.datasets.curation.components.selection) SelectDataPointsSchema (class in openff.evaluator.datasets.curation.components.selection) SelectSubstances (class in openff.evaluator.datasets.curation.components.selection) SelectSubstancesSchema (class in openff.evaluator.datasets.curation.components.selection) server_address (openff.evaluator.client.ConnectionOptions attribute) (openff.evaluator.client.EvaluatorClient property) server_port (openff.evaluator.client.ConnectionOptions attribute) (openff.evaluator.client.EvaluatorClient property) set_uuid() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) set_value() (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) setdefault() (openff.evaluator.utils.observables.ObservableFrame method) setup_only (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) simulation_data_path (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) SimulationDataQuery (class in openff.evaluator.storage.query) SimulationLayer (class in openff.evaluator.layers.simulation) SimulationProtocols (class in openff.evaluator.protocols.utils) SimulationSchema (class in openff.evaluator.layers.simulation) smiles (openff.evaluator.substances.Component attribute) SmirnoffForceFieldSource (class in openff.evaluator.forcefield) solute (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solute_coordinate_file (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) solution_1_coordinates (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solution_1_free_energy (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solution_1_system (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solution_1_trajectory_path (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solution_2_coordinates (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solution_2_free_energy (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solution_2_system (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solution_2_trajectory_path (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solvated_complex_coordinates (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) solvated_complex_system (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) solvated_complex_trajectory_path (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) solvated_ligand_coordinates (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) solvated_ligand_system (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) solvated_ligand_trajectory_path (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) SolvateExistingStructure (class in openff.evaluator.protocols.coordinates) SolvationFreeEnergy (class in openff.evaluator.properties) SolvationYankProtocol (class in openff.evaluator.protocols.yank) solvent_1 (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solvent_1_coordinate_path (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solvent_1_trajectory_path (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solvent_2 (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solvent_2_coordinate_path (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) solvent_2_trajectory_path (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) Source (class in openff.evaluator.datasets) source (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) source_calculation_id (openff.evaluator.storage.data.BaseSimulationData attribute) (openff.evaluator.storage.data.StoredFreeEnergyData attribute) (openff.evaluator.storage.data.StoredSimulationData attribute) (openff.evaluator.storage.query.BaseSimulationDataQuery attribute) (openff.evaluator.storage.query.FreeEnergyDataQuery attribute) (openff.evaluator.storage.query.SimulationDataQuery attribute) sources (openff.evaluator.datasets.PhysicalPropertyDataSet property) (openff.evaluator.datasets.taproom.TaproomDataSet property) (openff.evaluator.datasets.thermoml.ThermoMLDataSet property) split() (openff.evaluator.storage.attributes.FilePath method) splitlines() (openff.evaluator.storage.attributes.FilePath method) start() (openff.evaluator.backends.CalculationBackend method) (openff.evaluator.backends.dask.BaseDaskBackend method) (openff.evaluator.backends.dask.BaseDaskJobQueueBackend method) (openff.evaluator.backends.dask.DaskLocalCluster method) (openff.evaluator.backends.dask.DaskLSFBackend method) (openff.evaluator.backends.dask.DaskPBSBackend method) (openff.evaluator.server.EvaluatorServer method) start_protocol (openff.evaluator.workflow.utils.ProtocolPath property) start_state_trajectory (openff.evaluator.storage.data.StoredFreeEnergyData attribute) started (openff.evaluator.backends.CalculationBackend property) (openff.evaluator.backends.dask.BaseDaskBackend property) (openff.evaluator.backends.dask.BaseDaskJobQueueBackend property) (openff.evaluator.backends.dask.DaskLocalCluster property) (openff.evaluator.backends.dask.DaskLSFBackend property) (openff.evaluator.backends.dask.DaskPBSBackend property) startswith() (openff.evaluator.storage.attributes.FilePath method) State (class in openff.evaluator.datasets.curation.components.selection) statistical_inefficiency (openff.evaluator.storage.data.StoredSimulationData attribute) steps_per_iteration (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) steric_lambdas_1 (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) steric_lambdas_2 (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) stop() (openff.evaluator.backends.CalculationBackend method) (openff.evaluator.backends.dask.BaseDaskBackend method) (openff.evaluator.backends.dask.BaseDaskJobQueueBackend method) (openff.evaluator.backends.dask.DaskLocalCluster method) (openff.evaluator.backends.dask.DaskLSFBackend method) (openff.evaluator.backends.dask.DaskPBSBackend method) (openff.evaluator.server.EvaluatorServer method) storage_queries (openff.evaluator.layers.reweighting.ReweightingSchema attribute) StorageAttribute (class in openff.evaluator.storage.attributes) StorageBackend (class in openff.evaluator.storage) store_force_field() (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.StorageBackend method) store_object() (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.StorageBackend method) StoredFreeEnergyData (class in openff.evaluator.storage.data) StoredSimulationData (class in openff.evaluator.storage.data) strip() (openff.evaluator.storage.attributes.FilePath method) submit_task() (openff.evaluator.backends.CalculationBackend method) (openff.evaluator.backends.dask.BaseDaskBackend method) (openff.evaluator.backends.dask.BaseDaskJobQueueBackend method) (openff.evaluator.backends.dask.DaskLocalCluster method) (openff.evaluator.backends.dask.DaskLSFBackend method) (openff.evaluator.backends.dask.DaskPBSBackend method) subset() (openff.evaluator.utils.observables.ObservableArray method) (openff.evaluator.utils.observables.ObservableFrame method) Substance (class in openff.evaluator.substances) substance (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) (openff.evaluator.protocols.forcefield.BaseBuildSystem attribute) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem attribute) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem attribute) (openff.evaluator.protocols.forcefield.BuildTLeapSystem attribute) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms attribute) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates attribute) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) (openff.evaluator.storage.data.BaseSimulationData attribute) (openff.evaluator.storage.data.StoredFreeEnergyData attribute) (openff.evaluator.storage.data.StoredSimulationData attribute) (openff.evaluator.storage.query.BaseSimulationDataQuery attribute) (openff.evaluator.storage.query.FreeEnergyDataQuery attribute) (openff.evaluator.storage.query.SimulationDataQuery attribute) substance_query (openff.evaluator.storage.query.BaseSimulationDataQuery attribute) (openff.evaluator.storage.query.FreeEnergyDataQuery attribute) (openff.evaluator.storage.query.SimulationDataQuery attribute) SubstanceQuery (class in openff.evaluator.storage.query) substances (openff.evaluator.datasets.PhysicalPropertyDataSet property) (openff.evaluator.datasets.taproom.TaproomDataSet property) (openff.evaluator.datasets.thermoml.ThermoMLDataSet property) SubtractValues (class in openff.evaluator.protocols.miscellaneous) swapcase() (openff.evaluator.storage.attributes.FilePath method) T TaproomDataSet (class in openff.evaluator.datasets.taproom) TaproomSource (class in openff.evaluator.datasets.taproom) target_reduced_potentials (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) TargetState (class in openff.evaluator.datasets.curation.components.selection) temperature (openff.evaluator.thermodynamics.ThermodynamicState attribute) temperature_cutoff (openff.evaluator.layers.reweighting.ReweightingSchema attribute) thermodynamic_state (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.AverageFreeEnergies attribute) (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.analysis.BaseAverageObservable attribute) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork attribute) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection attribute) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) (openff.evaluator.storage.data.BaseSimulationData attribute) (openff.evaluator.storage.data.StoredFreeEnergyData attribute) (openff.evaluator.storage.data.StoredSimulationData attribute) (openff.evaluator.storage.query.BaseSimulationDataQuery attribute) (openff.evaluator.storage.query.FreeEnergyDataQuery attribute) (openff.evaluator.storage.query.SimulationDataQuery attribute) ThermodynamicState (class in openff.evaluator.thermodynamics) thermoml_property() (in module openff.evaluator.datasets.thermoml) ThermoMLDataSet (class in openff.evaluator.datasets.thermoml) thermostat_friction (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) time_series_statistics (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.analysis.BaseAverageObservable attribute) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol attribute) (openff.evaluator.protocols.analysis.DecorrelateObservables attribute) (openff.evaluator.protocols.analysis.DecorrelateTrajectory attribute) timestep (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) title() (openff.evaluator.storage.attributes.FilePath method) TLeapForceFieldSource (class in openff.evaluator.forcefield) to_force_field() (openff.evaluator.forcefield.SmirnoffForceFieldSource method) to_graph() (openff.evaluator.workflow.Workflow method) to_number_of_molecules() (openff.evaluator.substances.Amount method) (openff.evaluator.substances.ExactAmount method) (openff.evaluator.substances.MoleFraction method) to_pandas() (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.taproom.TaproomDataSet method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) to_protocol() (openff.evaluator.workflow.schemas.ProtocolGroupSchema method) (openff.evaluator.workflow.schemas.ProtocolSchema method) to_storage_query() (openff.evaluator.storage.data.BaseSimulationData method) (openff.evaluator.storage.data.BaseStoredData method) (openff.evaluator.storage.data.ForceFieldData method) (openff.evaluator.storage.data.HashableStoredData method) (openff.evaluator.storage.data.ReplaceableData method) (openff.evaluator.storage.data.StoredFreeEnergyData method) (openff.evaluator.storage.data.StoredSimulationData method) tolerance (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation attribute) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation attribute) topology_file_name (openff.evaluator.storage.data.StoredFreeEnergyData attribute) topology_path (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase attribute) total_number_of_iterations (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) total_number_of_molecules (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) trajectory_file_name (openff.evaluator.storage.data.StoredSimulationData attribute) trajectory_file_path (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies attribute) (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) trajectory_path (openff.evaluator.protocols.analysis.ComputeDipoleMoments attribute) trajectory_paths (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase attribute) translate() (openff.evaluator.storage.attributes.FilePath method) type (openff.evaluator.protocols.groups.ConditionalGroup.Condition attribute) (openff.evaluator.workflow.schemas.ProtocolGroupSchema attribute) (openff.evaluator.workflow.schemas.ProtocolSchema attribute) U uncertainty (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) UNDEFINED (in module openff.evaluator.attributes) UnpackStoredSimulationData (class in openff.evaluator.protocols.storage) unsuccessful_properties (openff.evaluator.client.RequestResult attribute) (openff.evaluator.server.Batch attribute) update() (openff.evaluator.utils.observables.ObservableFrame method) update_forward_refs() (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema class method) (openff.evaluator.datasets.curation.components.CurationComponentSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByChargedSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByElementsSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByEnvironmentsSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByIonicLiquidSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByMoleFractionSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByNComponentsSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByPressureSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByPropertyTypesSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByRacemicSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmilesSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySmirksSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByStereochemistrySchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterBySubstancesSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterByTemperatureSchema class method) (openff.evaluator.datasets.curation.components.filtering.FilterDuplicatesSchema class method) (openff.evaluator.datasets.curation.components.freesolv.ImportFreeSolvSchema class method) (openff.evaluator.datasets.curation.components.selection.SelectDataPointsSchema class method) (openff.evaluator.datasets.curation.components.selection.SelectSubstancesSchema class method) (openff.evaluator.datasets.curation.components.selection.State class method) (openff.evaluator.datasets.curation.components.selection.TargetState class method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema class method) (openff.evaluator.datasets.curation.workflow.CurationWorkflowSchema class method) update_references() (openff.evaluator.workflow.schemas.ProtocolReplicator method) upper() (openff.evaluator.storage.attributes.FilePath method) V validate() (openff.evaluator.attributes.AttributeClass method) (openff.evaluator.client.ConnectionOptions method) (openff.evaluator.client.Request method) (openff.evaluator.client.RequestOptions method) (openff.evaluator.client.RequestResult method) (openff.evaluator.datasets.PhysicalProperty method) (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.taproom.TaproomDataSet method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) (openff.evaluator.layers.CalculationLayerResult method) (openff.evaluator.layers.CalculationLayerSchema method) (openff.evaluator.layers.reweighting.ReweightingSchema method) (openff.evaluator.layers.simulation.SimulationSchema method) (openff.evaluator.layers.workflow.WorkflowCalculationSchema method) (openff.evaluator.properties.Density method) (openff.evaluator.properties.DielectricConstant method) (openff.evaluator.properties.EnthalpyOfMixing method) (openff.evaluator.properties.EnthalpyOfVaporization method) (openff.evaluator.properties.ExcessMolarVolume method) (openff.evaluator.properties.HostGuestBindingAffinity method) (openff.evaluator.properties.SolvationFreeEnergy method) (openff.evaluator.protocols.analysis.AverageDielectricConstant method) (openff.evaluator.protocols.analysis.AverageFreeEnergies method) (openff.evaluator.protocols.analysis.AverageObservable method) (openff.evaluator.protocols.analysis.BaseAverageObservable method) (openff.evaluator.protocols.analysis.BaseDecorrelateProtocol method) (openff.evaluator.protocols.analysis.ComputeDipoleMoments method) (openff.evaluator.protocols.analysis.DecorrelateObservables method) (openff.evaluator.protocols.analysis.DecorrelateTrajectory method) (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol method) (openff.evaluator.protocols.coordinates.BuildDockedCoordinates method) (openff.evaluator.protocols.coordinates.SolvateExistingStructure method) (openff.evaluator.protocols.forcefield.BaseBuildSystem method) (openff.evaluator.protocols.forcefield.BuildLigParGenSystem method) (openff.evaluator.protocols.forcefield.BuildSmirnoffSystem method) (openff.evaluator.protocols.forcefield.BuildTLeapSystem method) (openff.evaluator.protocols.gradients.ZeroGradients method) (openff.evaluator.protocols.groups.ConditionalGroup method) (openff.evaluator.protocols.groups.ConditionalGroup.Condition method) (openff.evaluator.protocols.miscellaneous.AddValues method) (openff.evaluator.protocols.miscellaneous.DivideValue method) (openff.evaluator.protocols.miscellaneous.DummyProtocol method) (openff.evaluator.protocols.miscellaneous.FilterSubstanceByRole method) (openff.evaluator.protocols.miscellaneous.MultiplyValue method) (openff.evaluator.protocols.miscellaneous.SubtractValues method) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction method) (openff.evaluator.protocols.openmm.OpenMMEnergyMinimisation method) (openff.evaluator.protocols.openmm.OpenMMEvaluateEnergies method) (openff.evaluator.protocols.openmm.OpenMMSimulation method) (openff.evaluator.protocols.paprika.analysis.AnalyzeAPRPhase method) (openff.evaluator.protocols.paprika.analysis.ComputeReferenceWork method) (openff.evaluator.protocols.paprika.analysis.ComputeSymmetryCorrection method) (openff.evaluator.protocols.paprika.coordinates.AddDummyAtoms method) (openff.evaluator.protocols.paprika.coordinates.PreparePullCoordinates method) (openff.evaluator.protocols.paprika.coordinates.PrepareReleaseCoordinates method) (openff.evaluator.protocols.paprika.restraints.ApplyRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateAttachRestraints method) (openff.evaluator.protocols.paprika.restraints.GeneratePullRestraints method) (openff.evaluator.protocols.paprika.restraints.GenerateReleaseRestraints method) (openff.evaluator.protocols.reweighting.BaseEvaluateEnergies method) (openff.evaluator.protocols.reweighting.BaseMBARProtocol method) (openff.evaluator.protocols.reweighting.ConcatenateObservables method) (openff.evaluator.protocols.reweighting.ConcatenateTrajectories method) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant method) (openff.evaluator.protocols.reweighting.ReweightObservable method) (openff.evaluator.protocols.simulation.BaseEnergyMinimisation method) (openff.evaluator.protocols.simulation.BaseSimulation method) (openff.evaluator.protocols.storage.UnpackStoredSimulationData method) (openff.evaluator.protocols.yank.BaseYankProtocol method) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol method) (openff.evaluator.protocols.yank.SolvationYankProtocol method) (openff.evaluator.server.Batch method) (openff.evaluator.storage.data.BaseSimulationData method) (openff.evaluator.storage.data.BaseStoredData method) (openff.evaluator.storage.data.ForceFieldData method) (openff.evaluator.storage.data.HashableStoredData method) (openff.evaluator.storage.data.ReplaceableData method) (openff.evaluator.storage.data.StoredFreeEnergyData method) (openff.evaluator.storage.data.StoredSimulationData method) (openff.evaluator.storage.query.BaseDataQuery method) (openff.evaluator.storage.query.BaseSimulationDataQuery method) (openff.evaluator.storage.query.ForceFieldQuery method) (openff.evaluator.storage.query.FreeEnergyDataQuery method) (openff.evaluator.storage.query.SimulationDataQuery method) (openff.evaluator.storage.query.SubstanceQuery method) (openff.evaluator.substances.Amount method) (openff.evaluator.substances.Component method) (openff.evaluator.substances.ExactAmount method) (openff.evaluator.substances.MoleFraction method) (openff.evaluator.substances.Substance method) (openff.evaluator.thermodynamics.ThermodynamicState method) (openff.evaluator.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) (openff.evaluator.workflow.schemas.ProtocolGroupSchema method) (openff.evaluator.workflow.schemas.ProtocolSchema method) (openff.evaluator.workflow.schemas.WorkflowSchema method) (openff.evaluator.workflow.WorkflowResult method) value (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.properties.Density attribute) (openff.evaluator.properties.DielectricConstant attribute) (openff.evaluator.properties.EnthalpyOfMixing attribute) (openff.evaluator.properties.EnthalpyOfVaporization attribute) (openff.evaluator.properties.ExcessMolarVolume attribute) (openff.evaluator.properties.HostGuestBindingAffinity attribute) (openff.evaluator.properties.SolvationFreeEnergy attribute) (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.analysis.AverageObservable attribute) (openff.evaluator.protocols.analysis.BaseAverageObservable attribute) (openff.evaluator.protocols.miscellaneous.DivideValue attribute) (openff.evaluator.protocols.miscellaneous.MultiplyValue attribute) (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction attribute) (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) (openff.evaluator.substances.Amount attribute) (openff.evaluator.substances.ExactAmount attribute) (openff.evaluator.substances.MoleFraction attribute) (openff.evaluator.utils.observables.ObservableArray property) (openff.evaluator.workflow.WorkflowResult attribute) value_a (openff.evaluator.protocols.miscellaneous.SubtractValues attribute) value_b (openff.evaluator.protocols.miscellaneous.SubtractValues attribute) values (openff.evaluator.protocols.analysis.AverageFreeEnergies attribute) (openff.evaluator.protocols.miscellaneous.AddValues attribute) values() (openff.evaluator.utils.observables.ObservableFrame method) verbose (openff.evaluator.protocols.yank.BaseYankProtocol attribute) (openff.evaluator.protocols.yank.LigandReceptorYankProtocol attribute) (openff.evaluator.protocols.yank.SolvationYankProtocol attribute) verbose_packmol (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) volumes (openff.evaluator.protocols.analysis.AverageDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) W wallclock_time_limit (openff.evaluator.backends.QueueWorkerResources property) water_model (openff.evaluator.protocols.forcefield.BuildLigParGenSystem attribute) (openff.evaluator.protocols.forcefield.BuildTLeapSystem attribute) WeightByMoleFraction (class in openff.evaluator.protocols.miscellaneous) weighted_value (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction attribute) window_index (openff.evaluator.protocols.paprika.restraints.ApplyRestraints attribute) with_traceback() (openff.evaluator.utils.exceptions.EvaluatorException method) (openff.evaluator.workflow.WorkflowException method) Workflow (class in openff.evaluator.workflow) workflow_id (openff.evaluator.workflow.WorkflowResult attribute) workflow_protocol() (in module openff.evaluator.workflow) workflow_schema (openff.evaluator.layers.reweighting.ReweightingSchema attribute) (openff.evaluator.layers.simulation.SimulationSchema attribute) (openff.evaluator.layers.workflow.WorkflowCalculationSchema attribute) workflow_to_layer_result() (openff.evaluator.layers.reweighting.ReweightingLayer static method) (openff.evaluator.layers.simulation.SimulationLayer static method) (openff.evaluator.layers.workflow.WorkflowCalculationLayer static method) WorkflowCalculationLayer (class in openff.evaluator.layers.workflow) WorkflowCalculationSchema (class in openff.evaluator.layers.workflow) WorkflowException WorkflowGraph (class in openff.evaluator.workflow) WorkflowResult (class in openff.evaluator.workflow) WorkflowSchema (class in openff.evaluator.workflow.schemas) Z ZeroGradients (class in openff.evaluator.protocols.gradients) zfill() (openff.evaluator.storage.attributes.FilePath method)