OpenFF Evaluator documentation

openff-evaluator

Index

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__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.QueueWorkerResources 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.thermoml.ImportThermoMLData method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema 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.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.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.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.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.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_note() (openff.evaluator.utils.exceptions.EvaluatorException method) (openff.evaluator.workflow.WorkflowException method) add_properties() (openff.evaluator.datasets.PhysicalPropertyDataSet 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_workflows() (openff.evaluator.workflow.WorkflowGraph method) 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.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.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.workflow.Protocol attribute) (openff.evaluator.workflow.ProtocolGroup attribute) Amount (class in openff.evaluator.substances)

amounts (openff.evaluator.substances.Substance attribute) 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.thermoml.ImportThermoMLData 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.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.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.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method) as_integer_ratio() (openff.evaluator.datasets.PropertyPhase method) assigned_residue_names (openff.evaluator.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure 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) 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) beta (openff.evaluator.thermodynamics.ThermodynamicState property) bit_count() (openff.evaluator.datasets.PropertyPhase method) bit_length() (openff.evaluator.datasets.PropertyPhase method) 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)

C

calculate_aqueous_ionic_mole_fraction() (openff.evaluator.substances.Substance static method) calculation_layer() (in module openff.evaluator.layers) 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.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.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.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)

checkpoint_frequency (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation 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) 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) ComputeResources (class in openff.evaluator.backends) ComputeResources.GPUPrecision (class in openff.evaluator.backends) ComputeResources.GPUToolkit (class in openff.evaluator.backends) ConcatenateObservables (class in openff.evaluator.protocols.reweighting) ConcatenateTrajectories (class in openff.evaluator.protocols.reweighting) condition_aggregation_behavior (openff.evaluator.protocols.groups.ConditionalGroup attribute) 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) conjugate() (openff.evaluator.datasets.PropertyPhase method) construct() (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema class method) (openff.evaluator.datasets.curation.components.CurationComponentSchema class method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema 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.storage.UnpackStoredSimulationData attribute) copy() (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema method) (openff.evaluator.datasets.curation.components.CurationComponentSchema method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema 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) current_iteration (openff.evaluator.protocols.groups.ConditionalGroup attribute) cutoff (openff.evaluator.forcefield.LigParGenForceFieldSource property) (openff.evaluator.forcefield.TLeapForceFieldSource property)

D

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_storage_query() (in module openff.evaluator.layers.reweighting) default_unit() (openff.evaluator.datasets.PhysicalProperty class method) denominator (openff.evaluator.datasets.PropertyPhase attribute) 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.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.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.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.thermoml.ImportThermoMLDataSchema method) 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) 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) error_on_failure (openff.evaluator.protocols.groups.ConditionalGroup attribute) EvaluatorException ExactAmount (class in openff.evaluator.substances) exceptions (openff.evaluator.layers.CalculationLayerResult attribute) (openff.evaluator.workflow.WorkflowResult attribute) 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.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.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.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) 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) force_field_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) force_field_path (openff.evaluator.protocols.gradients.ZeroGradients attribute) (openff.evaluator.protocols.storage.UnpackStoredSimulationData 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.storage.data.StoredFreeEnergyData attribute) FreeEnergyDataQuery (class in openff.evaluator.storage.query) from_bytes() (openff.evaluator.datasets.PropertyPhase method) 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.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.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.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.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.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.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.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.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.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.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_default_metadata() (openff.evaluator.workflow.Workflow static method) get() (openff.evaluator.utils.observables.ObservableFrame method) get_amounts() (openff.evaluator.substances.Substance method) get_attributes() (openff.evaluator.attributes.AttributeClass 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.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.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.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.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.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.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.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method)

get_molecules_per_component() (openff.evaluator.substances.Substance method) get_property_hash() (openff.evaluator.datasets.PhysicalProperty 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.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.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.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.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.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.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) gradients (openff.evaluator.datasets.PhysicalProperty attribute) (openff.evaluator.workflow.WorkflowResult 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)

I

id (openff.evaluator.datasets.PhysicalProperty 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.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.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.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)

imag (openff.evaluator.datasets.PropertyPhase attribute) 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_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_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

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.datasets.CalculationSource method) (openff.evaluator.datasets.curation.components.conversion.ConvertExcessDensityDataSchema method) (openff.evaluator.datasets.curation.components.CurationComponentSchema method) (openff.evaluator.datasets.curation.components.thermoml.ImportThermoMLDataSchema method) (openff.evaluator.datasets.MeasurementSource method) (openff.evaluator.datasets.PhysicalProperty method) (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.Source 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.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.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.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.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_residue_name (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) ligand_substance (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute)

LigParGenForceFieldSource (class in openff.evaluator.forcefield) LigParGenForceFieldSource.ChargeModel (class in openff.evaluator.forcefield) ljust() (openff.evaluator.storage.attributes.FilePath 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.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.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.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.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method)

MergeBehavior (class in openff.evaluator.workflow.attributes) metadata (openff.evaluator.datasets.PhysicalProperty 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

number_of_components (openff.evaluator.substances.Substance property) number_of_gpus (openff.evaluator.backends.ComputeResources property) (openff.evaluator.backends.QueueWorkerResources property) 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) numerator (openff.evaluator.datasets.PropertyPhase attribute)

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) OpenMMEnergyMinimisation (class in openff.evaluator.protocols.openmm) OpenMMEvaluateEnergies (class in openff.evaluator.protocols.openmm) OpenMMSimulation (class in openff.evaluator.protocols.openmm) 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.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_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.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.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.workflow.Protocol property) (openff.evaluator.workflow.ProtocolGroup property)

outputs_to_store (openff.evaluator.workflow.schemas.WorkflowSchema attribute) (openff.evaluator.workflow.Workflow property)

P

ParameterGradient (class in openff.evaluator.forcefield) ParameterGradientKey (class in openff.evaluator.forcefield) parameterized_system (openff.evaluator.protocols.analysis.ComputeDipoleMoments 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.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.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.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.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.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.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) 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) prepend_protocol_id() (openff.evaluator.workflow.utils.ProtocolPath method) pressure (openff.evaluator.thermodynamics.ThermodynamicState attribute) properties (openff.evaluator.datasets.PhysicalPropertyDataSet property) (openff.evaluator.datasets.thermoml.ThermoMLDataSet property) properties_by_substance() (openff.evaluator.datasets.PhysicalPropertyDataSet method) (openff.evaluator.datasets.thermoml.ThermoMLDataSet method) properties_by_type() (openff.evaluator.datasets.PhysicalPropertyDataSet 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.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)

Q

query() (openff.evaluator.storage.LocalFileStorage method) (openff.evaluator.storage.StorageBackend method) QueryAttribute (class in openff.evaluator.storage.attributes)

QueueWorkerResources (class in openff.evaluator.backends) QueueWorkerResources.GPUPrecision (class in openff.evaluator.backends) QueueWorkerResources.GPUToolkit (class in openff.evaluator.backends)

R

real (openff.evaluator.datasets.PropertyPhase attribute) receptor_coordinate_file (openff.evaluator.protocols.coordinates.BuildDockedCoordinates attribute) receptor_residue_name (openff.evaluator.protocols.coordinates.BuildDockedCoordinates 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) 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.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.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.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_url (openff.evaluator.forcefield.LigParGenForceFieldSource property) 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.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.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.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) 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) 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) ReweightDielectricConstant (class in openff.evaluator.protocols.reweighting) ReweightingLayer (class in openff.evaluator.layers.reweighting) 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.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.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.workflow.Protocol property) (openff.evaluator.workflow.ProtocolGroup 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.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.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.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.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.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.workflow.Protocol method) (openff.evaluator.workflow.ProtocolGroup method)

setdefault() (openff.evaluator.utils.observables.ObservableFrame method) should_execute (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.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.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.workflow.Protocol attribute) (openff.evaluator.workflow.ProtocolGroup attribute) simulation_data_path (openff.evaluator.protocols.storage.UnpackStoredSimulationData attribute) SimulationDataQuery (class in openff.evaluator.storage.query) SimulationLayer (class in openff.evaluator.layers.simulation) SimulationSchema (class in openff.evaluator.layers.simulation) smiles (openff.evaluator.substances.Component attribute) SmirnoffForceFieldSource (class in openff.evaluator.forcefield) solute_coordinate_file (openff.evaluator.protocols.coordinates.SolvateExistingStructure attribute) SolvateExistingStructure (class in openff.evaluator.protocols.coordinates) Source (class in openff.evaluator.datasets) source (openff.evaluator.datasets.PhysicalProperty 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.thermoml.ThermoMLDataSet property) split() (openff.evaluator.storage.attributes.FilePath method) splitlines() (openff.evaluator.storage.attributes.FilePath method) start() (openff.evaluator.backends.CalculationBackend method) start_protocol (openff.evaluator.workflow.utils.ProtocolPath property) start_state_trajectory (openff.evaluator.storage.data.StoredFreeEnergyData attribute) started (openff.evaluator.backends.CalculationBackend property) startswith() (openff.evaluator.storage.attributes.FilePath method) statistical_inefficiency (openff.evaluator.storage.data.StoredSimulationData attribute) steps_per_iteration (openff.evaluator.protocols.openmm.OpenMMSimulation attribute) (openff.evaluator.protocols.simulation.BaseSimulation attribute) stop() (openff.evaluator.backends.CalculationBackend 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) 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.protocols.coordinates.BuildCoordinatesPackmol attribute) (openff.evaluator.protocols.coordinates.SolvateExistingStructure 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.thermoml.ThermoMLDataSet property) SubtractValues (class in openff.evaluator.protocols.miscellaneous) swapcase() (openff.evaluator.storage.attributes.FilePath method)

T

target_reduced_potentials (openff.evaluator.protocols.reweighting.BaseMBARProtocol attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.reweighting.ReweightObservable attribute) temperature (openff.evaluator.thermodynamics.ThermodynamicState attribute) temperature_cutoff (openff.evaluator.layers.reweighting.ReweightingSchema attribute) thermodynamic_state (openff.evaluator.datasets.PhysicalProperty 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.reweighting.BaseEvaluateEnergies attribute) (openff.evaluator.protocols.reweighting.ReweightDielectricConstant attribute) (openff.evaluator.protocols.simulation.BaseSimulation 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) 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) title() (openff.evaluator.storage.attributes.FilePath method) TLeapForceFieldSource (class in openff.evaluator.forcefield)

to_bytes() (openff.evaluator.datasets.PropertyPhase method) 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.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) to_substance_n_molecules() (openff.evaluator.substances.Substance 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) 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) 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) UNDEFINED (in module openff.evaluator.attributes) UnpackStoredSimulationData (class in openff.evaluator.protocols.storage) 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.thermoml.ImportThermoMLDataSchema 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.datasets.PhysicalProperty method) (openff.evaluator.datasets.PhysicalPropertyDataSet 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.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.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.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.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.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_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) WeightByMoleFraction (class in openff.evaluator.protocols.miscellaneous) weighted_value (openff.evaluator.protocols.miscellaneous.WeightByMoleFraction 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)