Property Estimator
0.0.7
User Guide
Installing the Property Estimator
Getting Started
Physical Property Measurements
Physical Property Data Sets
Developer Documentation
API
Release History
Release Process
Property Estimator
Docs
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Index
Edit on GitHub
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
_
__init__() (propertyestimator.backends.BaseDaskBackend method)
(propertyestimator.backends.ComputeResources method)
(propertyestimator.backends.DaskLocalCluster method)
(propertyestimator.backends.DaskLSFBackend method)
(propertyestimator.backends.PropertyEstimatorBackend method)
(propertyestimator.backends.QueueWorkerResources method)
(propertyestimator.client.ConnectionOptions method)
(propertyestimator.client.PropertyEstimatorClient method)
(propertyestimator.client.PropertyEstimatorOptions method)
(propertyestimator.client.PropertyEstimatorResult method)
(propertyestimator.client.PropertyEstimatorSubmission method)
(propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
(propertyestimator.forcefield.ForceFieldSource method)
(propertyestimator.forcefield.LigParGenForceFieldSource method)
(propertyestimator.forcefield.SmirnoffForceFieldSource method)
(propertyestimator.forcefield.TLeapForceFieldSource method)
(propertyestimator.layers.PropertyCalculationLayer method)
(propertyestimator.layers.ReweightingLayer method)
(propertyestimator.layers.SimulationLayer method)
(propertyestimator.properties.CalculationSource method)
(propertyestimator.properties.Density method)
(propertyestimator.properties.DielectricConstant method)
(propertyestimator.properties.EnthalpyOfMixing method)
(propertyestimator.properties.EnthalpyOfVaporization method)
(propertyestimator.properties.ExcessMolarVolume method)
(propertyestimator.properties.HostGuestBindingAffinity method)
(propertyestimator.properties.MeasurementSource method)
(propertyestimator.properties.ParameterGradient method)
(propertyestimator.properties.ParameterGradientKey method)
(propertyestimator.properties.PhysicalProperty method)
(propertyestimator.properties.PropertyPhase method)
(propertyestimator.properties.Source method)
(propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.utils.BaseReweightingProtocols method)
(propertyestimator.protocols.utils.BaseSimulationProtocols method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.server.PropertyEstimatorServer method)
(propertyestimator.storage.dataclasses.BaseStoredData method)
(propertyestimator.storage.dataclasses.StoredDataCollection method)
(propertyestimator.storage.dataclasses.StoredSimulationData method)
(propertyestimator.storage.LocalFileStorage method)
(propertyestimator.storage.PropertyEstimatorStorage method)
(propertyestimator.substances.Substance method)
(propertyestimator.thermodynamics.ThermodynamicState method)
(propertyestimator.workflow.decorators.BaseProtocolAttribute method)
(propertyestimator.workflow.decorators.InequalityMergeBehaviour method)
(propertyestimator.workflow.decorators.MergeBehaviour method)
(propertyestimator.workflow.IWorkflowProperty method)
(propertyestimator.workflow.protocols.BaseProtocol method)
(propertyestimator.workflow.schemas.ProtocolGroupSchema method)
(propertyestimator.workflow.schemas.ProtocolReplicator method)
(propertyestimator.workflow.schemas.ProtocolSchema method)
(propertyestimator.workflow.schemas.WorkflowDataCollectionToStore method)
(propertyestimator.workflow.schemas.WorkflowOutputToStore method)
(propertyestimator.workflow.schemas.WorkflowSchema method)
(propertyestimator.workflow.schemas.WorkflowSimulationDataToStore method)
(propertyestimator.workflow.utils.PlaceholderInput method)
(propertyestimator.workflow.utils.ProtocolPath method)
(propertyestimator.workflow.utils.ReplicatorValue method)
(propertyestimator.workflow.Workflow method)
(propertyestimator.workflow.WorkflowGraph method)
(propertyestimator.workflow.WorkflowOptions method)
A
activate_site_location (propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
add_component() (propertyestimator.substances.Substance method)
add_condition() (propertyestimator.protocols.groups.ConditionalGroup method)
add_socket() (propertyestimator.server.PropertyEstimatorServer method)
add_sockets() (propertyestimator.server.PropertyEstimatorServer method)
add_workflow() (propertyestimator.workflow.WorkflowGraph method)
AddValues (class in propertyestimator.protocols.miscellaneous)
allow_gpu_platforms (propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
allow_merging (propertyestimator.protocols.analysis.AveragePropertyProtocol attribute)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
(propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData attribute)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem attribute)
(propertyestimator.protocols.forcefield.BuildTLeapSystem attribute)
(propertyestimator.protocols.gradients.CentralDifferenceGradient attribute)
(propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
(propertyestimator.protocols.groups.ConditionalGroup attribute)
(propertyestimator.protocols.groups.ProtocolGroup attribute)
(propertyestimator.protocols.miscellaneous.AddValues attribute)
(propertyestimator.protocols.miscellaneous.DivideValue attribute)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole attribute)
(propertyestimator.protocols.miscellaneous.MultiplyValue attribute)
(propertyestimator.protocols.miscellaneous.SubtractValues attribute)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction attribute)
(propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
(propertyestimator.protocols.reweighting.ConcatenateStatistics attribute)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
(propertyestimator.protocols.simulation.RunEnergyMinimisation attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
(propertyestimator.protocols.storage.UnpackStoredDataCollection attribute)
(propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
(propertyestimator.workflow.protocols.BaseProtocol attribute)
allow_protocol_merging (propertyestimator.client.PropertyEstimatorOptions attribute)
allowed_calculation_layers (propertyestimator.client.PropertyEstimatorOptions attribute)
analysis_protocol() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
(propertyestimator.protocols.utils.BaseSimulationProtocols property)
append_uuid() (propertyestimator.workflow.utils.ProtocolPath method)
apply() (propertyestimator.workflow.schemas.ProtocolReplicator method)
apply_known_charges (propertyestimator.protocols.forcefield.BuildSmirnoffSystem attribute)
apply_replicator() (propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.workflow.protocols.BaseProtocol method)
apply_restraints (propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
assign_parameters() (propertyestimator.protocols.utils.BaseSimulationProtocols property)
AveragePropertyProtocol (class in propertyestimator.protocols.analysis)
AverageTrajectoryProperty (class in propertyestimator.protocols.analysis)
B
BaseDaskBackend (class in propertyestimator.backends)
BaseMBARProtocol (class in propertyestimator.protocols.reweighting)
BaseProtocol (class in propertyestimator.workflow.protocols)
BaseProtocolAttribute (class in propertyestimator.workflow.decorators)
BaseReweightingProtocols (class in propertyestimator.protocols.utils)
BaseSimulationProtocols (class in propertyestimator.protocols.utils)
BaseStoredData (class in propertyestimator.storage.dataclasses)
BaseYankProtocol (class in propertyestimator.protocols.yank)
beta() (propertyestimator.thermodynamics.ThermodynamicState property)
bind() (propertyestimator.server.PropertyEstimatorServer method)
bootstrap_iterations (propertyestimator.protocols.analysis.AveragePropertyProtocol attribute)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
(propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
(propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
bootstrap_sample_size (propertyestimator.protocols.analysis.AveragePropertyProtocol attribute)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
(propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
(propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
bootstrap_uncertainties (propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
box_aspect_ratio (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
build_coordinates() (propertyestimator.protocols.utils.BaseSimulationProtocols property)
build_reference_system() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
build_target_system() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
BuildCoordinatesPackmol (class in propertyestimator.protocols.coordinates)
BuildDockedCoordinates (class in propertyestimator.protocols.coordinates)
BuildDockedCoordinates.ActivateSiteLocation (class in propertyestimator.protocols.coordinates)
BuildSmirnoffSystem (class in propertyestimator.protocols.forcefield)
BuildSmirnoffSystem.WaterModel (class in propertyestimator.protocols.forcefield)
BuildTLeapSystem (class in propertyestimator.protocols.forcefield)
BuildTLeapSystem.ChargeBackend (class in propertyestimator.protocols.forcefield)
BuildTLeapSystem.WaterModel (class in propertyestimator.protocols.forcefield)
C
calculate_aqueous_ionic_mole_fraction() (propertyestimator.substances.Substance static method)
CalculateReducedPotentialOpenMM (class in propertyestimator.protocols.reweighting)
CalculationSource (class in propertyestimator.properties)
can_merge() (propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.storage.dataclasses.BaseStoredData method)
(propertyestimator.storage.dataclasses.StoredDataCollection method)
(propertyestimator.storage.dataclasses.StoredSimulationData method)
(propertyestimator.workflow.protocols.BaseProtocol method)
CentralDifferenceGradient (class in propertyestimator.protocols.gradients)
charge_backend (propertyestimator.protocols.forcefield.BuildTLeapSystem attribute)
charged_molecule_paths (propertyestimator.protocols.forcefield.BuildSmirnoffSystem attribute)
checkpoint_frequency (propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
checkpoint_interval (propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
collection_data_paths (propertyestimator.protocols.storage.UnpackStoredDataCollection attribute)
component (propertyestimator.protocols.miscellaneous.WeightByMoleFraction attribute)
component_role (propertyestimator.protocols.miscellaneous.FilterSubstanceByRole attribute)
components() (propertyestimator.substances.Substance property)
ComputeResources (class in propertyestimator.backends)
ComputeResources.GPUToolkit (class in propertyestimator.backends)
concatenate_statistics() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
concatenate_trajectories() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
ConcatenateStatistics (class in propertyestimator.protocols.reweighting)
ConcatenateTrajectories (class in propertyestimator.protocols.reweighting)
ConditionalGroup (class in propertyestimator.protocols.groups)
ConditionalGroup.ConditionType (class in propertyestimator.protocols.groups)
ConnectionOptions (class in propertyestimator.client)
converge_uncertainty() (propertyestimator.protocols.utils.BaseSimulationProtocols property)
coordinate_file_name (propertyestimator.storage.dataclasses.StoredSimulationData attribute)
coordinate_file_path (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem attribute)
(propertyestimator.protocols.forcefield.BuildTLeapSystem attribute)
(propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
(propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.workflow.schemas.WorkflowSimulationDataToStore attribute)
count() (propertyestimator.protocols.utils.BaseReweightingProtocols method)
(propertyestimator.protocols.utils.BaseSimulationProtocols method)
current_iteration (propertyestimator.protocols.groups.ConditionalGroup attribute)
cutoff() (propertyestimator.forcefield.LigParGenForceFieldSource property)
(propertyestimator.forcefield.TLeapForceFieldSource property)
D
DaskLocalCluster (class in propertyestimator.backends)
DaskLSFBackend (class in propertyestimator.backends)
data (propertyestimator.storage.dataclasses.StoredDataCollection attribute)
(propertyestimator.workflow.schemas.WorkflowDataCollectionToStore attribute)
decorrelate_statistics() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
decorrelate_trajectory() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
Density (class in propertyestimator.properties)
dependants_graph() (propertyestimator.protocols.groups.ConditionalGroup property)
(propertyestimator.protocols.groups.ProtocolGroup property)
dependencies() (propertyestimator.protocols.analysis.AveragePropertyProtocol property)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty property)
(propertyestimator.protocols.analysis.ExtractAverageStatistic property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData property)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol property)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates property)
(propertyestimator.protocols.coordinates.SolvateExistingStructure property)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem property)
(propertyestimator.protocols.forcefield.BuildTLeapSystem property)
(propertyestimator.protocols.gradients.CentralDifferenceGradient property)
(propertyestimator.protocols.gradients.GradientReducedPotentials property)
(propertyestimator.protocols.groups.ConditionalGroup property)
(propertyestimator.protocols.groups.ProtocolGroup property)
(propertyestimator.protocols.miscellaneous.AddValues property)
(propertyestimator.protocols.miscellaneous.DivideValue property)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole property)
(propertyestimator.protocols.miscellaneous.MultiplyValue property)
(propertyestimator.protocols.miscellaneous.SubtractValues property)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction property)
(propertyestimator.protocols.reweighting.BaseMBARProtocol property)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM property)
(propertyestimator.protocols.reweighting.ConcatenateStatistics property)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories property)
(propertyestimator.protocols.reweighting.ReweightStatistics property)
(propertyestimator.protocols.simulation.RunEnergyMinimisation property)
(propertyestimator.protocols.simulation.RunOpenMMSimulation property)
(propertyestimator.protocols.storage.UnpackStoredDataCollection property)
(propertyestimator.protocols.storage.UnpackStoredSimulationData property)
(propertyestimator.protocols.yank.BaseYankProtocol property)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol property)
(propertyestimator.protocols.yank.SolvationYankProtocol property)
(propertyestimator.workflow.protocols.BaseProtocol property)
DielectricConstant (class in propertyestimator.properties)
DivideValue (class in propertyestimator.protocols.miscellaneous)
divisor (propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
(propertyestimator.protocols.miscellaneous.DivideValue attribute)
docked_complex_coordinate_path (propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
docked_ligand_coordinate_path (propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
doi (propertyestimator.properties.MeasurementSource attribute)
download_url() (propertyestimator.forcefield.LigParGenForceFieldSource property)
E
effective_sample_indices (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
(propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
effective_samples (propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
electrostatic_lambdas_1 (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
electrostatic_lambdas_2 (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
enable_pbc (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
(propertyestimator.protocols.simulation.RunEnergyMinimisation attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
energy_minimisation() (propertyestimator.protocols.utils.BaseSimulationProtocols property)
ensemble (propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
EnthalpyOfMixing (class in propertyestimator.properties)
EnthalpyOfVaporization (class in propertyestimator.properties)
EnthalpyWorkflow (propertyestimator.properties.EnthalpyOfMixing attribute)
equilibration_index (propertyestimator.protocols.analysis.AveragePropertyProtocol attribute)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
(propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData attribute)
equilibration_simulation() (propertyestimator.protocols.utils.BaseSimulationProtocols property)
estimated_free_energy (propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
estimated_properties (propertyestimator.client.PropertyEstimatorResult attribute)
exceptions (propertyestimator.client.PropertyEstimatorResult attribute)
ExcessMolarVolume (class in propertyestimator.properties)
execute() (propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.workflow.protocols.BaseProtocol method)
execution_order() (propertyestimator.protocols.groups.ConditionalGroup property)
(propertyestimator.protocols.groups.ProtocolGroup property)
expected_components (propertyestimator.protocols.miscellaneous.FilterSubstanceByRole attribute)
extract_uncorrelated_statistics() (propertyestimator.protocols.utils.BaseSimulationProtocols property)
extract_uncorrelated_trajectory() (propertyestimator.protocols.utils.BaseSimulationProtocols property)
ExtractAverageStatistic (class in propertyestimator.protocols.analysis)
ExtractUncorrelatedData (class in propertyestimator.protocols.analysis)
ExtractUncorrelatedStatisticsData (class in propertyestimator.protocols.analysis)
ExtractUncorrelatedTrajectoryData (class in propertyestimator.protocols.analysis)
F
fidelity (propertyestimator.properties.CalculationSource attribute)
filter_by_components() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
filter_by_elements() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
filter_by_function() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
filter_by_phases() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
filter_by_pressure() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
filter_by_property_types() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
filter_by_smiles() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
filter_by_temperature() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
filtered_substance (propertyestimator.protocols.miscellaneous.FilterSubstanceByRole attribute)
FilterSubstanceByRole (class in propertyestimator.protocols.miscellaneous)
force_field_id (propertyestimator.storage.dataclasses.BaseStoredData attribute)
force_field_path (propertyestimator.protocols.forcefield.BuildSmirnoffSystem attribute)
(propertyestimator.protocols.forcefield.BuildTLeapSystem attribute)
(propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
(propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
force_field_source (propertyestimator.client.PropertyEstimatorSubmission attribute)
ForceFieldSource (class in propertyestimator.forcefield)
forward_observable_value (propertyestimator.protocols.gradients.CentralDifferenceGradient attribute)
forward_parameter_value (propertyestimator.protocols.gradients.CentralDifferenceGradient attribute)
(propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
forward_potentials_path (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
frame_counts (propertyestimator.protocols.reweighting.ReweightStatistics attribute)
from_components() (propertyestimator.substances.Substance class method)
from_doi() (propertyestimator.datasets.ThermoMLDataSet class method)
from_file() (propertyestimator.datasets.ThermoMLDataSet class method)
from_json() (propertyestimator.client.PropertyEstimatorClient.Request class method)
from_object() (propertyestimator.forcefield.SmirnoffForceFieldSource class method)
from_path() (propertyestimator.forcefield.SmirnoffForceFieldSource class method)
from_url() (propertyestimator.datasets.ThermoMLDataSet class method)
from_xml() (propertyestimator.datasets.ThermoMLDataSet class method)
full_path() (propertyestimator.workflow.utils.ProtocolPath property)
full_substance (propertyestimator.protocols.miscellaneous.WeightByMoleFraction attribute)
G
generate_base_reweighting_protocols() (in module propertyestimator.protocols.utils)
generate_base_simulation_protocols() (in module propertyestimator.protocols.utils)
generate_default_metadata() (propertyestimator.workflow.Workflow static method)
generate_gradient_protocol_group() (in module propertyestimator.protocols.utils)
get_amounts() (propertyestimator.substances.Substance method)
get_class_attribute() (propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.workflow.protocols.BaseProtocol method)
get_default_reweighting_workflow_schema() (propertyestimator.properties.Density static method)
(propertyestimator.properties.DielectricConstant static method)
(propertyestimator.properties.EnthalpyOfMixing static method)
(propertyestimator.properties.EnthalpyOfVaporization static method)
(propertyestimator.properties.ExcessMolarVolume static method)
get_default_simulation_workflow_schema() (propertyestimator.properties.Density static method)
(propertyestimator.properties.DielectricConstant static method)
(propertyestimator.properties.EnthalpyOfMixing static method)
(propertyestimator.properties.EnthalpyOfVaporization static method)
(propertyestimator.properties.ExcessMolarVolume static method)
(propertyestimator.properties.HostGuestBindingAffinity static method)
get_default_workflow_schema() (propertyestimator.properties.Density static method)
(propertyestimator.properties.DielectricConstant static method)
(propertyestimator.properties.EnthalpyOfMixing static method)
(propertyestimator.properties.EnthalpyOfVaporization static method)
(propertyestimator.properties.ExcessMolarVolume static method)
(propertyestimator.properties.HostGuestBindingAffinity static method)
(propertyestimator.properties.PhysicalProperty static method)
get_molecules_per_component() (propertyestimator.substances.Substance method)
get_value() (propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.workflow.protocols.BaseProtocol method)
get_value_references() (propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.workflow.protocols.BaseProtocol method)
gpu_device_indices() (propertyestimator.backends.ComputeResources property)
(propertyestimator.backends.QueueWorkerResources property)
gradient (propertyestimator.protocols.gradients.CentralDifferenceGradient attribute)
GradientReducedPotentials (class in propertyestimator.protocols.gradients)
H
handle_stream() (propertyestimator.server.PropertyEstimatorServer method)
has_force_field() (propertyestimator.storage.LocalFileStorage method)
(propertyestimator.storage.PropertyEstimatorStorage method)
high_precision (propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
HostGuestBindingAffinity (class in propertyestimator.properties)
I
id (propertyestimator.client.PropertyEstimatorResult attribute)
id() (propertyestimator.client.PropertyEstimatorClient.Request property)
(propertyestimator.protocols.analysis.AveragePropertyProtocol property)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty property)
(propertyestimator.protocols.analysis.ExtractAverageStatistic property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData property)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol property)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates property)
(propertyestimator.protocols.coordinates.SolvateExistingStructure property)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem property)
(propertyestimator.protocols.forcefield.BuildTLeapSystem property)
(propertyestimator.protocols.gradients.CentralDifferenceGradient property)
(propertyestimator.protocols.gradients.GradientReducedPotentials property)
(propertyestimator.protocols.groups.ConditionalGroup property)
(propertyestimator.protocols.groups.ProtocolGroup property)
(propertyestimator.protocols.miscellaneous.AddValues property)
(propertyestimator.protocols.miscellaneous.DivideValue property)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole property)
(propertyestimator.protocols.miscellaneous.MultiplyValue property)
(propertyestimator.protocols.miscellaneous.SubtractValues property)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction property)
(propertyestimator.protocols.reweighting.BaseMBARProtocol property)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM property)
(propertyestimator.protocols.reweighting.ConcatenateStatistics property)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories property)
(propertyestimator.protocols.reweighting.ReweightStatistics property)
(propertyestimator.protocols.simulation.RunEnergyMinimisation property)
(propertyestimator.protocols.simulation.RunOpenMMSimulation property)
(propertyestimator.protocols.storage.UnpackStoredDataCollection property)
(propertyestimator.protocols.storage.UnpackStoredSimulationData property)
(propertyestimator.protocols.yank.BaseYankProtocol property)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol property)
(propertyestimator.protocols.yank.SolvationYankProtocol property)
(propertyestimator.workflow.protocols.BaseProtocol property)
identifier() (propertyestimator.substances.Substance property)
(propertyestimator.substances.Substance.Amount property)
(propertyestimator.substances.Substance.Component property)
(propertyestimator.substances.Substance.ExactAmount property)
(propertyestimator.substances.Substance.MoleFraction property)
index() (propertyestimator.protocols.utils.BaseReweightingProtocols method)
(propertyestimator.protocols.utils.BaseSimulationProtocols method)
InequalityMergeBehaviour (class in propertyestimator.workflow.decorators)
input_coordinate_file (propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData attribute)
(propertyestimator.protocols.simulation.RunEnergyMinimisation attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
input_coordinate_paths (propertyestimator.protocols.reweighting.ConcatenateTrajectories attribute)
input_data_path (propertyestimator.protocols.storage.UnpackStoredDataCollection attribute)
input_statistics_path (propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData attribute)
input_statistics_paths (propertyestimator.protocols.reweighting.ConcatenateStatistics attribute)
input_substance (propertyestimator.protocols.miscellaneous.FilterSubstanceByRole attribute)
input_trajectory_path (propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData attribute)
input_trajectory_paths (propertyestimator.protocols.reweighting.ConcatenateTrajectories attribute)
inverse_beta() (propertyestimator.thermodynamics.ThermodynamicState property)
IWorkflowProperty (class in propertyestimator.workflow)
J
job_script() (propertyestimator.backends.DaskLSFBackend method)
json() (propertyestimator.client.ConnectionOptions method)
(propertyestimator.client.PropertyEstimatorClient.Request method)
(propertyestimator.client.PropertyEstimatorOptions method)
(propertyestimator.client.PropertyEstimatorResult method)
(propertyestimator.client.PropertyEstimatorSubmission method)
(propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
(propertyestimator.forcefield.ForceFieldSource method)
(propertyestimator.forcefield.LigParGenForceFieldSource method)
(propertyestimator.forcefield.SmirnoffForceFieldSource method)
(propertyestimator.forcefield.TLeapForceFieldSource method)
(propertyestimator.properties.CalculationSource method)
(propertyestimator.properties.Density method)
(propertyestimator.properties.DielectricConstant method)
(propertyestimator.properties.EnthalpyOfMixing method)
(propertyestimator.properties.EnthalpyOfVaporization method)
(propertyestimator.properties.ExcessMolarVolume method)
(propertyestimator.properties.HostGuestBindingAffinity method)
(propertyestimator.properties.MeasurementSource method)
(propertyestimator.properties.PhysicalProperty method)
(propertyestimator.properties.Source method)
(propertyestimator.server.PropertyEstimatorServer.ServerEstimationRequest method)
(propertyestimator.substances.Substance method)
(propertyestimator.substances.Substance.Component method)
(propertyestimator.thermodynamics.ThermodynamicState method)
(propertyestimator.workflow.schemas.ProtocolGroupSchema method)
(propertyestimator.workflow.schemas.ProtocolReplicator method)
(propertyestimator.workflow.schemas.ProtocolSchema method)
(propertyestimator.workflow.schemas.WorkflowSchema method)
K
kinetic_energies_path (propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
L
label() (propertyestimator.substances.Substance.Component property)
last_protocol() (propertyestimator.workflow.utils.ProtocolPath property)
leap_source() (propertyestimator.forcefield.TLeapForceFieldSource property)
ligand_residue_name (propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
ligand_substance (propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
LigandReceptorYankProtocol (class in propertyestimator.protocols.yank)
LigandReceptorYankProtocol.RestraintType (class in propertyestimator.protocols.yank)
LigParGenForceFieldSource (class in propertyestimator.forcefield)
LigParGenForceFieldSource.ChargeModel (class in propertyestimator.forcefield)
listen() (propertyestimator.server.PropertyEstimatorServer method)
LocalFileStorage (class in propertyestimator.storage)
M
mass_density (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
max_iterations (propertyestimator.protocols.groups.ConditionalGroup attribute)
(propertyestimator.protocols.simulation.RunEnergyMinimisation attribute)
max_molecules (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
mbar_protocol() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
MeasurementSource (class in propertyestimator.properties)
merge() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
(propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.storage.dataclasses.BaseStoredData class method)
(propertyestimator.storage.dataclasses.StoredDataCollection class method)
(propertyestimator.storage.dataclasses.StoredSimulationData class method)
(propertyestimator.workflow.protocols.BaseProtocol method)
MergeBehaviour (class in propertyestimator.workflow.decorators)
metadata() (propertyestimator.properties.Density property)
(propertyestimator.properties.DielectricConstant property)
(propertyestimator.properties.EnthalpyOfMixing property)
(propertyestimator.properties.EnthalpyOfVaporization property)
(propertyestimator.properties.ExcessMolarVolume property)
(propertyestimator.properties.HostGuestBindingAffinity property)
(propertyestimator.properties.PhysicalProperty property)
multi_component_property() (propertyestimator.properties.EnthalpyOfVaporization property)
(propertyestimator.properties.HostGuestBindingAffinity property)
multiplier (propertyestimator.protocols.miscellaneous.MultiplyValue attribute)
MultiplyValue (class in propertyestimator.protocols.miscellaneous)
N
number_of_components() (propertyestimator.substances.Substance property)
number_of_equilibration_iterations (propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
number_of_gpus() (propertyestimator.backends.ComputeResources property)
(propertyestimator.backends.QueueWorkerResources property)
number_of_iterations (propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
number_of_ligand_conformers (propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
number_of_properties() (propertyestimator.datasets.PhysicalPropertyDataSet property)
(propertyestimator.datasets.ThermoMLDataSet property)
number_of_threads() (propertyestimator.backends.ComputeResources property)
(propertyestimator.backends.QueueWorkerResources property)
number_of_uncorrelated_samples (propertyestimator.protocols.analysis.ExtractUncorrelatedData attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData attribute)
O
options (propertyestimator.client.PropertyEstimatorSubmission attribute)
output_coordinate_file (propertyestimator.protocols.simulation.RunEnergyMinimisation attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
output_coordinate_path (propertyestimator.protocols.reweighting.ConcatenateTrajectories attribute)
output_frequency (propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
output_number_of_molecules (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
output_statistics_path (propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData attribute)
(propertyestimator.protocols.reweighting.ConcatenateStatistics attribute)
output_substance (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
output_trajectory_path (propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData attribute)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories attribute)
P
parameter_key (propertyestimator.protocols.gradients.CentralDifferenceGradient attribute)
(propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
ParameterGradient (class in propertyestimator.properties)
ParameterGradientKey (class in propertyestimator.properties)
parse_json() (propertyestimator.client.ConnectionOptions class method)
(propertyestimator.client.PropertyEstimatorOptions class method)
(propertyestimator.client.PropertyEstimatorResult class method)
(propertyestimator.client.PropertyEstimatorSubmission class method)
(propertyestimator.datasets.PhysicalPropertyDataSet class method)
(propertyestimator.datasets.ThermoMLDataSet class method)
(propertyestimator.forcefield.ForceFieldSource class method)
(propertyestimator.forcefield.LigParGenForceFieldSource class method)
(propertyestimator.forcefield.SmirnoffForceFieldSource class method)
(propertyestimator.forcefield.TLeapForceFieldSource class method)
(propertyestimator.properties.CalculationSource class method)
(propertyestimator.properties.Density class method)
(propertyestimator.properties.DielectricConstant class method)
(propertyestimator.properties.EnthalpyOfMixing class method)
(propertyestimator.properties.EnthalpyOfVaporization class method)
(propertyestimator.properties.ExcessMolarVolume class method)
(propertyestimator.properties.HostGuestBindingAffinity class method)
(propertyestimator.properties.MeasurementSource class method)
(propertyestimator.properties.PhysicalProperty class method)
(propertyestimator.properties.Source class method)
(propertyestimator.server.PropertyEstimatorServer.ServerEstimationRequest class method)
(propertyestimator.substances.Substance class method)
(propertyestimator.substances.Substance.Component class method)
(propertyestimator.thermodynamics.ThermodynamicState class method)
(propertyestimator.workflow.schemas.ProtocolGroupSchema class method)
(propertyestimator.workflow.schemas.ProtocolReplicator class method)
(propertyestimator.workflow.schemas.ProtocolSchema class method)
(propertyestimator.workflow.schemas.WorkflowSchema class method)
per_thread_memory_limit() (propertyestimator.backends.QueueWorkerResources property)
perturbation_scale (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
PhysicalProperty (class in propertyestimator.properties)
PhysicalPropertyDataSet (class in propertyestimator.datasets)
placeholder_id() (propertyestimator.workflow.schemas.ProtocolReplicator property)
PlaceholderInput (class in propertyestimator.workflow.utils)
pop_next_in_path() (propertyestimator.workflow.utils.ProtocolPath method)
preferred_charge_model() (propertyestimator.forcefield.LigParGenForceFieldSource property)
preferred_gpu_toolkit() (propertyestimator.backends.ComputeResources property)
(propertyestimator.backends.QueueWorkerResources property)
prepend_protocol_id() (propertyestimator.workflow.utils.ProtocolPath method)
pressure (propertyestimator.thermodynamics.ThermodynamicState attribute)
pressure() (propertyestimator.properties.Density property)
(propertyestimator.properties.DielectricConstant property)
(propertyestimator.properties.EnthalpyOfMixing property)
(propertyestimator.properties.EnthalpyOfVaporization property)
(propertyestimator.properties.ExcessMolarVolume property)
(propertyestimator.properties.HostGuestBindingAffinity property)
(propertyestimator.properties.PhysicalProperty property)
production_simulation() (propertyestimator.protocols.utils.BaseSimulationProtocols property)
properties (propertyestimator.client.PropertyEstimatorSubmission attribute)
properties() (propertyestimator.datasets.PhysicalPropertyDataSet property)
(propertyestimator.datasets.ThermoMLDataSet property)
property_name() (propertyestimator.workflow.utils.ProtocolPath property)
PropertyCalculationLayer (class in propertyestimator.layers)
PropertyEstimatorBackend (class in propertyestimator.backends)
PropertyEstimatorClient (class in propertyestimator.client)
PropertyEstimatorClient.Request (class in propertyestimator.client)
PropertyEstimatorOptions (class in propertyestimator.client)
PropertyEstimatorResult (class in propertyestimator.client)
PropertyEstimatorServer (class in propertyestimator.server)
PropertyEstimatorServer.ServerEstimationRequest (class in propertyestimator.server)
PropertyEstimatorStorage (class in propertyestimator.storage)
PropertyEstimatorSubmission (class in propertyestimator.client)
PropertyPhase (class in propertyestimator.properties)
protocol_input (in module propertyestimator.workflow.decorators)
protocol_output (in module propertyestimator.workflow.decorators)
protocol_path() (propertyestimator.workflow.utils.ProtocolPath property)
ProtocolGroup (class in propertyestimator.protocols.groups)
ProtocolGroupSchema (class in propertyestimator.workflow.schemas)
ProtocolPath (class in propertyestimator.workflow.utils)
ProtocolReplicator (class in propertyestimator.workflow.schemas)
protocols() (propertyestimator.protocols.groups.ConditionalGroup property)
(propertyestimator.protocols.groups.ProtocolGroup property)
ProtocolSchema (class in propertyestimator.workflow.schemas)
provenance (propertyestimator.properties.CalculationSource attribute)
(propertyestimator.storage.dataclasses.BaseStoredData attribute)
Q
queued_properties (propertyestimator.client.PropertyEstimatorResult attribute)
QueueWorkerResources (class in propertyestimator.backends)
QueueWorkerResources.GPUToolkit (class in propertyestimator.backends)
R
receptor_coordinate_file (propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
receptor_residue_name (propertyestimator.protocols.coordinates.BuildDockedCoordinates attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
reduced_reference_potential() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
reduced_target_potential() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
reference (propertyestimator.properties.MeasurementSource attribute)
reference_force_field_paths (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
reference_potential_paths (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
reference_reduced_potentials (propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
reference_statistics_path (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
register_calculation_layer() (in module propertyestimator.layers)
register_thermoml_property() (in module propertyestimator.datasets)
replace_protocol() (propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.workflow.protocols.BaseProtocol method)
(propertyestimator.workflow.utils.ProtocolPath method)
(propertyestimator.workflow.Workflow method)
replace_protocol_types() (propertyestimator.workflow.schemas.WorkflowSchema method)
ReplicatorValue (class in propertyestimator.workflow.utils)
request_estimate() (propertyestimator.client.PropertyEstimatorClient method)
request_url() (propertyestimator.forcefield.LigParGenForceFieldSource property)
required_effective_samples (propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
restraint_type (propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
result (propertyestimator.protocols.miscellaneous.AddValues attribute)
(propertyestimator.protocols.miscellaneous.DivideValue attribute)
(propertyestimator.protocols.miscellaneous.MultiplyValue attribute)
(propertyestimator.protocols.miscellaneous.SubtractValues attribute)
results() (propertyestimator.client.PropertyEstimatorClient.Request method)
retain_packmol_files (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
retrieve_force_field() (propertyestimator.storage.LocalFileStorage method)
(propertyestimator.storage.PropertyEstimatorStorage method)
retrieve_simulation_data() (propertyestimator.storage.LocalFileStorage method)
(propertyestimator.storage.PropertyEstimatorStorage method)
retrieve_simulation_data_by_id() (propertyestimator.storage.LocalFileStorage method)
(propertyestimator.storage.PropertyEstimatorStorage method)
reverse_observable_value (propertyestimator.protocols.gradients.CentralDifferenceGradient attribute)
reverse_parameter_value (propertyestimator.protocols.gradients.CentralDifferenceGradient attribute)
(propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
reverse_potentials_path (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
ReweightingLayer (class in propertyestimator.layers)
ReweightStatistics (class in propertyestimator.protocols.reweighting)
role() (propertyestimator.substances.Substance.Component property)
root_directory() (propertyestimator.storage.LocalFileStorage property)
root_protocols() (propertyestimator.protocols.groups.ConditionalGroup property)
(propertyestimator.protocols.groups.ProtocolGroup property)
RunEnergyMinimisation (class in propertyestimator.protocols.simulation)
RunOpenMMSimulation (class in propertyestimator.protocols.simulation)
S
schedule_calculation() (propertyestimator.layers.PropertyCalculationLayer static method)
(propertyestimator.layers.ReweightingLayer static method)
(propertyestimator.layers.SimulationLayer static method)
schema() (propertyestimator.protocols.analysis.AveragePropertyProtocol property)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty property)
(propertyestimator.protocols.analysis.ExtractAverageStatistic property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData property)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData property)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol property)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates property)
(propertyestimator.protocols.coordinates.SolvateExistingStructure property)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem property)
(propertyestimator.protocols.forcefield.BuildTLeapSystem property)
(propertyestimator.protocols.gradients.CentralDifferenceGradient property)
(propertyestimator.protocols.gradients.GradientReducedPotentials property)
(propertyestimator.protocols.groups.ConditionalGroup property)
(propertyestimator.protocols.groups.ProtocolGroup property)
(propertyestimator.protocols.miscellaneous.AddValues property)
(propertyestimator.protocols.miscellaneous.DivideValue property)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole property)
(propertyestimator.protocols.miscellaneous.MultiplyValue property)
(propertyestimator.protocols.miscellaneous.SubtractValues property)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction property)
(propertyestimator.protocols.reweighting.BaseMBARProtocol property)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM property)
(propertyestimator.protocols.reweighting.ConcatenateStatistics property)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories property)
(propertyestimator.protocols.reweighting.ReweightStatistics property)
(propertyestimator.protocols.simulation.RunEnergyMinimisation property)
(propertyestimator.protocols.simulation.RunOpenMMSimulation property)
(propertyestimator.protocols.storage.UnpackStoredDataCollection property)
(propertyestimator.protocols.storage.UnpackStoredSimulationData property)
(propertyestimator.protocols.yank.BaseYankProtocol property)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol property)
(propertyestimator.protocols.yank.SolvationYankProtocol property)
(propertyestimator.workflow.protocols.BaseProtocol property)
server_address (propertyestimator.client.ConnectionOptions attribute)
server_address() (propertyestimator.client.PropertyEstimatorClient.Request property)
server_port (propertyestimator.client.ConnectionOptions attribute)
server_port() (propertyestimator.client.PropertyEstimatorClient.Request property)
set_uuid() (propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.workflow.protocols.BaseProtocol method)
set_value() (propertyestimator.properties.Density method)
(propertyestimator.properties.DielectricConstant method)
(propertyestimator.properties.EnthalpyOfMixing method)
(propertyestimator.properties.EnthalpyOfVaporization method)
(propertyestimator.properties.ExcessMolarVolume method)
(propertyestimator.properties.HostGuestBindingAffinity method)
(propertyestimator.properties.PhysicalProperty method)
(propertyestimator.protocols.analysis.AveragePropertyProtocol method)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty method)
(propertyestimator.protocols.analysis.ExtractAverageStatistic method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData method)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData method)
(propertyestimator.protocols.coordinates.BuildCoordinatesPackmol method)
(propertyestimator.protocols.coordinates.BuildDockedCoordinates method)
(propertyestimator.protocols.coordinates.SolvateExistingStructure method)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem method)
(propertyestimator.protocols.forcefield.BuildTLeapSystem method)
(propertyestimator.protocols.gradients.CentralDifferenceGradient method)
(propertyestimator.protocols.gradients.GradientReducedPotentials method)
(propertyestimator.protocols.groups.ConditionalGroup method)
(propertyestimator.protocols.groups.ProtocolGroup method)
(propertyestimator.protocols.miscellaneous.AddValues method)
(propertyestimator.protocols.miscellaneous.DivideValue method)
(propertyestimator.protocols.miscellaneous.FilterSubstanceByRole method)
(propertyestimator.protocols.miscellaneous.MultiplyValue method)
(propertyestimator.protocols.miscellaneous.SubtractValues method)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction method)
(propertyestimator.protocols.reweighting.BaseMBARProtocol method)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM method)
(propertyestimator.protocols.reweighting.ConcatenateStatistics method)
(propertyestimator.protocols.reweighting.ConcatenateTrajectories method)
(propertyestimator.protocols.reweighting.ReweightStatistics method)
(propertyestimator.protocols.simulation.RunEnergyMinimisation method)
(propertyestimator.protocols.simulation.RunOpenMMSimulation method)
(propertyestimator.protocols.storage.UnpackStoredDataCollection method)
(propertyestimator.protocols.storage.UnpackStoredSimulationData method)
(propertyestimator.protocols.yank.BaseYankProtocol method)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol method)
(propertyestimator.protocols.yank.SolvationYankProtocol method)
(propertyestimator.workflow.protocols.BaseProtocol method)
setup_only (propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
simulation_data_path (propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
SimulationLayer (class in propertyestimator.layers)
smiles() (propertyestimator.substances.Substance.Component property)
SmirnoffForceFieldSource (class in propertyestimator.forcefield)
solute (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
solute_coordinate_file (propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
solvated_complex_coordinates (propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
solvated_complex_system (propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
solvated_complex_trajectory_path (propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
solvated_ligand_coordinates (propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
solvated_ligand_system (propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
solvated_ligand_trajectory_path (propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
SolvateExistingStructure (class in propertyestimator.protocols.coordinates)
SolvationYankProtocol (class in propertyestimator.protocols.yank)
solvent_1 (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
solvent_1_coordinates (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
solvent_1_system (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
solvent_1_trajectory_path (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
solvent_2 (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
solvent_2_coordinates (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
solvent_2_system (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
solvent_2_trajectory_path (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
Source (class in propertyestimator.properties)
source_calculation_id (propertyestimator.storage.dataclasses.BaseStoredData attribute)
sources() (propertyestimator.datasets.PhysicalPropertyDataSet property)
(propertyestimator.datasets.ThermoMLDataSet property)
start() (propertyestimator.backends.BaseDaskBackend method)
(propertyestimator.backends.DaskLocalCluster method)
(propertyestimator.backends.DaskLSFBackend method)
(propertyestimator.backends.PropertyEstimatorBackend method)
(propertyestimator.server.PropertyEstimatorServer method)
start_listening_loop() (propertyestimator.server.PropertyEstimatorServer method)
start_protocol() (propertyestimator.workflow.utils.ProtocolPath property)
statistical_inefficiency (propertyestimator.protocols.analysis.AveragePropertyProtocol attribute)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
(propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedData attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedStatisticsData attribute)
(propertyestimator.protocols.analysis.ExtractUncorrelatedTrajectoryData attribute)
(propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.storage.dataclasses.StoredSimulationData attribute)
(propertyestimator.workflow.schemas.WorkflowSimulationDataToStore attribute)
statistics_file_name (propertyestimator.storage.dataclasses.StoredSimulationData attribute)
statistics_file_path (propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
(propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.workflow.schemas.WorkflowSimulationDataToStore attribute)
statistics_path (propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
statistics_paths (propertyestimator.protocols.reweighting.ReweightStatistics attribute)
statistics_type (propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
steps_per_iteration (propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
(propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
steric_lambdas_1 (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
steric_lambdas_2 (propertyestimator.protocols.yank.SolvationYankProtocol attribute)
stop() (propertyestimator.backends.BaseDaskBackend method)
(propertyestimator.backends.DaskLocalCluster method)
(propertyestimator.backends.DaskLSFBackend method)
(propertyestimator.backends.PropertyEstimatorBackend method)
(propertyestimator.server.PropertyEstimatorServer method)
store_force_field() (propertyestimator.storage.LocalFileStorage method)
(propertyestimator.storage.PropertyEstimatorStorage method)
store_simulation_data() (propertyestimator.storage.LocalFileStorage method)
(propertyestimator.storage.PropertyEstimatorStorage method)
StoredDataCollection (class in propertyestimator.storage.dataclasses)
StoredSimulationData (class in propertyestimator.storage.dataclasses)
submit() (propertyestimator.workflow.WorkflowGraph method)
submit_task() (propertyestimator.backends.BaseDaskBackend method)
(propertyestimator.backends.DaskLocalCluster method)
(propertyestimator.backends.DaskLSFBackend method)
(propertyestimator.backends.PropertyEstimatorBackend method)
Substance (class in propertyestimator.substances)
substance (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
(propertyestimator.protocols.forcefield.BuildSmirnoffSystem attribute)
(propertyestimator.protocols.forcefield.BuildTLeapSystem attribute)
(propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
(propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.storage.dataclasses.BaseStoredData attribute)
(propertyestimator.workflow.schemas.WorkflowOutputToStore attribute)
Substance.Amount (class in propertyestimator.substances)
Substance.Component (class in propertyestimator.substances)
Substance.ComponentRole (class in propertyestimator.substances)
Substance.ExactAmount (class in propertyestimator.substances)
Substance.MoleFraction (class in propertyestimator.substances)
SubtractValues (class in propertyestimator.protocols.miscellaneous)
system_path (propertyestimator.protocols.forcefield.BuildSmirnoffSystem attribute)
(propertyestimator.protocols.forcefield.BuildTLeapSystem attribute)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
(propertyestimator.protocols.simulation.RunEnergyMinimisation attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
T
target_reduced_potentials (propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
temperature (propertyestimator.thermodynamics.ThermodynamicState attribute)
temperature() (propertyestimator.properties.Density property)
(propertyestimator.properties.DielectricConstant property)
(propertyestimator.properties.EnthalpyOfMixing property)
(propertyestimator.properties.EnthalpyOfVaporization property)
(propertyestimator.properties.ExcessMolarVolume property)
(propertyestimator.properties.HostGuestBindingAffinity property)
(propertyestimator.properties.PhysicalProperty property)
thermodynamic_state (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
(propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
(propertyestimator.storage.dataclasses.BaseStoredData attribute)
ThermodynamicState (class in propertyestimator.thermodynamics)
ThermoMLDataSet (class in propertyestimator.datasets)
thermostat_friction (propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
timestep (propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
(propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
TLeapForceFieldSource (class in propertyestimator.forcefield)
to_components() (propertyestimator.workflow.utils.ProtocolPath static method)
to_force_field() (propertyestimator.forcefield.SmirnoffForceFieldSource method)
to_number_of_molecules() (propertyestimator.substances.Substance.Amount method)
(propertyestimator.substances.Substance.ExactAmount method)
(propertyestimator.substances.Substance.MoleFraction method)
to_pandas() (propertyestimator.datasets.PhysicalPropertyDataSet method)
(propertyestimator.datasets.ThermoMLDataSet method)
tolerance (propertyestimator.protocols.simulation.RunEnergyMinimisation attribute)
total_number_of_iterations (propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
total_number_of_molecules (propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.storage.dataclasses.StoredSimulationData attribute)
(propertyestimator.workflow.schemas.WorkflowSimulationDataToStore attribute)
trajectory_file_name (propertyestimator.storage.dataclasses.StoredSimulationData attribute)
trajectory_file_path (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
(propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
(propertyestimator.protocols.simulation.RunOpenMMSimulation attribute)
(propertyestimator.protocols.storage.UnpackStoredSimulationData attribute)
(propertyestimator.workflow.schemas.WorkflowSimulationDataToStore attribute)
trajectory_path (propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
U
uncorrelated_values (propertyestimator.protocols.analysis.AveragePropertyProtocol attribute)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
(propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
unpack_stored_data() (propertyestimator.protocols.utils.BaseReweightingProtocols property)
UnpackStoredDataCollection (class in propertyestimator.protocols.storage)
UnpackStoredSimulationData (class in propertyestimator.protocols.storage)
unsuccessful_properties (propertyestimator.client.PropertyEstimatorResult attribute)
update_references() (propertyestimator.workflow.schemas.ProtocolReplicator method)
use_internal_energy (propertyestimator.protocols.reweighting.CalculateReducedPotentialOpenMM attribute)
use_subset_of_force_field (propertyestimator.protocols.gradients.GradientReducedPotentials attribute)
V
validate_interfaces() (propertyestimator.workflow.schemas.WorkflowSchema method)
value (propertyestimator.protocols.analysis.AveragePropertyProtocol attribute)
(propertyestimator.protocols.analysis.AverageTrajectoryProperty attribute)
(propertyestimator.protocols.analysis.ExtractAverageStatistic attribute)
(propertyestimator.protocols.miscellaneous.DivideValue attribute)
(propertyestimator.protocols.miscellaneous.MultiplyValue attribute)
(propertyestimator.protocols.miscellaneous.WeightByMoleFraction attribute)
(propertyestimator.protocols.reweighting.BaseMBARProtocol attribute)
(propertyestimator.protocols.reweighting.ReweightStatistics attribute)
value() (propertyestimator.substances.Substance.Amount property)
(propertyestimator.substances.Substance.ExactAmount property)
(propertyestimator.substances.Substance.MoleFraction property)
value_a (propertyestimator.protocols.miscellaneous.SubtractValues attribute)
value_b (propertyestimator.protocols.miscellaneous.SubtractValues attribute)
values (propertyestimator.protocols.miscellaneous.AddValues attribute)
verbose (propertyestimator.protocols.yank.BaseYankProtocol attribute)
(propertyestimator.protocols.yank.LigandReceptorYankProtocol attribute)
(propertyestimator.protocols.yank.SolvationYankProtocol attribute)
verbose_packmol (propertyestimator.protocols.coordinates.BuildCoordinatesPackmol attribute)
(propertyestimator.protocols.coordinates.SolvateExistingStructure attribute)
W
wallclock_time_limit() (propertyestimator.backends.QueueWorkerResources property)
water_model (propertyestimator.protocols.forcefield.BuildSmirnoffSystem attribute)
(propertyestimator.protocols.forcefield.BuildTLeapSystem attribute)
WeightByMoleFraction (class in propertyestimator.protocols.miscellaneous)
weighted_value (propertyestimator.protocols.miscellaneous.WeightByMoleFraction attribute)
Workflow (class in propertyestimator.workflow)
workflow_options (propertyestimator.client.PropertyEstimatorOptions attribute)
workflow_schemas (propertyestimator.client.PropertyEstimatorOptions attribute)
WorkflowDataCollectionToStore (class in propertyestimator.workflow.schemas)
WorkflowGraph (class in propertyestimator.workflow)
WorkflowOptions (class in propertyestimator.workflow)
WorkflowOptions.ConvergenceMode (class in propertyestimator.workflow)
WorkflowOutputToStore (class in propertyestimator.workflow.schemas)
WorkflowSchema (class in propertyestimator.workflow.schemas)
WorkflowSimulationDataToStore (class in propertyestimator.workflow.schemas)
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