API¶
A set of API documents for this projects classes and modules.
Client Side API¶
The PropertyEstimatorClient is the main object that users of the property estimator will interface with. |
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Represents the options options that can be passed to the property estimation server backend. |
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Represents a set of properties to be estimated by the server backend, the parameters which will be used to estimate them, and options about how the properties will be estimated. |
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Represents the results of attempting to estimate a set of physical properties using the property estimator server backend. |
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The set of options to use when connecting to a PropertyEstimatorServer |
Force Field Sources
A helper object to define the source of a force field and any associated meta data, such as version, file paths, or generation options. |
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A wrapper around force fields based on the SMIRks Native Open Force Field (SMIRNOFF) specification. |
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A wrapper around Amber force fields which may be applied via the tleap software package. |
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A wrapper and the OPLSAAM force field which can be applied via the LigParGen server. |
Gradient Estimation
Server Side API¶
The object responsible for coordinating all properties estimations to to be ran using the property estimator, in addition to deciding at which fidelity a property will be calculated. |
Physical Property API¶
Represents the value of any physical property and it’s uncertainty. |
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An enum describing the phase a property was collected in. |
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Container class for information about how a property was measured / calculated. |
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Contains any metadata about how a physical property was measured by experiment. |
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Contains any metadata about how a physical property was calculated. |
Built-in Properties
A class representation of a density property |
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A class representation of an excess molar volume property |
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A class representation of a dielectric property |
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A class representation of an enthalpy of mixing property |
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A class representation of an enthalpy of vaporization property |
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A class representation of a host-guest binding affinity property |
Substance Definition
Defines the components, their amounts, and their roles in a system. |
State Definition
Data specifying a physical thermodynamic state obeying Boltzmann statistics. |
Metadata
An enum describing the phase a property was collected in. |
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Container class for information about how a property was measured / calculated. |
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Contains any metadata about how a physical property was measured by experiment. |
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Contains any metadata about how a physical property was calculated. |
Data Set API¶
An object for storing and curating data sets of both physical property measurements and estimated. |
NIST ThermoML Archive
A dataset of physical property measurements created from a ThermoML dataset. |
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A decorator which registers information on how to parse a given ThermoML property |
Calculation Layers API¶
An abstract representation of a calculation layer whose goal is to estimate a set of physical properties using a single approach, such as a layer which employs direct simulations to estimate properties, or one which reweights cached simulation data to the same end. |
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A decorator which registers a class as being a calculation layer which may be used in property calculations. |
Built-in Calculation Layers
A calculation layer which aims to calculate physical properties by reweighting the results of previous calculations. |
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A calculation layer which aims to calculate physical properties directly from molecular simulation. |
Calculation Backends API¶
An abstract base representation of a property estimator backend. |
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An object which stores how many of each type of computational resource (threads or gpu’s) is available to a calculation worker. |
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An extended resource object with properties specific to calculations which will run on queue based resources, such as LSF, PBS or SLURM. |
Dask Backends
A base dask backend class, which implements functionality which is common to all other dask based backends. |
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A property estimator backend which uses a dask LocalCluster object to run calculations on a single machine. |
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A property estimator backend which uses a dask_jobqueue.LSFCluster object to run calculations within an existing LSF queue. |
Storage Backends API¶
An abstract base representation of how the property estimator will interact with and store simulation data. |
Built-in Storage Backends
A storage backend which stores files in directories on the local disk. |
Data Classes
A base representation of cached data to be stored by a storage backend. |
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A representation of data which has been cached from a single previous simulation. |
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A collection of stored StoredSimulationData objects, all generated at the same state and using the same force field parameters. |
Workflow API¶
Encapsulates and prepares a workflow which is able to estimate a physical property. |
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A hierarchical structure for storing and submitting the workflows which will estimate a set of physical properties.. |
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A set of convenience options used when creating estimation workflows. |
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Defines the interface a property must implement to be estimable by a workflow. |
Schema
Outlines the workflow which should be followed when calculating a certain property. |
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A json serializable representation of a workflow protocol. |
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A json serializable representation of a workflow protocol group. |
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A protocol replicator contains the information necessary to replicate parts of a property estimation workflow. |
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An object which describes which data should be cached after a workflow has finished executing, and from which completed protocols should the data be collected from. |
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An object which describes which data should be cached after a workflow has finished executing, and from which completed protocols should the data be collected from. |
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An object which describes which data should be cached after a workflow has finished executing, and from which completed protocols should the data be collected from. |
Base Protocol API
The base class for a protocol which would form one step of a larger property calculation workflow. |
Input / Output Utilities
A class to act as a place holder for a protocols input value, for when the value of an input is not known a priori, and does not come from another protocol. |
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A placeholder value which will be set by a protocol replicator with the specified id. |
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Represents a pointer to the output of another protocol. |
Decorators
alias of |
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alias of |
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A custom descriptor used to mark class attributes as being either a required input, or provided output of a protocol. |
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A enum which describes how attributes should be handled when attempting to merge similar protocols. |
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A enum which describes how attributes which can be compared with inequalities should be merged. |
Built-in Workflow Protocols¶
Coordinate Generation
Creates a set of 3D coordinates with a specified composition using the PACKMOL package. |
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Solvates a set of 3D coordinates with a specified solvent using the PACKMOL package. |
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Creates a set of coordinates for a ligand bound to some receptor. |
Force Field Assignment
Parametrise a set of molecules with a given smirnoff force field using the OpenFF toolkit. |
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Parametrise a set of molecules with an Amber based force field. |
Simulation
A protocol to minimise the potential energy of a system. |
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Performs a molecular dynamics simulation in a given ensemble using an OpenMM backend. |
YANK Free Energies
An abstract base class for protocols which will performs a set of alchemical free energy simulations using the YANK framework. |
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A protocol for performing ligand-receptor alchemical free energy calculations using the YANK framework. |
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A protocol for performing solvation alchemical free energy calculations using the YANK framework. |
Simulation Analysis
An abstract base class for protocols which will calculate the average of a property and its uncertainty via bootstrapping. |
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An abstract base class for protocols which will calculate the average of a property from a simulation trajectory. |
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Extracts the average value from a statistics file which was generated during a simulation. |
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An abstract base class for protocols which will subsample a data set, yielding only equilibrated, uncorrelated data. |
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A protocol which will subsample frames from a trajectory, yielding only uncorrelated frames as determined from a provided statistical inefficiency and equilibration time. |
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A protocol which will subsample entries from a statistics array, yielding only uncorrelated entries as determined from a provided statistical inefficiency and equilibration time. |
Reweighting
A protocol which concatenates multiple trajectories into a single one. |
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A protocol which concatenates multiple trajectories into a single one. |
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Calculates the reduced potential for a given set of configurations. |
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Reweights a set of observables using MBAR to calculate the average value of the observables at a different state than they were originally measured. |
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Reweights a set of observables from a StatisticsArray using MBAR. |
Gradients
A protocol to estimates the the reduced potential of the configurations of a trajectory using reverse and forward perturbed simulation parameters for use with estimating reweighted gradients using the central difference method. |
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A protocol which employs the central diference method to estimate the gradient of an observable A, such that |
Groups
A collection of protocols to be executed in one batch. |
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A collection of protocols which are to execute until a given condition is met. |
Storage
Loads a StoredDataCollection object from disk, and makes its inner data objects easily accessible to other protocols. |
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Loads a StoredSimulationData object from disk, and makes its attributes easily accessible to other protocols. |
Miscellaneous
A protocol to add together a list of values. |
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A protocol to subtract one value from another such that: |
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A protocol which multiplies a value by a specified scalar |
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A protocol which divides a value by a specified scalar |
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A protocol which takes a substance as input, and returns a substance which only contains components whose role match a given criteria. |
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Multiplies a value by the mole fraction of a component in a Substance. |
Workflow Construction Utilities¶
Constructs a set of protocols which, when combined in a workflow schema, may be executed to reweight a set of existing data to estimate a particular property. |
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Constructs a set of protocols which, when combined in a workflow schema, may be executed to run a single simulation to estimate a particular property. |
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Constructs a set of protocols which, when combined in a workflow schema, may be executed to reweight a set of existing data to estimate a particular property. |