class openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationSolventUnit(*, protocol: gufe.Protocol, stateA: ChemicalSystem, stateB: ChemicalSystem, alchemical_components: dict[str, list[Component]], generation: int = 0, repeat_id: int = 0, name: str | None = None)#

Protocol Unit for the solvent phase of an absolute solvation free energy

Parameters:

  • protocol (gufe.Protocol) – protocol used to create this Unit. Contains key information such as the settings.

  • stateA (ChemicalSystem) – ChemicalSystem containing the components defining the state at lambda 0.

  • stateB (ChemicalSystem) – ChemicalSystem containing the components defining the state at lambda 1.

  • alchemical_components (dict[str, Component]) – the alchemical components for each state in this Unit

  • name (str, optional) – Human-readable identifier for this Unit

  • repeat_id (int, optional) – Identifier for which repeat (aka replica/clone) this Unit is, default 0

  • generation (int, optional) – Generation counter which keeps track of how many times this repeat has been extended, default 0.

property dependencies: list[gufe.protocols.protocolunit.ProtocolUnit]#

All units that this unit is dependent on (parents)

execute(*, context: Context, raise_error: bool = False, **inputs) → ProtocolUnitResult | ProtocolUnitFailure#

Given ProtocolUnitResult s from dependencies, execute this ProtocolUnit.

Parameters:

  • context (Context) – Execution context for this ProtocolUnit; includes e.g. shared and scratch Path s.

  • raise_error (bool) – If True, raise any errors instead of catching and returning a ProtocolUnitFailure default False

  • **inputs – Keyword arguments giving the named inputs to _execute. These can include ProtocolUnitResult objects from ProtocolUnit objects this unit is dependent on.

property inputs: Dict[str, Any]#

Inputs to the ProtocolUnit.

Includes any ProtocolUnit instances this ProtocolUnit depends on.

property name: str | None#

Optional name for the ProtocolUnit.

run(dry=False, verbose=True, scratch_basepath=None, shared_basepath=None) → dict[str, Any]#

Run the absolute free energy calculation.

Parameters:

  • dry (bool) – Do a dry run of the calculation, creating all necessary alchemical system components (topology, system, sampler, etc…) but without running the simulation, default False

  • verbose (bool) – Verbose output of the simulation progress. Output is provided via INFO level logging, default True

  • scratch_basepath (pathlib.Path) – Path to the scratch (temporary) directory space.

  • shared_basepath (pathlib.Path) – Path to the shared (persistent) directory space.

Returns:

Outputs created in the basepath directory or the debug objects (i.e. sampler) if dry==True.

Return type:

dict