class openfe.protocols.openmm_rfe.equil_rfe_methods.HybridTopologyMultiStateSimulationUnit(*, name: str | None = None, **inputs)

Create an instance of a ProtocolUnit.

Parameters:

• name (str) – Custom name to give this

• **inputs – Keyword arguments, which can include other ProtocolUnit`s on which this `ProtocolUnit is dependent. Should be either gufe objects or JSON-serializables.

run(*, system: System, positions: Quantity, selection_indices: ndarray[tuple[Any, ...], dtype[_ScalarT]], dry: bool = False, verbose: bool = True, scratch_basepath: Path | None = None, shared_basepath: Path | None = None) → dict[str, Any]

Run the free energy calculation using a multistate sampler.

Parameters:

• system (openmm.System) – The System to simulate.

• positions (openmm.unit.Quantity) – The positions of the System.

• selection_indices (npt.NDArray) – Indices of the System particles to write to file.

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

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

• scratch_basepath (pathlib.Path | None) – Where to store temporary files, defaults to current working directory

• shared_basepath (pathlib.Path | None) – Where to run the calculation, defaults to current working directory

Returns:

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

Return type:

dict

Raises:

error – Exception if anything failed

property dependencies: list[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.