class openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolUnit(*, protocol: RelativeHybridTopologyProtocol, stateA: ChemicalSystem, stateB: ChemicalSystem, ligandmapping: LigandAtomMapping, generation: int, repeat_id: int, name: str | None = None)

Calculates the relative free energy of an alchemical ligand transformation.

Parameters:

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

• stateA (ChemicalSystem) – the two ligand SmallMoleculeComponents to transform between. The transformation will go from ligandA to ligandB.

• stateB (ChemicalSystem) – the two ligand SmallMoleculeComponents to transform between. The transformation will go from ligandA to ligandB.

• ligandmapping (LigandAtomMapping) – the mapping of atoms between the two ligand components

• repeat_id (int) – identifier for which repeat (aka replica/clone) this Unit is

• generation (int) – counter for how many times this repeat has been extended

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

Notes

The mapping used must not involve any elemental changes. A check for this is done on class creation.

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

Run the relative free energy calculation.

Parameters:

• 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 (Pathlike, optional) – Where to store temporary files, defaults to current working directory

• shared_basepath (Pathlike, optional) – 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

static analyse(where) → dict

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.