TransformationBase

class gufe.transformations.transformation.TransformationBase(protocol: Protocol, name: str | None = None)

Transformation base class.

Parameters:

• protocol (Protocol) – The sampling method to use for the transformation.

• name (str, optional) – A human-readable name for this transformation.

Methods

create	Returns a ProtocolDAG executing this Transformation.protocol.
dump	Dump this Transformation to a JSON file.
gather	Gather multiple ProtocolDAGResult s into a single ProtocolResult.
load	Create a Transformation from a JSON file.

Attributes

name	Optional identifier for the transformation; used as part of its hash.
protocol	The Protocol used to perform the transformation.
stateA	The starting ChemicalSystem for the transformation.
stateB	The ending ChemicalSystem for the transformation.

abstract create(*, extends: ProtocolDAGResult | None = None, name: str | None = None) → ProtocolDAG

Returns a ProtocolDAG executing this Transformation.protocol.

dump(file)

Dump this Transformation to a JSON file.

Note that this is not space-efficient: for example, any Component which is used in both ChemicalSystem objects will be represented twice in the JSON output.

Parameters:

file (Union[PathLike, FileLike]) – A pathlike of filelike to save this transformation to.

gather(protocol_dag_results: Iterable[ProtocolDAGResult]) → ProtocolResult

Gather multiple ProtocolDAGResult s into a single ProtocolResult.

Parameters:

protocol_dag_results (Iterable[ProtocolDAGResult]) – The ProtocolDAGResult objects to assemble aggregate quantities from.

Returns:

Aggregated results from many ProtocolDAGResult objects, all from a given Protocol.

Return type:

ProtocolResult

classmethod load(file)

Create a Transformation from a JSON file.

Parameters:

file (Union[PathLike, FileLike]) – A pathlike or filelike to read this transformation from.

property name: str | None

Optional identifier for the transformation; used as part of its hash.

Set this to a unique value if adding multiple, otherwise identical transformations to the same AlchemicalNetwork to avoid deduplication.

property protocol: Protocol

The Protocol used to perform the transformation.

The protocol estimates the free energy differences between stateA and stateB ChemicalSystem objects. It includes all details needed to perform required simulations/calculations and encodes the alchemical or non-alchemical pathway used.

abstract property stateA: ChemicalSystem

The starting ChemicalSystem for the transformation.

abstract property stateB: ChemicalSystem

The ending ChemicalSystem for the transformation.