NonTransformation

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

A non-alchemical edge of an alchemical network.

A “transformation” that performs no transformation at all. Technically a self-loop, or an edge with the same ChemicalSystem at either end.

Functionally used for applying a dynamics protocol to a ChemicalSystem that performs no alchemical transformation at all. This allows e.g. equilibrium MD to be performed on a ChemicalSystem as desired alongside alchemical protocols between it and and other ChemicalSystem objects.

Parameters:

• system (ChemicalSystem) – The system to be sampled, acting as both the starting and end state of the NonTransformation.

• protocol (Protocol) – The sampling method to use on the system

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

Methods

create

Returns a ProtocolDAG executing this NonTransformation.protocol.

Attributes

stateA	The ChemicalSystem this NonTransformation samples.
stateB	The ChemicalSystem this NonTransformation samples.
system	The ChemicalSystem this "transformation" samples.

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

Returns a ProtocolDAG executing this NonTransformation.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.

property stateA: ChemicalSystem

The ChemicalSystem this NonTransformation samples.

Synonomous with system attribute and identical to stateB.

property stateB: ChemicalSystem

The ChemicalSystem this NonTransformation samples.

Synonomous with system attribute and identical to stateA.

property system: ChemicalSystem

The ChemicalSystem this “transformation” samples.