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.

Two chemical states with a method for estimating free energy difference

Connects two ChemicalSystem objects, with directionality, and relates this to a Protocol which will provide an estimate of the free energy difference of moving between these systems. Used as an edge of an AlchemicalNetwork.

Parameters:

• stateA (ChemicalSystem) – The start (A) and end (B) states of the transformation

• stateB (ChemicalSystem) – The start (A) and end (B) states of the transformation

• protocol (Protocol) – The method used to estimate the free energy difference between states A and B

• mapping (Optional[Union[ComponentMapping, list[ComponentMapping]]]) – the details of any transformations between Component s of the two states

• name (str, optional) – a human-readable tag for this transformation

Methods

create

Returns a ProtocolDAG executing this Transformation.protocol.

Attributes

protocol	The protocol for sampling dynamics of the ChemicalSystem.
stateA	The starting ChemicalSystem for the transformation.
stateB	The ending ChemicalSystem for the transformation.
system

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 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 mapping: ComponentMapping | list[ComponentMapping] | None

The mappings relevant for this Transformation

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

The protocol for sampling dynamics of the ChemicalSystem.

Includes all details needed to perform required simulations/calculations.

property stateA

The starting ChemicalSystem for the transformation.

property stateB

The ending ChemicalSystem for the transformation.

property system: ChemicalSystem