- class openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol(settings: Settings)#
Create a new
settings (Settings) – The full settings for this
- create(*, stateA: ChemicalSystem, stateB: ChemicalSystem, mapping: dict[str, gufe.mapping.componentmapping.ComponentMapping] | None, extends: ProtocolDAGResult | None = None, name: str | None = None, transformation_key: GufeKey | None = None) ProtocolDAG #
Prepare a ProtocolDAG with all information required for execution.
A ProtocolDAG is composed of ProtocolUnit`s, with dependencies established between them. These form a directed, acyclic graph, and each `ProtocolUnit can be executed once its dependencies have completed.
A ProtocolDAG can be passed to a Scheduler for execution on its resources. A ProtocolDAGResult can be retrieved from the Scheduler upon completion of all ProtocolUnit`s in the `ProtocolDAG.
stateA (ChemicalSystem) – The starting ChemicalSystem for the transformation.
stateB (ChemicalSystem) – The ending ChemicalSystem for the transformation.
- Mappings of e.g. atoms between a labelled component in the
stateA and stateB ChemicalSystem .
extends (Optional[ProtocolDAGResult]) – If provided, then the ProtocolDAG produced will start from the end state of the given ProtocolDAGResult. This allows for extension from a previously-run ProtocolDAG.
name (Optional[str]) – A user supplied identifier for the resulting DAG
transformation_key (Optional[GufeKey]) – Key of the Transformation that this Protocol corresponds to, if applicable. This will be used to label the resulting ProtocolDAG, and can be used for identifying its source. This label will be passed on to the ProtocolDAGResult resulting from execution of this ProtocolDAG.
A directed, acyclic graph that can be executed by a Scheduler.
- Return type:
- classmethod default_settings() Settings #
Get the default settings for this Protocol.
These can be modified and passed in as the settings for a new Protocol instance.
- gather(protocol_dag_results: Iterable[ProtocolDAGResult]) ProtocolResult #
Gather multiple ProtocolDAGResults into a single ProtocolResult.