- class openfe.protocols.openmm_rfe.equil_rfe_methods.HybridTopologySetupUnit(*, name: str | None = None, **inputs)#
Calculates the relative free energy of an alchemical ligand transformation.
Create an instance of a ProtocolUnit.
- Parameters:
name (str) – Custom name to give this
**inputs – Keyword arguments, which can include other ProtocolUnit`s on which this `ProtocolUnit is dependent. Should be either gufe objects or JSON-serializables.
- run(*, dry: bool = False, verbose: bool = True, scratch_basepath: Path | None = None, shared_basepath: Path | None = None) dict[str, Any]#
Setup a hybrid topology system.
- 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 (pathlib.Path | None) – Where to store temporary files, defaults to current working directory
shared_basepath (pathlib.Path | None) – Where to run the calculation, defaults to current working directory
- Returns:
Outputs created by the setup unit or the debug objects (e.g. HybridTopologyFactory) if
dry==True.- Return type:
- Raises:
error – Exception if anything failed
- property dependencies: list[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.
sharedandscratchPath 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.