class openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexRunUnit(*, name: str | None = None, **inputs)#

Protocol Unit for the complex phase of an relative SepTop free energy

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.

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. shared and scratch Path 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.

property inputs: dict[str, Any]#

Inputs to the ProtocolUnit.

Includes any ProtocolUnit instances this ProtocolUnit depends on.

property name: str | None#

Optional name for the ProtocolUnit.

run(serialized_system, serialized_topology, dry=False, verbose=True, scratch_basepath=None, shared_basepath=None) → dict[str, Any]#

Run the simulation part of the SepTop protocol.

Parameters:

  • serialized_system (pathlib.Path) – Path to the serialized OpenMM system

  • serialized_topology (pathlib.Path) – Path to the serialized topology of the system

  • dry (bool) – Do a dry run of the calculation, creating all necessary alchemical system components (topology, system, sampler, etc…) but without running the simulation, default False

  • verbose (bool) – Verbose output of the simulation progress. Output is provided via INFO level logging, default True

  • scratch_basepath (pathlib.Path) – Path to the scratch (temporary) directory space.

  • shared_basepath (pathlib.Path) – Path to the shared (persistent) directory space.

Returns:

dict – Dictionary of the outputs created in the basepath directory (e.g. path to the simulation .nc file, checkpoint file) or the sampler if dry==True.

Return type:

dict[str, Any]