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

Protocol Unit for the analysis of the solvent phase of a 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.

simtype = 'solvent'#
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(*, trajectory: Path, checkpoint: Path, pdb_file: Path, ligand_A_indices: list[int], ligand_B_indices: list[int], smc_A: SmallMoleculeComponent, smc_B: SmallMoleculeComponent, dry: bool = False, verbose: bool = True, scratch_basepath: Path | None = None, shared_basepath: Path | None = None) → dict[str, Any]#

Analyze the multistate simulation.

Parameters:

  • trajectory (pathlib.Path) – Path to the MultiStateReporter generated NetCDF file.

  • checkpoint (pathlib.Path) – Path to the checkpoint file generated by MultiStateReporter.

  • pdb_file (pathlib.Path) – Path to the subsampled PDB file.

  • ligand_A_indices (list[int]) – Atom indices of ligand A in the subsampled system.

  • ligand_B_indices (list[int]) – Atom indices of ligand B in the subsampled system.

  • smc_A (SmallMoleculeComponent) – SmallMoleculeComponent for ligand A.

  • smc_B (SmallMoleculeComponent) – SmallMoleculeComponent for ligand B.

  • 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 in the basepath directory or the debug objects (i.e. sampler) if dry==True.

Return type:

dict