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

Protocol Unit for 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'

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

Run the SepTop free energy calculation.

Parameters:

• 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:

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

Return type:

dict

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.

static get_smc_comps(alchem_comps: dict[str, list[Component]], smc_comps: dict[SmallMoleculeComponent, Molecule]) → tuple[dict[SmallMoleculeComponent, Molecule], dict[SmallMoleculeComponent, Molecule], dict[SmallMoleculeComponent, Molecule]]

get_system(solv_comp: SolventComponent, prot_comp: ProteinComponent, smc_comp: dict[SmallMoleculeComponent, Molecule], settings: dict[str, SettingsBaseModel])

Creates an OpenMM system, topology, positions, modeller and also residue IDs of the different components

Parameters:

• solv_comp (SolventComponent) –

• prot_comp (Optional[ProteinComponent]) –

• smc_comp (dict[SmallMoleculeComponent,OFFMolecule]) –

• settings (dict[str, SettingsBaseModel]) – A dictionary of settings object for the unit.

Returns:

• omm_system (openmm.app.System)

• omm_topology (openmm.app.Topology)

• positions (openmm.unit.Quantity)

• system_modeller (openmm.app.Modeller)

• comp_resids (dict[Component, npt.NDArray]) – A dictionary of residues for each component in the System.

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.