ASFEVacuumSetupUnit#

class pontibus.protocols.solvation.ASFEVacuumSetupUnit(*, name: str | None = None, **inputs)#

Protocol Unit for setting up the vacuum phase of an absolute solvation free energy 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.

Attributes

simtype

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(dry: bool = False, verbose: bool = True, scratch_basepath: Path | None = None, shared_basepath: Path | None = None) → dict[str, Any]#

Run the setup phase of an absolute free energy calculation.

Parameters:

  • dry (bool) – Do a dry run of the calculation, creating all necessary alchemical system components (topology, system, 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 | None) – Path to the scratch (temporary) directory space. Defaults to the current working directory if None.

  • shared_basepath (pathlib.Path | None) – Path to the shared (persistent) directory space. Defaults to the current working directory if None.

Returns:

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

Return type:

dict

simtype: str = 'vacuum'#