openmmslicer.integrators module

The integrators module contains some commonly used integrators which are compatible with openmmslicer

class openmmslicer.integrators.AlchemicalEnergyEvaluator(*args: Any, **kwargs: Any)

Bases: openmmtools.integrators.openmmtools.integrators.LangevinIntegrator._name

A dummy integrator which is only used for energy evaluation of states at different lambda values.

Parameters

alchemical_functions (dict) –

A dictionary containing the desired alchemical functions. Default is: alchemical_functions = {

’lambda_sterics’: ‘min(lambda, 1)’, ‘lambda_electrostatics’: ‘min(lambda, 1)’, ‘lambda_torsions’: ‘min(lambda, 1)’,

}

Note that these must be overloaded if no alchemical torsions are needed.

getPotentialEnergyFromLambda(lambda_)

openmm.unit.Quantity: Returns the potential energy of the current state at a desired lambda value.

class openmmslicer.integrators.AlchemicalGeodesicBAOABIntegrator(*args: Any, **kwargs: Any)

Bases: openmmtools.integrators.openmmtools.integrators.GeodesicBAOABIntegrator._name

An alchemical version of the openmmtools.integrators.AlchemicalGeodesicBAOABIntegrator.

Parameters

• alchemical_functions (dict) –

  A dictionary containing the desired alchemical functions. Default is: alchemical_functions = {

  ’lambda_sterics’: ‘min(lambda, 1)’, ‘lambda_electrostatics’: ‘min(lambda, 1)’, ‘lambda_torsions’: ‘min(lambda, 1)’,

  }

  Note that these must be overloaded if no alchemical torsions are needed.

• initial_lambda (float) – The initial lambda value to instantiate the integrator. Default is 0.

• args – Positional arguments to be passed to openmmtools.integrators.AlchemicalGeodesicBAOABIntegrator.

• kwargs – Keyword arguments to be passed to openmmtools.integrators.AlchemicalGeodesicBAOABIntegrator.

class openmmslicer.integrators.AlchemicalLangevinIntegrator(*args: Any, **kwargs: Any)

Bases: openmmtools.integrators.openmmtools.integrators.LangevinIntegrator._name

An alchemical version of the openmmtools.integrators.LangevinIntegrator.

Parameters

• alchemical_functions (dict) –

  A dictionary containing the desired alchemical functions. Default is: alchemical_functions = {

  ’lambda_sterics’: ‘min(lambda, 1)’, ‘lambda_electrostatics’: ‘min(lambda, 1)’, ‘lambda_torsions’: ‘min(lambda, 1)’,

  }

  Note that these must be overloaded if no alchemical torsions are needed.

• initial_lambda (float) – The initial lambda value to instantiate the integrator. Default is 0.

• args – Positional arguments to be passed to openmmtools.integrators.LangevinIntegrator.

• kwargs – Keyword arguments to be passed to openmmtools.integrators.LangevinIntegrator.

openmmslicer.integrators.make_alchemical(cls)

A decorator which can be used to make integrators alchemical.