perses.rjmc.topology_proposal.SystemGenerator

class perses.rjmc.topology_proposal.SystemGenerator(forcefields_to_use, forcefield_kwargs=None, metadata=None, use_antechamber=True, barostat=None)

This is a utility class to generate OpenMM Systems from topology objects.

Parameters:

forcefields_to_use : list of string

List of the names of ffxml files that will be used in system creation.

forcefield_kwargs : dict of arguments to createSystem, optional

Allows specification of various aspects of system creation.

metadata : dict, optional

Metadata associated with the SystemGenerator.

use_antechamber : bool, optional, default=True

If True, will add the GAFF residue template generator.

barostat : MonteCarloBarostat, optional, default=None

If provided, a matching barostat will be added to the generated system.

Attributes:

ffxmls

forcefield

Methods

build_system(new_topology)	Build a system from the new_topology, adding templates for the molecules in oemol_list
getForceField()	Return the associated ForceField object.

__init__(forcefields_to_use, forcefield_kwargs=None, metadata=None, use_antechamber=True, barostat=None)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(forcefields_to_use[, …])	Initialize self.
build_system(new_topology)	Build a system from the new_topology, adding templates for the molecules in oemol_list
getForceField()	Return the associated ForceField object.

Attributes

ffxmls
forcefield

build_system(new_topology)

Build a system from the new_topology, adding templates for the molecules in oemol_list

Parameters:

new_topology : simtk.openmm.app.Topology object

The topology of the system

Returns:

new_system : openmm.System

A system object generated from the topology

getForceField()

Return the associated ForceField object.

Returns:

forcefield : simtk.openmm.app.ForceField

The current ForceField object.