ForceField

class simtk.openmm.app.forcefield.ForceField(*files)

A ForceField constructs OpenMM System objects based on a Topology.

__init__(*files)

Load one or more XML files and create a ForceField object based on them.

Parameters:files (list) – A list of XML files defining the force field. Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module’s data subdirectory (for built in force fields), or an open file-like object with a read() method from which the forcefield XML data can be loaded.

Methods

__init__(*files) Load one or more XML files and create a ForceField object based on them.
createSystem(topology[, nonbondedMethod, ...]) Construct an OpenMM System representing a Topology with this force field.
generateTemplatesForUnmatchedResidues(topology) Generate forcefield residue templates for residues in specified topology for which no forcefield templates are available.
getGenerators() Get the list of all registered generators.
getMatchingTemplates(topology[, ...]) Return a list of forcefield residue templates matching residues in the specified topology.
getUnmatchedResidues(topology) Return a list of Residue objects from specified topology for which no forcefield templates are available.
loadFile(files) Load an XML file and add the definitions from it to this ForceField.
registerAtomType(parameters) Register a new atom type.
registerGenerator(generator) Register a new generator.
registerPatch(patch) Register a new patch that can be applied to templates.
registerResidueTemplate(template) Register a new residue template.
registerScript(script) Register a new script to be executed after building the System.
registerTemplateGenerator(generator) Register a residue template generator that can be used to parameterize residues that do not match existing forcefield templates.
registerTemplatePatch(residue, patch, ...) Register that a particular patch can be used with a particular residue.
loadFile(files)

Load an XML file and add the definitions from it to this ForceField.

Parameters:files (string or file or tuple) – An XML file or tuple of XML files containing force field definitions. Each entry may be either an absolute file path, a path relative to the current working directory, a path relative to this module’s data subdirectory (for built in force fields), or an open file-like object with a read() method from which the forcefield XML data can be loaded.
getGenerators()

Get the list of all registered generators.

registerGenerator(generator)

Register a new generator.

registerAtomType(parameters)

Register a new atom type.

registerResidueTemplate(template)

Register a new residue template.

registerPatch(patch)

Register a new patch that can be applied to templates.

registerTemplatePatch(residue, patch, patchResidueIndex)

Register that a particular patch can be used with a particular residue.

registerScript(script)

Register a new script to be executed after building the System.

registerTemplateGenerator(generator)

Register a residue template generator that can be used to parameterize residues that do not match existing forcefield templates.

This functionality can be used to add handlers to parameterize small molecules or unnatural/modified residues.

Caution

This method is experimental, and its API is subject to change.

Parameters:
  • generator (function) – A function that will be called when a residue is encountered that does not match an existing forcefield template.
  • a residue without a template is encountered, the generator function is called with (When) –

:param ::: success = generator(forcefield, residue) :param where forcefield is the calling ForceField object and residue is a simtk.openmm.app.topology.Residue object.: :param generator must conform to the following API: :param ::: generator API

param forcefield:
 

The ForceField object to which residue templates and/or parameters are to be added.

type forcefield:
 

simtk.openmm.app.ForceField

param residue:

The residue topology for which a template is to be generated.

type residue:

simtk.openmm.app.Topology.Residue

returns:
  • success (bool) – If the generator is able to successfully parameterize the residue, True is returned. If the generator cannot parameterize the residue, it should return False and not modify forcefield.
  • The generator should either register a residue template directly with forcefield.registerResidueTemplate(template)
  • or it should call forcefield.loadFile(file) to load residue definitions from an ffxml file.
  • It can also use the ForceField programmatic API to add additional atom types (via forcefield.registerAtomType(parameters))
  • or additional parameters.
getUnmatchedResidues(topology)

Return a list of Residue objects from specified topology for which no forcefield templates are available.

Caution

This method is experimental, and its API is subject to change.

Parameters:topology (Topology) – The Topology whose residues are to be checked against the forcefield residue templates.
Returns:
  • unmatched_residues (list of Residue) – List of Residue objects from topology for which no forcefield residue templates are available. Note that multiple instances of the same residue appearing at different points in the topology may be returned.
  • This method may be of use in generating missing residue templates or diagnosing parameterization failures.
getMatchingTemplates(topology, ignoreExternalBonds=False)

Return a list of forcefield residue templates matching residues in the specified topology.

Caution

This method is experimental, and its API is subject to change.

Parameters:
  • topology (Topology) – The Topology whose residues are to be checked against the forcefield residue templates.
  • ignoreExternalBonds (bool=False) – If true, ignore external bonds when matching residues to templates.
Returns:

  • templates (list of _TemplateData) – List of forcefield residue templates corresponding to residues in the topology. templates[index] is template corresponding to residue index in topology.residues()
  • This method may be of use in debugging issues related to parameter assignment.

generateTemplatesForUnmatchedResidues(topology)

Generate forcefield residue templates for residues in specified topology for which no forcefield templates are available.

Caution

This method is experimental, and its API is subject to change.

Parameters:topology (Topology) – The Topology whose residues are to be checked against the forcefield residue templates.
Returns:
  • templates (list of _TemplateData) – List of forcefield residue templates corresponding to residues in topology for which no forcefield templates are currently available. Atom types will be set to None, but template name, atom names, elements, and connectivity will be taken from corresponding Residue objects.
  • residues (list of Residue) – List of Residue objects that were used to generate the templates. residues[index] is the Residue that was used to generate the template templates[index]
createSystem(topology, nonbondedMethod=NoCutoff, nonbondedCutoff=Quantity(value=1.0, unit=nanometer), constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, residueTemplates={}, ignoreExternalBonds=False, switchDistance=None, flexibleConstraints=False, **args)

Construct an OpenMM System representing a Topology with this force field.

Parameters:
  • topology (Topology) – The Topology for which to create a System
  • nonbondedMethod (object=NoCutoff) – The method to use for nonbonded interactions. Allowed values are NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
  • nonbondedCutoff (distance=1*nanometer) – The cutoff distance to use for nonbonded interactions
  • constraints (object=None) – Specifies which bonds and angles should be implemented with constraints. Allowed values are None, HBonds, AllBonds, or HAngles.
  • rigidWater (boolean=True) – If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
  • removeCMMotion (boolean=True) – If true, a CMMotionRemover will be added to the System
  • hydrogenMass (mass=None) – The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same.
  • residueTemplates (dict=dict()) – Key: Topology Residue object Value: string, name of _TemplateData residue template object to use for (Key) residue. This allows user to specify which template to apply to particular Residues in the event that multiple matching templates are available (e.g Fe2+ and Fe3+ templates in the ForceField for a monoatomic iron ion in the topology).
  • ignoreExternalBonds (boolean=False) – If true, ignore external bonds when matching residues to templates. This is useful when the Topology represents one piece of a larger molecule, so chains are not terminated properly. This option can create ambiguities where multiple templates match the same residue. If that happens, use the residueTemplates argument to specify which one to use.
  • switchDistance (float=None) – The distance at which the potential energy switching function is turned on for Lennard-Jones interactions. If this is None, no switching function will be used.
  • flexibleConstraints (boolean=False) – If True, parameters for constrained degrees of freedom will be added to the System
  • args – Arbitrary additional keyword arguments may also be specified. This allows extra parameters to be specified that are specific to particular force fields.
Returns:

the newly created System

Return type:

system

__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__
__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__