openforcefield.typing.engines.smirnoff.forcefield.ForceField¶

class openforcefield.typing.engines.smirnoff.forcefield.ForceField(*sources, parameter_handler_classes=None, parameter_io_handler_classes=None, disable_version_check=False, allow_cosmetic_attributes=False)[source]¶

A factory that assigns SMIRNOFF parameters to a molecular system

ForceField is a factory that constructs an OpenMM simtk.openmm.System object from a openforcefield.topology.Topology object defining a (bio)molecular system containing one or more molecules.

When a ForceField object is created from one or more specified SMIRNOFF serialized representations, all ParameterHandler subclasses currently imported are identified and registered to handle different sections of the SMIRNOFF force field definition file(s).

All ParameterIOHandler subclasses currently imported are identified and registered to handle different serialization formats (such as XML).

The force field definition is processed by these handlers to populate the ForceField object model data structures that can easily be manipulated via the API:

Processing a Topology object defining a chemical system will then call all :class`ParameterHandler` objects in an order guaranteed to satisfy the declared processing order constraints of each :class`ParameterHandler`.

Examples

Create a new ForceField containing the smirnoff99Frosst parameter set:

>>> from openforcefield.typing.engines.smirnoff import ForceField
>>> forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml')

Create an OpenMM system from a openforcefield.topology.Topology object:

>>> from openforcefield.topology import Molecule, Topology
>>> ethanol = Molecule.from_smiles('CCO')
>>> topology = Topology.from_molecules(molecules=[ethanol])
>>> system = forcefield.create_openmm_system(topology)

Modify the long-range electrostatics method:

>>> forcefield.get_parameter_handler('Electrostatics').method = 'PME'

Inspect the first few vdW parameters:

>>> low_precedence_parameters = forcefield.get_parameter_handler('vdW').parameters[0:3]

Retrieve the vdW parameters by SMIRKS string and manipulate it:

>>> parameter = forcefield.get_parameter_handler('vdW').parameters['[#1:1]-[#7]']
>>> parameter.rmin_half += 0.1 * unit.angstroms
>>> parameter.epsilon *= 1.02

Make a child vdW type more specific (checking modified SMIRKS for validity):

>>> forcefield.get_parameter_handler('vdW').parameters[-1].smirks += '~[#53]'

Warning

While we check whether the modified SMIRKS is still valid and has the appropriate valence type, we currently don’t check whether the typing remains hierarchical, which could result in some types no longer being assignable because more general types now come below them and preferentially match.

Delete a parameter:

>>> del forcefield.get_parameter_handler('vdW').parameters['[#1:1]-[#6X4]']

Insert a parameter at a specific point in the parameter tree:

>>> from openforcefield.typing.engines.smirnoff import vdWHandler
>>> new_parameter = vdWHandler.vdWType(smirks='[*:1]', epsilon=0.0157*unit.kilocalories_per_mole, rmin_half=0.6000*unit.angstroms)
>>> forcefield.get_parameter_handler('vdW').parameters.insert(0, new_parameter)

Warning

We currently don’t check whether removing a parameter could accidentally remove the root type, so it’s possible to no longer type all molecules this way.

Attributes

parametersdict of str: parameters[tagname] is the instantiated ParameterHandler class that handles parameters associated with the force tagname. This is the primary means of retrieving and modifying parameters, such as parameters['vdW'][0].sigma *= 1.1
parameter_object_handlersdict of str: Registered list of ParameterHandler classes that will handle different forcefield tags to create the parameter object model. parameter_object_handlers[tagname] is the ParameterHandler that will be instantiated to process the force field definition section tagname. ParameterHandler classes are registered when the ForceField object is created, but can be manipulated afterwards.
parameter_io_handlersdict of str: Registered list of ParameterIOHandler classes that will handle serializing/deserializing the parameter object model to string or file representations, such as XML. parameter_io_handlers[iotype] is the ParameterHandler that will be instantiated to process the serialization scheme iotype. ParameterIOHandler classes are registered when the ForceField object is created, but can be manipulated afterwards.

Methods

`create_openmm_system`(self, topology, \\kwargs)	Create an OpenMM System representing the interactions for the specified Topology with the current force field
`create_parmed_structure`(self, topology, …)	Create a ParmEd Structure object representing the interactions for the specified Topology with the current force field
`get_parameter_handler`(self, tagname[, …])	Retrieve the parameter handlers associated with the provided tagname.
`get_parameter_io_handler`(self, io_format)	Retrieve the parameter handlers associated with the provided tagname.
`label_molecules`(self, topology)	Return labels for a list of molecules corresponding to parameters from this force field.
`parse_smirnoff_from_source`(self, source)	Reads a SMIRNOFF data structure from a source, which can be one of many types.
`parse_sources`(self, sources[, …])	Parse a SMIRNOFF force field definition.
`register_parameter_handler`(self, …)	Register a new ParameterHandler for a specific tag, making it available for lookup in the ForceField.
`register_parameter_io_handler`(self, …)	Register a new ParameterIOHandler, making it available for lookup in the ForceField.
`to_file`(self, filename[, io_format, …])	Write this Forcefield and all its associated parameters to a string in a given format which complies with the SMIRNOFF spec.
`to_string`(self[, io_format, …])	Write this Forcefield and all its associated parameters to a string in a given format which complies with the SMIRNOFF spec.

__init__(self, *sources, parameter_handler_classes=None, parameter_io_handler_classes=None, disable_version_check=False, allow_cosmetic_attributes=False)[source]¶

Create a new ForceField object from one or more SMIRNOFF parameter definition files.

Parameters

sourcesstring or file-like object or open file handle or URL (or iterable of these): A list of files defining the SMIRNOFF force field to be loaded. Currently, only the SMIRNOFF XML format is supported. 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. If multiple files are specified, any top-level tags that are repeated will be merged if they are compatible, with files appearing later in the sequence resulting in parameters that have higher precedence. Support for multiple files is primarily intended to allow solvent parameters to be specified by listing them last in the sequence.
parameter_handler_classesiterable of ParameterHandler classes, optional, default=None: If not None, the specified set of ParameterHandler classes will be instantiated to create the parameter object model. By default, all imported subclasses of ParameterHandler are automatically registered.
parameter_io_handler_classesiterable of ParameterIOHandler classes: If not None, the specified set of ParameterIOHandler classes will be used to parse/generate serialized parameter sets. By default, all imported subclasses of ParameterIOHandler are automatically registered.
disable_version_checkbool, optional, default=False: If True, will disable checks against the current highest supported forcefield version. This option is primarily intended for forcefield development.
allow_cosmetic_attributesbool, optional. Default = False: Whether to retain non-spec kwargs from data sources.

Examples

Load one SMIRNOFF parameter set in XML format (searching the package data directory by default, which includes some standard parameter sets):

>>> forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml')

Load multiple SMIRNOFF parameter sets:

forcefield = ForceField(‘test_forcefields/smirnoff99Frosst.offxml’, ‘test_forcefields/tip3p.offxml’)

Load a parameter set from a string:

>>> offxml = '<SMIRNOFF version="0.2" aromaticity_model="OEAroModel_MDL"/>'
>>> forcefield = ForceField(offxml)

Methods

`__init__`(self, \*sources[, …])	Create a new `ForceField` object from one or more SMIRNOFF parameter definition files.
`create_openmm_system`(self, topology, \\kwargs)	Create an OpenMM System representing the interactions for the specified Topology with the current force field
`create_parmed_structure`(self, topology, …)	Create a ParmEd Structure object representing the interactions for the specified Topology with the current force field
`get_parameter_handler`(self, tagname[, …])	Retrieve the parameter handlers associated with the provided tagname.
`get_parameter_io_handler`(self, io_format)	Retrieve the parameter handlers associated with the provided tagname.
`label_molecules`(self, topology)	Return labels for a list of molecules corresponding to parameters from this force field.
`parse_smirnoff_from_source`(self, source)	Reads a SMIRNOFF data structure from a source, which can be one of many types.
`parse_sources`(self, sources[, …])	Parse a SMIRNOFF force field definition.
`register_parameter_handler`(self, …)	Register a new ParameterHandler for a specific tag, making it available for lookup in the ForceField.
`register_parameter_io_handler`(self, …)	Register a new ParameterIOHandler, making it available for lookup in the ForceField.
`to_file`(self, filename[, io_format, …])	Write this Forcefield and all its associated parameters to a string in a given format which complies with the SMIRNOFF spec.
`to_string`(self[, io_format, …])	Write this Forcefield and all its associated parameters to a string in a given format which complies with the SMIRNOFF spec.

Attributes

`author`	Returns the author data for this ForceField object.
`date`	Returns the date data for this ForceField object.

property author¶

Returns the author data for this ForceField object. If not defined in any loaded files, this will be None.

Returns

authorstr: The author data for this forcefield.

property date¶

Returns the date data for this ForceField object. If not defined in any loaded files, this will be None.

Returns

datestr: The date data for this forcefield.

register_parameter_handler(self, parameter_handler)[source]¶

Warning

This API is experimental and subject to change.

Parameters

parameter_handlerA ParameterHandler object: The ParameterHandler to register. The TAGNAME attribute of this object will be used as the key for registration.

register_parameter_io_handler(self, parameter_io_handler)[source]¶

Warning

This API is experimental and subject to change.

Parameters

parameter_io_handlerA ParameterIOHandler object: The ParameterIOHandler to register. The FORMAT attribute of this object will be used to associate it to a file format/suffix.

get_parameter_handler(self, tagname, handler_kwargs=None, allow_cosmetic_attributes=False)[source]¶

Retrieve the parameter handlers associated with the provided tagname.

If the parameter handler has not yet been instantiated, it will be created and returned. If a parameter handler object already exists, it will be checked for compatibility and an Exception raised if it is incompatible with the provided kwargs. If compatible, the existing ParameterHandler will be returned.

Parameters

tagnamestr: The name of the parameter to be handled.
handler_kwargsdict, optional. Default = None: Dict to be passed to the handler for construction or checking compatibility. If this is None and no existing ParameterHandler exists for the desired tag, a handler will be initialized with all default values. If this is None and a handler for the desired tag exists, the existing ParameterHandler will be returned.
allow_cosmetic_attributesbool, optional. Default = False: Whether to permit non-spec kwargs in smirnoff_data.

Returns

handlerAn openforcefield.engines.typing.smirnoff.ParameterHandler

Raises

KeyError if there is no ParameterHandler for the given tagname

get_parameter_io_handler(self, io_format)[source]¶

Retrieve the parameter handlers associated with the provided tagname. If the parameter IO handler has not yet been instantiated, it will be created.

Parameters

io_formatstr: The name of the io format to be handled.

Returns

io_handlerAn openforcefield.engines.typing.smirnoff.ParameterIOHandler

Raises

KeyError if there is no ParameterIOHandler for the given tagname

parse_sources(self, sources, allow_cosmetic_attributes=True)[source]¶

Parse a SMIRNOFF force field definition.

Parameters

sourcesstring or file-like object or open file handle or URL (or iterable of these)

A list of files defining the SMIRNOFF force field to be loaded. Currently, only the SMIRNOFF XML format is supported. 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. If multiple files are specified, any top-level tags that are repeated will be merged if they are compatible, with files appearing later in the sequence resulting in parameters that have higher precedence. Support for multiple files is primarily intended to allow solvent parameters to be specified by listing them last in the sequence.

allow_cosmetic_attributesbool, optional. Default = False

Whether to permit non-spec kwargs present in the source.

.. notes ::

New SMIRNOFF sections are handled independently, as if they were specified in the same file.
If a SMIRNOFF section that has already been read appears again, its definitions are appended to the end of the previously-read definitions if the sections are configured with compatible attributes; otherwise, an IncompatibleTagException is raised.

parse_smirnoff_from_source(self, source)[source]¶

Reads a SMIRNOFF data structure from a source, which can be one of many types.

Parameters

sourcestr or bytes: sources : string or file-like object or open file handle or URL (or iterable of these) A list of files defining the SMIRNOFF force field to be loaded Currently, only the SMIRNOFF XML format is supported. 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.

Returns

smirnoff_dataOrderedDict: A representation of a SMIRNOFF-format data structure. Begins at top-level ‘SMIRNOFF’ key.

to_string(self, io_format='XML', discard_cosmetic_attributes=False)[source]¶

Write this Forcefield and all its associated parameters to a string in a given format which complies with the SMIRNOFF spec.

Parameters

io_formatstr or ParameterIOHandler, optional. Default=’XML’: The serialization format to write to
discard_cosmetic_attributesbool, default=False: Whether to discard any non-spec attributes stored in the ForceField.

Returns

forcefield_stringstr: The string representation of the serialized forcefield

to_file(self, filename, io_format=None, discard_cosmetic_attributes=False)[source]¶

Write this Forcefield and all its associated parameters to a string in a given format which complies with the SMIRNOFF spec.

Parameters

filenamestr: The filename to write to
io_formatstr or ParameterIOHandler, optional. Default=None: The serialization format to write out. If None, will attempt to be inferred from the filename.
discard_cosmetic_attributesbool, default=False: Whether to discard any non-spec attributes stored in the ForceField.

Returns

forcefield_stringstr: The string representation of the serialized forcefield

create_openmm_system(self, topology, **kwargs)[source]¶

Create an OpenMM System representing the interactions for the specified Topology with the current force field

Parameters

topologyopenforcefield.topology.Topology: The Topology corresponding to the system to be parameterized
charge_from_moleculesList[openforcefield.molecule.Molecule], optional: If specified, partial charges will be taken from the given molecules instead of being determined by the force field.

Returns

systemsimtk.openmm.System: The newly created OpenMM System corresponding to the specified topology

create_parmed_structure(self, topology, positions, **kwargs)[source]¶

Create a ParmEd Structure object representing the interactions for the specified Topology with the current force field

This method creates a ParmEd Structure object containing a topology, positions, and parameters.

Parameters

topologyopenforcefield.topology.Topology: The Topology corresponding to the System object to be created.
positionssimtk.unit.Quantity of dimension (natoms,3) with units compatible with angstroms: The positions corresponding to the System object to be created

Returns

structureparmed.Structure: The newly created parmed.Structure object

label_molecules(self, topology)[source]¶

Return labels for a list of molecules corresponding to parameters from this force field. For each molecule, a dictionary of force types is returned, and for each force type, each force term is provided with the atoms involved, the parameter id assigned, and the corresponding SMIRKS.

Parameters

topologyopenforcefield.topology.Topology: A Topology object containing one or more unique molecules to be labeled

Returns

molecule_labelslist: List of labels for unique molecules. Each entry in the list corresponds to one unique molecule in the Topology and is a dictionary keyed by force type, i.e., molecule_labels[0]['HarmonicBondForce'] gives details for the harmonic bond parameters for the first molecule. Each element is a list of the form: [ ( [ atom1, ..., atomN], parameter_id, SMIRKS), ... ].