openforcefield.typing.engines.smirnoff.forcefield.ForceField

class openforcefield.typing.engines.smirnoff.forcefield.ForceField(*sources, aromaticity_model='OEAroModel_MDL', parameter_handler_classes=None, parameter_io_handler_classes=None, disable_version_check=False, allow_cosmetic_attributes=False, load_plugins=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(topology, **kwargs)

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

create_parmed_structure(topology, positions, …)

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

get_parameter_handler(tagname[, …])

Retrieve the parameter handlers associated with the provided tagname.

get_parameter_io_handler(io_format)

Retrieve the parameter handlers associated with the provided tagname.

label_molecules(topology)

Return labels for a list of molecules corresponding to parameters from this force field.

parse_smirnoff_from_source(source)

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

parse_sources(sources[, …])

Parse a SMIRNOFF force field definition.

register_parameter_handler(parameter_handler)

Register a new ParameterHandler for a specific tag, making it available for lookup in the ForceField.

register_parameter_io_handler(…)

Register a new ParameterIOHandler, making it available for lookup in the ForceField.

to_file(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([io_format, …])

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

__init__(*sources, aromaticity_model='OEAroModel_MDL', parameter_handler_classes=None, parameter_io_handler_classes=None, disable_version_check=False, allow_cosmetic_attributes=False, load_plugins=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.

aromaticity_modelstring, default=’OEAroModel_MDL’

The aromaticity model used by the force field. Currently, only ‘OEAroModel_MDL’ is supported

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.

load_plugins: bool, optional. Default = False

Whether to load ParameterHandler classes which have been registered by installed plugins.

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__(*sources[, aromaticity_model, …])

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

create_openmm_system(topology, **kwargs)

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

create_parmed_structure(topology, positions, …)

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

get_parameter_handler(tagname[, …])

Retrieve the parameter handlers associated with the provided tagname.

get_parameter_io_handler(io_format)

Retrieve the parameter handlers associated with the provided tagname.

label_molecules(topology)

Return labels for a list of molecules corresponding to parameters from this force field.

parse_smirnoff_from_source(source)

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

parse_sources(sources[, …])

Parse a SMIRNOFF force field definition.

register_parameter_handler(parameter_handler)

Register a new ParameterHandler for a specific tag, making it available for lookup in the ForceField.

register_parameter_io_handler(…)

Register a new ParameterIOHandler, making it available for lookup in the ForceField.

to_file(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([io_format, …])

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

Attributes

aromaticity_model

Returns the aromaticity model for this ForceField object.

author

Returns the author data for this ForceField object.

date

Returns the date data for this ForceField object.

registered_parameter_handlers

Return the list of registered parameter handlers by name