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 OpenMMsimtk.openmm.System
object from aopenforcefield.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, allParameterHandler
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 instantiatedParameterHandler
class that handles parameters associated with the forcetagname
. This is the primary means of retrieving and modifying parameters, such asparameters['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 theParameterHandler
that will be instantiated to process the force field definition sectiontagname
.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 theParameterHandler
that will be instantiated to process the serialization schemeiotype
.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 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 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
Returns the aromaticity model for this ForceField object.
Returns the author data for this ForceField object.
Returns the date data for this ForceField object.
Return the list of registered parameter handlers by name
-
property
aromaticity_model
¶ Returns the aromaticity model for this ForceField object.
- Returns
- aromaticity_model
The aromaticity model for this force field.
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
(parameter_handler)[source]¶ Register a new ParameterHandler for a specific tag, making it available for lookup in the ForceField.
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
(parameter_io_handler)[source]¶ Register a new ParameterIOHandler, making it available for lookup in the ForceField.
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.
-
property
registered_parameter_handlers
¶ Return the list of registered parameter handlers by name
Warning
This API is experimental and subject to change.
- Returns
- registered_parameter_handlers: iterable of names of ParameterHandler objects in this ForceField
-
get_parameter_handler
(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
(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
(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
(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
(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
(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
(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. default =[]
If specified, partial charges will be taken from the given molecules instead of being determined by the force field.
- partial_bond_orders_from_moleculesList[openforcefield.molecule.Molecule], optional. default=[]
If specified, partial bond orders will be taken from the given molecules instead of being determined by the force field. All bonds on each molecule given must have
fractional_bond_order
specified. A ValueError will be raised if any bonds havefractional_bond_order=None
. Molecules in the topology not represented in this list will have fractional bond orders calculated using underlying toolkits as needed.- return_topologybool, optional. default=False
If
True
, return tuple of(system, topology)
, wheretopology
is the processed topology. DefaultFalse
. This topology will have the final partial charges assigned on its reference_molecules attribute, as well as partial bond orders (if they were calculated).
- Returns
- systemsimtk.openmm.System
The newly created OpenMM System corresponding to the specified
topology
- topologyopenforcefield.topology.Topology, optional.
If the return_topology keyword argument is used, this method will also return a Topology. This can be used to inspect the partial charges and partial bond orders assigned to the molecules during parameterization.
-
create_parmed_structure
(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 theSystem
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
(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), ... ]
.