openforcefield.typing.engines.smirnoff.parameters.BondHandler¶

class openforcefield.typing.engines.smirnoff.parameters.BondHandler(**kwargs)[source]¶

Handle SMIRNOFF <Bonds> tags

Warning

This API is experimental and subject to change.

Attributes

known_kwargs

List of kwargs that can be parsed by the function.

parameters

The ParameterList that holds this ParameterHandler’s parameter objects

Methods

BondType(**kwargs)	A SMIRNOFF bond type
add_parameter(self, parameter_kwargs)	Add a parameter to the forcefield, ensuring all parameters are valid.
assign_parameters(self, topology, system)	Assign parameters for the given Topology to the specified System object.
check_handler_compatibility(self, other_handler)	Checks whether this ParameterHandler encodes compatible physics as another ParameterHandler.
check_parameter_compatibility(self, …)	Check to make sure that the fields requiring defined units are compatible with the required units for the Parameters handled by this ParameterHandler
find_matches(self, entity)	Find the elements of the topology/molecule matched by a parameter type.
get_parameter(self, parameter_attrs)	Return the parameters in this ParameterHandler that match the parameter_attrs argument
postprocess_system(self, topology, system, …)	Allow the force to perform a a final post-processing pass on the System following parameter assignment, if needed.
to_dict(self[, output_units, …])	Convert this ParameterHandler to an OrderedDict, compliant with the SMIRNOFF data spec.

create_force

__init__(self, **kwargs)[source]¶

Initialize a ParameterHandler, optionally with a list of parameters and other kwargs.

Parameters

allow_cosmetic_attributesbool, optional. Default = False

Whether to permit non-spec kwargs. If True, non-spec kwargs will be stored as attributes of this object and can be accessed and modified. Otherwise an exception will be raised if a non-spec kwarg is encountered.

**kwargsdict

The dict representation of the SMIRNOFF data source

Methods

__init__(self, \*\*kwargs)	Initialize a ParameterHandler, optionally with a list of parameters and other kwargs.
add_parameter(self, parameter_kwargs)	Add a parameter to the forcefield, ensuring all parameters are valid.
assign_parameters(self, topology, system)	Assign parameters for the given Topology to the specified System object.
check_handler_compatibility(self, other_handler)	Checks whether this ParameterHandler encodes compatible physics as another ParameterHandler.
check_parameter_compatibility(self, …)	Check to make sure that the fields requiring defined units are compatible with the required units for the Parameters handled by this ParameterHandler
create_force(self, system, topology, \*\*kwargs)
find_matches(self, entity)	Find the elements of the topology/molecule matched by a parameter type.
get_parameter(self, parameter_attrs)	Return the parameters in this ParameterHandler that match the parameter_attrs argument
postprocess_system(self, topology, system, …)	Allow the force to perform a a final post-processing pass on the System following parameter assignment, if needed.
to_dict(self[, output_units, …])	Convert this ParameterHandler to an OrderedDict, compliant with the SMIRNOFF data spec.

Attributes

known_kwargs	List of kwargs that can be parsed by the function.
parameters	The ParameterList that holds this ParameterHandler’s parameter objects

class BondType(**kwargs)[source]¶

A SMIRNOFF bond type

Warning

This API is experimental and subject to change.

Attributes

smirks

Methods

to_dict(self[, discard_cosmetic_attributes])

Convert this ParameterType object to dict.

to_dict(self, discard_cosmetic_attributes=True)¶

Convert this ParameterType object to dict. A unit-bearing attribute (‘X’) will be converted to two dict entries, one ([‘X’] containing the unitless value, and another ([‘X_unit’]) containing a string representation of its unit.

Parameters

discard_cosmetic_attributesbool, optional. Default = True

Whether to discard non-spec attributes of this ParameterType

Returns

smirnoff_dictdict

The SMIRNOFF-compliant dict representation of this ParameterType object.

output_unitsdict[str: simtk.unit.Unit]

A mapping from each simtk.unit.Quanitity-valued ParameterType attribute to the unit it was converted to during serialization.

check_handler_compatibility(self, other_handler)[source]¶

Checks whether this ParameterHandler encodes compatible physics as another ParameterHandler. This is called if a second handler is attempted to be initialized for the same tag.

Parameters

other_handlera ParameterHandler object

The handler to compare to.

Raises

IncompatibleParameterError if handler_kwargs are incompatible with existing parameters.

add_parameter(self, parameter_kwargs)¶

Add a parameter to the forcefield, ensuring all parameters are valid.

Parameters

parameter_kwargsdict

The kwargs to pass to the ParameterHandler.INFOTYPE (a ParameterType) constructor

assign_parameters(self, topology, system)¶

Assign parameters for the given Topology to the specified System object.

Parameters

topologyopenforcefield.topology.Topology

The Topology for which parameters are to be assigned. Either a new Force will be created or parameters will be appended to an existing Force.

systemsimtk.openmm.System

The OpenMM System object to add the Force (or append new parameters) to.

check_parameter_compatibility(self, parameter_kwargs)¶

Check to make sure that the fields requiring defined units are compatible with the required units for the Parameters handled by this ParameterHandler

Parameters

parameter_kwargs: dict

The dict that will be used to construct the ParameterType

Raises

Raises a ValueError if the parameters are incompatible.

find_matches(self, entity)¶

Find the elements of the topology/molecule matched by a parameter type.

Parameters

entityopenforcefield.topology.Topology or openforcefield.topology.Molecule

Topology or molecule to search.

Returns

matchesValenceDict[Tuple[int], ParameterType]

matches[particle_indices] is the ParameterType object matching the tuple of particle indices in entity.

get_parameter(self, parameter_attrs)¶

Return the parameters in this ParameterHandler that match the parameter_attrs argument

Parameters

parameter_attrsdict of {attr: value}

The attrs mapped to desired values (for example {“smirks”: “[:1]~[#16:2]=,:[#6:3]~[:4]”, “id”: “t105”} )

Returns

list of ParameterType objects

A list of matching ParameterType objects

known_kwargs¶

List of kwargs that can be parsed by the function.

parameters¶

The ParameterList that holds this ParameterHandler’s parameter objects

postprocess_system(self, topology, system, **kwargs)¶

Allow the force to perform a a final post-processing pass on the System following parameter assignment, if needed.

Parameters

topologyopenforcefield.topology.Topology

The Topology for which parameters are to be assigned. Either a new Force will be created or parameters will be appended to an existing Force.

systemsimtk.openmm.System

The OpenMM System object to add the Force (or append new parameters) to.

to_dict(self, output_units=None, discard_cosmetic_attributes=True)¶

Convert this ParameterHandler to an OrderedDict, compliant with the SMIRNOFF data spec.

Parameters

output_unitsdict[str

A mapping from the ParameterType attribute name to the output unit its value should be converted to.

discard_cosmetic_attributesbool, optional. Default = True.

Whether to discard non-spec parameter and header attributes in this ParameterHandler.

Returns

smirnoff_dataOrderedDict

SMIRNOFF-spec compliant representation of this ParameterHandler and its internal ParameterList.