openforcefield.typing.engines.smirnoff.parameters.ElectrostaticsHandler¶

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

Handles SMIRNOFF <Electrostatics> tags.

Warning

This API is experimental and subject to change.

Attributes

cutoff

The cutoff used for long-range van der Waals interactions

known_kwargs

List of kwargs that can be parsed by the function.

method

The method used to model long-range electrostatic interactions

parameters

The ParameterList that holds this ParameterHandler’s parameter objects

switch_width

The switching width used for long-range electrostatics interactions

Methods

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

cutoff	The cutoff used for long-range van der Waals interactions
known_kwargs	List of kwargs that can be parsed by the function.
method	The method used to model long-range electrostatic interactions
parameters	The ParameterList that holds this ParameterHandler’s parameter objects
switch_width	The switching width used for long-range electrostatics interactions

method¶

The method used to model long-range electrostatic interactions

cutoff¶

The cutoff used for long-range van der Waals interactions

switch_width¶

The switching width used for long-range electrostatics interactions

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.