openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler

class openforcefield.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler(**kwargs)[source]

Handle SMIRNOFF <ToolkitAM1BCC> 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

add_parameter(parameter_kwargs) Add a parameter to the forcefield, ensuring all parameters are valid.
assign_charge_from_molecules(molecule, …) Given an input molecule, checks against a list of molecules for an isomorphic match.
assign_parameters(topology, system) Assign parameters for the given Topology to the specified System object.
check_handler_compatibility(handler_kwargs) Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler.
check_parameter_compatibility(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
find_matches(entity) Find the elements of the topology/molecule matched by a parameter type.
get_parameter(parameter_attrs) Return the parameters in this ParameterHandler that match the parameter_attrs argument
postprocess_system(system, topology, **kwargs) Allow the force to perform a a final post-processing pass on the System following parameter assignment, if needed.
to_dict([output_units, …]) Convert this ParameterHandler to an OrderedDict, compliant with the SMIRNOFF data spec.
create_force  
__init__(**kwargs)[source]

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

Parameters:
permit_cosmetic_attributes : bool

Whether to accept non-spec kwargs

**kwargs : dict

The dict representation of the SMIRNOFF data source

Methods

__init__(**kwargs) Initialize a ParameterHandler, optionally with a list of parameters and other kwargs.
add_parameter(parameter_kwargs) Add a parameter to the forcefield, ensuring all parameters are valid.
assign_charge_from_molecules(molecule, …) Given an input molecule, checks against a list of molecules for an isomorphic match.
assign_parameters(topology, system) Assign parameters for the given Topology to the specified System object.
check_handler_compatibility(handler_kwargs) Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler.
check_parameter_compatibility(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
create_force(system, topology, **kwargs)
find_matches(entity) Find the elements of the topology/molecule matched by a parameter type.
get_parameter(parameter_attrs) Return the parameters in this ParameterHandler that match the parameter_attrs argument
postprocess_system(system, topology, **kwargs) Allow the force to perform a a final post-processing pass on the System following parameter assignment, if needed.
to_dict([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
check_handler_compatibility(handler_kwargs, assume_missing_is_default=True)[source]

Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler. This is called if a second handler is attempted to be initialized for the same tag. If no value is given for a field, it will be assumed to expect the ParameterHandler class default.

Parameters:
handler_kwargs : dict

The kwargs that would be used to construct a ParameterHandler

assume_missing_is_default : bool

If True, will assume that parameters not specified in handler_kwargs would have been set to the default. Therefore, an exception is raised if the ParameterHandler is incompatible with the default value for a unspecified field.

Raises:
IncompatibleParameterError if handler_kwargs are incompatible with existing parameters.
assign_charge_from_molecules(molecule, charge_mols)[source]

Given an input molecule, checks against a list of molecules for an isomorphic match. If found, assigns partial charges from the match to the input molecule.

Parameters:
molecule : an openforcefield.topology.FrozenMolecule

The molecule to have partial charges assigned if a match is found.

charge_mols : list of [openforcefield.topology.FrozenMolecule]

A list of molecules with charges already assigned.

Returns:
match_found : bool

Whether a match was found. If True, the input molecule will have been modified in-place.

postprocess_system(system, topology, **kwargs)[source]

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

Parameters:
topology : openforcefield.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.

system : simtk.openmm.System

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

add_parameter(parameter_kwargs)

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

Parameters:
parameter_kwargs : dict

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

assign_parameters(topology, system)

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

Parameters:
topology : openforcefield.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.

system : simtk.openmm.System

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

check_parameter_compatibility(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(entity)

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

Parameters:
entity : openforcefield.topology.Topology or openforcefield.topology.Molecule

Topology or molecule to search.

Returns:
matches : ValenceDict[Tuple[int], ParameterType]

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

get_parameter(parameter_attrs)

Return the parameters in this ParameterHandler that match the parameter_attrs argument

Parameters:
parameter_attrs : dict of {attr: value}

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

Returns:
list of ParameterType-derived objects

A list of matching ParameterType-derived objects

known_kwargs

List of kwargs that can be parsed by the function.

parameters

The ParameterList that holds this ParameterHandler’s parameter objects

to_dict(output_units=None, return_cosmetic_attributes=False)

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

Parameters:
output_units : dict[str

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

return_cosmetic_attributes : bool, optional. Default = False.

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

Returns:
smirnoff_data : OrderedDict

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