openforcefield.typing.engines.smirnoff.parameters.ImproperTorsionHandler

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

Handle SMIRNOFF <ImproperTorsionForce> 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

ImproperTorsionType(**kwargs) A SMIRNOFF torsion type for improper torsions.
add_parameter(parameter_kwargs) Add a parameter to the forcefield, ensuring all parameters are valid.
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 improper torsions in 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(topology, system, **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_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 improper torsions in 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(topology, system, **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
class ImproperTorsionType(**kwargs)[source]

A SMIRNOFF torsion type for improper torsions.

Warning

This API is experimental and subject to change.

Attributes:
smirks

Methods

to_dict([return_cosmetic_attributes]) Convert this ParameterType-derived object to dict.
to_dict(return_cosmetic_attributes=False)

Convert this ParameterType-derived 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:
return_cosmetic_attributes : bool, optional. default = False

Whether to return non-spec attributes of this ParameterType

Returns:
smirnoff_dict : dict

The SMIRNOFF-compliant dict representation of this ParameterType-derived object.

output_units : dict[str: simtk.unit.Unit]

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

find_matches(entity)[source]

Find the improper torsions in the topology/molecule matched by a parameter type.

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

Topology or molecule to search.

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

matches[atom_indices] is the ParameterType object matching the 4-tuple of atom indices in entity.

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_handler_compatibility(handler_kwargs)

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.

Parameters:
handler_kwargs : dict

The kwargs that would be used to construct

Raises:
IncompatibleParameterError if handler_kwargs are incompatible with existing parameters.
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.
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

postprocess_system(topology, system, **kwargs)

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.

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.