openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler

class openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler(allow_cosmetic_attributes=False, skip_version_check=False, **kwargs)[source]

Handle SMIRNOFF <vdW> tags

Warning

This API is experimental and subject to change.

__init__(allow_cosmetic_attributes=False, skip_version_check=False, **kwargs)

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.
skip_version_check: bool, optional. Default = False: If False, the SMIRNOFF section version will not be checked, and the ParameterHandler will be initialized with version set to _MAX_SUPPORTED_SECTION_VERSION.
**kwargsdict: The dict representation of the SMIRNOFF data source

Methods

`__init__`([allow_cosmetic_attributes, ...])	Initialize a ParameterHandler, optionally with a list of parameters and other kwargs.
`add_cosmetic_attribute`(attr_name, attr_value)	Add a cosmetic attribute to this object.
`add_parameter`([parameter_kwargs, parameter, ...])	Add a parameter to the force field, ensuring all parameters are valid.
`assign_parameters`(topology, system)	Assign parameters for the given Topology to the specified OpenMM `System` object.
`assign_partial_bond_orders_from_molecules`(...)
`attribute_is_cosmetic`(attr_name)	Determine whether an attribute of this object is cosmetic.
`check_charges_assigned`(ref_mol, topology)	Check whether charges have been assigned for a reference molecule.
`check_handler_compatibility`(other_handler)	Checks whether this ParameterHandler encodes compatible physics as another ParameterHandler.
`check_partial_bond_orders_from_molecules_duplicates`(pb_mols)
`create_force`(system, topology, **kwargs)
`delete_cosmetic_attribute`(attr_name)	Delete a cosmetic attribute from this object.
`find_matches`(entity[, unique])	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.
`mark_charges_assigned`(ref_mol, topology)	Record that charges have been assigned for a reference molecule.
`postprocess_system`(topology, system, **kwargs)	Allow the force to perform a a final post-processing pass on the OpenMM `System` following parameter assignment, if needed.
`to_dict`([discard_cosmetic_attributes])	Convert this ParameterHandler to an OrderedDict, compliant with the SMIRNOFF data spec.

Attributes

`TAGNAME`	The name of this ParameterHandler corresponding to the SMIRNOFF tag name
`combining_rules`
`cutoff`
`known_kwargs`	List of kwargs that can be parsed by the function.
`method`
`parameters`	The ParameterList that holds this ParameterHandler's parameter objects
`potential`
`scale12`
`scale13`
`scale14`
`scale15`
`switch_width`
`version`

class vdWType(**kwargs)[source]

A SMIRNOFF vdWForce type.

Warning

This API is experimental and subject to change.

to_dict(discard_cosmetic_attributes=False, duplicate_attributes=None)[source]

Convert this object to dict format.

The returning dictionary contains all the ParameterAttribute and IndexedParameterAttribute as well as cosmetic attributes if discard_cosmetic_attributes is False.

Parameters

discard_cosmetic_attributesbool, optional. Default = False: Whether to discard non-spec attributes of this object
duplicate_attributeslist of string, optional. Default = None: A list of names of attributes that redundantly decsribe data and should be discarded during serializaiton

Returns

smirnoff_dictdict: The SMIRNOFF-compliant dict representation of this object.

add_cosmetic_attribute(attr_name, attr_value)

Add a cosmetic attribute to this object.

This attribute will not have a functional effect on the object in the Open Force Field Toolkit, but can be written out during output.

Warning

The API for modifying cosmetic attributes is experimental and may change in the future (see issue #338).

Parameters

attr_namestr: Name of the attribute to define for this object.
attr_valuestr: The value of the attribute to define for this object.

attribute_is_cosmetic(attr_name)

Determine whether an attribute of this object is cosmetic.

Warning

The API for modifying cosmetic attributes is experimental and may change in the future (see issue #338).

Parameters

attr_namestr: The attribute name to check

Returns

is_cosmeticbool: Returns True if the attribute is defined and is cosmetic. Returns False otherwise.

delete_cosmetic_attribute(attr_name)

Delete a cosmetic attribute from this object.

Warning

The API for modifying cosmetic attributes is experimental and may change in the future (see issue #338).

Parameters

attr_namestr: Name of the cosmetic attribute to delete.

check_handler_compatibility(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.

property TAGNAME

The name of this ParameterHandler corresponding to the SMIRNOFF tag name

Returns

handler_namestr: The name of this parameter handler

add_cosmetic_attribute(attr_name, attr_value)

Add a cosmetic attribute to this object.

This attribute will not have a functional effect on the object in the Open Force Field Toolkit, but can be written out during output.

Warning

The API for modifying cosmetic attributes is experimental and may change in the future (see issue #338).

Parameters

attr_namestr: Name of the attribute to define for this object.
attr_valuestr: The value of the attribute to define for this object.

add_parameter(parameter_kwargs=None, parameter=None, after=None, before=None)

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

Parameters

parameter_kwargs: dict, optional

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

parameter: ParameterType, optional

A ParameterType to add to the ParameterHandler

afterstr or int, optional

The SMIRKS pattern (if str) or index (if int) of the parameter directly before where the new parameter will be added

beforestr, optional

The SMIRKS pattern (if str) or index (if int) of the parameter directly after where the new parameter will be added

Note the following behavior:

Either parameter_kwargs or parameter must be specified.
When before and after are both None, the new parameter will be appended to the END of the parameter list.
When before and after are both specified, the new parameter will be added immediately after the parameter matching the after pattern or index.
The order of parameters in a parameter list can have significant impacts on parameter assignment. For details, see the [SMIRNOFF](https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html#smirnoff-parameter-specification-is-hierarchical) specification.

Examples

Add a ParameterType to an existing ParameterList at a specified position.

Given an existing parameter handler and a new parameter to add to it:

>>> from openmm import unit
>>> bh = BondHandler(skip_version_check=True)
>>> length = 1.5 * unit.angstrom
>>> k = 100 * unit.kilocalorie_per_mole / unit.angstrom ** 2
>>> bh.add_parameter({'smirks': '[*:1]-[*:2]', 'length': length, 'k': k, 'id': 'b1'})
>>> bh.add_parameter({'smirks': '[*:1]=[*:2]', 'length': length, 'k': k, 'id': 'b2'})
>>> bh.add_parameter({'smirks': '[*:1]#[*:2]', 'length': length, 'k': k, 'id': 'b3'})
>>> [p.id for p in bh.parameters]
['b1', 'b2', 'b3']

>>> param = {'smirks': '[#1:1]-[#6:2]', 'length': length, 'k': k, 'id': 'b4'}

Add a new parameter immediately after the parameter with the smirks ‘[:1]=[:2]’

>>> bh.add_parameter(param, after='[*:1]=[*:2]')
>>> [p.id for p in bh.parameters]
['b1', 'b2', 'b4', 'b3']

assign_parameters(topology, system)

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

Parameters

topologyopenff.toolkit.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.
systemopenmm.System: The OpenMM System object to add the Force (or append new parameters) to.

attribute_is_cosmetic(attr_name)

Determine whether an attribute of this object is cosmetic.

Warning

The API for modifying cosmetic attributes is experimental and may change in the future (see issue #338).

Parameters

attr_namestr: The attribute name to check

Returns

is_cosmeticbool: Returns True if the attribute is defined and is cosmetic. Returns False otherwise.

static check_charges_assigned(ref_mol, topology)

Check whether charges have been assigned for a reference molecule.

Parameters

ref_molopenff.toolkit.topology.Molecule: The molecule to check for having charges assigned
topologyopenff.toolkit.topology.Topology: The topology to query for this information

Returns

charges_assignedbool: Whether charges have already been assigned to this molecule

delete_cosmetic_attribute(attr_name)

Delete a cosmetic attribute from this object.

Warning

The API for modifying cosmetic attributes is experimental and may change in the future (see issue #338).

Parameters

attr_namestr: Name of the cosmetic attribute to delete.

find_matches(entity, unique=False)

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

Parameters

entityopenff.toolkit.topology.Topology: Topology to search.
uniquebool, default=False: If False, SMARTS matching will enumerate every valid permutation of matching atoms. If True, only one order of each unique match will be returned.

Returns

matchesValenceDict[Tuple[int], ParameterHandler._Match]: 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. When multiple attrs are passed, parameters that have any (not all) matching attributes are returned.

Parameters

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

Returns

paramslist of ParameterType objects: A list of matching ParameterType objects

Examples

Create a parameter handler and populate it with some data.

>>> from openmm import unit
>>> handler = BondHandler(skip_version_check=True)
>>> handler.add_parameter(
...     {
...         'smirks': '[*:1]-[*:2]',
...         'length': 1*unit.angstrom,
...         'k': 10*unit.kilocalorie_per_mole/unit.angstrom**2,
...     }
... )

Look up, from this handler, all parameters matching some SMIRKS pattern

>>> handler.get_parameter({'smirks': '[*:1]-[*:2]'})
[<BondType with smirks: [*:1]-[*:2]  length: 1 A  k: 10 kcal/(A**2 mol)  >]

property known_kwargs: List of kwargs that can be parsed by the function.

mark_charges_assigned(ref_mol, topology)

Record that charges have been assigned for a reference molecule.

Parameters

ref_molopenff.toolkit.topology.Molecule: The molecule to mark as having charges assigned
topologyopenff.toolkit.topology.Topology: The topology to record this information on.

property 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 OpenMM System following parameter assignment, if needed.

Parameters

topologyopenff.toolkit.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.
systemopenmm.System: The OpenMM System object to add the Force (or append new parameters) to.

to_dict(discard_cosmetic_attributes=False)

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

Parameters

discard_cosmetic_attributesbool, optional. Default = False.: 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.