openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler

class openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler(**kwargs)[source]

Handle SMIRNOFF <VirtualSites> tags

TODO: Add example usage/documentation

Warning

This API is experimental and subject to change.

__init__(**kwargs)[source]

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

Parameters

allow_cosmetic_attributes (bool, 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.
**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_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)
`create_openff_virtual_sites`(topology)	Modifies the input topology to contain VirtualSites assigned by this handler.
`delete_cosmetic_attribute`(attr_name)	Delete a cosmetic attribute from this object.
`find_matches`(entity[, expand_permutations, ...])	Find the virtual sites 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.
`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.
`register_virtual_site_type`(vsite_name, vsite_cls)	Register an implemented virtual site type.
`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
`exclusion_policy`
`known_kwargs`	List of kwargs that can be parsed by the function.
`parameters`	The ParameterList that holds this ParameterHandler's parameter objects
`version`
`virtual_site_types`	Return the dictionary of registered virtual site types

add_parameter(parameter_kwargs=None, parameter=None, after=None, before=None)[source]

Add a parameter to the force field, ensuring all parameters are valid. This method differs from other handlers in that it uses a plugin-style enable/disable type system

Parameters

parameter_kwargs (dict, optional) – The kwargs to pass to the ParameterHandler.INFOTYPE (a ParameterType) constructor
parameter (the new) – A ParameterType to add to the ParameterHandler
after (str or int, optional) – The SMIRKS pattern (if str) or index (if int) of the parameter directly before where the new parameter will be added
before (str, optional) – The SMIRKS pattern (if str) or index (if int) of the parameter directly after where the new parameter will be added
(parameter_kwargs (Note that one of) –
specified (Note that when before and after are both) –
None (Note that when before and after are both) – to the END of the parameter list.
appended (the new parameter will be) – to the END of the parameter list.
specified – will be added immediately after the parameter matching the after pattern or index.
parameter – will be added immediately after the parameter matching the after pattern or index.

register_virtual_site_type(vsite_name, vsite_cls, replace=False)[source]

Register an implemented virtual site type. Doing this must be done to pass the validation and option checking. To disable a type, register the name with None and replace=True

Parameters

vsite_name (str) – The name of the type. This name must be what is found in the “type” attribute in the OFFXML format
vsite_cls (Any) – The class to register the name with that implements the type.

Returns

None

property virtual_site_types

Return the dictionary of registered virtual site types

Parameters: None –
Returns: virtual_site_types (dict) – A list of virtual site types already registered, paired with their class that implements them

class VirtualSiteType(**kwargs)[source]

A SMIRNOFF virtual site base type

Warning

This API is experimental and subject to change.

transformed_dict_cls: alias of ValenceDict

classmethod vsite_type()[source]: The type of this virtual site as represented in the SMIRNOFF specification

Warning

This API is experimental and subject to change.

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_name (str) – Name of the attribute to define for this object.
attr_value (str) – 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_name (str) – The attribute name to check
Returns: is_cosmetic (bool) – 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_name (str) – Name of the cosmetic attribute to delete.

to_dict(discard_cosmetic_attributes=False, duplicate_attributes=None)

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_attributes (bool, optional. Default = False) – Whether to discard non-spec attributes of this object
duplicate_attributes (list of string, optional. Default = None) – A list of names of attributes that redundantly decsribe data and should be discarded during serializaiton

Returns

smirnoff_dict (dict) – The SMIRNOFF-compliant dict representation of this object.

class VirtualSiteBondChargeType(**kwargs)[source]

A SMIRNOFF virtual site bond charge type

Warning

This API is experimental and subject to change.

add_virtual_site(molecule, orientations, replace=False)[source]

Add a virtual site to the molecule

Parameters

molecule (openff.toolkit.topology.molecule.Molecule) – The molecule to add the virtual site to
orientations (List[Tuple[int]]) – A list of orientation tuples which define the permuations used to contruct the geometry of the virtual site particles
replace (bool, default=False) – Replace this virtual site if it already exists in the molecule

Returns

off_idx (int) – The index of the first particle added due to this virtual site
.. warning :: This API is experimental and subject to change.

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_name (str) – Name of the attribute to define for this object.
attr_value (str) – 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_name (str) – The attribute name to check
Returns: is_cosmetic (bool) – 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_name (str) – Name of the cosmetic attribute to delete.

to_dict(discard_cosmetic_attributes=False, duplicate_attributes=None)

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_attributes (bool, optional. Default = False) – Whether to discard non-spec attributes of this object
duplicate_attributes (list of string, optional. Default = None) – A list of names of attributes that redundantly decsribe data and should be discarded during serializaiton

Returns

smirnoff_dict (dict) – The SMIRNOFF-compliant dict representation of this object.

transformed_dict_cls: alias of ValenceDict

classmethod vsite_type(): The type of this virtual site as represented in the SMIRNOFF specification

Warning

This API is experimental and subject to change.

class VirtualSiteMonovalentLonePairType(**kwargs)[source]

A SMIRNOFF monovalent lone pair virtual site type

Warning

This API is experimental and subject to change.

add_virtual_site(molecule, orientations, replace=False)[source]

Add a virtual site to the molecule

Parameters

molecule (openff.toolkit.topology.molecule.Molecule) – The molecule to add the virtual site to
orientations (List[Tuple[int]]) – A list of orientation tuples which define the permuations used to contruct the geometry of the virtual site particles
replace (bool, default=False) – Replace this virtual site if it already exists in the molecule

Returns

off_idx (int) – The index of the first particle added due to this virtual site
.. warning :: This API is experimental and subject to change.

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_name (str) – Name of the attribute to define for this object.
attr_value (str) – 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_name (str) – The attribute name to check
Returns: is_cosmetic (bool) – 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_name (str) – Name of the cosmetic attribute to delete.

to_dict(discard_cosmetic_attributes=False, duplicate_attributes=None)

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_attributes (bool, optional. Default = False) – Whether to discard non-spec attributes of this object
duplicate_attributes (list of string, optional. Default = None) – A list of names of attributes that redundantly decsribe data and should be discarded during serializaiton

Returns

smirnoff_dict (dict) – The SMIRNOFF-compliant dict representation of this object.

transformed_dict_cls: alias of ValenceDict

classmethod vsite_type(): The type of this virtual site as represented in the SMIRNOFF specification

Warning

This API is experimental and subject to change.

class VirtualSiteDivalentLonePairType(**kwargs)[source]

A SMIRNOFF divalent lone pair virtual site type

Warning

This API is experimental and subject to change.

add_virtual_site(molecule, orientations, replace=False)[source]

Add a virtual site to the molecule

Parameters

molecule (openff.toolkit.topology.molecule.Molecule) – The molecule to add the virtual site to
orientations (List[Tuple[int]]) – A list of orientation tuples which define the permuations used to contruct the geometry of the virtual site particles
replace (bool, default=False) – Replace this virtual site if it already exists in the molecule

Returns

off_idx (int) – The index of the first particle added due to this virtual site
.. warning :: This API is experimental and subject to change.

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_name (str) – Name of the attribute to define for this object.
attr_value (str) – 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_name (str) – The attribute name to check
Returns: is_cosmetic (bool) – 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_name (str) – Name of the cosmetic attribute to delete.

to_dict(discard_cosmetic_attributes=False, duplicate_attributes=None)

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_attributes (bool, optional. Default = False) – Whether to discard non-spec attributes of this object
duplicate_attributes (list of string, optional. Default = None) – A list of names of attributes that redundantly decsribe data and should be discarded during serializaiton

Returns

smirnoff_dict (dict) – The SMIRNOFF-compliant dict representation of this object.

transformed_dict_cls: alias of ValenceDict

classmethod vsite_type(): The type of this virtual site as represented in the SMIRNOFF specification

Warning

This API is experimental and subject to change.

class VirtualSiteTrivalentLonePairType(**kwargs)[source]

A SMIRNOFF trivalent lone pair virtual site type

Warning

This API is experimental and subject to change.

transformed_dict_cls: alias of ImproperDict

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_name (str) – Name of the attribute to define for this object.
attr_value (str) – 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_name (str) – The attribute name to check
Returns: is_cosmetic (bool) – 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_name (str) – Name of the cosmetic attribute to delete.

to_dict(discard_cosmetic_attributes=False, duplicate_attributes=None)

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_attributes (bool, optional. Default = False) – Whether to discard non-spec attributes of this object
duplicate_attributes (list of string, optional. Default = None) – A list of names of attributes that redundantly decsribe data and should be discarded during serializaiton

Returns

smirnoff_dict (dict) – The SMIRNOFF-compliant dict representation of this object.

classmethod vsite_type(): The type of this virtual site as represented in the SMIRNOFF specification

Warning

This API is experimental and subject to change.

add_virtual_site(molecule, orientations, replace=False)[source]

Add a virtual site to the molecule

Parameters

molecule (openff.toolkit.topology.molecule.Molecule) – The molecule to add the virtual site to
orientations (List[Tuple[int]]) – A list of orientation tuples which define the permuations used to contruct the geometry of the virtual site particles
replace (bool, default=False) – Replace this virtual site if it already exists in the molecule

Returns

off_idx (int) – The index of the first particle added due to this virtual site
.. warning :: This API is experimental and subject to change.

property TAGNAME

The name of this ParameterHandler corresponding to the SMIRNOFF tag name

Returns: handler_name (str) – 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_name (str) – Name of the attribute to define for this object.
attr_value (str) – The value of the attribute to define for this object.

assign_parameters(topology, system)

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

Parameters

topology (openff.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.
system (openmm.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_name (str) – The attribute name to check
Returns: is_cosmetic (bool) – 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_mol (openff.toolkit.topology.Molecule) – The molecule to check for having charges assigned
topology (openff.toolkit.topology.Topology) – The topology to query for this information

Returns

charges_assigned (bool) – 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_name (str) – Name of the cosmetic attribute to delete.

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_attrs (dict of {attr: value}) – The attrs mapped to desired values (for example {“smirks”: “[:1]~[#16:2]=,:[#6:3]~[:4]”, “id”: “t105”} )
Returns: params (list 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_mol (openff.toolkit.topology.Molecule) – The molecule to mark as having charges assigned
topology (openff.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

topology (openff.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.
system (openmm.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_attributes (bool, optional. Default = False.) – Whether to discard non-spec parameter and header attributes in this ParameterHandler.
Returns: smirnoff_data (OrderedDict) – SMIRNOFF-spec compliant representation of this ParameterHandler and its internal ParameterList.

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

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_handler (a ParameterHandler object) – The handler to compare to.

Raises

IncompatibleParameterError if handler_kwargs are incompatible with –
existing parameters. –

find_matches(entity, expand_permutations=True, unique=False)[source]

Find the virtual sites in the topology/molecule matched by a parameter type.

Parameters: entity (openff.toolkit.topology.Topology) – Topology to search.
Returns: matches (Dict[Tuple[int], ParameterHandler._Match]) – matches[atom_indices] is the ParameterType object matching the n-tuple of atom indices in entity.

create_openff_virtual_sites(topology)[source]

Modifies the input topology to contain VirtualSites assigned by this handler.

Parameters: topology (openff.toolkit.topology.Topology) – Topology to add virtual sites to.