openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler¶
-
class
openff.toolkit.typing.engines.smirnoff.parameters.
ParameterHandler
(allow_cosmetic_attributes=False, skip_version_check=False, **kwargs)[source]¶ Base class for parameter handlers.
Parameter handlers are configured with some global parameters for a given section. They may also contain a
ParameterList
populated withParameterType
objects if they are responsible for assigning SMIRKS-based parameters.Warning
This API is experimental and subject to change.
- Attributes
TAGNAME
The name of this ParameterHandler corresponding to the SMIRNOFF tag name
known_kwargs
List of kwargs that can be parsed by the function.
parameters
The ParameterList that holds this ParameterHandler’s parameter objects
- version
Methods
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.attribute_is_cosmetic
(attr_name)Determine whether an attribute of this object is cosmetic.
check_handler_compatibility
(handler_kwargs)Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler.
delete_cosmetic_attribute
(attr_name)Delete a cosmetic attribute from this object.
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
(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.
assign_partial_bond_orders_from_molecules
check_partial_bond_orders_from_molecules_duplicates
-
__init__
(allow_cosmetic_attributes=False, skip_version_check=False, **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.
- 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_handler_compatibility
(handler_kwargs)Checks if a set of kwargs used to create a ParameterHandler are compatible with this ParameterHandler.
check_partial_bond_orders_from_molecules_duplicates
(pb_mols)delete_cosmetic_attribute
(attr_name)Delete a cosmetic attribute from this object.
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
(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
The name of this ParameterHandler corresponding to the SMIRNOFF tag name
List of kwargs that can be parsed by the function.
The ParameterList that holds this ParameterHandler’s parameter objects
version
-
property
parameters
¶ The ParameterList that holds this ParameterHandler’s parameter objects
-
property
TAGNAME
¶ The name of this ParameterHandler corresponding to the SMIRNOFF tag name
- Returns
- handler_namestr
The name of this parameter handler
-
property
known_kwargs
¶ List of kwargs that can be parsed by the function.
-
check_handler_compatibility
(handler_kwargs)[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.
- Parameters
- handler_kwargsdict
The kwargs that would be used to construct
- Raises
- IncompatibleParameterError if handler_kwargs are incompatible with existing parameters.
-
add_parameter
(parameter_kwargs=None, parameter=None, after=None, before=None)[source]¶ 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 that one of (parameter_kwargs, parameter) must be specified
- Note that when `before` and `after` are both None, the new parameter will be appended
to the END of the parameter list.
- Note that when `before` and `after` are both specified, the new parameter
will be added immediately after the parameter matching the after pattern or index.
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 simtk 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']
-
get_parameter
(parameter_attrs)[source]¶ 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 simtk 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) >]
-
find_matches
(entity)[source]¶ Find the elements of the topology/molecule matched by a parameter type.
- Parameters
- entityopenff.toolkit.topology.Topology
Topology to search.
- Returns
- matchesValenceDict[Tuple[int], ParameterHandler._Match]
matches[particle_indices]
is theParameterType
object matching the tuple of particle indices inentity
.
-
assign_parameters
(topology, system)[source]¶ 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.
- systemsimtk.openmm.System
The OpenMM System object to add the Force (or append new parameters) to.
-
postprocess_system
(topology, system, **kwargs)[source]¶ 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.
- systemsimtk.openmm.System
The OpenMM System object to add the Force (or append new parameters) to.
-
to_dict
(discard_cosmetic_attributes=False)[source]¶ 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.
-
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.