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>
tagsWarning
This API is experimental and subject to change.
- 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
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_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.
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.
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.
vdWType
(**kwargs)A SMIRNOFF vdWForce type.
assign_partial_bond_orders_from_molecules
check_partial_bond_orders_from_molecules_duplicates
create_force
-
__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)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
The name of this ParameterHandler corresponding to the SMIRNOFF tag name
combining_rules
cutoff
List of kwargs that can be parsed by the function.
method
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.
- Attributes
- epsilon
- id
- parent_id
- rmin_half
- sigma
- smirks
Methods
add_cosmetic_attribute
(attr_name, attr_value)Add a cosmetic attribute to this object.
attribute_is_cosmetic
(attr_name)Determine whether an attribute of this object is cosmetic.
delete_cosmetic_attribute
(attr_name)Delete a cosmetic attribute from this object.
to_dict
([discard_cosmetic_attributes, …])Convert this object to dict format.
-
to_dict
(discard_cosmetic_attributes=False, duplicate_attributes=None)[source]¶ Convert this object to dict format.
The returning dictionary contains all the
ParameterAttribute
andIndexedParameterAttribute
as well as cosmetic attributes ifdiscard_cosmetic_attributes
isFalse
.- 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 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']
-
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.
- systemsimtk.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_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)¶ 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
.
-
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 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) >]
-
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.
- systemsimtk.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_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.