BondHandler

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

Handle SMIRNOFF <Bonds> tags

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.

attribute_is_cosmetic(attr_name)

Determine whether an attribute of this object is cosmetic.

check_handler_compatibility(other_handler)

Checks whether this ParameterHandler encodes compatible physics as another ParameterHandler.

create_force(*args, **kwarsg)

Deprecated since version 0.11.0.

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.

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

fractional_bondorder_interpolation

fractional_bondorder_method

known_kwargs

List of kwargs that can be parsed by the function.

parameters

The ParameterList that holds this ParameterHandler's parameter objects

potential

version

class BondType(**kwargs)[source]

A SMIRNOFF bond type

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 OpenFF 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.

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.

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 OpenFF 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.

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

  • 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

  • behavior (Note the following) –

    • 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 specification: https://openforcefield.github.io/standards/standards/smirnoff/#smirnoff-parameter-specification-is-hierarchical

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 / unit.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']
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.

create_force(*args, **kwarsg)

Deprecated since version 0.11.0: This method was deprecated in v0.11.0, no longer has any functionality, and will soon be removed. Use the OpenFF Interchange package instead.

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.

find_matches(entity, unique=False)

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

Parameters
  • entity (Topology) – Topology to search.

  • unique (bool, 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

matches (ValenceDict[Tuple[int], ParameterHandler._Match]) – matches[atom_indices] is the ParameterType object matching the tuple of atom 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_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 / unit.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.

property parameters

The ParameterList that holds this ParameterHandler’s parameter objects

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.