openforcefield.typing.engines.smirnoff.parameters.ParameterType

class openforcefield.typing.engines.smirnoff.parameters.ParameterType(smirks, allow_cosmetic_attributes=False, **kwargs)

Base class for SMIRNOFF parameter types.

This base class provides utilities to create new parameter types. See the below for examples of how to do this.

Warning

This API is experimental and subject to change.

See also

ParameterAttribute

IndexedParameterAttribute

Examples

This class allows to define new parameter types by just listing its attributes. In the example below, _VALENCE_TYPE AND _ELEMENT_NAME are used for the validation of the SMIRKS pattern associated to the parameter and the automatic serialization/deserialization into a dict.

>>> class MyBondParameter(ParameterType):
...     _VALENCE_TYPE = 'Bond'
...     _ELEMENT_NAME = 'Bond'
...     length = ParameterAttribute(unit=unit.angstrom)
...     k = ParameterAttribute(unit=unit.kilocalorie_per_mole / unit.angstrom**2)
...

The parameter automatically inherits the required smirks attribute from ParameterType. Associating a unit to a ParameterAttribute cause the attribute to accept only values in compatible units and to parse string expressions.

>>> my_par = MyBondParameter(
...     smirks='[*:1]-[*:2]',
...     length='1.01 * angstrom',
...     k=5 * unit.kilocalorie_per_mole / unit.angstrom**2
... )
>>> my_par.length
Quantity(value=1.01, unit=angstrom)
>>> my_par.k = 3.0 * unit.gram
Traceback (most recent call last):
...
openforcefield.utils.utils.IncompatibleUnitError: k=3.0 g should have units of kilocalorie/(angstrom**2*mole)

Each attribute can be made optional by specifying a default value, and you can attach a converter function by passing a callable as an argument or through the decorator syntax.

>>> class MyParameterType(ParameterType):
...     _VALENCE_TYPE = 'Atom'
...     _ELEMENT_NAME = 'Atom'
...
...     attr_optional = ParameterAttribute(default=2)
...     attr_all_to_float = ParameterAttribute(converter=float)
...     attr_int_to_float = ParameterAttribute()
...
...     @attr_int_to_float.converter
...     def attr_int_to_float(self, attr, value):
...         # This converter converts only integers to floats
...         # and raise an exception for the other types.
...         if isinstance(value, int):
...             return float(value)
...         elif not isinstance(value, float):
...             raise TypeError(f"Cannot convert '{value}' to float")
...         return value
...
>>> my_par = MyParameterType(smirks='[*:1]', attr_all_to_float='3.0', attr_int_to_float=1)
>>> my_par.attr_optional
2
>>> my_par.attr_all_to_float
3.0
>>> my_par.attr_int_to_float
1.0

The float() function can convert strings to integers, but our custom converter forbids it

>>> my_par.attr_all_to_float = '2.0'
>>> my_par.attr_int_to_float = '4.0'
Traceback (most recent call last):
...
TypeError: Cannot convert '4.0' to float

Parameter attributes that can be indexed can be handled with the IndexedParameterAttribute. These support unit validation and converters exactly as ``ParameterAttribute``s, but the validation/conversion is performed for each indexed attribute.

>>> class MyTorsionType(ParameterType):
...     _VALENCE_TYPE = 'ProperTorsion'
...     _ELEMENT_NAME = 'Proper'
...     periodicity = IndexedParameterAttribute(converter=int)
...     k = IndexedParameterAttribute(unit=unit.kilocalorie_per_mole)
...
>>> my_par = MyTorsionType(
...     smirks='[*:1]-[*:2]-[*:3]-[*:4]',
...     periodicity1=2,
...     k1=5 * unit.kilocalorie_per_mole,
...     periodicity2='3',
...     k2=6 * unit.kilocalorie_per_mole,
... )
>>> my_par.periodicity
[2, 3]

Indexed attributes, can be accessed both as a list or as their indexed parameter name.

>>> my_par.periodicity2 = 6
>>> my_par.periodicity[0] = 1
>>> my_par.periodicity
[1, 6]

Attributes

smirksstr

The SMIRKS pattern that this parameter matches.

idstr or None

An optional identifier for the parameter.

parent_idstr or None

Optionally, the identifier of the parameter of which this parameter is a specialization.

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.

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

Create a ParameterType.

Parameters

smirksstr

The SMIRKS match for the provided parameter type.

allow_cosmetic_attributesbool optional. Default = False

Whether to permit non-spec kwargs (“cosmetic attributes”). If True, non-spec kwargs will be stored as an attribute of this parameter which can be accessed and written out. Otherwise an exception will be raised.

Methods

__init__(smirks[, allow_cosmetic_attributes])	Create a ParameterType.
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.

Attributes

id	A descriptor for ParameterType attributes.
parent_id	A descriptor for ParameterType attributes.
smirks	A descriptor for ParameterType attributes.