# Source code for openforcefield.typing.engines.smirnoff.parameters

    #!/usr/bin/env python

    #=============================================================================================
    # MODULE DOCSTRING
    #=============================================================================================
    """
    Parameter handlers for the SMIRNOFF force field engine

    This file contains standard parameter handlers for the SMIRNOFF force field engine.
    These classes implement the object model for self-contained parameter assignment.
    New pluggable handlers can be created by creating subclasses of :class:`ParameterHandler`.

    """

    __all__ = [
        'SMIRNOFFSpecError',
        'IncompatibleParameterError',
        'UnassignedValenceParameterException',
        'UnassignedBondParameterException',
        'UnassignedAngleParameterException',
        'NonbondedMethod',
        'ParameterList',
        'ParameterType',
        'ParameterHandler',
        'ParameterAttribute',
        'IndexedParameterAttribute',
        'IndexedMappedParameterAttribute',
        'ConstraintHandler',
        'BondHandler',
        'AngleHandler',
        'ProperTorsionHandler',
        'ImproperTorsionHandler',
        'vdWHandler',
        'GBSAHandler'
    ]

    #=============================================================================================
    # GLOBAL IMPORTS
    #=============================================================================================

    import copy
    from collections import OrderedDict, defaultdict
    from enum import Enum
    import functools
    import inspect
    import logging
    import re

    from simtk import openmm, unit

    from openforcefield.utils import attach_units,  \
        extract_serialized_units_from_dict, MessageException, \
        object_to_quantity, GLOBAL_TOOLKIT_REGISTRY
    from openforcefield.topology import ValenceDict, ImproperDict, SortedDict
    from openforcefield.topology.molecule import Molecule
    from openforcefield.typing.chemistry import ChemicalEnvironment
    from openforcefield.utils import IncompatibleUnitError
    from openforcefield.utils.collections import ValidatedList, ValidatedDict

    #=============================================================================================
    # CONFIGURE LOGGER
    #=============================================================================================

    logger = logging.getLogger(__name__)

    #======================================================================
    # CUSTOM EXCEPTIONS
    #======================================================================

    class SMIRNOFFSpecError(MessageException):
        """
        Exception for when data is noncompliant with the SMIRNOFF data specification.
        """
        pass

    class IncompatibleParameterError(MessageException):
        """
        Exception for when a set of parameters is scientifically/technically incompatible with another
        """
        pass

    class UnassignedValenceParameterException(Exception):
        """Exception raised when there are valence terms for which a ParameterHandler can't find parameters."""
        pass

    class UnassignedBondParameterException(UnassignedValenceParameterException):
        """Exception raised when there are bond terms for which a ParameterHandler can't find parameters."""
        pass

    class UnassignedAngleParameterException(UnassignedValenceParameterException):
        """Exception raised when there are angle terms for which a ParameterHandler can't find parameters."""
        pass

    class UnassignedProperTorsionParameterException(UnassignedValenceParameterException):
        """Exception raised when there are proper torsion terms for which a ParameterHandler can't find parameters."""
        pass

    class UnassignedMoleculeChargeException(Exception):
        """Exception raised when no charge method is able to assign charges to a molecule."""
        pass

    class NonintegralMoleculeChargeException(Exception):
        """Exception raised when the partial charges on a molecule do not sum up to its formal charge."""
        pass

    #======================================================================
    # ENUM TYPES
    #======================================================================

    class NonbondedMethod(Enum):
        """
        An enumeration of the nonbonded methods
        """
        NoCutoff = 0
        CutoffPeriodic = 1
        CutoffNonPeriodic = 2
        Ewald = 3
        PME = 4

    #======================================================================
    # PARAMETER ATTRIBUTES
    #======================================================================

    # TODO: Think about adding attrs to the dependencies and inherit from attr.ib
    class ParameterAttribute:
        """A descriptor for ``ParameterType`` attributes.

        The descriptors allows associating to the parameter a default value,
        which makes the attribute optional, a unit, and a custom converter.

        Because we may want to have ``None`` as a default value, required
        attributes have the ``default`` set to the special type ``UNDEFINED``.

        Converters can be both static or instance functions/methods with
        respective signatures

        converter(value): -> converted_value
        converter(instance, parameter_attribute, value): -> converted_value

        A decorator syntax is available (see example below).

        Parameters
        ----------
        default : object, optional
            When specified, the descriptor makes this attribute optional by
            attaching a default value to it.
        unit : simtk.unit.Quantity, optional
            When specified, only quantities with compatible units are allowed
            to be set, and string expressions are automatically parsed into a
            ``Quantity``.
        converter : callable, optional
            An optional function that can be used to convert values before
            setting the attribute.

        See Also
        --------
        IndexedParameterAttribute
            A parameter attribute with multiple terms.

        Examples
        --------

        Create a parameter type with an optional and a required attribute.

        >>> class MyParameter:
        ...     attr_required = ParameterAttribute()
        ...     attr_optional = ParameterAttribute(default=2)
        ...
        >>> my_par = MyParameter()

        Even without explicit assignment, the default value is returned.

        >>> my_par.attr_optional
        2

        If you try to access an attribute without setting it first, an
        exception is raised.

        >>> my_par.attr_required
        Traceback (most recent call last):
        ...
        AttributeError: 'MyParameter' object has no attribute '_attr_required'

        The attribute allow automatic conversion and validation of units.

        >>> from simtk import unit
        >>> class MyParameter:
        ...     attr_quantity = ParameterAttribute(unit=unit.angstrom)
        ...
        >>> my_par = MyParameter()
        >>> my_par.attr_quantity = '1.0 * nanometer'
        >>> my_par.attr_quantity
        Quantity(value=1.0, unit=nanometer)
        >>> my_par.attr_quantity = 3.0
        Traceback (most recent call last):
        ...
        openforcefield.utils.utils.IncompatibleUnitError: attr_quantity=3.0 dimensionless should have units of angstrom

        You can attach a custom converter to an attribute.

        >>> class MyParameter:
        ...     # Both strings and integers convert nicely to floats with float().
        ...     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 float
        ...         # 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 = MyParameter()

        attr_all_to_float accepts and convert to float both strings and integers

        >>> my_par.attr_all_to_float = 1
        >>> my_par.attr_all_to_float
        1.0
        >>> my_par.attr_all_to_float = '2.0'
        >>> my_par.attr_all_to_float
        2.0

        The custom converter associated to attr_int_to_float converts only integers instead.
        >>> my_par.attr_int_to_float = 3
        >>> my_par.attr_int_to_float
        3.0
        >>> my_par.attr_int_to_float = '4.0'
        Traceback (most recent call last):
        ...
        TypeError: Cannot convert '4.0' to float

        """

        class UNDEFINED:
            """Custom type used by ``ParameterAttribute`` to differentiate between ``None`` and undeclared default."""
            pass

        def __init__(self, default=UNDEFINED, unit=None, converter=None):
            self.default = default
            self._unit = unit
            self._converter = converter

        def __set_name__(self, owner, name):
            self._name = '_' + name

        @property
        def name(self):
            # Get rid of the initial underscore.
            return self._name[1:]

        def __get__(self, instance, owner):
            if instance is None:
                # This is called from the class. Return the descriptor object.
                return self

            try:
                return getattr(instance, self._name)
            except AttributeError:
                # The attribute has not initialized. Check if there's a default.
                if self.default is ParameterAttribute.UNDEFINED:
                    raise
                return self.default

        def __set__(self, instance, value):
            # Convert and validate the value.
            value = self._convert_and_validate(instance, value)
            setattr(instance, self._name, value)

        def converter(self, converter):
            """Create a new ParameterAttribute with an associated converter.

            This is meant to be used as a decorator (see main examples).
            """
            return self.__class__(default=self.default, converter=converter)

        def _convert_and_validate(self, instance, value):
            """Convert to Quantity, validate units, and call custom converter."""
            # The default value is always allowed.
            if self._is_valid_default(value):
                return value
            # Convert and validate units.
            value = self._validate_units(value)
            # Call the custom converter before setting the value.
            value = self._call_converter(value, instance)
            return value

        def _is_valid_default(self, value):
            """Return True if this is a defined default value."""
            return self.default is not ParameterAttribute.UNDEFINED and value == self.default

        def _validate_units(self, value):
            """Convert strings expressions to Quantity and validate the units if requested."""
            if self._unit is not None:
                # Convert eventual strings to Quantity objects.
                value = object_to_quantity(value)

                # Check if units are compatible.
                try:
                    if not self._unit.is_compatible(value.unit):
                        raise IncompatibleUnitError(f'{self.name}={value} should have units of {self._unit}')
                except AttributeError:
                    # This is not a Quantity object.
                    raise IncompatibleUnitError(f'{self.name}={value} should have units of {self._unit}')
            return value

        def _call_converter(self, value, instance):
            """Correctly calls static and instance converters."""
            if self._converter is not None:
                try:
                    # Static function.
                    return self._converter(value)
                except TypeError:
                    # Instance method.
                    return self._converter(instance, self, value)
            return value

    class IndexedParameterAttribute(ParameterAttribute):
        """The attribute of a parameter with an unspecified number of terms.

        Some parameters can be associated to multiple terms, For example,
        torsions have parameters such as k1, k2, ..., and ``IndexedParameterAttribute``
        can be used to encapsulate the sequence of terms.

        The only substantial difference with ``ParameterAttribute`` is that
        only sequences are supported as values and converters and units are
        checked on each element of the sequence.

        Currently, the descriptor makes the sequence immutable. This is to
        avoid that an element of the sequence could be set without being
        properly validated. In the future, the data could be wrapped in a
        safe list that would safely allow mutability.

        Parameters
        ----------
        default : object, optional
            When specified, the descriptor makes this attribute optional by
            attaching a default value to it.
        unit : simtk.unit.Quantity, optional
            When specified, only sequences of quantities with compatible units
            are allowed to be set.
        converter : callable, optional
            An optional function that can be used to validate and cast each
            element of the sequence before setting the attribute.

        See Also
        --------
        ParameterAttribute
            A simple parameter attribute.

        Examples
        --------

        Create an optional indexed attribute with unit of angstrom.

        >>> from simtk import unit
        >>> class MyParameter:
        ...     length = IndexedParameterAttribute(default=None, unit=unit.angstrom)
        ...
        >>> my_par = MyParameter()
        >>> my_par.length is None
        True

        Strings are parsed into Quantity objects.

        >>> my_par.length = ['1 * angstrom', 0.5 * unit.nanometer]
        >>> my_par.length[0]
        Quantity(value=1, unit=angstrom)

        Similarly, custom converters work as with ``ParameterAttribute``, but
        they are used to validate each value in the sequence.

        >>> class MyParameter:
        ...     attr_indexed = IndexedParameterAttribute(converter=float)
        ...
        >>> my_par = MyParameter()
        >>> my_par.attr_indexed = [1, '1.0', '1e-2', 4.0]
        >>> my_par.attr_indexed
        [1.0, 1.0, 0.01, 4.0]

        """
        def _convert_and_validate(self, instance, value):
            """Overwrite ParameterAttribute._convert_and_validate to make the value a ValidatedList."""
            # The default value is always allowed.
            if self._is_valid_default(value):
                return value

            # We push the converters into a ValidatedList so that we can make
            # sure that elements are validated correctly when they are modified
            # after their initialization.
            # ValidatedList expects converters that take the value as a single
            # argument so we create a partial function with the instance assigned.
            static_converter = functools.partial(self._call_converter, instance=instance)
            value = ValidatedList(value, converter=[self._validate_units, static_converter])

            return value

    class IndexedMappedParameterAttribute(ParameterAttribute):
        """The attribute of a parameter with an unspecified number of terms, where
        each term is a mapping.

        Some parameters can be associated to multiple terms,
        where those terms have multiple components.
        For example, torsions with fractional bond orders have parameters such as
        k1_bondorder1, k1_bondorder2, k2_bondorder1, k2_bondorder2, ..., and
        ``IndexedMappedParameterAttribute`` can be used to encapsulate the sequence of
        terms as mappings (typically, `dict`s) of their components.

        The only substantial difference with ``IndexedParameterAttribute`` is that
        only sequences of mappings are supported as values and converters and units are
        checked on each component of each element in the sequence.

        Currently, the descriptor makes the sequence immutable. This is to
        avoid that an element of the sequence could be set without being
        properly validated. In the future, the data could be wrapped in a
        safe list that would safely allow mutability.

        Parameters
        ----------
        default : object, optional
            When specified, the descriptor makes this attribute optional by
            attaching a default value to it.
        unit : simtk.unit.Quantity, optional
            When specified, only sequences of mappings where values are quantities with
            compatible units are allowed to be set.
        converter : callable, optional
            An optional function that can be used to validate and cast each
            component of each element of the sequence before setting the attribute.

        See Also
        --------
        IndexedParameterAttribute
            A parameter attribute representing a sequence.

        Examples
        --------

        Create an optional indexed attribute with unit of angstrom.

        >>> from simtk import unit
        >>> class MyParameter:
        ...     length = IndexedMappedParameterAttribute(default=None, unit=unit.angstrom)
        ...
        >>> my_par = MyParameter()
        >>> my_par.length is None
        True

        Strings are parsed into Quantity objects.

        >>> my_par.length = [{1:'1 * angstrom'}, {1: 0.5 * unit.nanometer}]
        >>> my_par.length[0]
        {1: Quantity(value=1, unit=angstrom)}

        Similarly, custom converters work as with ``ParameterAttribute``, but
        they are used to validate each value in the sequence.

        >>> class MyParameter:
        ...     attr_indexed = IndexedMappedParameterAttribute(converter=float)
        ...
        >>> my_par = MyParameter()
        >>> my_par.attr_indexed = [{1: 1}, {2: '1.0', 3: '1e-2'}, {4: 4.0}]
        >>> my_par.attr_indexed
        [{1: 1.0}, {2: 1.0, 3: 0.01}, {4: 4.0}]

        """
        def _convert_and_validate(self, instance, value):
            """Overwrite ParameterAttribute._convert_and_validate to make the value a ValidatedList."""
            # The default value is always allowed.
            if self._is_valid_default(value):
                return value

            # We push the converters into a ValidatedListMapping so that we can make
            # sure that elements are validated correctly when they are modified
            # after their initialization.
            # ValidatedListMapping expects converters that take the value as a single
            # argument so we create a partial function with the instance assigned.
            static_converter = functools.partial(self._call_converter, instance=instance)

            value = ValidatedList(
                    [ValidatedDict(element,
                                   converter=[self._validate_units, static_converter])
                        for element in value],
                    converter=self._index_converter)

            return value

        @staticmethod
        def _index_converter(x):
            return ValidatedDict(x)

    class _ParameterAttributeHandler:
        """A base class for ``ParameterType`` and ``ParameterHandler`` objects.

        Encapsulate shared code of ``ParameterType`` and ``ParameterHandler``.
        In particular, this base class provides an ``__init__`` method that
        automatically initialize the attributes defined through the ``ParameterAttribute``
        and ``IndexedParameterAttribute`` descriptors, as well as handling
        cosmetic attributes.

        See Also
        --------
        ParameterAttribute
            A simple parameter attribute.
        IndexedParameterAttribute
            A parameter attribute with multiple terms.

        Examples
        --------

        This base class was design to encapsulate shared code between ``ParameterType``
        and ``ParameterHandler``, which both need to deal with parameter and cosmetic
        attributes.

        To create a new type/handler, you can use the ``ParameterAttribute`` descriptors.

        >>> class ParameterTypeOrHandler(_ParameterAttributeHandler):
        ...     length = ParameterAttribute(unit=unit.angstrom)
        ...     k = ParameterAttribute(unit=unit.kilocalorie_per_mole / unit.angstrom**2)
        ...

        ``_ParameterAttributeHandler`` and the descriptors take care of performing
        sanity checks on initialization and assignment of the single attributes. Because
        we attached units to the parameters, we need to pass them with compatible units.

        >>> my_par = ParameterTypeOrHandler(
        ...     length='1.01 * angstrom',
        ...     k=5 * unit.kilocalorie_per_mole / unit.angstrom**2
        ... )

        Note that ``_ParameterAttributeHandler`` took care of implementing
        a constructor, and that unit parameters support string assignments.
        These are automatically converted to ``Quantity`` objects.

        >>> my_par.length
        Quantity(value=1.01, unit=angstrom)

        While assigning incompatible units is forbidden.

        >>> 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)

        On top of type checking, the constructor implemented in ``_ParameterAttributeHandler``
        checks if some required parameters are not given.

        >>> ParameterTypeOrHandler(length=3.0*unit.nanometer)
        Traceback (most recent call last):
        ...
        openforcefield.typing.engines.smirnoff.parameters.SMIRNOFFSpecError: <class 'openforcefield.typing.engines.smirnoff.parameters.ParameterTypeOrHandler'> require the following missing parameters: ['k']. Defined kwargs are ['length']

        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 ParameterTypeOrHandler(_ParameterAttributeHandler):
        ...     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 = ParameterTypeOrHandler(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(_ParameterAttributeHandler):
        ...     periodicity = IndexedParameterAttribute(converter=int)
        ...     k = IndexedParameterAttribute(unit=unit.kilocalorie_per_mole)
        ...
        >>> my_par = MyTorsionType(
        ...     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]

        """

        def __init__(self, allow_cosmetic_attributes=False, **kwargs):
            """
            Initialize parameter and cosmetic attributes.

            Parameters
            ----------
            allow_cosmetic_attributes : bool 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.

            """
            # A list that may be populated to record the cosmetic attributes
            # read from a SMIRNOFF data source.
            self._cosmetic_attribs = []

            # Do not modify the original data.
            smirnoff_data = copy.deepcopy(kwargs)

            smirnoff_data, indexed_mapped_attr_lengths = self._process_indexed_mapped_attributes(smirnoff_data)
            smirnoff_data = self._process_indexed_attributes(smirnoff_data, indexed_mapped_attr_lengths)

            # Check for missing required arguments.
            given_attributes = set(smirnoff_data.keys())
            required_attributes = set(self._get_required_parameter_attributes().keys())
            missing_attributes = required_attributes.difference(given_attributes)
            if len(missing_attributes) != 0:
                msg = (f"{self.__class__} require the following missing parameters: {sorted(missing_attributes)}."
                       f" Defined kwargs are {sorted(smirnoff_data.keys())}")
                raise SMIRNOFFSpecError(msg)

            # Finally, set attributes of this ParameterType and handle cosmetic attributes.
            allowed_attributes = set(self._get_parameter_attributes().keys())
            for key, val in smirnoff_data.items():
                if key in allowed_attributes:
                    setattr(self, key, val)
                # Handle all unknown kwargs as cosmetic so we can write them back out
                elif allow_cosmetic_attributes:
                    self.add_cosmetic_attribute(key, val)
                else:
                    msg = (f"Unexpected kwarg ({key}: {val})  passed to {self.__class__} constructor. "
                            "If this is a desired cosmetic attribute, consider setting "
                            "'allow_cosmetic_attributes=True'")
                    raise SMIRNOFFSpecError(msg)

        def _process_indexed_mapped_attributes(self, smirnoff_data):
            # TODO: construct data structure for holding indexed_mapped attrs, which
            # will get fed into setattr
            indexed_mapped_attr_lengths = {}
            reindex = set()
            reverse = defaultdict(dict)

            kwargs = list(smirnoff_data.keys())
            for kwarg in kwargs:
                attr_name, index, key = self._split_attribute_index_mapping(kwarg)

                # Check if this is an indexed_mapped attribute.
                if ((key is not None) and
                    (index is not None) and
                    attr_name in self._get_indexed_mapped_parameter_attributes()):

                    # we start with a dict because have no guarantee of order
                    # in which we will see each kwarg
                    # we'll switch this to a list later
                    if attr_name not in smirnoff_data:
                        smirnoff_data[attr_name] = dict()
                        reindex.add(attr_name)

                    if index not in smirnoff_data[attr_name]:
                        smirnoff_data[attr_name][index] = dict()

                    smirnoff_data[attr_name][index][key] = smirnoff_data[kwarg]
                    del smirnoff_data[kwarg]

                    # build reverse mapping; needed for contiguity check below
                    if index not in reverse[attr_name]:
                        reverse[attr_name][index] = dict()
                    reverse[attr_name][index][key] = kwarg

            # turn all our top-level dicts into lists
            # catch cases where we skip an index,
            # e.g. k1_bondorder*, k3_bondorder* defined, but not k2_bondorder*
            for attr_name in reindex:
                indexed_mapping = []
                j = 0
                for i in sorted(smirnoff_data[attr_name].keys()):
                    if int(i) == j:
                        indexed_mapping.append(smirnoff_data[attr_name][i])
                        j += 1
                    else:
                        # any key will do; we are sensitive only to top-level index
                        key = sorted(reverse[attr_name][i].keys())[0]
                        kwarg = reverse[attr_name][i][key]
                        val = smirnoff_data[attr_name][i][key]

                        msg = (f"Unexpected kwarg ({kwarg}: {val})  passed to {self.__class__} constructor. "
                                "If this is a desired cosmetic attribute, consider setting "
                                "'allow_cosmetic_attributes=True'")
                        raise SMIRNOFFSpecError(msg)

                smirnoff_data[attr_name] = indexed_mapping

                # keep track of lengths; used downstream for checking against other
                # indexed attributes
                indexed_mapped_attr_lengths[attr_name] = len(smirnoff_data[attr_name])

            return smirnoff_data, indexed_mapped_attr_lengths

        def _process_indexed_attributes(self, smirnoff_data, indexed_attr_lengths=None):
            # Check for indexed attributes and stack them into a list.
            # Keep track of how many indexed attribute we find to make sure they all have the same length.

            # TODO: REFACTOR ME; try looping over contents of `smirnoff_data`, using
            # `split_attribute_index` to extract values

            if indexed_attr_lengths is None:
                indexed_attr_lengths = {}

            for attrib_basename in self._get_indexed_parameter_attributes().keys():
                index = 1
                while True:
                    attrib_w_index = '{}{}'.format(attrib_basename, index)

                    # Exit the while loop if the indexed attribute is not given.
                    # this is the stop condition
                    try:
                        attrib_w_index_value = smirnoff_data[attrib_w_index]
                    except KeyError:
                        break

                    # Check if this is the first iteration.
                    if index == 1:
                        # Check if this attribute has been specified with and without index.
                        if attrib_basename in smirnoff_data:
                            err_msg = (f"The attribute '{attrib_basename}' has been specified "
                                       f"with and without index: '{attrib_w_index}'")
                            raise TypeError(err_msg)

                        # Otherwise create the list object.
                        smirnoff_data[attrib_basename] = list()

                    # Append the new value to the list.
                    smirnoff_data[attrib_basename].append(attrib_w_index_value)

                    # Remove the indexed attribute from the kwargs as it will
                    # be exposed only as an element of the list.
                    del smirnoff_data[attrib_w_index]
                    index += 1

                # Update the lengths with this attribute (if it was found).
                if index > 1:
                    indexed_attr_lengths[attrib_basename] = len(smirnoff_data[attrib_basename])

            # Raise an error if we there are different indexed
            # attributes with a different number of terms.
            if len(set(indexed_attr_lengths.values())) > 1:
                raise TypeError('The following indexed attributes have '
                                f'different lengths: {indexed_attr_lengths}')

            return smirnoff_data

        def to_dict(self, discard_cosmetic_attributes=False):
            """
            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

            Returns
            -------
            smirnoff_dict : dict
                The SMIRNOFF-compliant dict representation of this object.

            """
            # Make a list of all attribs that should be included in the
            # returned dict (call list() to make a copy). We discard
            # optional attributes that are set to None defaults.
            attribs_to_return = list(self._get_defined_parameter_attributes().keys())

            # Start populating a dict of the attribs.
            indexed_attribs = set(self._get_indexed_parameter_attributes().keys())
            indexed_mapped_attribs = set(self._get_indexed_mapped_parameter_attributes().keys())
            smirnoff_dict = OrderedDict()

            # If attribs_to_return is ordered here, that will effectively be an informal output ordering
            for attrib_name in attribs_to_return:
                attrib_value = getattr(self, attrib_name)

                if attrib_name in indexed_mapped_attribs:
                    for idx, mapping in enumerate(attrib_value):
                        for key, val in mapping.items():
                            attrib_name_indexed, attrib_name_mapped = attrib_name.split('_')
                            smirnoff_dict[f"{attrib_name_indexed}{str(idx+1)}_{attrib_name_mapped}{key}"] = val
                elif attrib_name in indexed_attribs:
                    for idx, val in enumerate(attrib_value):
                        smirnoff_dict[attrib_name + str(idx+1)] = val
                else:
                    smirnoff_dict[attrib_name] = attrib_value

            # Serialize cosmetic attributes.
            if not(discard_cosmetic_attributes):
                for cosmetic_attrib in self._cosmetic_attribs:
                    smirnoff_dict[cosmetic_attrib] = getattr(self, '_' + cosmetic_attrib)

            return smirnoff_dict

        def __getattr__(self, item):
            """Take care of mapping indexed attributes to their respective list elements."""

            # Try matching the case where there are two indices
            # this indicates a index_mapped parameter
            attr_name, index, key = self._split_attribute_index_mapping(item)

            # Check if this is an indexed_mapped attribute.
            if ((key is not None) and
                (index is not None) and
                attr_name in self._get_indexed_mapped_parameter_attributes()):
                indexed_mapped_attr_value = getattr(self, attr_name)
                try:
                    return indexed_mapped_attr_value[index][key]
                except (IndexError, KeyError) as err:
                    if not err.args:
                        err.args=('',)
                    err.args = err.args + (f"'{item}' is out of bound for indexed attribute '{attr_name}'",)
                    raise

            # Otherwise, try indexed attribute
            # Separate the indexed attribute name from the list index.
            attr_name, index = self._split_attribute_index(item)

            # Check if this is an indexed attribute.
            if (index is not None) and attr_name in self._get_indexed_parameter_attributes():
                indexed_attr_value = getattr(self, attr_name)
                try:
                    return indexed_attr_value[index]
                except IndexError:
                    raise IndexError(f"'{item}' is out of bound for indexed attribute '{attr_name}'")

            # Otherwise, forward the search to the next class in the MRO.
            try:
                return super().__getattr__(item)
            except AttributeError as e:
                # If this fails because the next classes in the MRO do not
                # implement __getattr__(), then raise the standard Attribute error.
                if '__getattr__' in str(e):
                    raise AttributeError(f"{self.__class__} object has no attribute '{item}'")
                # Otherwise, re-raise the error from the class in the MRO.
                raise

        def __setattr__(self, key, value):
            """Take care of mapping indexed attributes to their respective list elements."""

            # Try matching the case where there are two indices
            # this indicates a index_mapped parameter
            attr_name, index, mapkey = self._split_attribute_index_mapping(key)

            # Check if this is an index_mapped attribute. avoiding an infinite
            # recursion by calling getattr() with non-existing keys.
            if ((mapkey is not None) and
                (index is not None) and
                attr_name in self._get_indexed_mapped_parameter_attributes()):
                indexed_mapped_attr_value = getattr(self, attr_name)
                try:
                    indexed_mapped_attr_value[index][mapkey] = value
                    return
                except (IndexError, KeyError) as err:
                    if not err.args:
                        err.args=('',)
                    err.args = err.args + (f"'{key}' is out of bound for indexed attribute '{attr_name}'",)
                    raise

            # Otherwise, try indexed attribute
            # Separate the indexed attribute name from the list index.
            attr_name, index = self._split_attribute_index(key)

            # Check if this is an indexed attribute. avoiding an infinite
            # recursion by calling getattr() with non-existing keys.
            if (index is not None) and (attr_name in self._get_indexed_parameter_attributes()):
                indexed_attr_value = getattr(self, attr_name)
                try:
                    indexed_attr_value[index] = value
                    return
                except IndexError:
                    raise IndexError(f"'{key}' is out of bound for indexed attribute '{attr_name}'")

            # Forward the request to the next class in the MRO.
            super().__setattr__(key, value)

        def add_cosmetic_attribute(self, 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.

            """
            setattr(self, '_'+attr_name, attr_value)
            self._cosmetic_attribs.append(attr_name)

        def delete_cosmetic_attribute(self, 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.
            """
            # TODO: Can we handle this by overriding __delattr__ instead?
            #  Would we also need to override __del__ as well to cover both deletation methods?
            delattr(self, '_'+attr_name)
            self._cosmetic_attribs.remove(attr_name)

        def attribute_is_cosmetic(self, 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.
            """
            return attr_name in self._cosmetic_attribs

        @staticmethod
        def _split_attribute_index(item):
            """Split the attribute name from the final index.

            For example, the method takes 'k2' and returns the tuple ('k', 1).
            If attribute_name doesn't end with an integer, it returns (item, None).
            """

            # Match any number (\d+) at the end of the string ($).
            match = re.search(r'\d+$', item)
            if match is None:
                return item, None

            index = match.group()  # This is a str.
            attr_name = item[:-len(index)]
            index = int(match.group()) - 1
            return attr_name, index

        @staticmethod
        def _split_attribute_index_mapping(item):
            """Split the attribute name from the final index.

            For example, the method takes 'k2' and returns the tuple ('k', 1).
            If attribute_name doesn't end with an integer, it returns (item, None).
            """
            # Match items of the form <item><index>_<mapping><key>
            # where <index> and <key> always integers
            match = re.search(r'\d+_[A-z]+\d+$', item)
            if match is None:
                return item, None, None

            # Match any number (\d+) at the end of the string ($).
            i_match = r'\d+$'

            indexed, mapped = item.split('_')

            # process indexed component
            match_indexed = re.search(i_match, indexed)
            index = match_indexed.group()  # This is a str.
            attr_name = indexed[:-len(index)]
            index = int(index) - 1

            # process mapped component
            match_mapping = re.search(i_match, mapped)
            key = match_mapping.group()  # This is a str.
            attr_name = f"{attr_name}_{mapped[:-len(key)]}"
            key = int(key) # we don't subtract 1 here, because these are keys, not indices

            return attr_name, index, key

        @classmethod
        def _get_parameter_attributes(cls, filter=None):
            """Return all the attributes of the parameters.

            This is constructed dynamically by introspection gathering all
            the descriptors that are instances of the ParameterAttribute class.
            Parent classes of the parameter types are inspected as well.

            Note that since Python 3.6 the order of the class attribute definition
            is preserved (see PEP 520) so this function will return the attribute
            in their declaration order.

            Parameters
            ----------
            filter : Callable, optional
                An optional function with signature filter(ParameterAttribute) -> bool.
                If specified, only attributes for which this functions returns
                True are returned.

            Returns
            -------
            parameter_attributes : Dict[str, ParameterAttribute]
                A map from the name of the controlled parameter to the
                ParameterAttribute descriptor handling it.

            Examples
            --------
            >>> parameter_attributes = ParameterType._get_parameter_attributes()
            >>> sorted(parameter_attributes.keys())
            ['id', 'parent_id', 'smirks']
            >>> isinstance(parameter_attributes['id'], ParameterAttribute)
            True

            """
            # If no filter is specified, get all the parameters.
            if filter is None:
                filter = lambda x: True

            # Go through MRO and retrieve also parents descriptors. The function
            # inspect.getmembers() automatically resolves the MRO, but it also
            # sorts the attribute alphabetically by name. Here we want the order
            # to be the same as the declaration order, which is guaranteed by PEP 520,
            # starting from the parent class.
            parameter_attributes = OrderedDict((name, descriptor) for c in reversed(inspect.getmro(cls))
                                               for name, descriptor in c.__dict__.items()
                                               if isinstance(descriptor, ParameterAttribute) and filter(descriptor))
            return parameter_attributes

        @classmethod
        def _get_indexed_mapped_parameter_attributes(cls):
            """Shortcut to retrieve only IndexedMappedParameterAttributes."""
            return cls._get_parameter_attributes(filter=lambda x: isinstance(x, IndexedMappedParameterAttribute))

        @classmethod
        def _get_indexed_parameter_attributes(cls):
            """Shortcut to retrieve only IndexedParameterAttributes."""
            return cls._get_parameter_attributes(filter=lambda x: isinstance(x, IndexedParameterAttribute))

        @classmethod
        def _get_required_parameter_attributes(cls):
            """Shortcut to retrieve only required ParameterAttributes."""
            return cls._get_parameter_attributes(filter=lambda x: x.default is x.UNDEFINED)

        @classmethod
        def _get_optional_parameter_attributes(cls):
            """Shortcut to retrieve only required ParameterAttributes."""
            return cls._get_parameter_attributes(filter=lambda x: x.default is not x.UNDEFINED)

        def _get_defined_parameter_attributes(self):
            """Returns all the attributes except for the optional attributes that have None default value.

            This returns first the required attributes and then the defined optional
            attribute in their respective declaration order.
            """
            required = self._get_required_parameter_attributes()
            optional = self._get_optional_parameter_attributes()
            # Filter the optional parameters that are set to their default.
            optional = OrderedDict((name, descriptor) for name, descriptor in optional.items()
                                   if not(descriptor.default is None and getattr(self, name) == descriptor.default))
            required.update(optional)
            return required

    #======================================================================
    # PARAMETER TYPE/LIST
    #======================================================================

    # We can't actually make this derive from dict, because it's possible for the user to change SMIRKS
    # of parameters already in the list, which would cause the ParameterType object's SMIRKS and
    # the dictionary key's SMIRKS to be out of sync.
    class ParameterList(list):
        """
        Parameter list that also supports accessing items by SMARTS string.

        .. warning :: This API is experimental and subject to change.

        """

        # TODO: Make this faster by caching SMARTS -> index lookup?

        # TODO: Override __del__ to make sure we don't remove root atom type

        # TODO: Allow retrieval by `id` as well

        def __init__(self, input_parameter_list=None):
            """
            Initialize a new ParameterList, optionally providing a list of ParameterType objects
            to initially populate it.

            Parameters
            ----------
            input_parameter_list: list[ParameterType], default=None
                A pre-existing list of ParameterType-based objects. If None, this ParameterList
                will be initialized empty.
            """
            super().__init__()

            input_parameter_list = input_parameter_list or []
            # TODO: Should a ParameterList only contain a single kind of ParameterType?
            for input_parameter in input_parameter_list:
                self.append(input_parameter)

        def append(self, parameter):
            """
            Add a ParameterType object to the end of the ParameterList

            Parameters
            ----------
            parameter : a ParameterType object

            """
            # TODO: Ensure that newly added parameter is the same type as existing?
            super().append(parameter)

        def extend(self, other):
            """
            Add a ParameterList object to the end of the ParameterList

            Parameters
            ----------
            other : a ParameterList

            """
            if not isinstance(other, ParameterList):
                msg = 'ParameterList.extend(other) expected instance of ParameterList, ' \
                      'but received {} (type {}) instead'.format(other, type(other))
                raise TypeError(msg)
            # TODO: Check if other ParameterList contains the same ParameterTypes?
            super().extend(other)

        def index(self, item):
            """
            Get the numerical index of a ParameterType object or SMIRKS in this ParameterList. Raises ValueError
            if the item is not found.

            Parameters
            ----------
            item : ParameterType object or str
                The parameter or SMIRKS to look up in this ParameterList

            Returns
            -------
            index : int
                The index of the found item
            """
            if isinstance(item, ParameterType):
                return super().index(item)
            else:
                for parameter in self:
                    if parameter.smirks == item:
                        return self.index(parameter)
                raise IndexError('SMIRKS {item} not found in ParameterList'.format(item=item))

        def insert(self, index, parameter):
            """
            Add a ParameterType object as if this were a list

            Parameters
            ----------
            index : int
                The numerical position to insert the parameter at
            parameter : a ParameterType object
                The parameter to insert
            """
            # TODO: Ensure that newly added parameter is the same type as existing?
            super().insert(index, parameter)

        def __delitem__(self, item):
            """
            Delete item by index or SMIRKS.

            Parameters
            ----------
            item : str or int
                SMIRKS or numerical index of item in this ParameterList
            """
            if type(item) is int:
                index = item
            else:
                # Try to find by SMIRKS
                index = self.index(item)
            super().__delitem__(index)

        def __getitem__(self, item):
            """
            Retrieve item by index or SMIRKS

            Parameters
            ----------
            item : str or int
                SMIRKS or numerical index of item in this ParameterList
            """
            if type(item) is int:
                index = item
            elif type(item) is slice:
                index = item
            else:
                index = self.index(item)
            return super().__getitem__(index)

        # TODO: Override __setitem__ and __del__ to ensure we can slice by SMIRKS as well
        # This is needed for pickling. See https://github.com/openforcefield/openforcefield/issues/411
        # for more details.
        # TODO: Is there a cleaner way (getstate/setstate perhaps?) to allow FFs to be
        #       pickled?
        def __reduce__(self):
            return (__class__, ( list( self),), self.__dict__)

        def __contains__(self, item):
            """Check to see if either Parameter or SMIRKS is contained in parameter list.

            Parameters
            ----------
            item : str
                SMIRKS of item in this ParameterList
            """
            if isinstance(item, str):
                # Special case for SMIRKS strings
                if item in [result.smirks for result in self]:
                    return True
            # Fall back to traditional access
            return list.__contains__(self, item)

        def to_list(self, discard_cosmetic_attributes=True):
            """
            Render this ParameterList to a normal list, serializing each ParameterType object in it to dict.

            Parameters
            ----------

            discard_cosmetic_attributes : bool, optional. Default = True
                Whether to discard non-spec attributes of each ParameterType object.

            Returns
            -------
            parameter_list : List[dict]
                A serialized representation of a ParameterList, with each ParameterType it contains converted to dict.
            """
            parameter_list = list()

            for parameter in self:
                parameter_dict = parameter.to_dict(discard_cosmetic_attributes=discard_cosmetic_attributes)
                parameter_list.append(parameter_dict)

            return parameter_list

    # TODO: Rename to better reflect role as parameter base class?
    class ParameterType(_ParameterAttributeHandler):
        """
        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.

        Attributes
        ----------
        smirks : str
            The SMIRKS pattern that this parameter matches.
        id : str or None
            An optional identifier for the parameter.
        parent_id : str or None
            Optionally, the identifier of the parameter of which this parameter
            is a specialization.

        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]

        """

        # ChemicalEnvironment valence type string expected by SMARTS string for this Handler
        _VALENCE_TYPE = None
        # The string mapping to this ParameterType in a SMIRNOFF data source
        _ELEMENT_NAME = None

        # Parameter attributes shared among all parameter types.
        smirks = ParameterAttribute()
        id = ParameterAttribute(default=None)
        parent_id = ParameterAttribute(default=None)

        @smirks.converter
        def smirks(self, attr, smirks):
            # Validate the SMIRKS string to ensure it matches the expected
            # parameter type, raising an exception if it is invalid or doesn't
            # tag a valid set of atoms.

            # TODO: Add check to make sure we can't make tree non-hierarchical
            #       This would require parameter type knows which ParameterList it belongs to
            ChemicalEnvironment.validate_smirks(
                smirks, validate_valence_type=True)
            return smirks

        def __init__(self, smirks, allow_cosmetic_attributes=False, **kwargs):
            """
            Create a ParameterType.

            Parameters
            ----------
            smirks : str
                The SMIRKS match for the provided parameter type.
            allow_cosmetic_attributes : bool 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.

            """
            # This is just to make smirks a required positional argument.
            kwargs['smirks']  = smirks
            super().__init__(allow_cosmetic_attributes=allow_cosmetic_attributes, **kwargs)

        def __repr__(self):
            ret_str = '<{} with '.format(self.__class__.__name__)
            for attr, val in self.to_dict().items():
                ret_str += f'{attr}: {val}  '
            ret_str += '>'
            return ret_str

    #======================================================================
    # PARAMETER HANDLERS
    #
    # The following classes are Handlers that know how to create Force
    # subclasses and add them to a System that is being created. Each Handler
    # class must define three methods:
    # 1) a constructor which takes as input hierarchical dictionaries of data
    #    conformant to the SMIRNOFF spec;
    # 2) a create_force() method that constructs the Force object and adds it
    #    to the System; and
    # 3) a labelForce() method that provides access to which terms are applied
    #    to which atoms in specified mols.
    #======================================================================

    # TODO: Should we have a parameter handler registry?

    class ParameterHandler(_ParameterAttributeHandler):
        """Base class for parameter handlers.

        Parameter handlers are configured with some global parameters for a
        given section. They may also contain a :class:`ParameterList` populated
        with :class:`ParameterType` objects if they are responsible for assigning
        SMIRKS-based parameters.

        .. warning

           Parameter handler objects can only belong to a single :class:`ForceField` object.
           If you need to create a copy to attach to a different :class:`ForceField` object,
           use ``create_copy()``.

        .. warning :: This API is experimental and subject to change.

        """

        _TAGNAME = None  # str of section type handled by this ParameterHandler (XML element name for SMIRNOFF XML representation)
        _INFOTYPE = None  # container class with type information that will be stored in self._parameters
        _OPENMMTYPE = None  # OpenMM Force class (or None if no equivalent)
        _DEPENDENCIES = None  # list of ParameterHandler classes that must precede this, or None

        _KWARGS = [] # Kwargs to catch when create_force is called
        _SMIRNOFF_VERSION_INTRODUCED = 0.0  # the earliest version of SMIRNOFF spec that supports this ParameterHandler
        _SMIRNOFF_VERSION_DEPRECATED = None  # if deprecated, the first SMIRNOFF version number it is no longer used
        _MIN_SUPPORTED_SECTION_VERSION = 0.3
        _MAX_SUPPORTED_SECTION_VERSION = 0.3

        version = ParameterAttribute()

        @version.converter
        def version(self, attr, new_version):
            """
            Raise a parsing exception if the given section version is unsupported.

            Raises
            ------
            SMIRNOFFVersionError if an incompatible version is passed in.

            """
            import packaging.version
            from openforcefield.typing.engines.smirnoff import SMIRNOFFVersionError
            # Use PEP-440 compliant version number comparison, if requested
            if (
                    packaging.version.parse(str(new_version)) >
                    packaging.version.parse(str(self._MAX_SUPPORTED_SECTION_VERSION))
                    ) or (
                    packaging.version.parse(str(new_version)) <
                    packaging.version.parse(str(self._MIN_SUPPORTED_SECTION_VERSION))
            ):
                raise SMIRNOFFVersionError(
                    f'SMIRNOFF offxml file was written with version {new_version}, but this version '
                    f'of ForceField only supports version {self._MIN_SUPPORTED_SECTION_VERSION} '
                    f'to version {self._MAX_SUPPORTED_SECTION_VERSION}'
                )
            return new_version

        def __init__(self, allow_cosmetic_attributes=False, skip_version_check=False, **kwargs):
            """
            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

            """
            # Skip version check if requested.
            if 'version' not in kwargs:
                if skip_version_check:
                    kwargs['version'] = self._MAX_SUPPORTED_SECTION_VERSION
                else:
                    raise SMIRNOFFSpecError(
                        f"Missing version while trying to construct {self.__class__}. "
                        f"0.3 SMIRNOFF spec requires each parameter section to have its own version."
                    )

            # List of ParameterType objects (also behaves like an OrderedDict where keys are SMARTS).
            self._parameters = ParameterList()

            # Initialize ParameterAttributes and cosmetic attributes.
            super().__init__(allow_cosmetic_attributes=allow_cosmetic_attributes, **kwargs)

        def _add_parameters(self, section_dict, allow_cosmetic_attributes=False):
            """
            Extend the ParameterList in this ParameterHandler using a SMIRNOFF data source.

            Parameters
            ----------
            section_dict : dict
                The dict representation of a SMIRNOFF data source containing parameters to att to this ParameterHandler
            allow_cosmetic_attributes : bool, optional. Default = False
                Whether to allow non-spec fields in section_dict. If True, non-spec kwargs will be stored as an
                attribute of the parameter. If False, non-spec kwargs will raise an exception.

            """
            unitless_kwargs, attached_units = extract_serialized_units_from_dict(section_dict)
            smirnoff_data = attach_units(unitless_kwargs, attached_units)

            element_name = None
            if self._INFOTYPE is not None:
                element_name = self._INFOTYPE._ELEMENT_NAME

            for key, val in smirnoff_data.items():
                # Skip sections that aren't the parameter list
                if key != element_name:
                    continue
                # If there are multiple parameters, this will be a list. If there's just one, make it a list
                if not (isinstance(val, list)):
                    val = [val]
                # If we're reading the parameter list, iterate through and attach units to
                # each parameter_dict, then use it to initialize a ParameterType
                for unitless_param_dict in val:
                    param_dict = attach_units(unitless_param_dict, attached_units)
                    new_parameter = self._INFOTYPE(**param_dict,
                                                   allow_cosmetic_attributes=allow_cosmetic_attributes)
                    self._parameters.append(new_parameter)

        @property
        def parameters(self):
            """The ParameterList that holds this ParameterHandler's parameter objects"""
            return self._parameters

        # TODO: Do we need to return these, or can we handle this internally
        @property
        def known_kwargs(self):
            """List of kwargs that can be parsed by the function.
            """
            # TODO: Should we use introspection to inspect the function signature instead?
            return set(self._KWARGS)

        def check_handler_compatibility(self, handler_kwargs):
            """
            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_kwargs : dict
                The kwargs that would be used to construct

            Raises
            ------
            IncompatibleParameterError if handler_kwargs are incompatible with existing parameters.
            """
            pass

        # TODO: Can we ensure SMIRKS and other parameters remain valid after manipulation?
        def add_parameter(self, parameter_kwargs):
            """Add a parameter to the forcefield, ensuring all parameters are valid.

            Parameters
            ----------
            parameter_kwargs : dict
                The kwargs to pass to the ParameterHandler.INFOTYPE (a ParameterType) constructor
            """
            # TODO: Do we need to check for incompatibility with existing parameters?
            new_parameter = self._INFOTYPE(**parameter_kwargs)
            self._parameters.append(new_parameter)

        def get_parameter(self, 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 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)  >]

            """
            params = list()
            for attr, value in parameter_attrs.items():
                for param in self.parameters:
                    if param in params:
                        continue
                    # TODO: Cleaner accessing of cosmetic attributes
                    # See issue #338
                    if param.attribute_is_cosmetic(attr):
                        attr = '_' + attr
                    if hasattr(param, attr):
                        if getattr(param, attr) == value:
                            params.append(param)
            return params

        class _Match:
            """Represents a ParameterType which has been matched to
            a given chemical environment.
            """

            @property
            def parameter_type(self):
                """ParameterType: The matched parameter type."""
                return self._parameter_type

            @property
            def environment_match(self):
                """Topology._ChemicalEnvironmentMatch: The environment which matched the type."""
                return self._environment_match

            def __init__(self, parameter_type, environment_match):
                """Constructs a new ParameterHandlerMatch object.

                Parameters
                ----------
                parameter_type: ParameterType
                    The matched parameter type.
                environment_match: Topology._ChemicalEnvironmentMatch
                    The environment which matched the type.
                """
                self._parameter_type = parameter_type
                self._environment_match = environment_match

        def find_matches(self, entity):
            """Find the elements of the topology/molecule matched by a parameter type.

            Parameters
            ----------
            entity : openforcefield.topology.Topology
                Topology to search.

            Returns
            ---------
            matches : ValenceDict[Tuple[int], ParameterHandler._Match]
                ``matches[particle_indices]`` is the ``ParameterType`` object
                matching the tuple of particle indices in ``entity``.
            """

            # TODO: Right now, this method is only ever called with an entity that is a Topoogy.
            #  Should we reduce its scope and have a check here to make sure entity is a Topology?
            return self._find_matches(entity)

        def _find_matches(self, entity, transformed_dict_cls=ValenceDict):
            """Implement find_matches() and allow using a difference valence dictionary.

            Parameters
            ----------
            entity : openforcefield.topology.Topology
                Topology to search.
            transformed_dict_cls: class
                The type of dictionary to store the matches in. This
                will determine how groups of atom indices are stored
                and accessed (e.g for angles indices should be 0-1-2
                and not 2-1-0).

            Returns
            ---------
            matches : `transformed_dict_cls` of ParameterHandlerMatch
                ``matches[particle_indices]`` is the ``ParameterType`` object
                matching the tuple of particle indices in ``entity``.
            """
            logger.debug('Finding matches for {}'.format(self.__class__.__name__))

            matches = transformed_dict_cls()

            # TODO: There are probably performance gains to be had here
            #       by performing this loop in reverse order, and breaking early once
            #       all environments have been matched.
            for parameter_type in self._parameters:
                matches_for_this_type = {}

                for environment_match in entity.chemical_environment_matches(parameter_type.smirks):
                    # Update the matches for this parameter type.
                    handler_match = self._Match(parameter_type, environment_match)
                    matches_for_this_type[environment_match.topology_atom_indices] = handler_match

                # Update matches of all parameter types.
                matches.update(matches_for_this_type)

                logger.debug('{:64} : {:8} matches'.format(
                    parameter_type.smirks, len(matches_for_this_type)))

            logger.debug('{} matches identified'.format(len(matches)))
            return matches

        @staticmethod
        def _assert_correct_connectivity(match, expected_connectivity=None):
            """A more performant version of the `topology.assert_bonded` method
            to ensure that the results of `_find_matches` are valid.

            Raises
            ------
            ValueError
                Raise an exception when the atoms in the match don't have
                the correct connectivity.

            Parameters
            ----------
            match: ParameterHandler._Match
                The match found by `_find_matches`
            connectivity: list of tuple of int, optional
                The expected connectivity of the match (e.g. for a torsion
                expected_connectivity=[(0, 1), (1, 2), (2, 3)]). If `None`,
                a connectivity of [(0, 1), ... (n - 1, n)] is assumed.
            """

            # I'm not 100% sure this is really necessary... but this should do
            # the same checks as the more costly assert_bonded method in the
            # ParameterHandler.create_force methods.
            if expected_connectivity is None:
                return

            reference_molecule = match.environment_match.reference_molecule

            for connectivity in expected_connectivity:

                atom_i = match.environment_match.reference_atom_indices[connectivity[0]]
                atom_j = match.environment_match.reference_atom_indices[connectivity[1]]

                reference_molecule.get_bond_between(atom_i, atom_j)

        def assign_parameters(self, topology, system):
            """Assign parameters for the given Topology to the specified System object.

            Parameters
            ----------
            topology : openforcefield.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 : simtk.openmm.System
                The OpenMM System object to add the Force (or append new parameters) to.
            """
            pass

        def postprocess_system(self, topology, system, **kwargs):
            """Allow the force to perform a a final post-processing pass on the System following parameter assignment, if needed.

            Parameters
            ----------
            topology : openforcefield.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 : simtk.openmm.System
                The OpenMM System object to add the Force (or append new parameters) to.
            """
            pass

        def to_dict(self, 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.

            """
            smirnoff_data = OrderedDict()

            # Populate parameter list
            parameter_list = self._parameters.to_list(discard_cosmetic_attributes=discard_cosmetic_attributes)

            # NOTE: This assumes that a ParameterHandler will have just one homogenous ParameterList under it
            if self._INFOTYPE is not None:
                #smirnoff_data[self._INFOTYPE._ELEMENT_NAME] = unitless_parameter_list
                smirnoff_data[self._INFOTYPE._ELEMENT_NAME] = parameter_list

            # Collect parameter and cosmetic attributes.
            header_attribute_dict = super().to_dict(discard_cosmetic_attributes=discard_cosmetic_attributes)
            smirnoff_data.update(header_attribute_dict)

            return smirnoff_data

        # -------------------------------
        # Utilities for children classes.
        # -------------------------------

        @classmethod
        def _check_all_valence_terms_assigned(cls, assigned_terms, valence_terms,
                                              exception_cls=UnassignedValenceParameterException):
            """Check that all valence terms have been assigned and print a user-friendly error message.

            Parameters
            ----------
            assigned_terms : ValenceDict
                Atom index tuples defining added valence terms.
            valence_terms : Iterable[TopologyAtom] or Iterable[Iterable[TopologyAtom]]
                Atom or atom tuples defining topological valence terms.
            exception_cls : UnassignedValenceParameterException
                A specific exception class to raise to allow catching only specific
                types of errors.

            """
            from openforcefield.topology import TopologyAtom
            # Provided there are no duplicates in either list,
            # or something weird like a bond has been added to
            # a torsions list - this should work just fine I think.
            # If we expect either of those assumptions to be incorrect,
            # (i.e len(not_found_terms) > 0) we have bigger issues
            # in the code and should be catching those cases elsewhere!
            # The fact that we graph match all topol molecules to ref
            # molecules should avoid the len(not_found_terms) > 0 case.

            if len(assigned_terms) == len(valence_terms):
                return

            # Convert the valence term to a valence dictionary to make sure
            # the order of atom indices doesn't matter for comparison.
            valence_terms_dict = assigned_terms.__class__()
            for atoms in valence_terms:
                try:
                    # valence_terms is a list of TopologyAtom tuples.
                    atom_indices = (a.topology_particle_index for a in atoms)
                except TypeError:
                    # valence_terms is a list of TopologyAtom.
                    atom_indices = (atoms.topology_particle_index,)
                valence_terms_dict[atom_indices] = atoms

            # Check that both valence dictionaries have the same keys (i.e. terms).
            assigned_terms_set = set(assigned_terms.keys())
            valence_terms_set = set(valence_terms_dict.keys())
            unassigned_terms = valence_terms_set.difference(assigned_terms_set)
            not_found_terms = assigned_terms_set.difference(valence_terms_set)

            # Raise an error if there are unassigned terms.
            err_msg = ""

            if len(unassigned_terms) > 0:

                unassigned_topology_atom_tuples = []

                # Gain access to the relevant topology
                if type(valence_terms[0]) is TopologyAtom:
                    topology = valence_terms[0].topology_molecule.topology
                else:
                    topology = valence_terms[0][0].topology_molecule.topology
                unassigned_str = ''
                for unassigned_tuple in unassigned_terms:
                    unassigned_str += '\n- Topology indices ' + str(unassigned_tuple)
                    unassigned_str += ': names and elements '

                    unassigned_topology_atoms = []

                    # Pull and add additional helpful info on missing terms
                    for atom_idx in unassigned_tuple:
                        topology_atom = topology.atom(atom_idx)
                        unassigned_topology_atoms.append(topology_atom)
                        unassigned_str += f"({topology_atom.atom.name} {topology_atom.atom.element.symbol}), "
                    unassigned_topology_atom_tuples.append(tuple(unassigned_topology_atoms))
                err_msg += ("{parameter_handler} was not able to find parameters for the following valence terms:\n"
                            "{unassigned_str}").format(parameter_handler=cls.__name__,
                                                         unassigned_str=unassigned_str)
            if len(not_found_terms) > 0:
                if err_msg != "":
                    err_msg += '\n'
                not_found_str = '\n- '.join([str(x) for x in not_found_terms])
                err_msg += ("{parameter_handler} assigned terms that were not found in the topology:\n"
                            "- {not_found_str}").format(parameter_handler=cls.__name__,
                                                        not_found_str=not_found_str)
            if err_msg != "":
                err_msg += '\n'
                exception = exception_cls(err_msg)
                exception.unassigned_topology_atom_tuples = unassigned_topology_atom_tuples
                exception.handler_class = cls
                raise exception

        def _check_attributes_are_equal(self, other, identical_attrs=(),
                                        tolerance_attrs=(), tolerance=1e-6):
            """Utility function to check that the given attributes of the two handlers are equal.

            Parameters
            ----------
            identical_attrs : List[str]
                Names of the parameters that must be checked with the equality operator.
            tolerance_attrs : List[str]
                Names of the parameters that must be equal up to a tolerance.
            tolerance : float
                The absolute tolerance used to compare the parameters.
            """
            def get_unitless_values(attr):
                this_val = getattr(self, attr)
                other_val = getattr(other, attr)
                # Strip quantities of their units before comparison.
                try:
                    u = this_val.unit
                except AttributeError:
                    return this_val, other_val
                return this_val / u, other_val / u

            for attr in identical_attrs:
                this_val, other_val = get_unitless_values(attr)

                if this_val != other_val:
                    raise IncompatibleParameterError(
                        "{} values are not identical. "
                        "(handler value: {}, incompatible value: {}".format(
                            attr, this_val, other_val))

            for attr in tolerance_attrs:
                this_val, other_val = get_unitless_values(attr)
                if abs(this_val - other_val) > tolerance:
                    raise IncompatibleParameterError(
                        "Difference between '{}' values is beyond allowed tolerance {}. "
                        "(handler value: {}, incompatible value: {}".format(
                            attr, tolerance, this_val, other_val))

    #=============================================================================================

    class ConstraintHandler(ParameterHandler):
        """Handle SMIRNOFF ``<Constraints>`` tags

        ``ConstraintHandler`` must be applied before ``BondHandler`` and ``AngleHandler``,
        since those classes add constraints for which equilibrium geometries are needed from those tags.

        .. warning :: This API is experimental and subject to change.
        """

        class ConstraintType(ParameterType):
            """A SMIRNOFF constraint type

            .. warning :: This API is experimental and subject to change.
            """
            _VALENCE_TYPE = 'Bond'
            _ELEMENT_NAME = 'Constraint'

            distance = ParameterAttribute(default=None, unit=unit.angstrom)

        _TAGNAME = 'Constraints'
        _INFOTYPE = ConstraintType
        _OPENMMTYPE = None  # don't create a corresponding OpenMM Force class

        def create_force(self, system, topology, **kwargs):
            constraint_matches = self.find_matches(topology)
            for (atoms, constraint_match) in constraint_matches.items():
                # Update constrained atom pairs in topology
                #topology.add_constraint(*atoms, constraint.distance)
                # If a distance is specified (constraint.distance != True), add the constraint here.
                # Otherwise, the equilibrium bond length will be used to constrain the atoms in HarmonicBondHandler
                constraint = constraint_match.parameter_type

                if constraint.distance is None:
                    topology.add_constraint(*atoms, True)
                else:
                    system.addConstraint(*atoms, constraint.distance)
                    topology.add_constraint(*atoms, constraint.distance)

    #=============================================================================================

    class BondHandler(ParameterHandler):
        """Handle SMIRNOFF ``<Bonds>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        class BondType(ParameterType):
            """A SMIRNOFF bond type

            .. warning :: This API is experimental and subject to change.
            """
            # ChemicalEnvironment valence type string expected by SMARTS string for this Handler
            _VALENCE_TYPE = 'Bond'
            _ELEMENT_NAME = 'Bond'

            # These attributes may be indexed (by integer bond order) if fractional bond orders are used.
            length = ParameterAttribute(unit=unit.angstrom)
            k = ParameterAttribute(unit=unit.kilocalorie_per_mole / unit.angstrom**2)

        _TAGNAME = 'Bonds'  # SMIRNOFF tag name to process
        _INFOTYPE = BondType  # class to hold force type info
        _OPENMMTYPE = openmm.HarmonicBondForce  # OpenMM force class to create
        _DEPENDENCIES = [ConstraintHandler]  # ConstraintHandler must be executed first

        potential = ParameterAttribute(default='harmonic')
        fractional_bondorder_method = ParameterAttribute(default=None)
        fractional_bondorder_interpolation = ParameterAttribute(default='linear')

        def check_handler_compatibility(self,
                                        other_handler):
            """
            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.
            """
            string_attrs_to_compare = ['potential', 'fractional_bondorder_method', 'fractional_bondorder_interpolation']
            self._check_attributes_are_equal(other_handler, identical_attrs=string_attrs_to_compare)

        def create_force(self, system, topology, **kwargs):
            # Create or retrieve existing OpenMM Force object
            # TODO: The commented line below should replace the system.getForce search
            #force = super(BondHandler, self).create_force(system, topology, **kwargs)
            existing = [system.getForce(i) for i in range(system.getNumForces())]
            existing = [f for f in existing if type(f) == self._OPENMMTYPE]
            if len(existing) == 0:
                force = self._OPENMMTYPE()
                system.addForce(force)
            else:
                force = existing[0]

            # Add all bonds to the system.
            bond_matches = self.find_matches(topology)

            skipped_constrained_bonds = 0  # keep track of how many bonds were constrained (and hence skipped)
            for (topology_atom_indices, bond_match) in bond_matches.items():
                # Get corresponding particle indices in Topology
                #particle_indices = tuple([ atom.particle_index for atom in atoms ])

                # Ensure atoms are actually bonded correct pattern in Topology
                self._assert_correct_connectivity(bond_match)
                # topology.assert_bonded(atoms[0], atoms[1])
                bond_params = bond_match.parameter_type
                match = bond_match.environment_match

                # Compute equilibrium bond length and spring constant.
                bond = match.reference_molecule.get_bond_between(*match.reference_atom_indices)

                if hasattr(bond_params, 'k_bondorder1'):
                    raise NotImplementedError("Partial bondorder treatment is not implemented for bonds.")

                    # Interpolate using fractional bond orders
                    # TODO: Do we really want to allow per-bond specification of interpolation schemes?
                    #order = bond.fractional_bond_order
                    #if self.fractional_bondorder_interpolation == 'interpolate-linear':
                    #    k = bond_params.k[0] + (bond_params.k[1] - bond_params.k[0]) * (order - 1.)
                    #    length = bond_params.length[0] + (
                    #        bond_params.length[1] - bond_params.length[0]) * (order - 1.)
                    #else:
                    #    raise Exception(
                    #        "Partial bondorder treatment {} is not implemented.".
                    #        format(self.fractional_bondorder_method))
                else:
                    [k, length] = [bond_params.k, bond_params.length]

                is_constrained = topology.is_constrained(*topology_atom_indices)

                # Handle constraints.
                if is_constrained:
                    # Atom pair is constrained; we don't need to add a bond term.
                    skipped_constrained_bonds += 1
                    # Check if we need to add the constraint here to the equilibrium bond length.
                    if is_constrained is True:
                        # Mark that we have now assigned a specific constraint distance to this constraint.
                        topology.add_constraint(*topology_atom_indices, length)
                        # Add the constraint to the System.
                        system.addConstraint(*topology_atom_indices, length)
                        #system.addConstraint(*particle_indices, length)
                    continue

                # Add harmonic bond to HarmonicBondForce
                force.addBond(*topology_atom_indices, length, k)

            logger.info('{} bonds added ({} skipped due to constraints)'.format(
                len(bond_matches) - skipped_constrained_bonds, skipped_constrained_bonds))

            # Check that no topological bonds are missing force parameters.
            valence_terms = [list(b.atoms) for b in topology.topology_bonds]
            self._check_all_valence_terms_assigned(assigned_terms=bond_matches, valence_terms=valence_terms,
                                                   exception_cls=UnassignedBondParameterException)

    #=============================================================================================

    class AngleHandler(ParameterHandler):
        """Handle SMIRNOFF ``<AngleForce>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        class AngleType(ParameterType):
            """A SMIRNOFF angle type.

            .. warning :: This API is experimental and subject to change.
            """
            _VALENCE_TYPE = 'Angle'  # ChemicalEnvironment valence type string expected by SMARTS string for this Handler
            _ELEMENT_NAME = 'Angle'

            angle = ParameterAttribute(unit=unit.degree)
            k = ParameterAttribute(unit=unit.kilocalorie_per_mole / unit.degree**2)

        _TAGNAME = 'Angles'  # SMIRNOFF tag name to process
        _INFOTYPE = AngleType  # class to hold force type info
        _OPENMMTYPE = openmm.HarmonicAngleForce  # OpenMM force class to create
        _DEPENDENCIES = [ConstraintHandler]  # ConstraintHandler must be executed first

        potential = ParameterAttribute(default='harmonic')

        def check_handler_compatibility(self,
                                        other_handler):
            """
            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.
            """
            string_attrs_to_compare = ['potential']
            self._check_attributes_are_equal(other_handler, identical_attrs=string_attrs_to_compare)

        def create_force(self, system, topology, **kwargs):
            #force = super(AngleHandler, self).create_force(system, topology, **kwargs)
            existing = [system.getForce(i) for i in range(system.getNumForces())]
            existing = [f for f in existing if type(f) == self._OPENMMTYPE]
            if len(existing) == 0:
                force = self._OPENMMTYPE()
                system.addForce(force)
            else:
                force = existing[0]

            # Add all angles to the system.
            angle_matches = self.find_matches(topology)
            skipped_constrained_angles = 0  # keep track of how many angles were constrained (and hence skipped)
            for (atoms, angle_match) in angle_matches.items():
                # Ensure atoms are actually bonded correct pattern in Topology
                # for (i, j) in [(0, 1), (1, 2)]:
                #     topology.assert_bonded(atoms[i], atoms[j])
                self._assert_correct_connectivity(angle_match)

                if topology.is_constrained(
                        atoms[0], atoms[1]) and topology.is_constrained(
                            atoms[1], atoms[2]) and topology.is_constrained(
                                atoms[0], atoms[2]):
                    # Angle is constrained; we don't need to add an angle term.
                    skipped_constrained_angles += 1
                    continue

                angle = angle_match.parameter_type
                force.addAngle(*atoms, angle.angle, angle.k)

            logger.info('{} angles added ({} skipped due to constraints)'.format(
                len(angle_matches) - skipped_constrained_angles,
                skipped_constrained_angles))

            # Check that no topological angles are missing force parameters
            self._check_all_valence_terms_assigned(assigned_terms=angle_matches,
                                                   valence_terms=list(topology.angles),
                                                   exception_cls=UnassignedAngleParameterException)

    #=============================================================================================

    # TODO: This is technically a validator, not a converter, but ParameterAttribute doesn't support them yet (it'll be easy if we switch to use the attrs library).
    def _allow_only(allowed_values):
        """A converter that checks the new value is only in a set.
        """
        allowed_values = frozenset(allowed_values)
        def _value_checker(instance, attr, new_value):
            # This statement means that, in the "SMIRNOFF Data Dict" format, the string "None"
            # and the Python None are the same thing
            if new_value == "None":
                new_value = None

            # Ensure that the new value is in the list of allowed values
            if new_value not in allowed_values:

                err_msg = (f'Attempted to set {instance.__class__.__name__}.{attr.name} '
                           f'to {new_value}. Currently, only the following values '
                           f'are supported: {sorted(allowed_values)}.')
                raise SMIRNOFFSpecError(err_msg)
            return new_value
        return _value_checker

    # TODO: There's a lot of duplicated code in ProperTorsionHandler and ImproperTorsionHandler
    class ProperTorsionHandler(ParameterHandler):
        """Handle SMIRNOFF ``<ProperTorsionForce>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        class ProperTorsionType(ParameterType):
            """A SMIRNOFF torsion type for proper torsions.

            .. warning :: This API is experimental and subject to change.
            """

            _VALENCE_TYPE = 'ProperTorsion'
            _ELEMENT_NAME = 'Proper'

            periodicity = IndexedParameterAttribute(converter=int)
            phase = IndexedParameterAttribute(unit=unit.degree)
            k = IndexedParameterAttribute(default=None, unit=unit.kilocalorie_per_mole)
            idivf = IndexedParameterAttribute(default=None, converter=float)

            # fractional bond order params
            k_bondorder = IndexedMappedParameterAttribute(default=None,
                                                          unit=unit.kilocalorie_per_mole)

        _TAGNAME = 'ProperTorsions'  # SMIRNOFF tag name to process
        _KWARGS = ['partial_bond_orders_from_molecules']
        _INFOTYPE = ProperTorsionType  # info type to store
        _OPENMMTYPE = openmm.PeriodicTorsionForce  # OpenMM force class to create

        potential = ParameterAttribute(
            default='k*(1+cos(periodicity*theta-phase))',
            converter=_allow_only(['k*(1+cos(periodicity*theta-phase))'])
        )
        default_idivf = ParameterAttribute(default='auto')
        fractional_bondorder_method = ParameterAttribute(default='AM1-Wiberg')
        fractional_bondorder_interpolation = ParameterAttribute(default='linear')

        def check_handler_compatibility(self,
                                        other_handler):
            """
            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.
            """
            float_attrs_to_compare = []
            string_attrs_to_compare = ['potential',
                                       'fractional_bondorder_method',
                                       'fractional_bondorder_interpolation']

            if self.default_idivf == 'auto':
                string_attrs_to_compare.append('default_idivf')
            else:
                float_attrs_to_compare.append('default_idivf')

            self._check_attributes_are_equal(other_handler, identical_attrs=string_attrs_to_compare,
                                             tolerance_attrs=float_attrs_to_compare)

        def check_partial_bond_orders_from_molecules_duplicates(self, pb_mols):
            if len(set(map(Molecule.to_smiles, pb_mols))) < len(pb_mols):
                raise ValueError("At least two user-provided fractional bond order "
                                 "molecules are isomorphic")

        def assign_partial_bond_orders_from_molecules(self, topology, pbo_mols):

            # for each reference molecule in our topology, we'll walk through the provided partial bond order molecules
            # if we find a match, we'll apply the partial bond orders and skip to the next molecule
            for ref_mol in topology.reference_molecules:
                for pbo_mol in pbo_mols:
                    # we are as stringent as we are in the ElectrostaticsHandler
                    # TODO: figure out whether bond order matching is redundant with aromatic matching
                    isomorphic, topology_atom_map = Molecule.are_isomorphic(ref_mol, pbo_mol,
                                                                            return_atom_map=True,
                                                                            aromatic_matching=True,
                                                                            formal_charge_matching=True,
                                                                            bond_order_matching=True,
                                                                            atom_stereochemistry_matching=True,
                                                                            bond_stereochemistry_matching=True)

                    # if matching, assign bond orders and skip to next molecule
                    # first match wins
                    if isomorphic:
                        # walk through bonds on reference molecule
                        for bond in ref_mol.bonds:
                            # use atom mapping to translate to pbo_molecule bond
                            pbo_bond = pbo_mol.get_bond_between(topology_atom_map[bond.atom1_index],
                                                                topology_atom_map[bond.atom2_index])
                            # extract fractional bond order
                            # assign fractional bond order to reference molecule bond
                            if pbo_bond.fractional_bond_order is None:
                                raise ValueError(f"Molecule '{ref_mol}' was requested to be parameterized "
                                        f"with user-provided fractional bond orders from '{pbo_mol}', but not "
                                        "all bonds were provided with `fractional_bond_order` specified")

                            bond.fractional_bond_order = pbo_bond.fractional_bond_order

                        break
                    # not necessary, but explicit
                    else:
                        continue

        def create_force(self, system, topology, **kwargs):
            #force = super(ProperTorsionHandler, self).create_force(system, topology, **kwargs)
            existing = [system.getForce(i) for i in range(system.getNumForces())]
            existing = [f for f in existing if type(f) == self._OPENMMTYPE]

            if len(existing) == 0:
                force = self._OPENMMTYPE()
                system.addForce(force)
            else:
                force = existing[0]

            # check whether any of the reference molecules in the topology
            # are in the partial_bond_orders_from_molecules list
            if 'partial_bond_orders_from_molecules' in kwargs:
                # check whether molecules in the partial_bond_orders_from_molecules
                # list have any duplicates
                self.check_partial_bond_orders_from_molecules_duplicates(kwargs['partial_bond_orders_from_molecules'])

                self.assign_partial_bond_orders_from_molecules(topology, kwargs['partial_bond_orders_from_molecules'])

            # find all proper torsions for which we have parameters
            # operates on reference molecules in topology
            # but gives back matches for atoms for instance molecules
            torsion_matches = self.find_matches(topology)

            for (atom_indices, torsion_match) in torsion_matches.items():
                # Ensure atoms are actually bonded correct pattern in Topology
                # Currently does nothing
                self._assert_correct_connectivity(torsion_match)

                if torsion_match.parameter_type.k_bondorder is None:
                    # TODO: add a check here that we have same number of terms for
                    # `kX_bondorder*`, `periodicityX`, `phaseX`
                    # only count a given `kX_bondorder*` once

                    # assign torsion with no interpolation
                    self._assign_torsion(atom_indices, torsion_match, force)
                else:
                    # TODO: add a check here that we have same number of terms for
                    # `kX_bondorder*`, `periodicityX`, `phaseX`
                    # only count a given `kX_bondorder*` once

                    # assign torsion with interpolation
                    self._assign_fractional_bond_orders(atom_indices, torsion_match, force, **kwargs)

            logger.info('{} torsions added'.format(len(torsion_matches)))

            # Check that no topological torsions are missing force parameters

            # I can see the apeal of these kind of methods as an 'absolute' check
            # that things have gone well, but I think just making sure that the
            # reference molecule has been fully parametrised should have the same
            # effect! It would be good to eventually refactor things so that everything
            # is focused on the single unique molecules, and then simply just cloned
            # onto the system. It seems like John's proposed System object would do
            # exactly this.
            self._check_all_valence_terms_assigned(assigned_terms=torsion_matches,
                                                   valence_terms=list(topology.propers),
                                                   exception_cls=UnassignedProperTorsionParameterException)

        def _assign_torsion(self, atom_indices, torsion_match, force):

            torsion_params = torsion_match.parameter_type

            for (periodicity, phase, k, idivf) in zip(torsion_params.periodicity,
                                                      torsion_params.phase,
                                                      torsion_params.k,
                                                      torsion_params.idivf):

                if idivf == 'auto':
                    # TODO: Implement correct "auto" behavior
                    raise NotImplementedError("The OpenForceField toolkit hasn't implemented "
                                              "support for the torsion `idivf` value of 'auto'")

                force.addTorsion(atom_indices[0], atom_indices[1],
                                 atom_indices[2], atom_indices[3], periodicity,
                                 phase, k/idivf)

        def _assign_fractional_bond_orders(self, atom_indices, torsion_match, force, **kwargs):
            from openforcefield.utils.toolkits import GLOBAL_TOOLKIT_REGISTRY

            torsion_params = torsion_match.parameter_type
            match = torsion_match.environment_match

            for (periodicity, phase, k_bondorder, idivf) in zip(torsion_params.periodicity,
                                                                torsion_params.phase,
                                                                torsion_params.k_bondorder,
                                                                torsion_params.idivf):

                if len(k_bondorder) < 2:
                    raise ValueError("At least 2 bond order values required for `k_bondorder`; "
                                     "got {}".format(len(k_bondorder)))

                if idivf == 'auto':
                    # TODO: Implement correct "auto" behavior
                    raise NotImplementedError("The OpenForceField toolkit hasn't implemented "
                                              "support for the torsion `idivf` value of 'auto'")

                # get central bond for reference molecule
                central_bond = match.reference_molecule.get_bond_between(
                        match.reference_atom_indices[1], match.reference_atom_indices[2])

                # if fractional bond order not calculated yet, we calculate it
                # should only happen once per reference molecule for which we care
                # about fractional bond interpolation
                # and not at all for reference molecules we don't
                if central_bond.fractional_bond_order is None:
                        toolkit_registry = kwargs.get('toolkit_registry', GLOBAL_TOOLKIT_REGISTRY)
                        match.reference_molecule.assign_fractional_bond_orders(
                                toolkit_registry=toolkit_registry,
                                use_conformers=match.reference_molecule.conformers)

                # scale k based on the bondorder of the central bond
                if self.fractional_bondorder_interpolation == 'linear':
                    # we only interpolate on k
                    k = self._linear_interpolate_k(k_bondorder, central_bond.fractional_bond_order)
                else:
                    raise Exception(
                        "Fractional bondorder treatment {} is not implemented.".
                        format(self.fractional_bondorder_method))

                # add a torsion with given parameters for topology atoms
                force.addTorsion(atom_indices[0], atom_indices[1],
                                 atom_indices[2], atom_indices[3], periodicity,
                                 phase, k/idivf)

        @staticmethod
        def _linear_interpolate_k(k_bondorder, fractional_bond_order):

            # pre-empt case where no interpolation is necessary
            if fractional_bond_order in k_bondorder:
                return k_bondorder[fractional_bond_order]

            # TODO: error out for nonsensical fractional bond orders

            # find the nearest bond_order beneath our fractional value
            try:
                below = max(bo for bo in k_bondorder if bo < fractional_bond_order)
            except ValueError:
                below = None

            # find the nearest bond_order above our fractional value
            try:
                above = min(bo for bo in k_bondorder if bo > fractional_bond_order)
            except ValueError:
                above = None

            # handle case where we can clearly interpolate
            if (above is not None) and (below is not None):
                return (k_bondorder[below]
                        + (k_bondorder[above] - k_bondorder[below])
                        * ((fractional_bond_order - below)/(above - below)))

            # error if we can't hope to interpolate at all
            elif (above is None) and (below is None):
                raise NotImplementedError(
                        f"Failed to find interpolation references for "
                        f"`fractional bond order` '{fractional_bond_order}', "
                        f"with `k_bond_order` '{k_bondorder}'")

            # extrapolate for fractional bond orders below our lowest defined bond order
            elif below is None:
                bond_orders = sorted(k_bondorder)
                k = (k_bondorder[bond_orders[0]]
                        - ((k_bondorder[bond_orders[1]] - k_bondorder[bond_orders[0]])
                           /(bond_orders[1] - bond_orders[0]))
                        * (bond_orders[0] - fractional_bond_order))
                return k

            # extrapolate for fractional bond orders above our highest defined bond order
            elif above is None:
                bond_orders = sorted(k_bondorder)
                k = (k_bondorder[bond_orders[-1]]
                        + ((k_bondorder[bond_orders[-1]] - k_bondorder[bond_orders[-2]])
                           /(bond_orders[-1] - bond_orders[-2]))
                        * (fractional_bond_order - bond_orders[-1]))
                return k

    # TODO: There's a lot of duplicated code in ProperTorsionHandler and ImproperTorsionHandler
    class ImproperTorsionHandler(ParameterHandler):
        """Handle SMIRNOFF ``<ImproperTorsionForce>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        class ImproperTorsionType(ParameterType):
            """A SMIRNOFF torsion type for improper torsions.

            .. warning :: This API is experimental and subject to change.
            """
            _VALENCE_TYPE = 'ImproperTorsion'
            _ELEMENT_NAME = 'Improper'

            periodicity = IndexedParameterAttribute(converter=int)
            phase = IndexedParameterAttribute(unit=unit.degree)
            k = IndexedParameterAttribute(unit=unit.kilocalorie_per_mole)
            idivf = IndexedParameterAttribute(default=None, converter=float)

        _TAGNAME = 'ImproperTorsions'  # SMIRNOFF tag name to process
        _INFOTYPE = ImproperTorsionType  # info type to store
        _OPENMMTYPE = openmm.PeriodicTorsionForce  # OpenMM force class to create

        potential = ParameterAttribute(
            default='k*(1+cos(periodicity*theta-phase))',
            converter=_allow_only(['k*(1+cos(periodicity*theta-phase))'])
        )
        default_idivf = ParameterAttribute(default='auto')

        def check_handler_compatibility(self,
                                        other_handler):
            """
            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.
            """
            float_attrs_to_compare = []
            string_attrs_to_compare = ['potential']

            if self.default_idivf == 'auto':
                string_attrs_to_compare.append('default_idivf')
            else:
                float_attrs_to_compare.append('default_idivf')

            self._check_attributes_are_equal(other_handler, identical_attrs=string_attrs_to_compare,
                                             tolerance_attrs=float_attrs_to_compare)

        def find_matches(self, entity):
            """Find the improper torsions in the topology/molecule matched by a parameter type.

            Parameters
            ----------
            entity : openforcefield.topology.Topology
                Topology to search.

            Returns
            ---------
            matches : ImproperDict[Tuple[int], ParameterHandler._Match]
                ``matches[atom_indices]`` is the ``ParameterType`` object
                matching the 4-tuple of atom indices in ``entity``.

            """
            return self._find_matches(entity, transformed_dict_cls=ImproperDict)

        def create_force(self, system, topology, **kwargs):
            #force = super(ImproperTorsionHandler, self).create_force(system, topology, **kwargs)
            #force = super().create_force(system, topology, **kwargs)
            existing = [system.getForce(i) for i in range(system.getNumForces())]
            existing = [
                f for f in existing if type(f) == openmm.PeriodicTorsionForce
            ]
            if len(existing) == 0:
                force = openmm.PeriodicTorsionForce()
                system.addForce(force)
            else:
                force = existing[0]

            # Add all improper torsions to the system
            improper_matches = self.find_matches(topology)
            for (atom_indices, improper_match) in improper_matches.items():
                # Ensure atoms are actually bonded correct pattern in Topology
                # For impropers, central atom is atom 1
                # for (i, j) in [(0, 1), (1, 2), (1, 3)]:
                #     topology.assert_bonded(atom_indices[i], atom_indices[j])
                self._assert_correct_connectivity(improper_match, [(0, 1), (1, 2), (1, 3)])

                improper = improper_match.parameter_type

                # TODO: This is a lazy hack. idivf should be set according to the ParameterHandler's default_idivf attrib
                if improper.idivf is None:
                    improper.idivf = [3 for item in improper.k]
                # Impropers are applied in three paths around the trefoil having the same handedness
                for (improper_periodicity, improper_phase, improper_k, improper_idivf) in zip(improper.periodicity,
                                                   improper.phase, improper.k, improper.idivf):
                    # TODO: Implement correct "auto" behavior
                    if improper_idivf == 'auto':
                        improper_idivf = 3
                        logger.warning("The OpenForceField toolkit hasn't implemented "
                                       "support for the torsion `idivf` value of 'auto'."
                                       "Currently assuming a value of '3' for impropers.")
                    # Permute non-central atoms
                    others = [atom_indices[0], atom_indices[2], atom_indices[3]]
                    # ((0, 1, 2), (1, 2, 0), and (2, 0, 1)) are the three paths around the trefoil
                    for p in [(others[i], others[j], others[k]) for (i, j, k) in [(0, 1, 2), (1, 2, 0), (2, 0, 1)]]:
                        # The torsion force gets added three times, since the k is divided by three
                        force.addTorsion(atom_indices[1], p[0], p[1], p[2],
                                         improper_periodicity, improper_phase, improper_k/improper_idivf)
            logger.info(
                '{} impropers added, each applied in a six-fold trefoil'.format(
                    len(improper_matches)))

    class _NonbondedHandler(ParameterHandler):
        """Base class for ParameterHandlers that deal with OpenMM NonbondedForce objects."""
        _OPENMMTYPE = openmm.NonbondedForce

        def create_force(self, system, topology, **kwargs):
            # If we aren't yet keeping track of which molecules' charges have been assigned by which charge methods,
            # initialize a dict for that here.
            # TODO: This should be an attribute of the _system_, not the _topology_. However, since we're still using
            #  OpenMM's System class, I am storing this data on the OFF Topology until we make an OFF System class.
            if not hasattr(topology, "_ref_mol_to_charge_method"):
                topology._ref_mol_to_charge_method = {ref_mol: None for ref_mol in topology.reference_molecules}

            # Retrieve the system's OpenMM NonbondedForce
            existing = [system.getForce(i) for i in range(system.getNumForces())]
            existing = [f for f in existing if type(f) == self._OPENMMTYPE]

            # If there isn't yet one, initialize it and populate it with particles
            if len(existing) == 0:
                force = self._OPENMMTYPE()
                system.addForce(force)
                # Create all particles.
                for _ in topology.topology_particles:
                    force.addParticle(0.0, 1.0, 0.0)
            else:
                force = existing[0]

            return force

        def mark_charges_assigned(self, ref_mol, topology):
            """
            Record that charges have been assigned for a reference molecule.

            Parameters
            ----------
            ref_mol : openforcefield.topology.Molecule
                The molecule to mark as having charges assigned
            topology : openforcefield.topology.Topology
                The topology to record this information on.

            """
            # TODO: Change this to interface with system object instead of topology once we move away from OMM's System
            topology._ref_mol_to_charge_method[ref_mol] = self.__class__

        @staticmethod
        def check_charges_assigned(ref_mol, topology):
            """
            Check whether charges have been assigned for a reference molecule.

            Parameters
            ----------
            ref_mol : openforcefield.topology.Molecule
                The molecule to check for having charges assigned
            topology : openforcefield.topology.Topology
                The topology to query for this information

            Returns
            -------
            charges_assigned : bool
                Whether charges have already been assigned to this molecule

            """
            # TODO: Change this to interface with system object instead of topology once we move away from OMM's System
            return topology._ref_mol_to_charge_method[ref_mol] is not None

    class vdWHandler(_NonbondedHandler):
        """Handle SMIRNOFF ``<vdW>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        class vdWType(ParameterType):
            """A SMIRNOFF vdWForce type.

            .. warning :: This API is experimental and subject to change.
            """
            _VALENCE_TYPE = 'Atom'  # ChemicalEnvironment valence type expected for SMARTS
            _ELEMENT_NAME = 'Atom'

            epsilon = ParameterAttribute(unit=unit.kilocalorie_per_mole)
            sigma = ParameterAttribute(default=None, unit=unit.angstrom)
            rmin_half = ParameterAttribute(default=None, unit=unit.angstrom)

            def __init__(self, **kwargs):
                sigma = kwargs.get('sigma', None)
                rmin_half = kwargs.get('rmin_half', None)
                if (sigma is None) and (rmin_half is None):
                    raise SMIRNOFFSpecError("Either sigma or rmin_half must be specified.")
                if (sigma is not None) and (rmin_half is not None):
                    raise SMIRNOFFSpecError(
                        "BOTH sigma and rmin_half cannot be specified simultaneously."
                    )

                super().__init__(**kwargs)

        _TAGNAME = 'vdW'  # SMIRNOFF tag name to process
        _INFOTYPE = vdWType  # info type to store
        # _KWARGS = ['ewaldErrorTolerance',
        #            'useDispersionCorrection',
        #            'usePbc'] # Kwargs to catch when create_force is called

        potential = ParameterAttribute(
            default='Lennard-Jones-12-6',
            converter=_allow_only(['Lennard-Jones-12-6'])
        )
        combining_rules = ParameterAttribute(
            default='Lorentz-Berthelot',
            converter=_allow_only(['Lorentz-Berthelot'])
        )

        scale12 = ParameterAttribute(default=0.0, converter=float)
        scale13 = ParameterAttribute(default=0.0, converter=float)
        scale14 = ParameterAttribute(default=0.5, converter=float)
        scale15 = ParameterAttribute(default=1.0, converter=float)

        cutoff = ParameterAttribute(default=9.0 * unit.angstroms, unit=unit.angstrom)
        switch_width = ParameterAttribute(default=1.0 * unit.angstroms, unit=unit.angstrom)
        method = ParameterAttribute(
            default='cutoff',
            converter=_allow_only(['cutoff', 'PME'])
        )

        # TODO: Use _allow_only when ParameterAttribute will support multiple converters (it'll be easy when we switch to use the attrs library)
        @scale12.converter
        def scale12(self, attrs, new_scale12):
            if new_scale12 != 0.0:
                raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale12 values other than 0.0. "
                                        "Specified 1-2 scaling was {}".format(self._scale12))
            return new_scale12

        @scale13.converter
        def scale13(self, attrs, new_scale13):
            if new_scale13 != 0.0:
                raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale13 values other than 0.0. "
                                        "Specified 1-3 scaling was {}".format(self._scale13))
            return new_scale13

        @scale15.converter
        def scale15(self, attrs, new_scale15):
            if new_scale15 != 1.0:
                raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale15 values other than 1.0. "
                                        "Specified 1-5 scaling was {}".format(self._scale15))
            return new_scale15

        # Tolerance when comparing float attributes for handler compatibility.
        _SCALETOL = 1e-5

        def check_handler_compatibility(self,
                                        other_handler):
            """
            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.
            """
            float_attrs_to_compare = ['scale12', 'scale13', 'scale14', 'scale15']
            string_attrs_to_compare = ['potential', 'combining_rules', 'method']
            unit_attrs_to_compare = ['cutoff']

            self._check_attributes_are_equal(other_handler, identical_attrs=string_attrs_to_compare,
                                             tolerance_attrs=float_attrs_to_compare+unit_attrs_to_compare,
                                             tolerance=self._SCALETOL)

        def create_force(self, system, topology, **kwargs):
            force = super().create_force(system, topology, **kwargs)

            # If we're using PME, then the only possible openMM Nonbonded type is LJPME
            if self._method == 'PME':
                # If we're given a nonperiodic box, we always set NoCutoff. Later we'll add support for CutoffNonPeriodic
                if (topology.box_vectors is None):
                    force.setNonbondedMethod(openmm.NonbondedForce.NoCutoff)
                    # if (topology.box_vectors is None):
                    #     raise SMIRNOFFSpecError("If vdW method is  PME, a periodic Topology "
                    #                             "must be provided")
                else:
                    force.setNonbondedMethod(openmm.NonbondedForce.LJPME)
                    force.setCutoffDistance(9. * unit.angstrom)
                    force.setEwaldErrorTolerance(1.e-4)

            # If method is cutoff, then we currently support openMM's PME for periodic system and NoCutoff for nonperiodic
            elif self._method == 'cutoff':
                # If we're given a nonperiodic box, we always set NoCutoff. Later we'll add support for CutoffNonPeriodic
                if (topology.box_vectors is None):
                    force.setNonbondedMethod(openmm.NonbondedForce.NoCutoff)
                else:
                    force.setNonbondedMethod(openmm.NonbondedForce.PME)
                    force.setUseDispersionCorrection(True)
                    force.setCutoffDistance(self._cutoff)

            # Iterate over all defined Lennard-Jones types, allowing later matches to override earlier ones.
            atom_matches = self.find_matches(topology)

            # Set the particle Lennard-Jones terms.
            for atom_key, atom_match in atom_matches.items():
                atom_idx = atom_key[0]
                ljtype = atom_match.parameter_type
                if ljtype.sigma is None:
                    sigma = 2. * ljtype.rmin_half / (2.**(1. / 6.))
                else:
                    sigma = ljtype.sigma
                force.setParticleParameters(atom_idx, 0.0, sigma,
                                            ljtype.epsilon)

            # Check that no atoms (n.b. not particles) are missing force parameters.
            self._check_all_valence_terms_assigned(assigned_terms=atom_matches,
                                                   valence_terms=list(topology.topology_atoms))

        # TODO: Can we express separate constraints for postprocessing and normal processing?
        def postprocess_system(self, system, topology, **kwargs):
            # Create exceptions based on bonds.
            # TODO: This postprocessing must occur after the ChargeIncrementModelHandler
            # QUESTION: Will we want to do this for *all* cases, or would we ever want flexibility here?
            bond_particle_indices = []

            for topology_molecule in topology.topology_molecules:

                top_mol_particle_start_index = topology_molecule.atom_start_topology_index

                for topology_bond in topology_molecule.bonds:

                    top_index_1 = topology_molecule._ref_to_top_index[topology_bond.bond.atom1_index]
                    top_index_2 = topology_molecule._ref_to_top_index[topology_bond.bond.atom2_index]

                    top_index_1 += top_mol_particle_start_index
                    top_index_2 += top_mol_particle_start_index

                    bond_particle_indices.append((top_index_1, top_index_2))

            for force in system.getForces():
                # TODO: Should we just store which `Force` object we are adding to and use that instead,
                # to prevent interference with other kinds of forces in the future?
                # TODO: Can we generalize this to allow for `CustomNonbondedForce` implementations too?
                if isinstance(force, openmm.NonbondedForce):
                    #nonbonded.createExceptionsFromBonds(bond_particle_indices, self.coulomb14scale, self.lj14scale)

                    # TODO: Don't mess with electrostatic scaling here. Have a separate electrostatics handler.
                    force.createExceptionsFromBonds(bond_particle_indices, 0.83333,
                                                    self._scale14)
                    #force.createExceptionsFromBonds(bond_particle_indices, self.coulomb14scale, self._scale14)

    class ElectrostaticsHandler(_NonbondedHandler):
        """Handles SMIRNOFF ``<Electrostatics>`` tags.

        .. warning :: This API is experimental and subject to change.
        """
        _TAGNAME = 'Electrostatics'
        _DEPENDENCIES = [vdWHandler]
        _KWARGS = ['charge_from_molecules', 'allow_nonintegral_charges']

        scale12 = ParameterAttribute(default=0.0, converter=float)
        scale13 = ParameterAttribute(default=0.0, converter=float)
        scale14 = ParameterAttribute(default=0.833333, converter=float)
        scale15 = ParameterAttribute(default=1.0, converter=float)
        cutoff = ParameterAttribute(default=9.0 * unit.angstrom, unit=unit.angstrom)
        switch_width = ParameterAttribute(default=0.0 * unit.angstrom, unit=unit.angstrom)
        method = ParameterAttribute(
            default='PME',
            converter=_allow_only(['Coulomb', 'PME'])
        )

        # TODO: Use _allow_only when ParameterAttribute will support multiple converters (it'll be easy when we switch to use the attrs library)
        @scale12.converter
        def scale12(self, attrs, new_scale12):
            if new_scale12 != 0.0:
                raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale12 values other than 0.0. "
                                        "Specified 1-2 scaling was {}".format(self._scale12))
            return new_scale12

        @scale13.converter
        def scale13(self, attrs, new_scale13):
            if new_scale13 != 0.0:
                raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale13 values other than 0.0. "
                                        "Specified 1-3 scaling was {}".format(self._scale13))
            return new_scale13

        @scale15.converter
        def scale15(self, attrs, new_scale15):
            if new_scale15 != 1.0:
                raise SMIRNOFFSpecError("Current OFF toolkit is unable to handle scale15 values other than 1.0. "
                                        "Specified 1-5 scaling was {}".format(self._scale15))
            return new_scale15

        @switch_width.converter
        def switch_width(self, attr, new_switch_width):
            if self._switch_width != 0.0 * unit.angstrom:
                raise IncompatibleParameterError(
                    "The current implementation of the Open Force Field toolkit can not "
                    "support an electrostatic switching width. Currently only `0.0 angstroms` "
                    f"is supported (SMIRNOFF data specified {new_switch_width})"
                )

        # Tolerance when comparing float attributes for handler compatibility.
        _SCALETOL = 1e-5

        def check_handler_compatibility(self,
                                        other_handler):
            """
            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.
            """
            float_attrs_to_compare = ['scale12', 'scale13', 'scale14', 'scale15']
            string_attrs_to_compare = ['method']
            unit_attrs_to_compare = ['cutoff', 'switch_width']

            self._check_attributes_are_equal(other_handler, identical_attrs=string_attrs_to_compare,
                                             tolerance_attrs=float_attrs_to_compare+unit_attrs_to_compare,
                                             tolerance=self._SCALETOL)

        def assign_charge_from_molecules(self, molecule, charge_mols):
            """
            Given an input molecule, checks against a list of molecules for an isomorphic match. If found, assigns
            partial charges from the match to the input molecule.

            Parameters
            ----------
            molecule : an openforcefield.topology.FrozenMolecule
                The molecule to have partial charges assigned if a match is found.
            charge_mols : list of [openforcefield.topology.FrozenMolecule]
                A list of molecules with charges already assigned.

            Returns
            -------
            match_found : bool
                Whether a match was found. If True, the input molecule will have been modified in-place.
            """

            import simtk.unit

            # Check each charge_mol for whether it's isomorphic to the input molecule
            for charge_mol in charge_mols:
                ismorphic, topology_atom_map = Molecule.are_isomorphic(molecule, charge_mol,
                                                                       return_atom_map=True,
                                                                       aromatic_matching=True,
                                                                       formal_charge_matching=True,
                                                                       bond_order_matching=True,
                                                                       atom_stereochemistry_matching=True,
                                                                       bond_stereochemistry_matching=True)
                # if they are isomorphic then use the mapping
                if ismorphic:
                    # Take the first valid atom indexing map
                    # Set the partial charges
                    # Make a copy of the charge molecule's charges array (this way it's the right shape)
                    temp_mol_charges = copy.deepcopy(simtk.unit.Quantity(charge_mol.partial_charges))
                    for charge_idx, ref_idx in topology_atom_map.items():
                        temp_mol_charges[ref_idx] = charge_mol.partial_charges[charge_idx]
                    molecule.partial_charges = temp_mol_charges
                    return True

            # If no match was found, return False
            return False

        def create_force(self, system, topology, **kwargs):
            from openforcefield.topology import FrozenMolecule, TopologyAtom, TopologyVirtualSite

            force = super().create_force(system, topology, **kwargs)

            # See if each molecule should have charges assigned by the charge_from_molecules kwarg
            for ref_mol in topology.reference_molecules:

                # If charges were already assigned, skip this molecule
                if self.check_charges_assigned(ref_mol, topology):
                    continue

                # Make a temporary copy of ref_mol to assign charges from charge_mol
                temp_mol = FrozenMolecule(ref_mol)

                # First, check whether any of the reference molecules in the topology are in the charge_from_mol list
                charges_from_charge_mol = False
                if 'charge_from_molecules' in kwargs:
                    charges_from_charge_mol = self.assign_charge_from_molecules(temp_mol, kwargs['charge_from_molecules'])

                # If this reference molecule wasn't in the charge_from_molecules list, end this iteration
                if not(charges_from_charge_mol):
                    continue

                # Otherwise, the molecule is in the charge_from_molecules list, and we should assign charges to all
                # instances of it in this topology.
                for topology_molecule in topology._reference_molecule_to_topology_molecules[ref_mol]:

                    for topology_particle in topology_molecule.particles:

                        if type(topology_particle) is TopologyAtom:
                            ref_mol_particle_index = topology_particle.atom.molecule_particle_index
                        elif type(topology_particle) is TopologyVirtualSite:
                            ref_mol_particle_index = topology_particle.virtual_site.molecule_particle_index
                        else:
                            raise ValueError(f'Particles of type {type(topology_particle)} are not supported')

                        topology_particle_index = topology_particle.topology_particle_index

                        particle_charge = temp_mol._partial_charges[ref_mol_particle_index]

                        # Retrieve nonbonded parameters for reference atom (charge not set yet)
                        _, sigma, epsilon = force.getParticleParameters(topology_particle_index)
                        # Set the nonbonded force with the partial charge
                        force.setParticleParameters(topology_particle_index,
                                                    particle_charge, sigma,
                                                    epsilon)

                # Finally, mark that charges were assigned for this reference molecule
                self.mark_charges_assigned(ref_mol, topology)

            # Set the nonbonded method
            settings_matched = False
            current_nb_method = force.getNonbondedMethod()

            # First, check whether the vdWHandler set the nonbonded method to LJPME, because that means
            # that electrostatics also has to be PME
            if (current_nb_method == openmm.NonbondedForce.LJPME) and (self._method != 'PME'):
                raise IncompatibleParameterError("In current Open Force Field toolkit implementation, if vdW "
                                                 "treatment is set to LJPME, electrostatics must also be PME "
                                                 "(electrostatics treatment currently set to {}".format(self._method))

            # Then, set nonbonded methods based on method keyword
            if self._method == 'PME':
                # Check whether the topology is nonperiodic, in which case we always switch to NoCutoff
                # (vdWHandler will have already set this to NoCutoff)
                # TODO: This is an assumption right now, and a bad one. See issue #219
                if topology.box_vectors is None:
                    assert current_nb_method == openmm.NonbondedForce.NoCutoff
                    settings_matched = True
                    # raise IncompatibleParameterError("Electrostatics handler received PME method keyword, but a nonperiodic"
                    #                                  " topology. Use of PME electrostatics requires a periodic topology.")
                else:
                    if current_nb_method == openmm.NonbondedForce.LJPME:
                        pass
                        # There's no need to check for matching cutoff/tolerance here since both are hard-coded defaults
                    else:
                        force.setNonbondedMethod(openmm.NonbondedForce.PME)
                        force.setCutoffDistance(9. * unit.angstrom)
                        force.setEwaldErrorTolerance(1.e-4)

                settings_matched = True

            # If vdWHandler set the nonbonded method to NoCutoff, then we don't need to change anything
            elif self._method == 'Coulomb':
                if topology.box_vectors is None:
                    # (vdWHandler will have already set this to NoCutoff)
                    assert current_nb_method == openmm.NonbondedForce.NoCutoff
                    settings_matched = True
                else:
                    raise IncompatibleParameterError("Electrostatics method set to Coulomb, and topology is periodic. "
                                                     "In the future, this will lead to use of OpenMM's CutoffPeriodic "
                                                     "Nonbonded force method, however this is not supported in the "
                                                     "current Open Force Field toolkit.")

            # If the vdWHandler set the nonbonded method to PME, then ensure that it has the same cutoff
            elif self._method == 'reaction-field':
                if topology.box_vectors is None:
                    # (vdWHandler will have already set this to NoCutoff)
                    assert current_nb_method == openmm.NonbondedForce.NoCutoff
                    settings_matched = True
                else:
                    raise IncompatibleParameterError("Electrostatics method set to reaction-field. In the future, "
                                                     "this will lead to use of OpenMM's CutoffPeriodic or CutoffNonPeriodic"
                                                     " Nonbonded force method, however this is not supported in the "
                                                     "current Open Force Field toolkit")

            if not settings_matched:
                raise IncompatibleParameterError("Unable to support provided vdW method, electrostatics "
                                                 "method ({}), and topology periodicity ({}) selections. Additional "
                                                 "options for nonbonded treatment may be added in future versions "
                                                 "of the Open Force Field toolkit.".format(self._method,
                                                                                    topology.box_vectors is not None))

        def postprocess_system(self, system, topology, **kwargs):
            force = super().create_force(system, topology, **kwargs)
            # Check to ensure all molecules have had charges assigned
            uncharged_mols = []
            for ref_mol in topology.reference_molecules:
                if not self.check_charges_assigned(ref_mol, topology):
                    uncharged_mols.append(ref_mol)

            if len(uncharged_mols) != 0:
                msg = "The following molecules did not have charges assigned by any ParameterHandler in the ForceField:\n"
                for ref_mol in uncharged_mols:
                    msg += f"{ref_mol.to_smiles()}\n"
                raise UnassignedMoleculeChargeException(msg)

            # Unless check is disabled, ensure that the sum of partial charges on a molecule
            # add up to approximately its formal charge
            allow_nonintegral_charges = kwargs.get('allow_nonintegral_charges', False)
            for top_mol in topology.topology_molecules:
                # Skip check if user manually disables it.
                if allow_nonintegral_charges:
                    continue
                formal_charge_sum = top_mol.reference_molecule.total_charge
                partial_charge_sum = 0. * unit.elementary_charge
                for top_particle in top_mol.particles:
                    q, _, _ = force.getParticleParameters(top_particle.topology_particle_index)
                    partial_charge_sum += q
                if abs(formal_charge_sum - partial_charge_sum) > 0.01 * unit.elementary_charge:
                    msg = f"Partial charge sum ({partial_charge_sum}) " \
                          f"for molecule '{top_mol.reference_molecule.name}' (SMILES " \
                          f"{top_mol.reference_molecule.to_smiles()} does not equal formal charge sum " \
                          f"({formal_charge_sum}). To override this error, provide the " \
                          f"'allow_nonintegral_charges=True' keyword to ForceField.create_openmm_system"
                    raise NonintegralMoleculeChargeException(msg)

    class LibraryChargeHandler(_NonbondedHandler):
        """Handle SMIRNOFF ``<LibraryCharges>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        class LibraryChargeType(ParameterType):
            """A SMIRNOFF Library Charge type.

            .. warning :: This API is experimental and subject to change.
            """
            _VALENCE_TYPE = None  # This disables the connectivity check when parsing LibraryChargeType objects
            _ELEMENT_NAME = 'LibraryCharge'

            name = ParameterAttribute(default=None)
            charge = IndexedParameterAttribute(unit=unit.elementary_charge)

            def __init__(self, **kwargs):
                super().__init__(**kwargs)
                unique_tags, connectivity = GLOBAL_TOOLKIT_REGISTRY.call('get_tagged_smarts_connectivity', self.smirks)
                if len(self.charge) != len(unique_tags):
                    raise SMIRNOFFSpecError(f"LibraryCharge {self} was initialized with unequal number of "
                                            f"tagged atoms and charges")

        _TAGNAME = 'LibraryCharges'  # SMIRNOFF tag name to process
        _INFOTYPE = LibraryChargeType  # info type to store
        _DEPENDENCIES = [vdWHandler, ElectrostaticsHandler]

        def find_matches(self, entity):
            """Find the elements of the topology/molecule matched by a parameter type.

            Parameters
            ----------
            entity : openforcefield.topology.Topology
                Topology to search.

            Returns
            ---------
            matches : ValenceDict[Tuple[int], ParameterHandler._Match]
                ``matches[particle_indices]`` is the ``ParameterType`` object
                matching the tuple of particle indices in ``entity``.
            """

            return self._find_matches(entity, transformed_dict_cls=dict)

        def create_force(self, system, topology, **kwargs):
            from openforcefield.topology import FrozenMolecule

            force = super().create_force(system, topology, **kwargs)

            # Iterate over all defined library charge parameters, allowing later matches to override earlier ones.
            atom_matches = self.find_matches(topology)

            # Create a set of all the topology atom indices for which library charges can be applied
            assignable_atoms = set()
            atom_assignments = dict()
            # TODO: This assumes that later matches should always override earlier ones. This may require more
            #       thought, since matches can be partially overlapping
            for topology_indices, library_charge in atom_matches.items():
                for charge_idx, top_idx in enumerate(topology_indices):
                    if top_idx in assignable_atoms:
                        logger.debug(f'Multiple library charge assignments found for atom {top_idx}')
                    assignable_atoms.add(top_idx)
                    atom_assignments[top_idx] = library_charge.parameter_type.charge[charge_idx]
            # TODO: Should header include a residue separator delimiter? Maybe not, since it's not clear how having
            #       multiple LibraryChargeHandlers could return a single set of matches while respecting different
            #       separators.

            # Keep track of the reference molecules that this successfully assigns charges to, so we can
            # mark them and subsequent charge generation handlers won't override the values
            ref_mols_assigned = set()

            # Check to see whether the set contains any complete molecules, and remove the matches if not.
            for top_mol in topology.topology_molecules:

                # Make a temporary copy of ref_mol to assign charges from charge_mol
                temp_mol = FrozenMolecule(top_mol.reference_molecule)

                # If charges were already assigned, skip this molecule
                if self.check_charges_assigned(temp_mol, topology):
                    continue

                # Ensure all of the atoms in this mol are covered, otherwise skip it
                top_particle_idxs = [atom.topology_particle_index for atom in top_mol.atoms]
                if len(set(top_particle_idxs).intersection(assignable_atoms)) != top_mol.n_atoms:
                    logger.debug('Entire molecule is not covered. Skipping library charge assignment.')
                    continue

                # If we pass both tests above, go ahead and assign charges
                # TODO: We could probably save a little time by looking up this TopologyMolecule's _reference molecule_
                #       and assigning charges to all other instances of it in this topology
                for top_particle_idx in top_particle_idxs:
                    _, sigma, epsilon = force.getParticleParameters(top_particle_idx)
                    force.setParticleParameters(top_particle_idx,
                                                atom_assignments[top_particle_idx],
                                                sigma,
                                                epsilon)

                ref_mols_assigned.add(temp_mol)

            # Finally, mark that charges were assigned for this reference molecule
            for assigned_mol in ref_mols_assigned:
                self.mark_charges_assigned(assigned_mol, topology)

    class ToolkitAM1BCCHandler(_NonbondedHandler):
        """Handle SMIRNOFF ``<ToolkitAM1BCC>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        _TAGNAME = 'ToolkitAM1BCC'  # SMIRNOFF tag name to process
        _DEPENDENCIES = [vdWHandler, ElectrostaticsHandler, LibraryChargeHandler]
        _KWARGS = ['toolkit_registry'] # Kwargs to catch when create_force is called

        def check_handler_compatibility(self,
                                        other_handler,
                                        assume_missing_is_default=True):
            """
            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.
            """
            pass

        def create_force(self, system, topology, **kwargs):
            import warnings
            from openforcefield.utils.toolkits import GLOBAL_TOOLKIT_REGISTRY
            from openforcefield.topology import FrozenMolecule, TopologyAtom, TopologyVirtualSite

            force = super().create_force(system, topology, **kwargs)

            for ref_mol in topology.reference_molecules:

                # If charges were already assigned, skip this molecule
                if self.check_charges_assigned(ref_mol, topology):
                    continue

                # Make a temporary copy of ref_mol to assign charges
                temp_mol = FrozenMolecule(ref_mol)

                # If the molecule wasn't already assigned charge values, calculate them here
                toolkit_registry = kwargs.get('toolkit_registry', GLOBAL_TOOLKIT_REGISTRY)
                try:
                    # We don't need to generate conformers here, since that will be done by default in
                    # compute_partial_charges_am1bcc if the use_conformers kwarg isn't defined
                    temp_mol.compute_partial_charges_am1bcc(toolkit_registry=toolkit_registry)
                except Exception as e:
                    warnings.warn(str(e), Warning)
                    continue

                # Assign charges to relevant atoms
                for topology_molecule in topology._reference_molecule_to_topology_molecules[ref_mol]:
                    for topology_particle in topology_molecule.particles:
                        if type(topology_particle) is TopologyAtom:
                            ref_mol_particle_index = topology_particle.atom.molecule_particle_index
                        elif type(topology_particle) is TopologyVirtualSite:
                            ref_mol_particle_index = topology_particle.virtual_site.molecule_particle_index
                        else:
                            raise ValueError(f'Particles of type {type(topology_particle)} are not supported')

                        topology_particle_index = topology_particle.topology_particle_index

                        particle_charge = temp_mol._partial_charges[ref_mol_particle_index]

                        # Retrieve nonbonded parameters for reference atom (charge not set yet)
                        _, sigma, epsilon = force.getParticleParameters(topology_particle_index)
                        # Set the nonbonded force with the partial charge
                        force.setParticleParameters(topology_particle_index,
                                                    particle_charge, sigma,
                                                    epsilon)
                # Finally, mark that charges were assigned for this reference molecule
                self.mark_charges_assigned(ref_mol, topology)

        # TODO: Move chargeModel and library residue charges to SMIRNOFF spec
        def postprocess_system(self, system, topology, **kwargs):

            bond_matches = self.find_matches(topology)

            # Apply bond charge increments to all appropriate force groups
            # QUESTION: Should we instead apply this to the Topology in a preprocessing step, prior to spreading out charge onto virtual sites?
            for force in system.getForces():
                if force.__class__.__name__ in [
                        'NonbondedForce'
                ]:  # TODO: We need to apply this to all Force types that involve charges, such as (Custom)GBSA forces and CustomNonbondedForce
                    for (atoms, bond_match) in bond_matches.items():
                        # Get corresponding particle indices in Topology
                        bond = bond_match.parameter_type

                        particle_indices = tuple(
                            [atom.particle_index for atom in atoms])
                        # Retrieve parameters
                        [charge0, sigma0, epsilon0] = force.getParticleParameters(
                            particle_indices[0])
                        [charge1, sigma1, epsilon1] = force.getParticleParameters(
                            particle_indices[1])
                        # Apply bond charge increment
                        charge0 -= bond.increment
                        charge1 += bond.increment
                        # Update charges
                        force.setParticleParameters(particle_indices[0], charge0,
                                                    sigma0, epsilon0)
                        force.setParticleParameters(particle_indices[1], charge1,
                                                    sigma1, epsilon1)
                        # TODO: Calculate exceptions

    class ChargeIncrementModelHandler(_NonbondedHandler):
        """Handle SMIRNOFF ``<ChargeIncrementModel>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        class ChargeIncrementType(ParameterType):
            """A SMIRNOFF bond charge correction type.

            .. warning :: This API is experimental and subject to change.
            """
            _VALENCE_TYPE = None  # This disables the connectivity check when parsing LibraryChargeType objects
            _ELEMENT_NAME = 'ChargeIncrement'

            charge_increment = IndexedParameterAttribute(unit=unit.elementary_charge)

            def __init__(self, **kwargs):
                super().__init__(**kwargs)
                unique_tags, connectivity = GLOBAL_TOOLKIT_REGISTRY.call('get_tagged_smarts_connectivity', self.smirks)
                if len(self.charge_increment) != len(unique_tags):
                    raise SMIRNOFFSpecError(f"ChargeIncrement {self} was initialized with unequal number of "
                                            f"tagged atoms and charge increments")

        _TAGNAME = 'ChargeIncrementModel'  # SMIRNOFF tag name to process
        _INFOTYPE = ChargeIncrementType  # info type to store
        _DEPENDENCIES = [vdWHandler, ElectrostaticsHandler, LibraryChargeHandler, ToolkitAM1BCCHandler]

        number_of_conformers = ParameterAttribute(default=1, converter=int)

        partial_charge_method = ParameterAttribute(
            default='AM1-Mulliken', converter=str
        )

        def check_handler_compatibility(self,
                                        other_handler,
                                        assume_missing_is_default=True):
            """
            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.
            """

            int_attrs_to_compare = ['number_of_conformers']
            string_attrs_to_compare = ['partial_charge_method']

            self._check_attributes_are_equal(other_handler,
                                             identical_attrs=string_attrs_to_compare+int_attrs_to_compare)

        def find_matches(self, entity):
            """Find the elements of the topology/molecule matched by a parameter type.

            Parameters
            ----------
            entity : openforcefield.topology.Topology
                Topology to search.

            Returns
            ---------
            matches : ValenceDict[Tuple[int], ParameterHandler._Match]
                ``matches[particle_indices]`` is the ``ParameterType`` object
                matching the tuple of particle indices in ``entity``.
            """
            # Using SortedDict here leads to the desired deduplication behavior, BUT it mangles the order
            # of the atom indices in the keys. Thankfully, the Match objects that are values in `matches` contain
            # `match.environment_match.topology_atom_indices`, which has the tuple in the correct order
            matches = self._find_matches(entity, transformed_dict_cls=SortedDict)
            return matches

        def create_force(self, system, topology, **kwargs):
            import warnings
            from openforcefield.topology import FrozenMolecule, TopologyAtom, TopologyVirtualSite

            # We only want one instance of this force type
            existing = [system.getForce(i) for i in range(system.getNumForces())]
            existing = [f for f in existing if type(f) == self._OPENMMTYPE]
            if len(existing) == 0:
                force = self._OPENMMTYPE()
                system.addForce(force)
            else:
                force = existing[0]

            for ref_mol in topology.reference_molecules:

                # If charges were already assigned, skip this molecule
                if self.check_charges_assigned(ref_mol, topology):
                    continue

                # Make a temporary copy of ref_mol to assign charges from charge_mol
                temp_mol = FrozenMolecule(ref_mol)

                toolkit_registry = kwargs.get('toolkit_registry', GLOBAL_TOOLKIT_REGISTRY)
                try:
                    # If the molecule wasn't assigned parameters from a manually-input charge_mol, calculate them here
                    temp_mol.generate_conformers(n_conformers=self.number_of_conformers)
                    temp_mol.assign_partial_charges(partial_charge_method=self.partial_charge_method,
                                                    toolkit_registry=toolkit_registry)
                except Exception as e:
                    warnings.warn(str(e), Warning)
                    continue

                charges_to_assign = {}

                # Assign initial, un-incremented charges to relevant atoms
                for topology_molecule in topology._reference_molecule_to_topology_molecules[ref_mol]:
                    for topology_particle in topology_molecule.particles:
                        topology_particle_index = topology_particle.topology_particle_index
                        if type(topology_particle) is TopologyAtom:
                            ref_mol_particle_index = topology_particle.atom.molecule_particle_index
                        if type(topology_particle) is TopologyVirtualSite:
                            ref_mol_particle_index = topology_particle.virtual_site.molecule_particle_index
                        particle_charge = temp_mol._partial_charges[ref_mol_particle_index]
                        charges_to_assign[topology_particle_index] = particle_charge

                # Find SMARTS-based matches for charge increments
                charge_increment_matches = self.find_matches(topology)

                # We ignore the atom index order in the keys here, since they have been
                # sorted in order to deduplicate matches and let us identify when one parameter overwrites another
                # in the SMIRNOFF parameter hierarchy. Since they are sorted, the position of the atom index
                # in the key tuple DOES NOT correspond to the appropriate chargeincrementX value.
                # Instead, the correct ordering of the match indices is found in
                # charge_increment_match.environment_match.topology_atom_indices
                for (_, charge_increment_match) in charge_increment_matches.items():
                    # Adjust the values in the charges_to_assign dict by adding any
                    # charge increments onto the existing values
                    atom_indices = charge_increment_match.environment_match.topology_atom_indices
                    charge_increment = charge_increment_match.parameter_type
                    for top_particle_idx, charge_increment in zip(atom_indices, charge_increment.charge_increment):
                        if top_particle_idx in charges_to_assign:
                            charges_to_assign[top_particle_idx] += charge_increment

                # Set the incremented charges on the System particles
                for topology_particle_index, charge_to_assign in charges_to_assign.items():
                    _, sigma, epsilon = force.getParticleParameters(topology_particle_index)
                    force.setParticleParameters(topology_particle_index,
                                                charge_to_assign, sigma,
                                                epsilon)

                # Finally, mark that charges were assigned for this reference molecule
                self.mark_charges_assigned(ref_mol, topology)

    class GBSAHandler(ParameterHandler):
        """Handle SMIRNOFF ``<GBSA>`` tags

        .. warning :: This API is experimental and subject to change.
        """

        class GBSAType(ParameterType):
            """A SMIRNOFF GBSA type.

            .. warning :: This API is experimental and subject to change.
            """
            _VALENCE_TYPE = 'Atom'
            _ELEMENT_NAME = 'Atom'

            radius = ParameterAttribute(unit=unit.angstrom)
            scale = ParameterAttribute(converter=float)

        _TAGNAME = 'GBSA'
        _INFOTYPE = GBSAType
        _OPENMMTYPE = openmm.GBSAOBCForce
        # It's important that this runs AFTER partial charges are assigned to all particles, since this will need to
        # collect and assign them to the GBSA particles
        _DEPENDENCIES = [vdWHandler, ElectrostaticsHandler,
                         ToolkitAM1BCCHandler, ChargeIncrementModelHandler, LibraryChargeHandler]

        gb_model = ParameterAttribute(
            default='OBC1',
            converter=_allow_only(['HCT', 'OBC1', 'OBC2'])
        )
        solvent_dielectric = ParameterAttribute(default=78.5, converter=float)
        solute_dielectric = ParameterAttribute(default=1, converter=float)
        sa_model = ParameterAttribute(default='ACE', converter=_allow_only(['ACE', None])
        )
        surface_area_penalty = ParameterAttribute(default=5.4*unit.calorie / unit.mole / unit.angstrom**2,
                                                  unit=unit.calorie / unit.mole / unit.angstrom**2)
        solvent_radius = ParameterAttribute(default=1.4*unit.angstrom, unit=unit.angstrom)

        def _validate_parameters(self):
            """
            Checks internal attributes, raising an exception if they are configured in an invalid way.
            """
            # If we're using HCT via GBSAHCTForce(CustomAmberGBForceBase):, then we need to ensure that:
            #   surface_area_energy is 5.4 cal/mol/A^2
            #   solvent_radius is 1.4 A
            # Justification at https://github.com/openforcefield/openforcefield/pull/363
            if self.gb_model == 'HCT':
                if ((self.surface_area_penalty != 5.4 * unit.calorie / unit.mole / unit.angstrom**2) and
                    (self.sa_model is not None)):
                    raise IncompatibleParameterError(f"The current implementation of HCT GBSA does not "
                                                     f"support surface_area_penalty values other than 5.4 "
                                                     f"cal/mol A^2 (data source specified value of "
                                                     f"{self.surface_area_penalty})")

                if ((self.solvent_radius != 1.4 * unit.angstrom) and
                    (self.sa_model is not None)):
                    raise IncompatibleParameterError(f"The current implementation of HCT GBSA does not "
                                                     f"support solvent_radius values other than 1.4 "
                                                     f"A (data source specified value of "
                                                     f"{self.solvent_radius})")

            # If we're using OBC1 via GBSAOBC1Force(CustomAmberGBForceBase), then we need to ensure that:
            #   surface_area_energy is 5.4 cal/mol/A^2
            #   solvent_radius is 1.4 A
            # Justification at https://github.com/openforcefield/openforcefield/pull/363
            if self.gb_model == 'OBC1':
                if ((self.surface_area_penalty != 5.4 * unit.calorie / unit.mole / unit.angstrom**2) and
                    (self.sa_model is not None)):
                    raise IncompatibleParameterError(f"The current implementation of OBC1 GBSA does not "
                                                     f"support surface_area_penalty values other than 5.4 "
                                                     f"cal/mol A^2 (data source specified value of "
                                                     f"{self.surface_area_penalty})")

                if ((self.solvent_radius != 1.4 * unit.angstrom) and
                    (self.sa_model is not None)):
                    raise IncompatibleParameterError(f"The current implementation of OBC1 GBSA does not "
                                                     f"support solvent_radius values other than 1.4 "
                                                     f"A (data source specified value of "
                                                     f"{self.solvent_radius})")

            # If we're using OBC2 via GBSAOBCForce, then we need to ensure that
            #   solvent_radius is 1.4 A
            # Justification at https://github.com/openforcefield/openforcefield/pull/363
            if self.gb_model == 'OBC2':

                if ((self.solvent_radius != 1.4 * unit.angstrom) and
                    (self.sa_model is not None)):
                    raise IncompatibleParameterError(f"The current implementation of OBC1 GBSA does not "
                                                     f"support solvent_radius values other than 1.4 "
                                                     f"A (data source specified value of "
                                                     f"{self.solvent_radius})")

        # Tolerance when comparing float attributes for handler compatibility.
        _SCALETOL = 1e-5

        def check_handler_compatibility(self,
                                        other_handler):
            """
            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.
            """
            float_attrs_to_compare = ['solvent_dielectric', 'solute_dielectric']
            string_attrs_to_compare = ['gb_model', 'sa_model']
            unit_attrs_to_compare = ['surface_area_penalty', 'solvent_radius']

            self._check_attributes_are_equal(other_handler, identical_attrs=string_attrs_to_compare,
                                             tolerance_attrs=float_attrs_to_compare+unit_attrs_to_compare,
                                             tolerance=self._SCALETOL)

        def create_force(self, system, topology, **kwargs):
            import simtk

            self._validate_parameters()

            # Grab the existing nonbonded force (which will have particle charges)
            existing = [system.getForce(i) for i in range(system.getNumForces())]
            existing = [
                f for f in existing if type(f) == openmm.NonbondedForce
            ]
            assert len(existing) == 1

            nonbonded_force = existing[0]

            # No previous GBSAForce should exist, so we're safe just making one here.
            force_map = {
                'HCT': simtk.openmm.app.internal.customgbforces.GBSAHCTForce,
                'OBC1': simtk.openmm.app.internal.customgbforces.GBSAOBC1Force,
                'OBC2': simtk.openmm.GBSAOBCForce,
                # It's tempting to do use the class below, but the customgbforce
                # version of OBC2 doesn't provide setSolventRadius()
                #'OBC2': simtk.openmm.app.internal.customgbforces.GBSAOBC2Force,
            }
            openmm_force_type = force_map[self.gb_model]

            if nonbonded_force.getNonbondedMethod() == openmm.NonbondedForce.NoCutoff:
                amber_cutoff = None
            else:
                amber_cutoff = nonbonded_force.getCutoffDistance().value_in_unit(unit.nanometer)

            if self.gb_model == 'OBC2':
                gbsa_force = openmm_force_type()

            else:
                # We set these values in the constructor if we use the internal AMBER GBSA type wrapper
                gbsa_force = openmm_force_type(solventDielectric=self.solvent_dielectric,
                                               soluteDielectric=self.solute_dielectric,
                                               SA=self.sa_model,
                                               cutoff=amber_cutoff,
                                               kappa=0,
                                               )
                # WARNING: If using a CustomAmberGBForce, the functional form is affected by whether
                # the cutoff kwarg is None *during initialization*. So, if you initialize it with a
                # non-None value, and then try to change it to None, you're likely to get unphysical results.

            # Set the GBSAForce to have the same cutoff as NonbondedForce
            #gbsa_force.setCutoffDistance(nonbonded_force.getCutoffDistance())
            if amber_cutoff is not None:
                gbsa_force.setCutoffDistance(amber_cutoff)

            if nonbonded_force.usesPeriodicBoundaryConditions():
                # WARNING: The lines below aren't equivalent. The NonbondedForce and
                # CustomGBForce NonbondedMethod enums have different meanings.
                # More details:
                # http://docs.openmm.org/latest/api-python/generated/simtk.openmm.openmm.NonbondedForce.html
                # http://docs.openmm.org/latest/api-python/generated/simtk.openmm.openmm.GBSAOBCForce.html
                # http://docs.openmm.org/latest/api-python/generated/simtk.openmm.openmm.CustomGBForce.html

                #gbsa_force.setNonbondedMethod(simtk.openmm.NonbondedForce.CutoffPeriodic)
                gbsa_force.setNonbondedMethod(simtk.openmm.CustomGBForce.CutoffPeriodic)
            else:
                #gbsa_force.setNonbondedMethod(simtk.openmm.NonbondedForce.NoCutoff)
                gbsa_force.setNonbondedMethod(simtk.openmm.CustomGBForce.NoCutoff)

            # Add all GBSA terms to the system. Note that this will have been done above
            if self.gb_model == 'OBC2':
                gbsa_force.setSolventDielectric(self.solvent_dielectric)
                gbsa_force.setSoluteDielectric(self.solute_dielectric)
                if self.sa_model is None:
                    gbsa_force.setSurfaceAreaEnergy(0)
                else:
                    gbsa_force.setSurfaceAreaEnergy(self.surface_area_penalty)

            # Iterate over all defined GBSA types, allowing later matches to override earlier ones.
            atom_matches = self.find_matches(topology)

            # Create all particles.

            # !!! WARNING: CustomAmberGBForceBase expects different per-particle parameters
            # depending on whether you use addParticle or setParticleParameters. In
            # setParticleParameters, we have to apply the offset and scale BEFORE setting
            # parameters, whereas in addParticle, the offset is applied automatically, and the particle
            # parameters are not set until an auxillary finalize() method is called. !!!

            # To keep it simple, we DO NOT pre-populate the particles in the GBSA force here.
            # We call addParticle further below instead.
            # These lines are commented out intentionally as an example of what NOT to do.
            #for topology_particle in topology.topology_particles:
                #gbsa_force.addParticle([0.0, 1.0, 0.0])

            params_to_add = [[] for _ in topology.topology_particles]
            for atom_key, atom_match in atom_matches.items():
                atom_idx = atom_key[0]
                gbsatype = atom_match.parameter_type
                charge, _, _2 = nonbonded_force.getParticleParameters(atom_idx)
                params_to_add[atom_idx] = [charge, gbsatype.radius, gbsatype.scale]

            if self.gb_model == 'OBC2':
                for particle_param in params_to_add:
                    gbsa_force.addParticle(*particle_param)
            else:
                for particle_param in params_to_add:
                    gbsa_force.addParticle(particle_param)
                # We have to call finalize() for models that inherit from CustomAmberGBForceBase,
                # otherwise the added particles aren't actually passed to the underlying CustomGBForce
                gbsa_force.finalize()

            # Check that no atoms (n.b. not particles) are missing force parameters.
            self._check_all_valence_terms_assigned(assigned_terms=atom_matches,
                                                   valence_terms=list(topology.topology_atoms))

            system.addForce(gbsa_force)

    if __name__ == '__main__':
        import doctest
        doctest.testmod()
        # doctest.run_docstring_examples(_ParameterAttributeHandler, globals())