chemistry.py

# -*- coding: utf-8 -*-

from collections import OrderedDict, defaultdict
from functools import reduce
from itertools import chain, product
from operator import mul, add
import copy
import math
import warnings

from .util.arithmeticdict import ArithmeticDict
from .util._expr import Expr
from .util.periodic import mass_from_composition
from .util.parsing import (
    formula_to_composition,
    to_reaction,
    formula_to_latex,
    formula_to_unicode,
    formula_to_html,
)

from .units import default_units, is_quantity, unit_of, to_unitless
from ._util import intdiv
from .util.pyutil import deprecated, DeferredImport, ChemPyDeprecationWarning


ReactionSystem = DeferredImport(
    "chempy.reactionsystem",
    "ReactionSystem",
    [deprecated(use_instead="chempy.ReactionSystem")],
)


class Substance(object):
    """ Class representing a chemical substance

    Parameters
    ----------
    name : str
    charge : int (optional, default: None)
        Will be stored in composition[0], prefer composition when possible.
    latex_name : str
    unicode_name : str
    html_name : str
    composition : dict or None (default)
        Dictionary (int -> number) e.g. {atomic number: count}, zero has special
        meaning (net charge). Avoid using the key 0 unless you specifically mean
        net charge. The motivation behind this is that it is easier to track a
        net-charge of e.g. 6 for U(VI) than it is to remember that uranium has 92
        electrons and use 86 as the value).
    data : dict
        Free form dictionary. Could be simple such as ``{'mp': 0, 'bp': 100}``
        or considerably more involved, e.g.: ``{'diffusion_coefficient': {\
 'water': lambda T: 2.1*m**2/s/K*(T - 273.15*K)}}``.

    Attributes
    ----------
    mass
        Maps to data['mass'], and when unavailable looks for ``formula.mass``.
    attrs
        A tuple of attribute names for serialization.
    composition : dict or None
        Dictionary mapping fragment key (str) to amount (int).
    data
        Free form dictionary.

    Examples
    --------
    >>> ammonium = Substance('NH4+', 1, 'NH_4^+', composition={7: 1, 1: 4},
    ...     data={'mass': 18.0385, 'pKa': 9.24})
    >>> ammonium.name
    'NH4+'
    >>> ammonium.composition == {0: 1, 1: 4, 7: 1}  # charge represented by key '0'
    True
    >>> ammonium.data['mass']
    18.0385
    >>> ammonium.data['pKa']
    9.24
    >>> ammonium.mass  # mass is a special case (also attribute)
    18.0385
    >>> ammonium.pKa
    Traceback (most recent call last):
        ...
    AttributeError: 'Substance' object has no attribute 'pKa'
    >>> nh4p = Substance.from_formula('NH4+')  # simpler
    >>> nh4p.composition == {7: 1, 1: 4, 0: 1}
    True
    >>> nh4p.latex_name
    'NH_{4}^{+}'

    """

    attrs = ("name", "latex_name", "unicode_name", "html_name", "composition", "data")

    def __eq__(self, other):
        for attr in self.attrs:
            if getattr(self, attr) != getattr(other, attr):
                return False
        return True

    def __hash__(self) -> int:
        hashed_values = []
        for key in self.attrs:
            value = getattr(self, key)
            if isinstance(value, dict):
                hashed_values.append(hash(tuple(sorted(value.items()))))
            else:
                hashed_values.append(hash(value))
        return sum(hashed_values)

    @property
    def charge(self):
        """Convenience property for accessing ``composition[0]``"""
        return self.composition.get(0, 0)  # electron (net) deficiency

    @property
    def mass(self):
        """Convenience property for accessing ``data['mass']``

        when ``data['mass']`` is missing the mass is calculated
        from the :attr:`composition` using
        :func:`chempy.util.parsing.mass_from_composition`.
        """
        try:
            return self.data["mass"]
        except KeyError:
            if self.composition is not None:
                return mass_from_composition(self.composition)

    @mass.setter
    def mass(self, value):
        self.data["mass"] = value

    def molar_mass(self, units=None):
        """Returns the molar mass (with units) of the substance

        Examples
        --------
        >>> nh4p = Substance.from_formula('NH4+')  # simpler
        >>> from chempy.units import default_units as u
        >>> nh4p.molar_mass(u)
        array(18.0384511...) * g/mol

        """
        if units is None:
            units = default_units
        return self.mass * units.g / units.mol

    def __init__(
        self,
        name=None,
        charge=None,
        latex_name=None,
        unicode_name=None,
        html_name=None,
        composition=None,
        data=None,
    ):
        self.name = name
        self.latex_name = latex_name
        self.unicode_name = unicode_name
        self.html_name = html_name
        self.composition = composition

        if self.composition is not None and 0 in self.composition:
            if charge is not None:
                raise KeyError("Cannot give both charge and composition[0]")
        else:
            if charge is not None and composition is not None:
                self.composition[0] = charge
        self.data = data or {}

    @classmethod
    def from_formula(cls, formula, **kwargs):
        """Creates a :class:`Substance` instance from its formula

        Parameters
        ----------
        formula: str
            e.g. 'Na+', 'H2O', 'Fe(CN)6-4'
        \\*\\*kwargs:
            keyword arguments passed on to `.Substance`

        Examples
        --------
        >>> NH3 = Substance.from_formula('NH3')
        >>> NH3.composition == {1: 3, 7: 1}
        True
        >>> '%.2f' % NH3.mass
        '17.03'
        >>> NH3.charge
        0
        >>> NH3.latex_name
        'NH_{3}'

        """
        return cls(
            formula,
            latex_name=formula_to_latex(formula),
            unicode_name=formula_to_unicode(formula),
            html_name=formula_to_html(formula),
            composition=formula_to_composition(formula),
            **kwargs
        )

    def __repr__(self):
        kw = ["name=" + self.name + ", ..."]  # Too verbose to print all
        return "<{}({})>".format(self.__class__.__name__, ",".join(kw))

    def __str__(self):
        return str(self.name)

    def _repr_html_(self):
        return self.html_name

    @staticmethod
    def composition_keys(substance_iter, skip_keys=()):
        """Occurring :attr:`composition` keys among a series of substances"""
        keys = set()
        for s in substance_iter:
            if s.composition is None:
                continue
            for k in s.composition.keys():
                if k in skip_keys:
                    continue
                keys.add(k)
        return sorted(keys)


class Species(Substance):
    """Substance belonging to a phase

    Species extends :class:`Substance` with the new attribute :attr:`phase_idx`

    Attributes
    ----------
    phase_idx: int
        Index of the phase (default is 0)
    """

    def __init__(self, *args, **kwargs):
        phase_idx = kwargs.pop("phase_idx", 0)
        super(Species, self).__init__(*args, **kwargs)
        self.phase_idx = phase_idx

    @property
    @deprecated(last_supported_version="0.3.0", will_be_missing_in="0.8.0")
    def precipitate(self):
        """deprecated attribute, provided for compatibility for now"""
        return self.phase_idx > 0

    @classmethod
    def from_formula(
        cls, formula, phases=("(s)", "(l)", "(g)"), default_phase_idx=0, **kwargs
    ):
        """Create a :class:`Species` instance from its formula

        Analogous to :meth:`Substance.from_formula` but with the addition that
        phase_idx is determined from the formula (and a mapping provided by
        ``phases``)

        Parameters
        ----------
        formula: str
            e.g. 'H2O', 'NaCl(s)', 'CO2(aq)', 'CO2(g)'
        phases: iterable of str or dict mapping str -> int
            if not in \\*\\*kwargs, ``phase_idx`` is determined from the suffix
            of ``formula`` where the suffixes is mapped from phases:
                if ``phases`` is a dictionary:
                    ``phase_idx = phases[suffix]``
                else:
                    ``phase_idx = phases.index(suffix) + 1``
            and if suffixes is missing in phases phase_idx is taken to be 0
        default_phase_idx: int or None (default: 0)
            If ``default_phase_idx`` is ``None``, ``ValueError`` is raised for
                unknown suffixes.
            Else ``default_phase_idx`` is used as ``phase_idx`` in those cases.
        \\*\\*kwargs:
            Keyword arguments passed on.

        Examples
        --------
        >>> water = Species.from_formula('H2O')
        >>> water.phase_idx
        0
        >>> NaCl = Species.from_formula('NaCl(s)')
        >>> NaCl.phase_idx
        1
        >>> Hg_l = Species.from_formula('Hg(l)')
        >>> Hg_l.phase_idx
        2
        >>> CO2g = Species.from_formula('CO2(g)')
        >>> CO2g.phase_idx
        3
        >>> CO2aq = Species.from_formula('CO2(aq)', default_phase_idx=None)
        Traceback (most recent call last):
            ...
        ValueError: Could not determine phase_idx
        >>> CO2aq = Species.from_formula('CO2(aq)')
        >>> CO2aq.phase_idx
        0
        >>> CO2aq = Species.from_formula('CO2(aq)', ['(aq)'],
        ...     default_phase_idx=None)
        >>> CO2aq.phase_idx
        1
        >>> Species.from_formula('CO2(aq)', {'(aq)': 0}, None).phase_idx
        0


        Raises
        ------
        ValueError:
            if ``default_phase_idx`` is ``None`` and no suffix found in phases

        """
        if "phase_idx" in kwargs:
            p_i = kwargs.pop("phase_idx")
        else:
            p_i = None
            if isinstance(phases, dict):
                for k, v in phases.items():
                    if formula.endswith(k):
                        p_i = v
                        break
            else:
                for idx, phase in enumerate(phases):
                    if formula.endswith(phase):
                        p_i = idx + 1
                        break
            if p_i is None:
                if default_phase_idx is None:
                    raise ValueError("Could not determine phase_idx")
                else:
                    p_i = default_phase_idx
        return cls(
            formula,
            latex_name=formula_to_latex(formula, suffixes=phases),
            unicode_name=formula_to_unicode(formula, suffixes=phases),
            html_name=formula_to_html(formula, suffixes=phases),
            composition=formula_to_composition(formula, suffixes=phases),
            phase_idx=p_i,
            **kwargs
        )


@deprecated(
    last_supported_version="0.3.0", will_be_missing_in="0.8.0", use_instead=Species
)
class Solute(Substance):
    """[DEPRECATED] Use `.Species` instead

    Counter-intuitive to its name Solute has an additional
    property 'precipitate'

    """

    def __init__(self, *args, **kwargs):
        precipitate = kwargs.pop("precipitate", False)
        Substance.__init__(self, *args, **kwargs)
        self.precipitate = precipitate

    @classmethod
    def from_formula(cls, formula, **kwargs):
        if formula.endswith("(s)"):
            kwargs["precipitate"] = True
        return cls(
            formula,
            latex_name=formula_to_latex(formula),
            unicode_name=formula_to_unicode(formula),
            html_name=formula_to_html(formula),
            composition=formula_to_composition(formula),
            **kwargs
        )


class Reaction(object):
    """Class representing a chemical reaction

    Consider for example:

        2 R --> A + P; r = k*A*R*R

    this would be represented as ``Reaction({'A': 1, 'R': 2},
    {'A': 2, 'P': 1}, param=k)``. Some reactions have a larger
    stoichiometric coefficient than what appears in the rate
    expression, e.g.:

        5 A + B --> C; r = k*A*B

    this can be represented as ``Reaction({'C1': 1, 'C2': 1},
    {'B': 1}, inact_reac={'C1': 4}, param=k)``.

    The rate constant information in ``param`` may be a subclass of
    :class:`chempy.kinetics.rates.RateExpr` or carry a :meth:`as_RateExpr`,
    if neither: `param` will be assumed to be a rate constant for a mass-action
    type of kinetic expression.

    Additional data may be stored in the ``data`` dict.


    Parameters
    ----------
    reac : dict (str -> int)
        If ``reac`` is a ``set``, then multiplicities are assumed to be 1.
    prod : dict (str -> int)
        If ``prod`` is a ``set``, then multiplicities are assumed to be 1.
    param : float or callable
        Special case (side-effect): if param is a subclass of
        :class:`.kinetics.rates.RateExpr` and its :attr:`rxn`
        is `None` it will be set to `self`.
    inact_reac : dict (optional)
    inact_prod : dict (optional)
    name : str (optional)
    k : deprecated (alias for param)
    ref : object
        Reference (e.g. a string containing doi number).
    data : dict (optional)
    checks : iterable of str
        Raises ``ValueError`` if any method ``check_%s`` returns False
        for all ``%s`` in ``checks``. Default: ``Reaction.default_checks``.

    Attributes
    ----------
    reac : OrderedDict
    prod : OrderedDict
    param : object
    inact_reac : OrderedDict
    inact_prod : OrderedDict
    name : str
    ref : str
    data : dict

    Examples
    --------
    >>> r = Reaction({'H2': 2, 'O2': 1}, {'H2O': 2})
    >>> r.keys() == {'H2', 'O2', 'H2O'}
    True
    >>> r.order()
    3
    >>> r.net_stoich(['H2', 'H2O', 'O2'])
    (-2, 2, -1)
    >>> print(r)
    2 H2 + O2 -> 2 H2O

    """

    _cmp_attr = ("reac", "prod", "param", "inact_reac", "inact_prod")
    _all_attr = _cmp_attr + ("name", "ref", "data")
    _str_arrow = "->"

    param_char = "k"  # convention
    default_checks = {"any_effect", "all_positive", "all_integral", "consistent_units"}

    @staticmethod
    def _init_stoich(container):
        if isinstance(container, set):
            container = {k: 1 for k in container}
        container = container or {}
        if type(container) == dict:  # noqa
            # we don't want isinstance here in case of OrderedDict
            container = OrderedDict(sorted(container.items(), key=lambda kv: kv[0]))
        return container

    def __init__(
        self,
        reac,
        prod,
        param=None,
        inact_reac=None,
        inact_prod=None,
        name=None,
        ref=None,
        data=None,
        checks=None,
        dont_check=None,
    ):
        self.reac = self._init_stoich(reac)
        self.inact_reac = self._init_stoich(inact_reac)
        self.prod = self._init_stoich(prod)
        self.inact_prod = self._init_stoich(inact_prod)
        self.param = param
        self.name = name
        self.ref = ref
        self.data = data or {}
        if checks is not None and dont_check is not None:
            raise ValueError("Cannot specify both checks and dont_check")
        if checks is None:
            checks = self.default_checks ^ (dont_check or set())

        for check in checks:
            getattr(self, "check_" + check)(throw=True)

    @classmethod
    def from_string(cls, string, substance_keys=None, globals_=None, **kwargs):
        """Parses a string into a Reaction instance

        Parameters
        ----------
        string : str
            String representation of the reaction.
        substance_keys : convertible to iterable of strings or string or None
            Used prevent e.g. misspelling.
            if str: split is invoked, if None: no checking done.
        globals_ : dict (optional)
            Dictionary for eval for (default: None -> {'chempy': chempy})
            If ``False``: no eval will be called (useful for web-apps).
        \\*\\*kwargs :
            Passed on to constructor.

        Examples
        --------
        >>> r = Reaction.from_string("H2O -> H+ + OH-; 1e-4", 'H2O H+ OH-')
        >>> r.reac == {'H2O': 1} and r.prod == {'H+': 1, 'OH-': 1}
        True
        >>> r2 = Reaction.from_string("2 H2O -> 2 H2 + O2", 'H2O H2 O2')
        >>> r2.reac == {'H2O': 2} and r2.prod == {'H2': 2, 'O2': 1}
        True
        >>> r3 = Reaction.from_string("A -> B; 1/second", 'A B')
        >>> from chempy.units import to_unitless, default_units as u
        >>> to_unitless(r3.param, u.hour**-1)
        3600.0
        >>> r4 = Reaction.from_string("A -> 2 B; 'k'", 'A B')
        >>> r4.rate(dict(A=3, B=5, k=7)) == {'A': -3*7, 'B': 2*3*7}
        True
        >>> r5 = Reaction.from_string("A -> B; 1/molar/second", 'A B')
        Traceback (most recent call last):
            ...
        ValueError: Unable to convert between units ...


        Notes
        -----
        :func:`chempy.util.parsing.to_reaction` is used which in turn calls
        :func:`eval` which is a severe security concern for untrusted input.

        """
        if isinstance(substance_keys, str):
            if " " in substance_keys:
                substance_keys = substance_keys.split()
        return to_reaction(
            string, substance_keys, cls._str_arrow, cls, globals_, **kwargs
        )

    def copy(self, **kwargs):
        if "checks" not in kwargs:
            kwargs["checks"] = ()
        for k in self._all_attr:
            if k not in kwargs:
                kwargs[k] = copy.copy(getattr(self, k))
        return self.__class__(**kwargs)

    def check_any_effect(self, throw=False):
        """Checks if the reaction has any effect"""
        if not any(self.net_stoich(self.keys())):
            if throw:
                raise ValueError(
                    "The net stoichiometry change of all species are zero."
                )
            else:
                return False
        return True

    def check_all_positive(self, throw=False):
        """Checks if all stoichiometric coefficients are positive"""
        for nam, cont in [
            (nam, getattr(self, nam))
            for nam in "reac prod inact_reac inact_prod".split()
        ]:
            for k, v in cont.items():
                if v < 0:
                    if throw:
                        raise ValueError(
                            "Found a negative stoichiometry for %s in %s." % (k, nam)
                        )
                    else:
                        return False
        return True

    def check_all_integral(self, throw=False):
        """Checks if all stoichiometric coefficients are integers"""
        for nam, cont in [
            (nam, getattr(self, nam))
            for nam in "reac prod inact_reac inact_prod".split()
        ]:
            for k, v in cont.items():
                if v != int(v) and v != type(v)(int(v)):
                    if throw:
                        raise ValueError(
                            "Found a non-integer stoichiometric coefficient for %s in %s."
                            % (k, nam)
                        )
                    else:
                        return False
        return True

    def check_consistent_units(self, throw=False):
        if is_quantity(self.param):  # This will assume mass action
            if isinstance(self.param.item(), Expr):
                param = (
                    self.param.item()({"temperature": 1 * default_units.K})
                    * self.param.units
                )
            else:
                param = self.param
            try:
                to_unitless(
                    param
                    / (default_units.molar ** (1 - self.order()) / default_units.s)
                )
            except Exception:
                if throw:
                    raise
                else:
                    return False
            else:
                return True
        else:
            return True  # the user might not be using ``chempy.units``

    def __eq__(lhs, rhs):
        if lhs is rhs:
            return True
        if not isinstance(lhs, Reaction) or not isinstance(rhs, Reaction):
            return NotImplemented
        for attr in lhs._cmp_attr:
            if getattr(lhs, attr) != getattr(rhs, attr):
                return False
        return True

    def __hash__(self):
        return sum(
            map(
                hash,
                (
                    getattr(self, k)
                    for k in ["reac", "prod", "param", "inact_reac", "inact_prod"]
                ),
            )
        )

    def order(self):
        """Sum of (active) reactant stoichiometries"""
        return sum(self.reac.values())

    def keys(self):
        return set(
            chain(
                self.reac.keys(),
                self.prod.keys(),
                self.inact_reac.keys(),
                self.inact_prod.keys(),
            )
        )

    def net_stoich(self, substance_keys):
        """Per substance net stoichiometry tuple (active & inactive)"""
        return tuple(
            self.prod.get(k, 0)
            - self.reac.get(k, 0)
            + self.inact_prod.get(k, 0)
            - self.inact_reac.get(k, 0)
            for k in substance_keys
        )

    def all_reac_stoich(self, substances):
        """Per substance reactant stoichiometry tuple (active & inactive)"""
        return tuple(
            self.reac.get(k, 0) + self.inact_reac.get(k, 0) for k in substances
        )

    def active_reac_stoich(self, substances):
        """Per substance reactant stoichiometry tuple (active)"""
        return tuple(self.reac.get(k, 0) for k in substances)

    def all_prod_stoich(self, substances):
        """Per substance product stoichiometry tuple (active & inactive)"""
        return tuple(
            self.prod.get(k, 0) + self.inact_prod.get(k, 0) for k in substances
        )

    def active_prod_stoich(self, substances):
        """Per substance product stoichiometry tuple (active)"""
        return tuple(self.prod.get(k, 0) for k in substances)

    def _xprecipitate_stoich(self, substances, xor):
        return tuple(
            (
                0
                if xor ^ (getattr(v, "phase_idx", 0) > 0)
                else self.prod.get(k, 0)
                + self.inact_prod.get(k, 0)
                - self.reac.get(k, 0)
                - self.inact_reac.get(k, 0)
            )
            for k, v in substances.items()
        )

    def precipitate_stoich(self, substances):
        """Only stoichiometry of precipitates"""
        net = self._xprecipitate_stoich(substances, True)
        found1 = -1
        for idx in range(len(net)):
            if net[idx] != 0:
                if found1 == -1:
                    found1 = idx
                else:
                    raise NotImplementedError("Only one precipitate assumed.")
        return net, net[found1], found1

    def non_precipitate_stoich(self, substances):
        """Only stoichiometry of non-precipitates"""
        return self._xprecipitate_stoich(substances, False)

    def has_precipitates(self, substances):
        for s_name in chain(
            self.reac.keys(),
            self.prod.keys(),
            self.inact_reac.keys(),
            self.inact_prod.keys(),
        ):
            if getattr(substances[s_name], "phase_idx", 0) > 0:
                return True
        return False

    def string(self, substances=None, with_param=False, with_name=False, **kwargs):
        """Returns a string representation of the reaction

        Parameters
        ----------
        substances: dict
            mapping substance keys to Substance instances
        with_param: bool
            whether to print the parameter (default: False)
        with_name: bool
            whether to print the name (default: False)

        Examples
        --------
        >>> r = Reaction({'H+': 1, 'Cl-': 1}, {'HCl': 1}, 1e10)
        >>> r.string(with_param=False)
        'Cl- + H+ -> HCl'

        """
        from .printing import str_

        return str_(
            self,
            substances=substances,
            with_param=with_param,
            with_name=with_name,
            **kwargs
        )

    def __str__(self):
        return self.string(with_param=True, with_name=True)

    def latex(self, substances, with_param=False, with_name=False, **kwargs):
        r"""Returns a LaTeX representation of the reaction

        Parameters
        ----------
        substances: dict
            mapping substance keys to Substance instances
        with_param: bool
            whether to print the parameter (default: False)
        with_name: bool
            whether to print the name (default: False)

        Examples
        --------
        >>> keys = 'H2O H+ OH-'.split()
        >>> subst = {k: Substance.from_formula(k) for k in keys}
        >>> r = Reaction.from_string("H2O -> H+ + OH-; 1e-4", subst)
        >>> r.latex(subst) == r'H_{2}O \rightarrow H^{+} + OH^{-}'
        True
        >>> r2 = Reaction.from_string("H+ + OH- -> H2O; 1e8/molar/second", subst)
        >>> ref = r'H^{+} + OH^{-} \rightarrow H_{2}O; 10^{8} $\mathrm{\frac{1}{(s{\cdot}M)}}$'
        >>> r2.latex(subst, with_param=True) == ref
        True

        """
        from .printing import latex

        return latex(
            self,
            substances=substances,
            with_param=with_param,
            with_name=with_name,
            **kwargs
        )

    def unicode(self, substances, with_param=False, with_name=False, **kwargs):
        u"""Returns a unicode string representation of the reaction

        Examples
        --------
        >>> keys = 'H2O H+ OH-'.split()
        >>> subst = {k: Substance.from_formula(k) for k in keys}
        >>> r = Reaction.from_string("H2O -> H+ + OH-; 1e-4", subst)
        >>> r.unicode(subst) == u'H₂O → H⁺ + OH⁻'
        True
        >>> r2 = Reaction.from_string("H+ + OH- -> H2O; 1e8/molar/second", subst)
        >>> r2.unicode(subst, with_param=True) == u'H⁺ + OH⁻ → H₂O; 10⁸ 1/(s·M)'
        True

        """
        from .printing import unicode_

        return unicode_(
            self,
            substances=substances,
            with_param=with_param,
            with_name=with_name,
            **kwargs
        )

    def html(self, substances, with_param=False, with_name=False, **kwargs):
        """Returns a HTML representation of the reaction

        Examples
        --------
        >>> keys = 'H2O H+ OH-'.split()
        >>> subst = {k: Substance.from_formula(k) for k in keys}
        >>> r = Reaction.from_string("H2O -> H+ + OH-; 1e-4", subst)
        >>> r.html(subst)
        'H<sub>2</sub>O &rarr; H<sup>+</sup> + OH<sup>-</sup>'
        >>> r2 = Reaction.from_string("H+ + OH- -> H2O; 1e8/molar/second", subst)
        >>> r2.html(subst, with_param=True)
        'H<sup>+</sup> + OH<sup>-</sup> &rarr; H<sub>2</sub>O&#59; 10<sup>8</sup> 1/(s*M)'

        """
        from .printing import html

        return html(
            self,
            with_param=with_param,
            with_name=with_name,
            substances=substances,
            **kwargs
        )

    def _repr_html_(self):
        return self.html({k: k for k in self.keys()})

    def _violation(self, substances, attr):
        net = 0.0
        for substance, coeff in zip(
            substances.values(), self.net_stoich(substances.keys())
        ):
            net += getattr(substance, attr) * coeff
        return net

    def mass_balance_violation(self, substances):
        """Net amount of mass produced

        Parameters
        ----------
        substances: dict

        Returns
        -------
        float: amount of net mass produced/consumed

        """
        return self._violation(substances, "mass")

    def charge_neutrality_violation(self, substances):
        """Net amount of charge produced

        Parameters
        ----------
        substances: dict

        Returns
        -------
        float: amount of net charge produced/consumed

        """
        return self._violation(substances, "charge")

    def composition_violation(self, substances, composition_keys=None):
        """Net amount of constituent produced

        If composition keys correspond to conserved entities e.g. atoms
        in chemical reactions, this function should return a list of zeros.

        Parameters
        ----------
        substances : dict
        composition_keys : iterable of str, ``None`` or ``True``
            When ``None`` or True: composition keys are taken from substances.
            When ``True`` the keys are also return as an extra return value

        Returns
        -------
        - If ``composition_keys == True``: a tuple: (violations, composition_keys)
        - Otherwise: violations (list of coefficients)

        """
        keys, values = zip(*substances.items())
        ret_comp_keys = composition_keys is True
        if composition_keys in (None, True):
            composition_keys = Substance.composition_keys(values)
        net = [0] * len(composition_keys)
        for substance, coeff in zip(values, self.net_stoich(keys)):
            for idx, key in enumerate(composition_keys):
                net[idx] += substance.composition.get(key, 0) * coeff
        if ret_comp_keys:
            return net, composition_keys
        else:
            return net

    def rate_expr(self):
        """Turns self.param into a RateExpr instance (if not already)

        Default is to create a ``MassAction`` instance. The parameter will
        be used as single instance in ``unique_keys`` if it is a string,
        otherwise it will be used as ``args``.

        Examples
        --------
        >>> r = Reaction.from_string('2 A + B -> 3 C; 7')
        >>> ratex = r.rate_expr()
        >>> ratex.args[0] == 7
        True

        """
        from .util._expr import Expr
        from .kinetics import MassAction

        if isinstance(self.param, Expr):
            return self.param
        else:
            try:
                convertible = self.param.as_RateExpr
            except AttributeError:
                if isinstance(self.param, str):
                    return MassAction.fk(self.param)
                else:
                    return MassAction([self.param])
            else:
                return convertible()

    def rate(self, variables=None, backend=math, substance_keys=None, ratex=None):
        """Evaluate the rate of a reaction

        Parameters
        ----------
        variables : dict
        backend : module, optional
        substance_keys : iterable of str, optional
        ratex : RateExpr

        Returns
        -------
        Dictionary mapping substance keys to the reactions contribution to overall rates.

        Examples
        --------
        >>> rxn1 = Reaction.from_string('2 H2 + O2 -> 2 H2O; 3')
        >>> ref1 = 3*5*5*7
        >>> rxn1.rate({'H2': 5, 'O2': 7}) == {'H2': -2*ref1, 'O2': -ref1, 'H2O': 2*ref1}
        True
        >>> from sympy import Symbol
        >>> k = Symbol('k')
        >>> rxn2 = Reaction(rxn1.reac, rxn1.prod, k)
        >>> concentrations = {key: Symbol(key) for key in set.union(set(rxn1.reac), set(rxn1.prod))}
        >>> import pprint
        >>> pprint.pprint(rxn2.rate(concentrations))
        {'H2': -2*H2**2*O2*k, 'H2O': 2*H2**2*O2*k, 'O2': -H2**2*O2*k}

        """
        if variables is None:
            variables = {}
        if substance_keys is None:
            substance_keys = self.keys()
        if ratex is None:
            ratex = self.rate_expr()

        if isinstance(ratex, Expr):
            srat = ratex(variables, backend=backend, reaction=self)
        else:
            srat = ratex
        return {
            k: srat * v for k, v in zip(substance_keys, self.net_stoich(substance_keys))
        }


def equilibrium_quotient(concs, stoich):
    """Calculates the equilibrium quotient of an equilbrium

    Parameters
    ----------
    concs: array_like
        per substance concentration
    stoich: iterable of integers
        per substance stoichiometric coefficient

    Examples
    --------
    >>> '%.12g' % equilibrium_quotient([1.0, 1e-7, 1e-7], [-1, 1, 1])
    '1e-14'

    """
    import numpy as np

    if not hasattr(concs, "ndim") or concs.ndim == 1:
        tot = 1
    else:
        tot = np.ones(concs.shape[0])
        concs = concs.T

    for nr, conc in zip(stoich, concs):
        tot *= conc ** nr
    return tot


class Equilibrium(Reaction):
    """Represents an equilibrium reaction

    See :class:`Reaction` for parameters

    """

    _str_arrow = "="
    param_char = "K"  # convention

    def check_consistent_units(self, throw=False):
        if is_quantity(self.param):  # This will assume mass action
            exponent = sum(self.prod.values()) - sum(self.reac.values())
            unit_param = unit_of(self.param, simplified=True)
            unit_expected = unit_of(default_units.molar ** exponent, simplified=True)
            if unit_param == unit_expected:
                return True
            else:
                if throw:
                    raise ValueError(
                        "Inconsistent units in equilibrium: %s vs %s"
                        % (unit_param, unit_expected)
                    )
                else:
                    return False
        else:
            return True  # the user might not be using ``chempy.units``

    def as_reactions(
        self,
        kf=None,
        kb=None,
        units=None,
        variables=None,
        backend=math,
        new_name=None,
        **kwargs
    ):
        """Creates a forward and backward :class:`Reaction` pair

        Parameters
        ----------
        kf : float or RateExpr
        kb : float or RateExpr
        units : module
        variables : dict, optional
        backend : module

        """
        nb = sum(self.prod.values())
        nf = sum(self.reac.values())
        if units is None:
            if hasattr(kf, "units") or hasattr(kb, "units"):
                raise ValueError("units missing")
            c0 = 1
        else:
            c0 = 1 * units.molar  # standard concentration IUPAC

        if kf is None:
            fw_name = self.name
            bw_name = new_name
            if kb is None:
                try:
                    kf, kb = self.param
                except TypeError:
                    raise ValueError("Exactly one rate needs to be provided")
            else:
                kf = kb * self.param * c0 ** (nb - nf)
        elif kb is None:
            kb = kf / (self.param * c0 ** (nb - nf))
            fw_name = new_name
            bw_name = self.name
        else:
            raise ValueError("Exactly one rate needs to be provided")

        return (
            Reaction(
                self.reac,
                self.prod,
                kf,
                self.inact_reac,
                self.inact_prod,
                ref=self.ref,
                name=fw_name,
                **kwargs
            ),
            Reaction(
                self.prod,
                self.reac,
                kb,
                self.inact_prod,
                self.inact_reac,
                ref=self.ref,
                name=bw_name,
                **kwargs
            ),
        )

    def equilibrium_expr(self):
        """Turns self.param into a :class:`EqExpr` instance (if not already)

        Examples
        --------
        >>> r = Equilibrium.from_string('2 A + B = 3 C; 7')
        >>> eqex = r.equilibrium_expr()
        >>> eqex.args[0] == 7
        True

        """
        from .util._expr import Expr
        from .thermodynamics import MassActionEq

        if isinstance(self.param, Expr):
            return self.param
        else:
            try:
                convertible = self.param.as_EqExpr
            except AttributeError:
                return MassActionEq([self.param])
            else:
                return convertible()

    def equilibrium_constant(self, variables=None, backend=math):
        """Return equilibrium constant

        Parameters
        ----------
        variables : dict, optional
        backend : module, optional

        """
        return self.equilibrium_expr().eq_const(variables, backend=backend)

    def equilibrium_equation(self, variables, backend=None, **kwargs):
        return self.equilibrium_expr().equilibrium_equation(
            variables, equilibrium=self, backend=backend, **kwargs
        )

    @deprecated(use_instead=equilibrium_constant)
    def K(self, *args, **kwargs):
        return self.equilibrium_constant(*args, **kwargs)

    def Q(self, substances, concs):
        """Calculates the equilibrium qoutient"""
        stoich = self.non_precipitate_stoich(substances)
        return equilibrium_quotient(concs, stoich)

    def precipitate_factor(self, substances, sc_concs):
        factor = 1
        for r, n in self.reac.items():
            if r.precipitate:
                factor *= sc_concs[substances.index(r)] ** -n
        for p, n in self.prod.items():
            if p.precipitate:
                factor *= sc_concs[substances.index(p)] ** n
        return factor

    def dimensionality(self, substances):
        result = 0
        for r, n in self.reac.items():
            if getattr(substances[r], "phase_idx", 0) > 0:
                continue
            result -= n
        for p, n in self.prod.items():
            if getattr(substances[p], "phase_idx", 0) > 0:
                continue
            result += n
        return result

    def __rmul__(self, other):  # This works on both Py2 and Py3
        try:
            other_is_int = other.is_integer
        except AttributeError:
            other_is_int = isinstance(other, int)
        if not other_is_int or not isinstance(self, Equilibrium):
            return NotImplemented
        param = None if self.param is None else self.param ** other
        if other < 0:
            other *= -1
            flip = True
        else:
            flip = False
        other = int(other)  # convert SymPy "Integer" to Python "int"
        reac = dict(other * ArithmeticDict(int, self.reac))
        prod = dict(other * ArithmeticDict(int, self.prod))
        inact_reac = dict(other * ArithmeticDict(int, self.inact_reac))
        inact_prod = dict(other * ArithmeticDict(int, self.inact_prod))
        if flip:
            reac, prod = prod, reac
            inact_reac, inact_prod = inact_prod, inact_reac
        return Equilibrium(
            reac, prod, param, inact_reac=inact_reac, inact_prod=inact_prod
        )

    def __neg__(self):
        return -1 * self

    def __mul__(self, other):
        return other * self

    def __add__(self, other):
        keys = set()
        for key in chain(
            self.reac.keys(), self.prod.keys(), other.reac.keys(), other.prod.keys()
        ):
            keys.add(key)
        reac, prod = {}, {}
        for key in keys:
            n = (
                self.prod.get(key, 0)
                - self.reac.get(key, 0)
                + other.prod.get(key, 0)
                - other.reac.get(key, 0)
            )
            if n < 0:
                reac[key] = -n
            elif n > 0:
                prod[key] = n
            else:
                pass  # n == 0
        if (self.param, other.param) == (None, None):
            param = None
        else:
            param = self.param * other.param
        return Equilibrium(reac, prod, param)

    def __sub__(self, other):
        return self + -1 * other

    @staticmethod
    def eliminate(rxns, wrt):
        """Linear combination coefficients for elimination of a substance

        Parameters
        ----------
        rxns : iterable of Equilibrium instances
        wrt : str (substance key)

        Examples
        --------
        >>> e1 = Equilibrium({'Cd+2': 4, 'H2O': 4}, {'Cd4(OH)4+4': 1, 'H+': 4}, 10**-32.5)
        >>> e2 = Equilibrium({'Cd(OH)2(s)': 1}, {'Cd+2': 1, 'OH-': 2}, 10**-14.4)
        >>> Equilibrium.eliminate([e1, e2], 'Cd+2')
        [1, 4]
        >>> print(1*e1 + 4*e2)
        4 Cd(OH)2(s) + 4 H2O = Cd4(OH)4+4 + 4 H+ + 8 OH-; 7.94e-91

        """
        import sympy

        viol = [r.net_stoich([wrt])[0] for r in rxns]
        factors = defaultdict(int)
        for v in viol:
            for f in sympy.primefactors(v):
                factors[f] = max(factors[f], sympy.Abs(v // f))
        rcd = reduce(mul, (k ** v for k, v in factors.items()))
        viol[0] *= -1
        return [rcd // v for v in viol]

    def cancel(self, rxn):
        """Multiplier of how many times rxn can be added/subtracted.

        Parameters
        ----------
        rxn : Equilibrium

        Examples
        --------
        >>> e1 = Equilibrium({'Cd(OH)2(s)': 4, 'H2O': 4},
        ...                  {'Cd4(OH)4+4': 1, 'H+': 4, 'OH-': 8}, 7.94e-91)
        >>> e2 = Equilibrium({'H2O': 1}, {'H+': 1, 'OH-': 1}, 10**-14)
        >>> e1.cancel(e2)
        -4
        >>> print(e1 - 4*e2)
        4 Cd(OH)2(s) = Cd4(OH)4+4 + 4 OH-; 7.94e-35

        """
        keys = rxn.keys()
        s1 = self.net_stoich(keys)
        s2 = rxn.net_stoich(keys)
        candidate = float("inf")
        for v1, v2 in zip(s1, s2):
            r = intdiv(-v1, v2)
            candidate = min(candidate, r, key=abs)
        return candidate


def _solve_balancing_ilp_pulp(A):
    import pulp

    x = [
        pulp.LpVariable("x%d" % i, lowBound=1, cat="Integer") for i in range(A.shape[1])
    ]
    prob = pulp.LpProblem("chempy_balancing_problem", pulp.LpMinimize)
    prob += reduce(add, x)
    for expr in [
        pulp.lpSum([x[i] * e for i, e in enumerate(row)]) for row in A.tolist()
    ]:
        prob += expr == 0
    prob.solve(pulp.PULP_CBC_CMD(msg=False))
    return [pulp.value(_) for _ in x]


def balance_stoichiometry(
    reactants,
    products,
    substances=None,
    substance_factory=Substance.from_formula,
    parametric_symbols=None,
    underdetermined=True,
    allow_duplicates=False,
):
    """Balances stoichiometric coefficients of a reaction

    Parameters
    ----------
    reactants : iterable of reactant keys
    products : iterable of product keys
    substances : OrderedDict or string or None
        Mapping reactant/product keys to instances of :class:`Substance`.
    substance_factory : callback
    parametric_symbols : generator of symbols
        Used to generate symbols for parametric solution for
        under-determined system of equations. Default is numbered "x-symbols" starting
        from 1.
    underdetermined : bool
        Allows to find a non-unique solution (in addition to a constant factor
        across all terms). Set to ``False`` to disallow (raise ValueError) on
        e.g. "C + O2 -> CO + CO2". Set to ``None`` if you want the symbols replaced
        so that the coefficients are the smallest possible positive (non-zero) integers.
    allow_duplicates : bool
        If False: raises an exception if keys appear in both ``reactants`` and ``products``.

    Examples
    --------
    >>> ref = {'C2H2': 2, 'O2': 3}, {'CO': 4, 'H2O': 2}
    >>> balance_stoichiometry({'C2H2', 'O2'}, {'CO', 'H2O'}) == ref
    True
    >>> ref2 = {'H2': 1, 'O2': 1}, {'H2O2': 1}
    >>> balance_stoichiometry('H2 O2'.split(), ['H2O2'], 'H2 O2 H2O2') == ref2
    True
    >>> reac, prod = 'CuSCN KIO3 HCl'.split(), 'CuSO4 KCl HCN ICl H2O'.split()
    >>> Reaction(*balance_stoichiometry(reac, prod)).string()
    '4 CuSCN + 7 KIO3 + 14 HCl -> 4 CuSO4 + 7 KCl + 4 HCN + 7 ICl + 5 H2O'
    >>> balance_stoichiometry({'Fe', 'O2'}, {'FeO', 'Fe2O3'}, underdetermined=False)
    Traceback (most recent call last):
        ...
    ValueError: The system was under-determined
    >>> r, p = balance_stoichiometry({'Fe', 'O2'}, {'FeO', 'Fe2O3'})
    >>> list(set.union(*[v.free_symbols for v in r.values()]))
    [x1]
    >>> b = balance_stoichiometry({'Fe', 'O2'}, {'FeO', 'Fe2O3'}, underdetermined=None)
    >>> b == ({'Fe': 3, 'O2': 2}, {'FeO': 1, 'Fe2O3': 1})
    True
    >>> d = balance_stoichiometry({'C', 'CO'}, {'C', 'CO', 'CO2'}, underdetermined=None, allow_duplicates=True)
    >>> d == ({'CO': 2}, {'C': 1, 'CO2': 1})
    True

    Returns
    -------
    balanced reactants : dict
    balanced products : dict

    """
    import sympy
    from sympy import (
        MutableDenseMatrix,
        gcd,
        zeros,
        linsolve,
        numbered_symbols,
        nsimplify,
        Wild,
        Symbol,
        Integer,
        Tuple,
        preorder_traversal as pre,
    )

    _intersect = sorted(set.intersection(*map(set, (reactants, products))))
    if _intersect:
        if allow_duplicates:
            if underdetermined is not None:
                raise NotImplementedError(
                    "allow_duplicates currently requires underdetermined=None"
                )
            if set(reactants) == set(products):
                raise ValueError("cannot balance: reactants and products identical")

            # For each duplicate, try to drop it completely:
            for dupl in _intersect:
                try:
                    result = balance_stoichiometry(
                        [sp for sp in reactants if sp != dupl],
                        [sp for sp in products if sp != dupl],
                        substances=substances,
                        substance_factory=substance_factory,
                        underdetermined=underdetermined,
                        allow_duplicates=True,
                    )
                except Exception:
                    continue
                else:
                    return result
            for perm in product(
                *[(False, True)] * len(_intersect)
            ):  # brute force (naive)
                r = set(reactants)
                p = set(products)
                for remove_reac, dupl in zip(perm, _intersect):
                    if remove_reac:
                        r.remove(dupl)
                    else:
                        p.remove(dupl)
                try:
                    result = balance_stoichiometry(
                        r,
                        p,
                        substances=substances,
                        substance_factory=substance_factory,
                        parametric_symbols=parametric_symbols,
                        underdetermined=underdetermined,
                        allow_duplicates=False,
                    )
                except ValueError:
                    continue
                else:
                    return result
            else:
                raise ValueError("Failed to remove duplicate keys: %s" % _intersect)
        else:
            raise ValueError("Substances on both sides: %s" % str(_intersect))
    if substances is None:
        substances = OrderedDict(
            [(k, substance_factory(k)) for k in chain(reactants, products)]
        )
    if isinstance(substances, str):
        substances = OrderedDict(
            [(k, substance_factory(k)) for k in substances.split()]
        )
    if type(reactants) == set:  # noqa
        # we don't want isinstance since it might be "OrderedSet"
        reactants = sorted(reactants)
    if type(products) == set:  # noqa
        products = sorted(products)
    subst_keys = list(reactants) + list(products)

    cks = Substance.composition_keys(substances.values())

    if parametric_symbols is None:
        parametric_symbols = numbered_symbols("x", start=1, integer=True, positive=True)

    # ?C2H2 + ?O2 -> ?CO + ?H2O
    # Ax = 0
    #   A:                    x:
    #
    #   C2H2   O2  CO  H2O
    # C -2     0    1   0      x0    =   0
    # H -2     0    0   2      x1        0
    # O  0    -2    1   1      x2        0
    #                          x3

    def _get(ck, sk):
        return substances[sk].composition.get(ck, 0) * (-1 if sk in reactants else 1)

    for ck in cks:  # check that all components are present on reactant & product sides
        for rk in reactants:
            if substances[rk].composition.get(ck, 0) != 0:
                break
        else:
            any_pos = any(substances[pk].composition.get(ck, 0) > 0 for pk in products)
            any_neg = any(substances[pk].composition.get(ck, 0) < 0 for pk in products)
            if any_pos and any_neg:
                pass  # negative and positive parts among products, no worries
            else:
                raise ValueError("Component '%s' not among reactants" % ck)

        for pk in products:
            if substances[pk].composition.get(ck, 0) != 0:
                break
        else:
            any_pos = any(substances[pk].composition.get(ck, 0) > 0 for pk in reactants)
            any_neg = any(substances[pk].composition.get(ck, 0) < 0 for pk in reactants)
            if any_pos and any_neg:
                pass  # negative and positive parts among reactants, no worries
            else:
                raise ValueError("Component '%s' not among products" % ck)

    A = MutableDenseMatrix([[_get(ck, sk) for sk in subst_keys] for ck in cks])
    A = nsimplify(A)
    symbs = list(reversed([next(parametric_symbols) for _ in range(len(subst_keys))]))
    (sol,) = linsolve((A, zeros(len(cks), 1)), symbs)
    try:
        sol = nsimplify(sol)
    except (AttributeError):
        pass

    wi = Wild("wi", properties=[lambda k: not k.has(Symbol)])
    cd = reduce(
        gcd,
        [1]
        + [
            1 / m[wi]
            for m in map(lambda n: n.match(symbs[-1] / wi), pre(sol))
            if m is not None
        ],
    )
    sol = sol.func(*[arg / cd for arg in sol.args])

    def remove(cont, symb, remaining):
        subsd = dict(zip(remaining / symb, remaining))
        cont = cont.func(*[(arg / symb).expand().subs(subsd) for arg in cont.args])
        if cont.has(symb):
            raise ValueError(
                "Bug, please report an issue at https://github.com/bjodah/chempy"
            )
        return cont

    done = False
    for idx, symb in enumerate(symbs):
        for expr in sol:
            iterable = expr.args if expr.is_Add else [expr]
            for term in iterable:
                if term.is_number:
                    done = True
                    break
            if done:
                break
        if done:
            break
        for expr in sol:
            if (expr / symb).is_number:
                sol = remove(sol, symb, MutableDenseMatrix(symbs[idx + 1 :]))
                break
    for symb in symbs:
        cd = 1
        for expr in sol:
            iterable = expr.args if expr.is_Add else [expr]
            for term in iterable:
                if term.is_Mul and term.args[0].is_number and term.args[1] == symb:
                    cd = gcd(cd, term.args[0])
        if cd != 1:
            sol = sol.func(*[arg.subs(symb, symb / cd) for arg in sol.args])
    integer_one = 1  # need 'is' check, SyntaxWarning when checking against literal
    if underdetermined is integer_one:
        from ._release import __version__

        if int(__version__.split(".")[1]) > 6:
            warnings.warn(  # deprecated because comparison with ``1`` problematic (True==1)
                (
                    "Pass underdetermined == None instead of ``1`` (deprecated since 0.7.0,"
                    " will_be_missing_in='0.9.0')"
                ),
                ChemPyDeprecationWarning,
            )
        underdetermined = None
    if underdetermined is None:
        sol = Tuple(*[Integer(x) for x in _solve_balancing_ilp_pulp(A)])

    fact = gcd(sol)
    sol = MutableDenseMatrix([e / fact for e in sol]).reshape(len(sol), 1)
    sol /= reduce(gcd, sol)
    sol = nsimplify(sol)

    if 0 in sol:
        raise ValueError("Superfluous species given.")
    if underdetermined:
        if any(x == sympy.nan for x in sol):
            raise ValueError("Failed to balance reaction")
    else:
        for x in sol:
            if len(x.free_symbols) != 0:
                raise ValueError("The system was under-determined")
        if not all(residual == 0 for residual in A * sol):
            raise ValueError("Failed to balance reaction")

    def _x(k):
        coeff = sol[subst_keys.index(k)]
        return int(coeff) if underdetermined is None else coeff

    return (
        OrderedDict([(k, _x(k)) for k in reactants]),
        OrderedDict([(k, _x(k)) for k in products]),
    )


def mass_fractions(
    stoichiometries, substances=None, substance_factory=Substance.from_formula
):
    """Calculates weight fractions of each substance in a stoichiometric dict

    Parameters
    ----------
    stoichiometries : dict or set
        If a ``set``: all entries are assumed to correspond to unit multiplicity.
    substances: dict or None

    Examples
    --------
    >>> r = mass_fractions({'H2': 1, 'O2': 1})
    >>> mH2, mO2 = 1.008*2, 15.999*2
    >>> abs(r['H2'] - mH2/(mH2+mO2)) < 1e-4
    True
    >>> abs(r['O2'] - mO2/(mH2+mO2)) < 1e-4
    True
    >>> mass_fractions({'H2O2'}) == {'H2O2': 1.0}
    True

    """
    if isinstance(stoichiometries, set):
        stoichiometries = {k: 1 for k in stoichiometries}
    if substances is None:
        substances = OrderedDict([(k, substance_factory(k)) for k in stoichiometries])
    tot_mass = sum([substances[k].mass * v for k, v in stoichiometries.items()])
    return {k: substances[k].mass * v / tot_mass for k, v in stoichiometries.items()}