.. _py-Chem:

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Chem
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.. default-domain:: py

.. py:currentmodule:: mod
.. cpp:namespace:: mod


Class ``AtomId``
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.. py:class:: AtomId

    Representation of the chemical element of an atom.

    .. py:method:: __init__(self, id=AtomIds.Invalid)

        Construct an atom ID from an integer.

        :param int id: the atomic number to construct from, or :py:const:`AtomIds.Invalid` to explicitly signal an invalid atom.
            Must be at most the same value as :py:const:`AtomIds.Max`.
    .. py:attribute:: symbol

        (Read-only) The symbol represented by the atom id.

        :type: str
        :raises: :py:class:`LogicError` if the id is invalid.
    .. py:method:: __int__(self)

        Implicit conversion to an integer type.

Class ``Isotope``
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.. py:class:: Isotope

    Representation of the isotope of an atom.

    .. py:method:: __init__(self)
                   __init__(self, i)

        Construct a representation of an isotope.
        If an isotope number is given, that specific one is constructed,
        otherwise the most abundant one is implicitly constructed.
    
        .. note:: There is a difference between constructing the most abundant isotope implicitly and explicitly.

        :param int i: An isotope number for explicit construction. Passing -1 is equivalent to default-construction.
            The number must be either -1 or at least 1.
    .. py:method:: __int__(self)

        Implicit conversion to an integer type.

Class ``Charge``
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.. py:class:: Charge

    Representation of the charge of an atom.

    .. py:method:: __init__(self, c=0)

        Construct a charge.

        :param int c: The charge to construct. Must be in the range :math:`[-9, 9]`.
    .. py:method:: __int__(self)

        Implicit conversion to an integer type.

Class ``AtomData``
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.. py:class:: AtomData

    Representation of basic data of an atom.

    .. py:method:: __init__(self, atomId=AtomIds.Invalid, istotope=Isotope(), charge=Charge(), radical=False)

        Construct an atom data object.

    .. py:attribute:: atomId

        (Read-only) The atom id.

        :type: AtomId
    .. py:attribute:: isotope

        (Read-only) The isotope.

        :type: Isotope
    .. py:attribute:: charge

        (Read-only) The charge.

        :type: Charge
    .. py::attribute:: radical

        (Read-only) The radical.

        :type: bool
    .. py::method:: __str__(self)

        :returns: A string representation of the atom data adhering to the string encoding of atoms (see :ref:`mol-enc`).
        :raises: :py::class:`LogicError` if the atom id is :py:const:`AtomIds.Invalid`.

Class ``BondType``
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.. py:class:: BondType

    Representation of a bond type.

    .. py:attribute:: Invalid
    .. py:attribute:: Single
    .. py:attribute:: Aromatic
    .. py:attribute:: Double
    .. py:attribute:: Triple
    .. py:method:: __str__(self)

        :returns: A string representation of the bond type adhering to the string encoding of bonds (see :ref:`mol-enc`).
        :raises: :py:class:`LogicError` if the bond type is :py:const:`Invalid`.

Class ``AtomIds``
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.. py:class:: AtomIds

    This class contains constants for each chemical element, both as their abbreviations and their full names.
    Two additional constants are provided for convenience.

    .. py:attribute:: Invalid

        Constant for the invalid atom id.

        :type: AtomId

    .. py:attribute:: Max

        An atom id equal to the atom id with the maximum valid id.

        :type: AtomId