cobra.core.species
==================

.. py:module:: cobra.core.species

.. autoapi-nested-parse::

   Define the Species class, used as a base for Gene and Metabolite.



Classes
-------

.. autoapisummary::

   cobra.core.species.Species


Module Contents
---------------

.. py:class:: Species(id: Optional[str] = None, name: Optional[str] = None, **kwargs)

   Bases: :py:obj:`cobra.core.object.Object`


   Species is a base class in Cobrapy.

   Species is a class for holding information regarding
   a chemical Species

   :param id: An identifier for the chemical species
   :type id: string
   :param name: A human readable name.
   :type name: string


   .. py:attribute:: _model
      :value: None



   .. py:attribute:: _reaction


   .. py:property:: reactions
      :type: FrozenSet


      Return a frozenset of reactions.

      :returns: A frozenset that includes the reactions of the species.
      :rtype: FrozenSet


   .. py:method:: __getstate__() -> dict

      Return the state of the species.

      Remove the references to container reactions when serializing to
      avoid problems associated with recursion.

      :returns: A dictionary describing the state, without the self._reaction to avoid
                recursion.
      :rtype: dict



   .. py:method:: copy() -> Species

      Copy a species.

      When copying a reaction, it is necessary to deepcopy the
      components so the list references aren't carried over.

      Additionally, a copy of a reaction is no longer in a cobra.Model.

      This should be fixed with self.__deepcopy__ if possible

      :returns: A copy of the species.
      :rtype: Species



   .. py:property:: model
      :type: Optional[cobra.Model]


      Return the model.

      :returns: Returns the cobra model that the species is associated with. None if there
                is no model associated with this species.
      :rtype: model