:py:mod:`bayflux.core.reactionNetwork`
======================================

.. py:module:: bayflux.core.reactionNetwork


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

Classes
~~~~~~~

.. autoapisummary::

   bayflux.core.reactionNetwork.ReactionNetwork
   bayflux.core.reactionNetwork.EnhancedReaction
   bayflux.core.reactionNetwork.AtomTransition




.. py:class:: ReactionNetwork(cobrapyModel)


   Bases: :py:obj:`cobra.Model`

   ReactionNetwork contains a genome scale model with atom transitions.

   This inherits from a cobra.Model but reactions are replaced with
   EnhancedReaction to add in atom transitions.

   Args:
       cobrapyModel (cobra.Model): A cobra.Model to inherit from.


   .. py:method:: copy()

      Provides a partial 'deepcopy' of the Model.  All of the Metabolite,
      Gene, and Reaction objects are created anew but in a faster fashion
      than deepcopy

      This code was taken verbatim from cobrapy, but modified
      to add EnhancedReactions.


   .. py:method:: writeFluxConstraints(outputFileName, format='csv', exchangesOnly=True)


   .. py:method:: readFluxConstraints(inputFileName, format='csv')


   .. py:method:: writeAtomTransitions(outputFileName, format='bayflux')


   .. py:method:: readAtomTransitions(inputFileName, format='bayflux')



.. py:class:: EnhancedReaction(cobrapyReaction, transitions=None)


   Bases: :py:obj:`cobra.Reaction`

   like a cobra.Reaction, but with atom transitions.

   See the attributes for cobra.Reaction in cobrapy

   Args:
       cobrapyReaction (cobra.Reaction): a cobra.Reaction object to 
           inherit from.
       transitions (list, optional): a list of AtomTransition objects.

   Attributes:
       transitions (list, optional): a list of AtomTransition objects.


   .. py:method:: _repr_html_()



.. py:class:: AtomTransition(reactants, products)


   Class for storing atom transitions associated with a reaction.

   Overview
   reactant and product transitions are
   stored as a tuple of two value tuples where the first value of each
   two value tuple is a cobra.Metabolite
   and the second value is a tuple of integers where the position
   in the tuple represents an atom (in left to right order)
   from the canonical SMILES representation of the metabolite,
   and the values in the tuples are integers, whereby the same
   atom in a product and reactant have the same integer label.
   Specific values of the integers are arbitrary.

   Special cases:

   Reactions with multiple atom transitions
   MetaCyc reaction SUCCCOASYN-RXN is an example
   with multiple atom transitions. We accommodate this
   by associating multiple atom transition objects with the
   same EnhancedReaction.

   Equivalent atoms
   Biochemically indistinguishable atoms should be represented
   with the same integer value in the atom transition tuple. This
   will be used to generate a set of equivalent EMUs. 

   Args:
       reactants (tuple): A tuple of two valued tuples as described above. 
       products (tuple): A tuple of two valued tuples as described above. 

   Attributes:
       reactants (tuple): A tuple of two valued tuples as described above. 
       products (tuple): A tuple of two valued tuples as described above. 


   .. py:method:: reverse()


   .. py:method:: __repr__()

      Return repr(self).