:mod:`memote.support.thermodynamics`
====================================

.. py:module:: memote.support.thermodynamics

.. autoapi-nested-parse::

   Supporting functions for checks requiring the eQuilibrator API.

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


Functions
~~~~~~~~~

.. autoapisummary::

   memote.support.thermodynamics.get_smallest_compound_id
   memote.support.thermodynamics.map_metabolite2kegg
   memote.support.thermodynamics.translate_reaction
   memote.support.thermodynamics.find_thermodynamic_reversibility_index


.. data:: compound_matcher
   

   

.. data:: logger
   

   

.. function:: get_smallest_compound_id(compounds_identifiers)

   Return the smallest KEGG compound identifier from a list.

   KEGG identifiers may map to compounds, drugs or glycans prefixed
   respectively with "C", "D", and "G" followed by at least 5 digits. We
   choose the lowest KEGG identifier with the assumption that several
   identifiers are due to chirality and that the lower one represents the
   more common form.

   :Parameters:

       **compounds_identifiers** : list
           A list of mixed KEGG identifiers.

   :Returns:

       str
           The KEGG compound identifier with the smallest number.




   :Raises:

       ValueError
           When compound_identifiers contains no KEGG compound identifiers.









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.. function:: map_metabolite2kegg(metabolite)

   Return a KEGG compound identifier for the metabolite if it exists.

   First see if there is an unambiguous mapping to a single KEGG compound ID
   provided with the model. If not, check if there is any KEGG compound ID in
   a list of mappings. KEGG IDs may map to compounds, drugs and glycans. KEGG
   compound IDs are sorted so we keep the lowest that is there. If none of
   this works try mapping to KEGG via the CompoundMatcher by the name of the
   metabolite. If the metabolite cannot be mapped at all we simply map it back
   to its own ID.

   :Parameters:

       **metabolite** : cobra.Metabolite
           The metabolite to be mapped to its KEGG compound identifier.

   :Returns:

       None
           If the metabolite could not be mapped.

       str
           The smallest KEGG compound identifier that was found.













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.. function:: translate_reaction(reaction, metabolite_mapping)

   Return a mapping from KEGG compound identifiers to coefficients.


   :Parameters:

       **reaction** : cobra.Reaction
           The reaction whose metabolites are to be translated.

       **metabolite_mapping** : dict
           An existing mapping from cobra.Metabolite to KEGG compound identifier
           that may already contain the metabolites in question or will have to be
           extended.

   :Returns:

       dict
           The stoichiometry of the reaction given as a mapping from metabolite
           KEGG identifier to coefficient.













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.. function:: find_thermodynamic_reversibility_index(reactions)

   Return the reversibility index of the given reactions.

   To determine the reversibility index, we calculate
   the reversibility index ln_gamma (see [R7b2151b2cd73-1]_ section 3.5) of each reaction
   using the eQuilibrator API [R7b2151b2cd73-2]_.

   :Parameters:

       **reactions: list of cobra.Reaction**
           A list of reactions for which to calculate the reversibility index.

   :Returns:

       tuple
           list of cobra.Reaction, index pairs
               A list of pairs of reactions and their reversibility indexes.
           list of cobra.Reaction
               A list of reactions which contain at least one metabolite that
               could not be mapped to KEGG on the basis of its annotation.
           list of cobra.Reaction
               A list of reactions for which it is not possible to calculate the
               standard change in Gibbs free energy potential. Reasons of failure
               include that participating metabolites cannot be broken down with
               the group contribution method.
           list of cobra.Reaction
               A list of reactions that are not chemically or redox balanced.









   .. rubric:: References

   .. [R7b2151b2cd73-1] Elad Noor, Arren Bar-Even, Avi Flamholz, Yaniv Lubling, Dan Davidi,
          Ron Milo; An integrated open framework for thermodynamics of
          reactions that combines accuracy and coverage, Bioinformatics,
          Volume 28, Issue 15, 1 August 2012, Pages 2037–2044,
          https://doi.org/10.1093/bioinformatics/bts317
   .. [R7b2151b2cd73-2] https://pypi.org/project/equilibrator-api/

   .. only:: latex

      [R7b2151b2cd73-1]_, [R7b2151b2cd73-2]_




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