:py:mod:`micom.solution`
========================

.. py:module:: micom.solution

.. autoapi-nested-parse::

   A community solution object.



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

Classes
~~~~~~~

.. autoapisummary::

   micom.solution.CommunitySolution



Functions
~~~~~~~~~

.. autoapisummary::

   micom.solution._group_taxa
   micom.solution.add_pfba_objective
   micom.solution.solve
   micom.solution.reset_solver
   micom.solution.optimize_with_retry
   micom.solution.crossover
   micom.solution.optimize_with_fraction



Attributes
~~~~~~~~~~

.. autoapisummary::

   micom.solution.good


.. py:data:: good

   Solver states that permit returning the solution.

.. py:function:: _group_taxa(values, ids, taxa, what='reaction')

   Format a list of values by id and taxa.


.. py:class:: CommunitySolution(community, slim=False, reactions=None, metabolites=None)


   Bases: :py:obj:`cobra.core.Solution`

   An FBA solution for an entire community.

   .. attribute:: objective_value

      The (optimal) value for the objective function.

      :type: float

   .. attribute:: members

      Contains basic info about the individual compartments/members of the
      community such as id, abundance and growth rates. Will also include
      one row for the external medium (without abundance and growth rate).

      :type: pandas.Series

   .. attribute:: growth_rate

      The overall growth rate for the community normalized to 1 gDW.

      :type: float

   .. attribute:: status

      The solver status related to the solution.

      :type: str

   .. attribute:: strategy

      The optimization strategy used to obtain the solution (may be empty).

      :type: str

   .. attribute:: fluxes

      Contains the reaction fluxes (primal values of variables) stratified
      by compartment. Columns denote individual fluxes and rows denote
      compartments: one for every taxon plus one for the external medium.
      Fluxes will be NA if the reaction does not exist in the organism.

      :type: pandas.DataFrame

   .. attribute:: reduced_costs

      Contains reaction reduced costs (dual values of variables) stratified
      by taxa. Columns denote individual fluxes and rows denote taxa.
      Reduced costs will be NA if the reaction does not exist in the
      organism.

      :type: pandas.Series

   .. attribute:: shadow_prices

      Contains metabolite shadow prices (dual values of constraints)
      stratified by taxa. Columns denote individual metabolites and rows
      denote taxa. Shadow prices will be NA if the metabolite does not
      exist in the organism.

      :type: pandas.Series

   .. py:method:: _repr_html_()

      Return a rich HTML representation of the solution.


   .. py:method:: __repr__()

      Convert CommunitySolution instance to string representation.



.. py:function:: add_pfba_objective(community, atol=1e-06, rtol=1e-06)

   Add pFBA objective.

   Add objective to minimize the summed flux of all reactions to the
   current objective. This one will work with any objective (even non-linear
   ones).

   .. seealso:: :obj:`pfba`

   :param community: The community to add the objective to.
   :type community: micom.Community


.. py:function:: solve(community, fluxes=True, pfba=True, raise_error=False, atol=1e-06, rtol=1e-06)

   Get all fluxes stratified by taxa.


.. py:function:: reset_solver(community)

   Reset the solver.


.. py:function:: optimize_with_retry(com, message='could not get optimum.')

   Try to reset the solver.


.. py:function:: crossover(community, sol, fluxes=False)

   Get the crossover solution.


.. py:function:: optimize_with_fraction(com, fraction, growth_rate=None, fluxes=False)

   Optimize with a constrained community growth rate.