cobra.medium.minimal_medium
===========================

.. py:module:: cobra.medium.minimal_medium

.. autoapi-nested-parse::

   Provide functions and helpers to obtain minimal growth media.



Attributes
----------

.. autoapisummary::

   cobra.medium.minimal_medium.logger


Functions
---------

.. autoapisummary::

   cobra.medium.minimal_medium.add_linear_obj
   cobra.medium.minimal_medium.add_mip_obj
   cobra.medium.minimal_medium._as_medium
   cobra.medium.minimal_medium.minimal_medium


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

.. py:data:: logger

.. py:function:: add_linear_obj(model: cobra.Model) -> None

   Add a linear version of a minimal medium to the model solver.

   Changes the optimization objective to finding the growth medium
   requiring the smallest total import flux:

   ..math:: minimize \sum_{r_i in import_reactions} |r_i|

   :param model: The cobra model to modify.
   :type model: cobra.Model


.. py:function:: add_mip_obj(model: cobra.Model) -> None

   Add a mixed-integer version of a minimal medium to the model.

   Changes the optimization objective to finding the medium with the least
   components:

   minimize size(R) where R part of import_reactions

   :param model: The model to modify.
   :type model: cobra.model


.. py:function:: _as_medium(exchanges: Iterable[cobra.Reaction], tolerance: float = 1e-06, exports: bool = False) -> pandas.Series

   Convert a solution to medium.

   :param exchanges: The exchange reactions to consider.
   :type exchanges: list of cobra.reaction
   :param tolerance: The absolute tolerance for fluxes. Fluxes with an absolute value
                     smaller than this number will be ignored (default 1e-6).
   :type tolerance: float > 0, optional
   :param exports: Whether to return export fluxes as well (default False).
   :type exports: bool, optional

   :returns: The "medium", meaning all active import fluxes in the solution.
   :rtype: pandas.Series


.. py:function:: minimal_medium(model: cobra.Model, min_objective_value: float = 0.1, exports: bool = False, minimize_components: Union[bool, int] = False, open_exchanges: bool = False) -> Union[pandas.Series, pandas.DataFrame, None]

   Find the minimal growth medium for the `model`.

   Finds the minimal growth medium for the `model` which allows for
   model as well as individual growth. Here, a minimal medium can either
   be the medium requiring the smallest total import flux or the medium
   requiring the least components (ergo ingredients), which will be much
   slower due to being a mixed integer problem (MIP).

   :param model: The model to modify.
   :type model: cobra.model
   :param min_objective_value: The minimum growth rate (objective) that has to be achieved
                               (default 0.1).
   :type min_objective_value: float > 0 or array-like object, optional
   :param exports: Whether to include export fluxes in the returned medium.
                   Defaults to False which will only return import fluxes
                   (default False).
   :type exports: bool, optional
   :param minimize_components: Whether to minimize the number of components instead of the total
                               import flux. Might be more intuitive if set to True, but may also
                               be slow to calculate for large communities. If set to a number `n`
                               will return up to `n` alternative solutions all with the same
                               number of components (default False).
   :type minimize_components: bool or int > 0, optional
   :param open_exchanges: Whether to ignore currently set bounds and make all exchange
                          reactions in the `model` possible. If set to a `number`, all
                          exchange reactions will be opened with (-`number`, `number`) as
                          bounds (default False).
   :type open_exchanges: bool or number, optional

   :returns: A pandas.Series giving the import flux for each required import
             reaction and (optionally) the associated export fluxes. All exchange
             fluxes are oriented into the import reaction e.g. positive fluxes
             denote imports and negative fluxes exports. If `minimize_components`
             is a number larger than 1, may return a pandas.DataFrame where each
             column is a minimal medium. Returns None, if the minimization is
             infeasible (for instance if min_growth > maximum growth rate).
   :rtype: pandas.Series, pandas.DataFrame or None

   .. rubric:: Notes

   Due to numerical issues, the `minimize_components` option will usually
   only minimize the number of "large" import fluxes. Specifically, the
   detection limit is given by ``integrality_tolerance * max_bound`` where
   ``max_bound`` is the largest bound on an import reaction. Thus, if you
   are interested in small import fluxes as well you may have to adjust the
   solver tolerance at first with `model.tolerance = 1e-7` for instance.
   However, this will be *very* slow for large models especially with GLPK.