:py:mod:`cobra.medium.boundary_types`
=====================================

.. py:module:: cobra.medium.boundary_types

.. autoapi-nested-parse::

   Provide functions to identify the type of boundary reactions.

   This module uses various heuristics to decide whether a boundary reaction
   is an exchange, demand or sink reaction. It mostly orientates on the
   following paper:

   Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for
   generating a high-quality genome-scale metabolic reconstruction.
   Nature protocols. Nature Publishing Group.
   http://doi.org/10.1038/nprot.2009.203



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


Functions
~~~~~~~~~

.. autoapisummary::

   cobra.medium.boundary_types.find_external_compartment
   cobra.medium.boundary_types.is_boundary_type
   cobra.medium.boundary_types.find_boundary_types



Attributes
~~~~~~~~~~

.. autoapisummary::

   cobra.medium.boundary_types.logger


.. py:data:: logger

   

.. py:function:: find_external_compartment(model: cobra.Model) -> str

   Find the external compartment in the model.

   Uses a simple heuristic where the external compartment should be the
   one with the most exchange reactions.

   :param model: The cobra model whose external compartments are to be identified.
   :type model: cobra.Model

   :returns: The putative external compartment.
   :rtype: str

   :raises RuntimeError: If several compartments are similar and thus difficult to identify,
       or, recognized names usually used for external compartment are
       absent.


.. py:function:: is_boundary_type(reaction: cobra.Reaction, boundary_type: str, external_compartment: str) -> bool

   Check whether a reaction is an exchange reaction.

   :param reaction: The reaction to check.
   :type reaction: cobra.Reaction
   :param boundary_type: Boundary type to check for.
   :type boundary_type: {"exchange", "demand", "sink"}
   :param external_compartment: The ID for the external compartment.
   :type external_compartment: str

   :returns: Whether the reaction looks like the requested type. Might be based
             on a heuristic.
   :rtype: bool


.. py:function:: find_boundary_types(model: cobra.Model, boundary_type: str, external_compartment: Optional[str] = None) -> List[cobra.Reaction]

   Find specific boundary reactions.

   :param model: The cobra model whose boundary reactions are to be found.
   :type model: cobra.Model
   :param boundary_type: Boundary type to check for.
   :type boundary_type: {"exchange", "demand", "sink"}
   :param external_compartment: The ID for the external compartment. If None, it will be detected
                                automatically (default None).
   :type external_compartment: str, optional

   :returns: A list of likely boundary reactions of a user defined type.
   :rtype: list of cobra.Reaction or an empty list