:py:mod:`gempipe.interface.medium`
==================================

.. py:module:: gempipe.interface.medium


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


Functions
~~~~~~~~~

.. autoapisummary::

   gempipe.interface.medium.reset_growth_env
   gempipe.interface.medium.set_bounded_uptakes
   gempipe.interface.medium.set_bounded_secretions
   gempipe.interface.medium.set_unbounded_exchanges



.. py:function:: reset_growth_env(model)

   Set all the EX_change reactions to (0, 1000).

   :param model: target model.
   :type model: cobra.Model


.. py:function:: set_bounded_uptakes(model, uptakes)

   Set uptake of nutrients.

   Can be expressed as either concentrations [mmol/L] or fluxes [mmol/(h*gDW)], depending on your aims.

   :param model: target model.
   :type model: cobra.Model
   :param secretions: dictionary keyed by EX_change reaction ID. Expressing values as tuples, the user can provide the standard deviation.
   :type secretions: dict


.. py:function:: set_bounded_secretions(model, secretions)

   Set secretion of metabolites.

   Can be expressed as either concentrations [mmol/L] or fluxes [mmol/(h*gDW)], depending on your aims.

   :param model: target model.
   :type model: cobra.Model
   :param secretions: dictionary keyed by EX_change reaction ID. Expressing values as tuples, the user can provide the standard deviation.
   :type secretions: dict


.. py:function:: set_unbounded_exchanges(model, exrs)

   Define which melecules require a free exchange (-1000, 1000).

   :param model: target model.
   :type model: cobra.Model
   :param exrs: IDs of EX_change reactions to unbound.
   :type exrs: list