skimpy.analysis.oracle.minimum_fluxes
=====================================

.. py:module:: skimpy.analysis.oracle.minimum_fluxes

.. autoapi-nested-parse::

   .. module:: skimpy
      :platform: Unix, Windows
      :synopsis: Simple Kinetic Models in Python

   .. moduleauthor:: SKiMPy team

   [---------]

   Copyright 2018 Laboratory of Computational Systems Biotechnology (LCSB),
   Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.



Attributes
----------

.. autoapisummary::

   skimpy.analysis.oracle.minimum_fluxes.BIGM
   skimpy.analysis.oracle.minimum_fluxes.BIGM_THERMO
   skimpy.analysis.oracle.minimum_fluxes.BIGM_DG
   skimpy.analysis.oracle.minimum_fluxes.BIGM_P
   skimpy.analysis.oracle.minimum_fluxes.EPSILON
   skimpy.analysis.oracle.minimum_fluxes.BIGM
   skimpy.analysis.oracle.minimum_fluxes.BIGM_THERMO
   skimpy.analysis.oracle.minimum_fluxes.BIGM_DG
   skimpy.analysis.oracle.minimum_fluxes.BIGM_P
   skimpy.analysis.oracle.minimum_fluxes.EPSILON


Classes
-------

.. autoapisummary::

   skimpy.analysis.oracle.minimum_fluxes.MinFLuxVariable
   skimpy.analysis.oracle.minimum_fluxes.MinFLux


Functions
---------

.. autoapisummary::

   skimpy.analysis.oracle.minimum_fluxes.add_min_flux_requirements
   skimpy.analysis.oracle.minimum_fluxes.relax_min_flux


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

.. py:data:: BIGM

.. py:data:: BIGM_THERMO

.. py:data:: BIGM_DG

.. py:data:: BIGM_P

.. py:data:: EPSILON

.. py:class:: MinFLuxVariable(reaction, **kwargs)

   Bases: :py:obj:`pytfa.optim.variables.ReactionVariable`


   Class to represent a negative slack variable for relaxation problems


   .. py:attribute:: prefix
      :value: 'MinFluxVar_'



.. py:class:: MinFLux(reaction, expr, **kwargs)

   Bases: :py:obj:`pytfa.optim.constraints.ReactionConstraint`


   Class to represent thermodynamics constraints.
   G: Flux_FW + Fluw_BW > min_flux


   .. py:attribute:: prefix
      :value: 'MF_'



.. py:data:: BIGM

.. py:data:: BIGM_THERMO

.. py:data:: BIGM_DG

.. py:data:: BIGM_P

.. py:data:: EPSILON

.. py:function:: add_min_flux_requirements(tmodel, flux, inplace=True, exclude=[])

.. py:function:: relax_min_flux(tmodel, reactions_to_ignore=(), solver=None, in_place=False)

   :param t_tmodel:
   :type t_tmodel: pytfa.thermo.ThermoModel:
   :param reactions_to_ignore: Iterable of reactions that should not be relaxed
   :param solver: solver to use (e.g. 'optlang-glpk', 'optlang-cplex',
       'optlang-gurobi'
   :return: a cobra_model with relaxed bounds on standard Gibbs free energy