skimpy.core.reactor
===================

.. py:module:: skimpy.core.reactor

.. autoapi-nested-parse::

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

   .. moduleauthor:: SKiMPy team

   [---------]

   Copyright 2020 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.



Classes
-------

.. autoapisummary::

   skimpy.core.reactor.Reactor


Functions
---------

.. autoapisummary::

   skimpy.core.reactor.make_reactor_ode_fun


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

.. py:class:: Reactor(models, biomass_reactions, biomass_scaling, boundary_conditions=None, extracellular_compartment='e', custom_variables=[])

   Bases: :py:obj:`abc.ABC`


       


   .. py:attribute:: extracellular_compartment
      :value: 'e'



   .. py:attribute:: medium


   .. py:attribute:: biomass_reactions


   .. py:attribute:: biomass_scaling


   .. py:attribute:: biomass_variables


   .. py:attribute:: models


   .. py:attribute:: boundary_conditions


   .. py:attribute:: initial_conditions


   .. py:attribute:: _modified
      :value: True



   .. py:attribute:: custom_variables


   .. py:property:: variables


   .. py:property:: parameters


   .. py:method:: parametrize(value_dict, model_name)

      Set the parameters of a specified model
      :param value_dict:
      :param model_name:
      :return:



   .. py:method:: add_boundary_condition(boundary_condition)

      Enforces a boundary condition (e.g. a constant concentration) on the
      kinetic model

      :param boundary_condition: the boundary condition to enforce
      :type boundary_condition: skimpy.core.BoundaryCondition
      :return:



   .. py:method:: add_to_tabdict(element, kind)


   .. py:method:: compile_ode(sim_type=QSSA, ncpu=1, add_dilution=False, custom_ode_update=None)

      :param sim_type:
      :param ncpu:
      :return:



   .. py:method:: initialize(value_dict, model_name)

      Set the initial conditions for a single strain (excluding medium)
      :param value_dict:
      :param model_name:
      :return:



   .. py:method:: solve_ode(time_out, solver_type='cvode', **kwargs)

      The solver types are from ::scikits.odes::, and can be found at
      <https://scikits-odes.readthedocs.io/en/latest/solvers.html>`_.
      :param time_out: The times at which the solution is evaluated
      :type time_out:  list(float) or similar
      :param solver_type: must be among ['cvode','ida','dopri5','dop853']
      :param kwargs:
      :return:



.. py:function:: make_reactor_ode_fun(reactor, sim_type, pool=None, add_dilution=False, custom_ode_update=None)

   This function generates the symbolic expressions for a reactor model

   :param reactor:
   :param sim_type:
   :param pool:
   :return: