skimpy.core.kinmodel
====================

.. py:module:: skimpy.core.kinmodel

.. autoapi-nested-parse::

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

   .. moduleauthor:: SKiMPy team

   [---------]

   Copyright 2017 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.kinmodel.KineticModel


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

.. py:class:: KineticModel(reactions=None, boundary_conditions=None, constraints=None, name='Unnamed')

   Bases: :py:obj:`object`


   This class contains the kinetic model as described by reaction and
   boundary conditions and constratins.

   :param :
   :return:


   .. py:attribute:: name
      :value: 'Unnamed'



   .. py:attribute:: reactions


   .. py:attribute:: boundary_conditions


   .. py:attribute:: constraints


   .. py:attribute:: initial_conditions


   .. py:attribute:: logger


   .. py:attribute:: _simtype
      :value: None



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



   .. py:attribute:: _recompiled
      :value: False



   .. py:attribute:: compartments


   .. py:property:: reactants


   .. py:property:: parameters


   .. py:property:: moieties


   .. py:method:: add_reaction(reaction)

      Adds a SKiMPy reaction to the model

      :param reaction: The reaction to add
      :type reaction: skimpy.core.Reaction
      :return:



   .. py:method:: add_compartment(compartment)

      :param compartment:
      :return:



   .. py:method:: add_constraint(constraint)


   .. 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:: parametrize_by_reaction(param_dict)

      If has input: apply as dict to reactions in the model by
          reaction.parametrize(args)
      :return:



   .. py:method:: parametrize(param_dict)


   .. py:method:: repair()

      Link inhibitors and activators to reactants
      FIXME: Any idea to avoid this is dearly welcome
      :return:



   .. py:property:: sim_type


   .. py:method:: prepare(mca=True, ode=True, **kwargs)

      Model preparation for different analysis types. The preparation is done before the compiling step
      to be able to curate the model in between

      :param mca:
      :param ode:
      :return:



   .. py:method:: compile_jacobian(type=NUMERICAL, sim_type=QSSA, ncpu=1)


   .. py:method:: compile_ode(sim_type=QSSA, ncpu=1)


   .. 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:method:: compile_mca(parameter_list=[], mca_type=NET, sim_type=QSSA, ncpu=1)

      Compile MCA expressions: elasticities, jacobian
      and control coeffcients