skimpy.analysis.modal
=====================

.. py:module:: skimpy.analysis.modal

.. 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.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/skimpy/analysis/modal/modal_matrix/index


Classes
-------

.. autoapisummary::

   skimpy.analysis.modal.TabDict
   skimpy.analysis.modal.FluxFunction


Functions
---------

.. autoapisummary::

   skimpy.analysis.modal.modal_matrix


Package Contents
----------------

.. py:class:: TabDict

   Bases: :py:obj:`collections.OrderedDict`


   Really just an ordered dict with tab completion in interactive terminals


   .. py:method:: __dir__()

      Default dir() implementation.



   .. py:method:: __getattr__(attr)


   .. py:method:: iloc(ix)


.. py:class:: FluxFunction(variables, expr, parameters, pool=None)

   .. py:attribute:: variables


   .. py:attribute:: expr


   .. py:attribute:: parameters


   .. py:attribute:: function


   .. py:method:: __call__(concentrations, parameters)


.. py:function:: modal_matrix(kmodel, concentration_dict, parameters, flux_modes=False, tolerance=1e-12)

   This function computes the transformation matrix W as described in Chapter 4 of
   Heinrich, Reinhart, and Stefan Schuster. The regulation of cellular systems.
   Springer Science & Business Media, 2012.

   The matrix W describes the composition of each pool variable X[i] whos
   dynamics are given by the eigenvalue lam[i] as a linear combination of
   the model variables S, which are concentrations.


   :param kmodel: A skimpy.core.KineticModel with compiled mca functions
   :param concentration_dict: A dict {'variable_name': value,  }
   :param parameters: A dict {'param_name': value,  }
   :return: