skimpy.analysis.mca
===================

.. py:module:: skimpy.analysis.mca

.. 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.



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/skimpy/analysis/mca/concentration_control_fun/index
   /autoapi/skimpy/analysis/mca/elasticity_fun/index
   /autoapi/skimpy/analysis/mca/flux_control_fun/index
   /autoapi/skimpy/analysis/mca/jacobian_fun/index
   /autoapi/skimpy/analysis/mca/make/index
   /autoapi/skimpy/analysis/mca/prepare/index
   /autoapi/skimpy/analysis/mca/utils/index
   /autoapi/skimpy/analysis/mca/volume_ratio_function/index


Attributes
----------

.. autoapisummary::

   skimpy.analysis.mca.SPLIT
   skimpy.analysis.mca.NET
   skimpy.analysis.mca.SPLIT
   skimpy.analysis.mca.NET


Classes
-------

.. autoapisummary::

   skimpy.analysis.mca.JacobianFunction
   skimpy.analysis.mca.Tensor
   skimpy.analysis.mca.ConcentrationControlFunction
   skimpy.analysis.mca.Tensor
   skimpy.analysis.mca.FluxControlFunction


Functions
---------

.. autoapisummary::

   skimpy.analysis.mca.get_reversible_fluxes


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

.. py:class:: JacobianFunction(reduced_stoichometry, independent_elasticity_function, dependent_elasticity_function, volume_ratio_function, conservation_relation, independent_variable_ix, dependent_variable_ix)

   .. py:attribute:: reduced_stoichometry


   .. py:attribute:: dependent_elasticity_function


   .. py:attribute:: independent_elasticity_function


   .. py:attribute:: volume_ratio_function


   .. py:attribute:: independent_variable_ix


   .. py:attribute:: dependent_variable_ix


   .. py:attribute:: conservation_relation


   .. py:method:: __call__(fluxes, concentrations, parameters, flux_jacobian=False)

      :param fluxes: `Dict` or `pd.Series` of reference flux vector
      :param concentrations: `Dict` or `pd.Series` of reference concentration vector
      :param parameters: `Dict` or `pd.Series` of reference parameters vector



.. py:class:: Tensor(data, indexes, *args, **kwargs)

   Bases: :py:obj:`object`


   .. py:attribute:: _data


   .. py:attribute:: complementary_indexes


   .. py:attribute:: _i


   .. py:attribute:: _j


   .. py:attribute:: _k


   .. py:method:: build_index_dict(index_names)


   .. py:method:: slice_by(slicer, value)

      Returns a slice of the tensor along a value on a specific index

      :param slicer:
      :type slicer: str or pandas.Index
      :param value:
      :return:



   .. py:method:: get_slice_index(slicer)

      Utility function for getting the integer number of the index (0,1, or 2)

      :param slicer:
      :return:



   .. py:method:: mean(slicer, *args, **kwargs)

      Flatten using the mean along an index

      :param slicer:
      :param args:
      :param kwargs:
      :return:



   .. py:method:: std(slicer, *args, **kwargs)

      Flatten using the standard deviation along an index
      :param slicer:
      :param args:
      :param kwargs:
      :return:



   .. py:method:: quantile(slicer, quantile, *args, **kwargs)

      Flatten using the standard deviation along an index
      :param slicer:
      :param args:
      :param kwargs:
      :return:



   .. py:method:: make_df(data, index1, index2)


.. py:data:: SPLIT
   :value: 'split'


   Item types 


.. py:data:: NET
   :value: 'net'


.. py:function:: get_reversible_fluxes(net_fluxes, displacements, reactions)

   :param net_fluxes: dict of net-fluxes
   :param displacements: dict of displacements for reversible reactions
   :param reactions: list of reaction names
   :return:


.. py:class:: ConcentrationControlFunction(model, reduced_stoichometry, independent_elasticity_function, dependent_elasticity_function, parameter_elasticity_function, volume_ratio_function, conservation_relation, independent_variable_ix, dependent_variable_ix, mca_type=NET, displacement_function=None)

   .. py:attribute:: model


   .. py:attribute:: reduced_stoichometry


   .. py:attribute:: dependent_elasticity_function


   .. py:attribute:: independent_elasticity_function


   .. py:attribute:: parameter_elasticity_function


   .. py:attribute:: independent_variable_ix


   .. py:attribute:: dependent_variable_ix


   .. py:attribute:: conservation_relation


   .. py:attribute:: volume_ratio_function


   .. py:attribute:: displacement_function
      :value: None



   .. py:attribute:: mca_type
      :value: 'net'



   .. py:method:: __call__(flux_dict, concentration_dict, parameter_population)


.. py:class:: Tensor(data, indexes, *args, **kwargs)

   Bases: :py:obj:`object`


   .. py:attribute:: _data


   .. py:attribute:: complementary_indexes


   .. py:attribute:: _i


   .. py:attribute:: _j


   .. py:attribute:: _k


   .. py:method:: build_index_dict(index_names)


   .. py:method:: slice_by(slicer, value)

      Returns a slice of the tensor along a value on a specific index

      :param slicer:
      :type slicer: str or pandas.Index
      :param value:
      :return:



   .. py:method:: get_slice_index(slicer)

      Utility function for getting the integer number of the index (0,1, or 2)

      :param slicer:
      :return:



   .. py:method:: mean(slicer, *args, **kwargs)

      Flatten using the mean along an index

      :param slicer:
      :param args:
      :param kwargs:
      :return:



   .. py:method:: std(slicer, *args, **kwargs)

      Flatten using the standard deviation along an index
      :param slicer:
      :param args:
      :param kwargs:
      :return:



   .. py:method:: quantile(slicer, quantile, *args, **kwargs)

      Flatten using the standard deviation along an index
      :param slicer:
      :param args:
      :param kwargs:
      :return:



   .. py:method:: make_df(data, index1, index2)


.. py:data:: SPLIT
   :value: 'split'


   Item types 


.. py:data:: NET
   :value: 'net'


.. py:class:: FluxControlFunction(model, reduced_stoichometry, independent_elasticity_function, dependent_elasticity_function, parameter_elasticity_function, conservation_relation, independent_variable_ix, dependent_variable_ix, concentration_control_fun, mca_type=NET)

   .. py:attribute:: model


   .. py:attribute:: reduced_stoichometry


   .. py:attribute:: dependent_elasticity_function


   .. py:attribute:: independent_elasticity_function


   .. py:attribute:: parameter_elasticity_function


   .. py:attribute:: independent_variable_ix


   .. py:attribute:: dependent_variable_ix


   .. py:attribute:: conservation_relation


   .. py:attribute:: concentration_control_fun


   .. py:attribute:: mca_type
      :value: 'net'



   .. py:method:: __call__(flux_dict, concentration_dict, parameter_population)