skimpy.core.modifiers
=====================

.. py:module:: skimpy.core.modifiers

.. 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.modifiers.ExpressionModifier
   skimpy.core.modifiers.BoundaryCondition
   skimpy.core.modifiers.ConstantConcentration
   skimpy.core.modifiers.AdditiveConcentrationRate
   skimpy.core.modifiers.BoundaryFlux
   skimpy.core.modifiers.FirstOrderSmallMoleculeModifier
   skimpy.core.modifiers.DisplacementSmallMoleculeModifier
   skimpy.core.modifiers.ActivationModifier
   skimpy.core.modifiers.InhibitionModifier
   skimpy.core.modifiers.HillActivationModifier
   skimpy.core.modifiers.SimpleHillActivationModifier
   skimpy.core.modifiers.HillInhibitionModifier


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

.. py:class:: ExpressionModifier(name, reaction=None, modifier=None)

   Bases: :py:obj:`object`


   This class describes a modifier to an expression, like a boundary condition
   or constraint.
   For example, changing a rate to a constant (boundary condition), or linking
   it to another variable of the model (constraint).
   It accepts as an argument a modifier.

   A modifier is a function which will look at all your expressions, and
   apply its transformation to them. As a result, its arguments have to be a
   TabDict of expressions, such as KinModel.ODEFun.expressions


   .. py:attribute:: prefix
      :value: 'MOD'



   .. py:attribute:: _name


   .. py:attribute:: _reaction
      :value: None



   .. py:method:: __call__(expressions)


   .. py:property:: modifier


   .. py:method:: link(model)

      Link the modifier to a model, to gain awareness of the inner/outer
      variables
      :param model:
      :return:



   .. py:property:: name


.. py:class:: BoundaryCondition(name, modifier=None, reaction=None)

   Bases: :py:obj:`ExpressionModifier`


   We differentiate boundary conditions as modifiers that define the boundaries
   of the observed system.


   .. py:attribute:: prefix
      :value: 'BC'



.. py:class:: ConstantConcentration(reactant, name=None, reaction=None)

   Bases: :py:obj:`BoundaryCondition`


       


   .. py:attribute:: prefix
      :value: 'CC'



   .. py:attribute:: reactant


   .. py:method:: modifier(expressions)

      Set the rate to 0
      :param expressions:
      :return:



   .. py:method:: __del__()


.. py:class:: AdditiveConcentrationRate(reactant, flux_value, name=None, reaction=None)

   Bases: :py:obj:`ExpressionModifier`


   Add a concentration rate term to your rate expression


   .. py:attribute:: prefix
      :value: 'ADDCR'



   .. py:attribute:: reactant


   .. py:attribute:: flux_value


   .. py:method:: modifier(expressions)

      Add to the rate expression
      :param expressions:
      :return:



.. py:class:: BoundaryFlux(reactant, flux_value, reaction=None)

   Bases: :py:obj:`BoundaryCondition`, :py:obj:`AdditiveConcentrationRate`


   We differentiate boundary conditions as modifiers that define the boundaries
   of the observed system.


   .. py:attribute:: prefix
      :value: 'BF'



   .. py:method:: check_dependency(expression)


.. py:class:: FirstOrderSmallMoleculeModifier(small_molecule, mechanism_stoichiometry, name=None, reaction=None)

   Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism`, :py:obj:`ExpressionModifier`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: prefix
      :value: 'HSM'



   .. py:attribute:: Reactants

      Class to define metabolites and their roles in the reaction
      :return:



   .. py:attribute:: Parameters

      Class to define parameters and their roles in the reaction
      :return:



   .. py:attribute:: parameter_reactant_links


   .. py:method:: modifier(expressions)

      change the flux reaction rate expressions
      :param expression: {vnet, vfwd, vbwd}
      :return:



   .. py:method:: get_qssa_rate_expression()


   .. py:method:: update_qssa_rate_expression()


   .. py:method:: get_full_rate_expression()
      :abstractmethod:



   .. py:method:: calculate_rate_constants()
      :abstractmethod:



.. py:class:: DisplacementSmallMoleculeModifier(small_molecule, mechanism_stoichiometry, name=None, reaction=None)

   Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism`, :py:obj:`ExpressionModifier`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: prefix
      :value: 'DSM'



   .. py:attribute:: Reactants

      Class to define metabolites and their roles in the reaction
      :return:



   .. py:attribute:: Parameters

      Class to define parameters and their roles in the reaction
      :return:



   .. py:attribute:: parameter_reactant_links


   .. py:method:: modifier(expressions)

      change the flux reaction rate expressions
      :param expression: {vnet, vfwd, vbwd}
      :return:



   .. py:method:: get_qssa_rate_expression()


   .. py:method:: update_qssa_rate_expression()


   .. py:method:: get_full_rate_expression()
      :abstractmethod:



   .. py:method:: calculate_rate_constants()
      :abstractmethod:



.. py:class:: ActivationModifier(activator, name=None, k_activation=None, reaction=None)

   Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism`, :py:obj:`ExpressionModifier`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: prefix
      :value: 'AM'



   .. py:attribute:: Reactants

      Class to define metabolites and their roles in the reaction
      :return:



   .. py:attribute:: Parameters

      Class to define parameters and their roles in the reaction
      :return:



   .. py:attribute:: parameter_reactant_links


   .. py:attribute:: reactant_stoichiometry


   .. py:method:: modifier(expressions)

      change the flux reaction rate expressions
      :param expression: {vnet, vfwd, vbwd}
      :return:



   .. py:method:: get_qssa_rate_expression()


   .. py:method:: update_qssa_rate_expression()


   .. py:method:: get_full_rate_expression()
      :abstractmethod:



   .. py:method:: calculate_rate_constants()
      :abstractmethod:



.. py:class:: InhibitionModifier(inhibitor, name=None, k_inhibition=None, reaction=None)

   Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism`, :py:obj:`ExpressionModifier`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: prefix
      :value: 'IM'



   .. py:attribute:: Reactants

      Class to define metabolites and their roles in the reaction
      :return:



   .. py:attribute:: Parameters

      Class to define parameters and their roles in the reaction
      :return:



   .. py:attribute:: parameter_reactant_links


   .. py:attribute:: reactant_stoichiometry


   .. py:method:: modifier(expressions)

      change the flux reaction rate expressions
      :param expression: {vnet, vfwd, vbwd}
      :return:



   .. py:method:: get_qssa_rate_expression()


   .. py:method:: update_qssa_rate_expression()


   .. py:method:: get_full_rate_expression()
      :abstractmethod:



   .. py:method:: calculate_rate_constants()
      :abstractmethod:



.. py:class:: HillActivationModifier(activator, name=None, k_activation=None, a_max=None, hill_coefficient=None, reaction=None)

   Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism`, :py:obj:`ExpressionModifier`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: prefix
      :value: 'HAM'



   .. py:attribute:: Reactants

      Class to define metabolites and their roles in the reaction
      :return:



   .. py:attribute:: Parameters

      Class to define parameters and their roles in the reaction
      :return:



   .. py:attribute:: parameter_reactant_links


   .. py:attribute:: reactant_stoichiometry


   .. py:method:: modifier(expressions)

      change the flux reaction rate expressions
      :param expression: {vnet, vfwd, vbwd}
      :return:



   .. py:method:: get_qssa_rate_expression()


   .. py:method:: update_qssa_rate_expression()


   .. py:method:: get_full_rate_expression()
      :abstractmethod:



   .. py:method:: calculate_rate_constants()
      :abstractmethod:



.. py:class:: SimpleHillActivationModifier(activator, name=None, k_activation=None, a_max=None, hill_coefficient=None, reaction=None)

   Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism`, :py:obj:`ExpressionModifier`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: prefix
      :value: 'SHAM'



   .. py:attribute:: Reactants

      Class to define metabolites and their roles in the reaction
      :return:



   .. py:attribute:: Parameters

      Class to define parameters and their roles in the reaction
      :return:



   .. py:attribute:: parameter_reactant_links


   .. py:attribute:: reactant_stoichiometry


   .. py:method:: modifier(expressions)

      change the flux reaction rate expressions
      :param expression: {vnet, vfwd, vbwd}
      :return:



   .. py:method:: get_qssa_rate_expression()


   .. py:method:: update_qssa_rate_expression()


   .. py:method:: get_full_rate_expression()
      :abstractmethod:



   .. py:method:: calculate_rate_constants()
      :abstractmethod:



.. py:class:: HillInhibitionModifier(inhibitor, name=None, k_inhibition=None, hill_coefficient=None, reaction=None)

   Bases: :py:obj:`skimpy.mechanisms.mechanism.KineticMechanism`, :py:obj:`ExpressionModifier`


   Helper class that provides a standard way to create an ABC using
   inheritance.


   .. py:attribute:: prefix
      :value: 'HIM'



   .. py:attribute:: Reactants

      Class to define metabolites and their roles in the reaction
      :return:



   .. py:attribute:: Parameters

      Class to define parameters and their roles in the reaction
      :return:



   .. py:attribute:: parameter_reactant_links


   .. py:attribute:: reactant_stoichiometry


   .. py:method:: modifier(expressions)

      change the flux reaction rate expressions
      :param expression: {vnet, vfwd, vbwd}
      :return:



   .. py:method:: get_qssa_rate_expression()


   .. py:method:: update_qssa_rate_expression()


   .. py:method:: get_full_rate_expression()
      :abstractmethod:



   .. py:method:: calculate_rate_constants()
      :abstractmethod: