booldog.continuous.ode_factory
==============================

.. py:module:: booldog.continuous.ode_factory


Attributes
----------

.. autoapisummary::

   booldog.continuous.ode_factory.logger
   booldog.continuous.ode_factory.ode_classes
   booldog.continuous.ode_factory.transforms


Classes
-------

.. autoapisummary::

   booldog.continuous.ode_factory.ODE
   booldog.continuous.ode_factory.BooleCubeODE
   booldog.continuous.ode_factory.SquadODE


Functions
---------

.. autoapisummary::

   booldog.continuous.ode_factory.ode_factory


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

.. py:data:: logger

.. py:function:: ode_factory(network, transform, **kwargs)

   Create a :py:class:`booldog.ode.ODE` from :py:class:`Network`.

   :param network: Input network.
   :type network: :py:class:`Network` or :py:class:`BooleanNetwork`
   :param transform: One of accepted transforms. See :py:data:`booldog.ode.transforms` or
                     :ref:`Notes <tagnotesode>` for options.
   :type transform: str

   :param \*\*kwargs: Additional arguments and keyword arguments passed to specific ODE class.

   :returns: **ode** -- A ODE system
   :rtype: :py:class:`booldog.ode.ODE`

   .. _tagnotesode:

   .. rubric:: Notes

   For specific transforms, see the relevant class for keyword
   arguments (`**kwargs`).

   The class per transform is defined in
   :py:data:`booldog.ode.ode_classes`.

   If the parameter is an int or float, the value is assigned for
   all variables. Otherwise the parameter argument should be a dict
   with keys as node names and values for their initial state. In
   this case, if the initial state is not defined for all nodes, a
   `default` key with the default value should also be present in the
   dict.

   Here follows a summary of the transform-specific keyword arguments

       'squad'

           - :py:class:`booldog.ode.SquadODE`
           - gamma : self-decay
           - h :  sigmoid gain

       'boolecube'

           - :py:class:`booldog.ode.BoolCubeODE`
           - tau : life-time of species

       'hillcube'

           - :py:class:`booldog.ode.BoolCubeODE`
           - tau : life-time of species
           - n : Hill coefficient
           - k : Hill dissociation constant

       'normalisedhillcube'

           - :py:class:`booldog.ode.BoolCubeODE`
           - tau : life-time of species
           - n : Hill coefficient
           - k : Hill dissociation constant


.. py:class:: ODE(network, transform)

   Generic ODE class produced by factory.

   Parent class is a variable, and defined by `transform` argument.


   .. py:attribute:: n


   .. py:attribute:: boolean_network


   .. py:attribute:: transform


   .. py:method:: event_function(t, x, event_t, *args)

      Event function for `events` of `scipy.integrate.solve_ivp`.

      :param t: Time-point of simulation
      :type t: float
      :param x:
      :type x: narray
      :param event_t: Time-point of event
      :type event_t: float
      :param \*args: ignored

      .. attribute:: terminal

         

         :type: True



   .. py:method:: update(off_nodes=None)

      Resets dxdt

      Shortcut to ODE class's `_get_system` method.

      :param off_nodes: List of node **indices** to set derivative to 0,
                        i.e. these nodes will remain constant in simulation.
      :type off_nodes: list of int, optional



.. py:class:: BooleCubeODE(network, transform, tau=1, n=3, k=0.5, **kwargs)

   Bases: :py:obj:`ODE`


   An ODE class.

   Use of multivariate polynomial interpolation for the transformation of a
    Boolean graph to a system of ODEs.

   .. attribute:: dxdt

      

      :type: function

   .. attribute:: param_tau

      life-time of species

      :type: arraylike

   .. attribute:: param_n

      Hill coefficient

      :type: arraylike

   .. attribute:: param_k

      Hill dissociation constant

      :type: arraylike

   .. attribute:: param_dict

      track parameters

      :type: dict


   .. py:attribute:: param_n


   .. py:attribute:: param_k


   .. py:attribute:: param_tau


   .. py:attribute:: param_dict


   .. py:attribute:: B1


   .. py:attribute:: dxdt


   .. py:method:: hill(x_array)


   .. py:method:: normalised_hill(x_array)


   .. py:method:: identity(x_array)


   .. py:method:: _get_system(off_nodes=None)


   .. py:method:: homologue_b1()

      Create function to calculate the multivariate polynomial
      interpolation of Boolean functions

      :returns: **B1**
      :rtype: function



   .. py:method:: write_c_code()


.. py:class:: SquadODE(network, transform, gamma=1, h=10, **kwargs)

   Bases: :py:obj:`ODE`


   An ODE parent class.

   Use of SQUAD for the transformation of a Boolean graph to a system of ODEs.

   .. attribute:: dxdt

      

      :type: function

   .. attribute:: param_gamma

      decay rate

      :type: arraylike

   .. attribute:: param_h

      sigmoidal gain

      :type: arraylike

   .. attribute:: activations

      activator matrix

      :type: arraylike

   .. attribute:: inhibitions

      inhibitor matrix

      :type: arraylike


   .. py:attribute:: param_gamma


   .. py:attribute:: param_h


   .. py:attribute:: _A1


   .. py:attribute:: _a1


   .. py:attribute:: _B1


   .. py:attribute:: _b1


   .. py:attribute:: dxdt


   .. py:method:: _omega(x)

      Equation (2) of Di Cara et al (2007)
      http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-462
      Based on Andre Blejec R code.



   .. py:method:: _dxdt_transform(x, w)

      Equation (2) of Di Cara et al (2007)



   .. py:method:: _get_system(off_nodes=[])


.. py:data:: ode_classes

   transform to ODE class translation

   :type: dict

.. py:data:: transforms

   list of accepted ODE transforms

   :type: set