skultrafast.kinetic_model
=========================

.. py:module:: skultrafast.kinetic_model

.. autoapi-nested-parse::

   This module helps to build a transfer matrix and applying it to an
   DAS.



Classes
-------

.. autoapisummary::

   skultrafast.kinetic_model.Transition
   skultrafast.kinetic_model.Model


Functions
---------

.. autoapisummary::

   skultrafast.kinetic_model.get_comparments
   skultrafast.kinetic_model.get_symbols


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

.. py:class:: Transition(from_comp, to_comp, rate=None, qy=None)

   Bases: :py:obj:`object`


   Represents a transtion between comparments.


   .. py:attribute:: from_comp


   .. py:attribute:: to_comp


   .. py:attribute:: qu_yield
      :value: None



.. py:class:: Model

   Bases: :py:obj:`object`


   Helper class to make a model


   .. py:attribute:: transitions
      :type:  List[Transition]
      :value: []



   .. py:method:: add_transition(from_comp, to_comp, rate=None, qy=None)

      Adds an transition to the model.

      :param from_comp: Start of the transition
      :type from_comp: str
      :param to_comp: Target of the transition
      :type to_comp: str
      :param rate: Name of the associated rate, by default None, which generates a
                   default name.
      :type rate: str, optional
      :param qy: The yield of the transition, by default 1
      :type qy: str of float, optional



   .. py:method:: build_matrix()

      Builds the n x n k-matrix as a symbolic representation (list of lists of tuples).
      Each entry contains a list of (coefficient, rate_name, yield_value) tuples.



   .. py:method:: build_mat_func()

      Creates a function that builds the K matrix from parameter values.
      Uses fully vectorized numpy operations for maximum speed.



   .. py:method:: get_compartments()


   .. py:method:: make_diff_equation()

      Creates a representation of the differential equations.
      Note: Full symbolic differential equation support removed with sympy dependency.



   .. py:method:: get_trans(y0, taus, t)

      Return the solution using vectorized matrix exponential computation.



.. py:function:: get_comparments(list_trans)

   Getting a list of transtions, return the compartments


.. py:function:: get_symbols(list_trans)

   Return the used symbols