:py:mod:`BioSANS2020.propagation.create_wxmaxima_command`
=========================================================

.. py:module:: BioSANS2020.propagation.create_wxmaxima_command

.. autoapi-nested-parse::

               This module is the create_wxmaxima_command module

   This module attempts to transforms topology file into wxmaxima ODE input
   that a user can copy and paste into wxmaxima to grab a symbolic solution




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


Functions
~~~~~~~~~

.. autoapisummary::

   BioSANS2020.propagation.create_wxmaxima_command.prepare_ffrrint
   BioSANS2020.propagation.create_wxmaxima_command.prepare_dict1
   BioSANS2020.propagation.create_wxmaxima_command.prepare_list1
   BioSANS2020.propagation.create_wxmaxima_command.prepare_list2
   BioSANS2020.propagation.create_wxmaxima_command.for_wxmaxima



.. py:function:: prepare_ffrrint(items)

   This function instantiate how the output will be printed by crea-
   thing the function ffprint

   Args:
       text (Text): text area where the outputs are written
       items (tuple): 3 item list of (canvas, scroll_x, scroll_y)

   Returns:
       function: either print in console or in text area


.. py:function:: prepare_dict1(sp_comp)

   This function prepares cs_var, cso_var, time

   Args:
       sp_comp (dict): dictionary of components position in reaction

   Returns:
       multitype: cs_var, cso_var, time


.. py:function:: prepare_list1(ks_dict)

   This function prepares a list of symbol for rate constant

   Args:
       ks_dict (dict): dictionary of rate constant positions

   Returns:
       list: rate constants symbols


.. py:function:: prepare_list2(stch_var, slabels)

   This function prepares two list from stoichiometric matrix

   Args:
       stch_var (np.ndarray): toichiometric matrix

   Returns:
       list: [non zero row values of  stch_var,
           nonzero rows index of stch_var]


.. py:function:: for_wxmaxima(sp_comp, ks_dict, conc, r_dict, p_dict, stch_var, items=None, rfile='')

   This function  transforms topology file  into wxmaxima  ODE input
   that a user can copy and paste into wxmaxima to grab a symbolic
   solution.

   Args:
       sp_comp (dict): dictionary of appearance or position of species
           or component in the reaction tag of BioSANS topology file.

           For example;

               #REACTIONS
               A => B, -kf1    # negative means to be estimated
               B => C, kf2

           The value of sp_comp is

               sp_comp = {'A': {0}, 'B': {0, 1}, 'C': {1}}

               A appears in first reaction with index 0
               B appears in first and second reaction with index 0, 1
               C appears in second reaction with index 1
       ks_dict (dict): dictionary of rate constant that appears in each
           reactions.

           For example;

               #REACTIONS
               A => B , 0.3        # first reaction
               B <=> C, 0.1, 0.2   # second reaction

           The value of ks_dict is

               ks_dict = {
                   0 : [0.3],      # first reaction
                   1 : [0.1, 0.2]  # second reaction
               }
       conc (dict): dictionary of initial concentration.

           For example;

               {'A': 100.0, 'B': -1.0, 'C': 0.0}
               negative means unknown or for estimation
       r_dict (dict): dictionary of reactant stoichiometry. For example

           r_dict = {
               0: {'A': 1},  # first reaction, coefficient of A is 1
               1: {'B': 1}   # second reaction, coefficient of B is 1
           }
       p_dict (dict): dictionary of product stoichiometry. For example

           p_dict = {
               0: {'B': 1},  # first reaction, coefficient of B is 1
               1: {'C': 1}   # second reaction, coefficient of C is 1
           }
       stch_var (numpy.ndarray): stoichiometric matrix. For example

           v_stoich = np.array([
               [   -1,           0   ]            # species A
               [    1,          -1   ]            # species B
               [    0,           1   ]            # species C
                 #1st rxn    2nd rxn
           ])
       items (list): list of [canvas, scroll_x, scroll_y]
       rfile (string, optional): name of topology file where some
           parameters or components are negative indicating  they  have
           to be estimated. Defaults to None.

   Returns:
       list: [0, 0] - contains nothing