:py:mod:`BioSANS2020.propagation.deterministic.ode_int`
=======================================================

.. py:module:: BioSANS2020.propagation.deterministic.ode_int

.. autoapi-nested-parse::

                     This module in the ode_int module

   This module uses the odeint integrator in python to propagate ODE trajec
   tory.



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


Functions
~~~~~~~~~

.. autoapisummary::

   BioSANS2020.propagation.deterministic.ode_int.ode_model
   BioSANS2020.propagation.deterministic.ode_int.ode_int



.. py:function:: ode_model(zlist, tvar, sp_comp, ks_dict, r_dict, p_dict, stch_var, molar=False)

   This function returns dx/dt where x are the components or species
   and t is time.

   Args:
       zlist (list): list of components or species amounts
       tvar (list): time stamp of trajectories i.e. [0, 0.1, 0.2, ...]
       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 appear 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
               }
       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 (np.ndarray): stoichiometric matrix
       molar : True if conc. is in molar else False

   Returns:
       np.ndarray: dx/dt where x are the components and t is time


.. py:function:: ode_int(conc, tvar, sp_comp, ks_dict, r_dict, p_dict, stch_var, molar=False, rfile='')

   This function returns the inetegration result of odeint

   Args:
       conc (dict): dictionary of initial concentration.

           For example;

               {'A': 100.0, 'B': -1.0, 'C': 0.0}
               negative means unknown or for estimation
       tvar (list): time stamp of trajectories i.e. [0, 0.1, 0.2, ...]
       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 appear 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
               }
       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
           }
       stoch_var (numpy.ndarray): stoichiometric matrix. For example

           stoch_var = np.array([
               [   -1,           0    ]            # species A
               [    1,          -1    ]            # species B
               [    0,           1    ]            # species C
                 #1st rxn    2nd rxn
           ])
       molar (bool, optional): If True, the units for any amount is in
           molar. Propensity will be macroscopic. Defaults to False.
       rfile (str): file name of BioSANS topology file.

   Returns:
       np.ndarray: trajectories