:py:mod:`BioSANS2020.model.fileconvert.convtopotosbml`
======================================================

.. py:module:: BioSANS2020.model.fileconvert.convtopotosbml

.. autoapi-nested-parse::

                This module is the convtopotosbml module

   The sole purpose of this module is to faciliate conversion of topology
   files into SBML files. Currently, this module still have a lot of
   problems and the converted file may not run properly.



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


Functions
~~~~~~~~~

.. autoapisummary::

   BioSANS2020.model.fileconvert.convtopotosbml.topo_to_sbml



.. py:function:: topo_to_sbml(sp_comp, ks_vals, conc, r_react, r_prods, vbig, v_volms, items=None, molar=False, rfile=None)

   This function helps in the conversion of topology file to SBML.
   Consider a file containing the following reaction topology;

       #REACTIONS
       A <=> B, 0.5, 0.3
       3 B => 2 C, 0.04

       @CONCENTRATION
       A, 100
       B, 90
       C, 80

   Args:
       sp_comp : dictionary of components where the key is the
                 component and the value is a set of integers that tell
                 the rank or order of that reaction as it appears in
                 the file. For the above topology
                 sp_comp = {'A': {0}, 'B': {0, 1}, 'C': {1}}
       ks_vals : dictioary of parameters where the key is the line in
                 the file and the value is the list of parameter found
                 i.e. for the above topology;
                 ks_vals = {0: [0.5, 0.3], 1: [0.04]}
       conc : dictionary of initial concentration i.e.
              conc = {'A': 100.0, 'B': 90.0, 'C': 80}
       r_react : dictionary where the key is the line in the file and
                 the value is a dictionary of reactants where the key
                 is the component and the value is its stoichiometric
                 coefficient in that line i.e. for the above topology;
                 r_react = {0: {'A': 1}, 1: {'B': 3}}
       r_prods : dictionary where the key is the line in the file and
                 the value is a dictionary of products where the key
                 is the component and the value is its stoichiometric
                 coefficient in that line i.e. for the above topology;
                 r_prods = {0: {'B': 1}, 1: {'C': 2}}
       vbig : not used but pertains to stoichiometric matrix
       v_volms : volume of compartment
       items : 3 item list of [canvas, scroll_x, scroll_y]
       molar : True if conc. is in molar otherwise False
       rfile : path of the topology file + name of topology file