BioSANS2020.model.fileconvert.convtopotosbml¶

Functions¶

BioSANS2020.model.fileconvert.convtopotosbml.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_compdictionary 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_valsdictioary 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]}

concdictionary of initial concentration i.e.

conc = {‘A’: 100.0, ‘B’: 90.0, ‘C’: 80}

r_reactdictionary 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_prodsdictionary 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