Location: Kraeutler_Logic_Models @ 3658dba9638e / python_cellml_text / write_cellml_script.py

Author:

Shelley Fong <s.fong@auckland.ac.nz>

Date:

2021-12-16 14:03:37+13:00

Desc:

Init

Permanent Source URI:

http://models.cellml.org/workspace/7e8/rawfile/3658dba9638e60010e18bef5e63e81168427d9d8/python_cellml_text/write_cellml_script.py

import csv

def read_IDs(path):
    data = []
    with open(path,'r') as f:
        reader = csv.reader(f)
        for row in reader:
            data.append(row[0])
        f.close()
    return data

Knames = read_IDs('..\\data\\Kname.txt')
rxnID = read_IDs('..\\data\\rxnID.txt')
rxnID_act = read_IDs('..\\data\\rxnID_act.txt')
rxnID_inh = read_IDs('..\\data\\rxnID_inh.txt')

with open('cellmlscript_temp.txt','w') as c:

    for name in rxnID:
        c.write('def import using "kraetler_functions.cellml" for\n\
    comp f_%s_module using comp f_module;\n\
    enddef;\n' %(name))
        
    for name in Knames:
        c.write('var %s: mM {init: 0, pub: out};\n' %name)
        
    for name in Knames:
        c.write('var tau_%s: second {init: 0, pub: out};\n' %name)
        
    for rx in rxnID:
        c.write('var EC50_%s: dimensionless {init: 0.5, pub: out};\n' %rx)
    for rx in rxnID:
        c.write('var W_%s: dimensionless {init: 1, pub: out};\n' %rx)

    for rx in rxnID_act:
        c.write('var f_act_%s: dimensionless {pub: in};\n' %rx)
    for rx in rxnID_inh:
        c.write('var f_inh_%s: dimensionless {pub: in};\n' %rx)

    for name in Knames:
        c.write('ode(%s, time) = (ppp)/tau_%s;\n' %(name, name))

    for rx in rxnID_act:
        reactant_name = rx.split('_')[0]
        c.write('    def map between env and f_%s_module for\n\
        vars W_%s and W;\n\
        vars n and n;\n\
        vars EC50_%s and EC50;\n\
        vars %s and X;\n\
        vars f_act_%s and f_act;\n\
    enddef;\n' %(rx,rx,rx,reactant_name,rx))
    for rx in rxnID_inh:
        reactant_name = rx.split('_')[0]
        c.write('    def map between env and f_%s_module for\n\
        vars W_%s and W;\n\
        vars n and n;\n\
        vars EC50_%s and EC50;\n\
        vars %s and X;\n\
        vars f_inh_%s and f_inhib;\n\
    enddef;\n' %(rx,rx,rx,reactant_name,rx))