qual_example1.py

An example of creating a model using SBML Level 3 Qualitative Models.

#!/usr/bin/env python
##
## @file    qual_example1.py
## @brief   Qual Example
## @author  Sarah Keating
##
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
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## Copyright (c) 2013-2018 by the California Institute of Technology
## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
## and the University of Heidelberg (Germany), with support from the National
## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
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import sys
import os.path
import libsbml
from libsbml import *


def main (args):
    # Creates an SBMLNamespaces object with the given SBML level, version
    # package name, package version.
    sbmlns = SBMLNamespaces(3, 1, "qual", 1)

    # Creates an SBMLDocument object
    document = SBMLDocument(sbmlns)

    # mark qual as required
    document.setPackageRequired("qual", True)

    # create the Model
    model = document.createModel()

    # create the Compartment
    compartment = model.createCompartment()
    compartment.setId("c")
    compartment.setConstant(True)

    # Get a QualModelPlugin object plugged in the model object.
    mplugin = model.getPlugin("qual")

    # create the QualitativeSpecies
    qs = mplugin.createQualitativeSpecies()
    qs.setId("s1")
    qs.setCompartment("c")
    qs.setConstant(False)
    qs.setInitialLevel(1)
    qs.setMaxLevel(4)
    qs.setName("sss")

    # create the Transition
    t = mplugin.createTransition()
    t.setId("d")
    t.setSBOTerm(1)

    i = t.createInput()
    i.setId("RD")
    i.setQualitativeSpecies("s1")
    i.setTransitionEffect(INPUT_TRANSITION_EFFECT_NONE)
    i.setSign(INPUT_SIGN_NEGATIVE)
    i.setThresholdLevel(2)
    i.setName("aa")

    o = t.createOutput()
    o.setId("wd")
    o.setQualitativeSpecies("s1")
    o.setTransitionEffect(OUTPUT_TRANSITION_EFFECT_PRODUCTION)
    o.setOutputLevel(2)
    o.setName("aa")

    ft = t.createFunctionTerm()
    math = parseL3Formula("geq(s1, 2)")
    ft.setResultLevel(1)
    ft.setMath(math)

    dt = t.createDefaultTerm()
    dt.setResultLevel(2)

    writeSBML(document, "qual_example1.xml")


if __name__ == '__main__':
  main(sys.argv)