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#!/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
## of libSBML. This program uses the open-source MIT license, as follows:
##
## Copyright (c) 2013-2014 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.
##
## Permission is hereby granted, free of charge, to any person obtaining a
## copy of this software and associated documentation files (the "Software"),
## to deal in the Software without restriction, including without limitation
## the rights to use, copy, modify, merge, publish, distribute, sublicense,
## and/or sell copies of the Software, and to permit persons to whom the
## Software is furnished to do so, subject to the following conditions:
##
## The above copyright notice and this permission notice shall be included in
## all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
## DEALINGS IN THE SOFTWARE.
##
## Neither the name of the California Institute of Technology (Caltech), nor
## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
## of Heidelberg, nor the names of any contributors, may be used to endorse
## or promote products derived from this software without specific prior
## written permission.
## ------------------------------------------------------------------------ -->
import sys
import os.path
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("none");
i.setSign("negative");
i.setThresholdLevel(2);
i.setName("aa");
o = t.createOutput();
o.setId("wd");
o.setQualitativeSpecies("s1");
o.setTransitionEffect("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)
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