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#!/usr/bin/python3
##
## @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) 2013-2018 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.
##
## 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
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)
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