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#
# @file multi_example3.cs
# @brief multi create example
# @author Sarah Keating
# @author Frank Bergmann
#
# <!--------------------------------------------------------------------------
# This file is part of libSBML. Please visit http://sbml.org for more
# information about SBML, and the latest version of libSBML.
#
# Copyright (C) 2009-2013 jointly by the following organizations:
# 1. California Institute of Technology, Pasadena, CA, USA
# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
#
# Copyright (C) 2006-2008 by the California Institute of Technology,
# Pasadena, CA, USA
#
# Copyright (C) 2002-2005 jointly by the following organizations:
# 1. California Institute of Technology, Pasadena, CA, USA
# 2. Japan Science and Technology Agency, Japan
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation. A copy of the license agreement is provided
# in the file named "LICENSE.txt" included with this software distribution
# and also available online as http://sbml.org/software/libsbml/license.html
# ------------------------------------------------------------------------ -->
#
#
from libsbml import *
sbmlns = SBMLNamespaces(3,1,"multi",1)
# create the document
document = SBMLDocument(sbmlns)
# set the required attribute to True
docPlug = document.getPlugin("multi")
docPlug.setRequired(True)
# create the Model
model=document.createModel()
# create the compartments
c = model.createCompartment()
c.setId("membrane")
c.setConstant(True)
# set the multi attribute isType via the compartmentPlugin
compPlug = c.getPlugin("multi")
compPlug.setIsType(True)
# create the speciesTypes
modelPlug = model.getPlugin("multi")
st = modelPlug.createMultiSpeciesType()
st.setId("stX")
st.setCompartment("membrane")
# create species
s = model.createSpecies()
s.setId("s1")
s.setCompartment("membrane")
s.setBoundaryCondition(False)
s.setHasOnlySubstanceUnits(False)
s.setConstant(False)
# set the multi attribute speciesType via the compartmentPlugin
spPlug = s.getPlugin("multi")
spPlug.setSpeciesType("stX")
# create species feature
sf = spPlug.createSpeciesFeature()
sf.setSpeciesFeatureType("a")
sf.setOccur(1)
sf.setComponent("b")
sfv = sf.createSpeciesFeatureValue()
sfv.setValue("c")
# create a subListOfSpeciesFeatures
subloSF = spPlug.createSubListOfSpeciesFeatures()
subloSF.setRelation(Relation_fromString("and"))
# add speciesFeatures to the subList
sf1 = SpeciesFeature(3, 1, 1)
sf1.setSpeciesFeatureType("a1")
sf1.setOccur(1)
sf1.setComponent("b1")
sfv1 = sf1.createSpeciesFeatureValue()
sfv1.setValue("c1")
subloSF.appendAndOwn(sf1)
sf1 = SpeciesFeature(3, 1, 1)
sf1.setSpeciesFeatureType("a2")
sf1.setOccur(1)
sf1.setComponent("b2")
sfv1 = sf1.createSpeciesFeatureValue()
sfv1.setValue("c2")
subloSF.appendAndOwn(sf1)
# create a second subListOfSpeciesfeatures
subloSF = spPlug.createSubListOfSpeciesFeatures()
subloSF.setRelation(Relation_fromString("or"))
sf1 = SpeciesFeature(3, 1, 1)
sf1.setSpeciesFeatureType("a3")
sf1.setOccur(1)
sf1.setComponent("b3")
sfv1 = sf1.createSpeciesFeatureValue()
sfv1.setValue("c3")
subloSF.appendAndOwn(sf1)
sf1 = SpeciesFeature(3, 1, 1)
sf1.setSpeciesFeatureType("a4")
sf1.setOccur(1)
sf1.setComponent("b4")
sfv1 = sf1.createSpeciesFeatureValue()
sfv1.setValue("c4")
subloSF.appendAndOwn(sf1)
writeSBML(document,"multi_example3.xml")
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