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#
# @file multi_example1.py
# @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)
c = model.createCompartment()
c.setId("inter_membrane")
c.setConstant(True)
# set the multi attribute isType via the compartmentPlugin
compPlug = c.getPlugin("multi")
compPlug.setIsType(True)
# create the compartmentReferences
compRef = compPlug.createCompartmentReference()
compRef.setId("m1")
compRef.setCompartment("membrane")
compRef = compPlug.createCompartmentReference()
compRef.setId("m2")
compRef.setCompartment("membrane")
# create the speciesTypes
modelPlug = model.getPlugin("multi")
st = modelPlug.createMultiSpeciesType()
st.setId("stX")
st.setCompartment("ct")
st = modelPlug.createMultiSpeciesType()
st.setId("stXXcis")
st.setCompartment("ct")
# create speciesTypeInstances
sti = st.createSpeciesTypeInstance()
sti.setId("stiX1")
sti.setSpeciesType("stX")
sti = st.createSpeciesTypeInstance()
sti.setId("stiX2")
sti.setSpeciesType("stX")
# create speciesTypeBond
istb = st.createInSpeciesTypeBond()
istb.setBindingSite1("stiX1")
istb.setBindingSite2("stiX2")
# another speciesType
st = modelPlug.createMultiSpeciesType()
st.setId("stXXtrans")
st.setCompartment("cct")
# create speciesTypeInstances
sti = st.createSpeciesTypeInstance()
sti.setId("stiX1")
sti.setSpeciesType("stX")
sti.setCompartmentReference("cr1")
sti = st.createSpeciesTypeInstance()
sti.setId("stiX2")
sti.setSpeciesType("stX")
sti.setCompartmentReference("cr2")
# create speciesTypeBond
istb = st.createInSpeciesTypeBond()
istb.setBindingSite1("stiX1")
istb.setBindingSite2("stiX2")
writeSBML(document,"multi_example1.xml")
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