# 
# @file    multi_example1.py
# @brief   multi create example
# @author  Sarah Keating
# @author  Frank Bergmann
# 
# <!--------------------------------------------------------------------------
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#     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
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# Copyright (C) 2006-2008 by the California Institute of Technology,
#     Pasadena, CA, USA 
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# Copyright (C) 2002-2005 jointly by the following organizations:
#     1. California Institute of Technology, Pasadena, CA, USA
#     2. Japan Science and Technology Agency, Japan
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# This library is free software; you can redistribute it and/or modify it
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# in the file named "LICENSE.txt" included with this software distribution
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# 

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")

