# 
# @file    multi_example1.py
# @brief   multi create example
# @author  Sarah Keating
# @author  Frank Bergmann
# 
# <!--------------------------------------------------------------------------
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# Copyright (C) 2009-2013 jointly by the following organizations:
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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
# under the terms of the GNU Lesser General Public License as published by
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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"); 

