#!/usr/bin/env python
## 
## @file    createExampleSBML.py
## @brief   Creates example SBML models presented in the SBML specification.
## @author  Akiya Jouraku
## @author  Michael Hucka
## @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) 2013-2016 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
from libsbml import *

#
# These variables are used in writeExampleSBML when writing an SBML
# document.  They are handed to libSBML functions in order to include
# the program information into comments within the SBML file.
#
ProgramName = "createExampleModels";
ProgramVersion = "1.0.0";

#
# The SBML Level and Version of the example SBML models.
#
Level = 2;
Version = 4;




#===============================================================================
#
#
# Functions for creating the Example SBML documents.
#
#
#===============================================================================


# 
# 
# Creates an SBML model represented in "7.1 A Simple example application of SBML"
# in the SBML Level 2 Version 4 Specification.
# 
# 

def createExampleEnzymaticReaction():
    level = Level;
    version = Version;

    #---------------------------------------------------------------------------
    #
    # Creates an SBMLDocument object 
    #
    #---------------------------------------------------------------------------

    sbmlDoc = SBMLDocument(level, version);

    #---------------------------------------------------------------------------
    #
    # Creates a Model object inside the SBMLDocument object. 
    #
    #---------------------------------------------------------------------------

    model = sbmlDoc.createModel();
    model.setId("EnzymaticReaction");

    #---------------------------------------------------------------------------
    #
    # Creates UnitDefinition objects inside the Model object.
    #
    #---------------------------------------------------------------------------
    
    #---------------------------------------------------------------------------  
    # (UnitDefinition1) Creates an UnitDefinition object ("per_second")
    #---------------------------------------------------------------------------

    unitdef = model.createUnitDefinition();
    unitdef.setId("per_second");

    #  Creates an Unit inside the UnitDefinition object 

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_SECOND);
    unit.setExponent(-1);

    #--------------------------------------------------------------------------------
    # (UnitDefinition2) Creates an UnitDefinition object ("litre_per_mole_per_second") 
    #--------------------------------------------------------------------------------

    # Note that we can reuse the pointers 'unitdef' and 'unit' because the
    # actual UnitDefinition object (along with the Unit objects within it)
    # is already attached to the Model object.

    unitdef = model.createUnitDefinition();
    unitdef.setId("litre_per_mole_per_second");

    #  Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_MOLE);
    unit.setExponent(-1);

    #  Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_LITRE);
    unit.setExponent(1);

    #  Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_SECOND);
    unit.setExponent(-1);


    #---------------------------------------------------------------------------
    #
    # Creates a Compartment object inside the Model object. 
    #
    #---------------------------------------------------------------------------

    compName = "cytosol";

    # Creates a Compartment object ("cytosol")

    comp = model.createCompartment();
    comp.setId(compName);

    # Sets the "size" attribute of the Compartment object.
    #
    # We are not setting the units on the compartment size explicitly, so
    # the units of this Compartment object will be the default SBML units of
    # volume, which are liters.
    #
    comp.setSize(1e-14);


    #---------------------------------------------------------------------------
    #
    # Creates Species objects inside the Model object. 
    #
    #---------------------------------------------------------------------------
    
    #---------------------------------------------------------------------------
    # (Species1) Creates a Species object ("ES")
    #---------------------------------------------------------------------------

    # Create the Species objects inside the Model object. 

    sp = model.createSpecies();
    sp.setId("ES");
    sp.setName("ES");

    # Sets the "compartment" attribute of the Species object to identify the 
    # compartment in which the Species object is located.

    sp.setCompartment(compName);

    # Sets the "initialAmount" attribute of the Species object.
    #
    #  In SBML, the units of a Species object's initial quantity are
    #  determined by two attributes, "substanceUnits" and
    #  "hasOnlySubstanceUnits", and the "spatialDimensions" attribute
    #  of the Compartment object ("cytosol") in which the species
    #  object is located.  Here, we are using the default values for
    #  "substanceUnits" (which is "mole") and "hasOnlySubstanceUnits"
    #  (which is "False").  The compartment in which the species is
    #  located uses volume units of liters, so the units of these
    #  species (when the species appear in numerical formulas in the
    #  model) will be moles/liters.  
    #
    sp.setInitialAmount(0);

    #---------------------------------------------------------------------------
    # (Species2) Creates a Species object ("P")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setCompartment(compName);
    sp.setId("P");
    sp.setName("P");
    sp.setInitialAmount(0);

    #---------------------------------------------------------------------------
    # (Species3) Creates a Species object ("S")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setCompartment(compName);
    sp.setId("S");
    sp.setName("S");
    sp.setInitialAmount(1e-20);

    #---------------------------------------------------------------------------
    # (Species4) Creates a Species object ("E")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setCompartment(compName);
    sp.setId("E");
    sp.setName("E");
    sp.setInitialAmount(5e-21);


    #---------------------------------------------------------------------------
    #
    # Creates Reaction objects inside the Model object. 
    #
    #---------------------------------------------------------------------------

    #---------------------------------------------------------------------------
    # (Reaction1) Creates a Reaction object ("veq").
    #---------------------------------------------------------------------------

    reaction = model.createReaction();
    reaction.setId("veq");

    # (Reactant1) Creates a Reactant object that references Species "E"
    # in the model.  The object will be created within the reaction in the
    # SBML <listOfReactants>.

    spr = reaction.createReactant();
    spr.setSpecies("E");

    # (Reactant2) Creates a Reactant object that references Species "S"
    # in the model.

    spr = reaction.createReactant();
    spr.setSpecies("S");

    #---------------------------------------------------------------------------
    # (Product1) Creates a Product object that references Species "ES" in
    # the model.
    #---------------------------------------------------------------------------

    spr = reaction.createProduct();
    spr.setSpecies("ES");

    #---------------------------------------------------------------------------
    # Creates a KineticLaw object inside the Reaction object ("veq"). 
    #---------------------------------------------------------------------------

    kl = reaction.createKineticLaw();

    #---------------------------------------------------------------------------
    # Creates an object which represents the following math of the
    # KineticLaw.
    #
    #      <math xmlns="http://www.w3.org/1998/Math/MathML">
    #        <apply>
    #          <times/>
    #          <ci> cytosol </ci>
    #          <apply>
    #            <minus/>
    #            <apply>
    #              <times/>
    #              <ci> kon </ci>
    #              <ci> E </ci>
    #              <ci> S </ci>
    #            </apply>
    #            <apply>
    #              <times/>
    #              <ci> koff </ci>
    #              <ci> ES </ci>
    #            </apply>
    #          </apply>
    #        </apply>
    #      </math>
    #
    #---------------------------------------------------------------------------

    #------------------------------------------
    #
    # create nodes representing the variables
    #
    #------------------------------------------

    astCytosol = ASTNode(AST_NAME);
    astCytosol.setName("cytosol");

    astKon = ASTNode(AST_NAME);
    astKon.setName("kon");

    astKoff = ASTNode(AST_NAME);
    astKoff.setName("koff");

    astE = ASTNode(AST_NAME);
    astE.setName("E");

    astS = ASTNode(AST_NAME);
    astS.setName("S");

    astES = ASTNode(AST_NAME);
    astES.setName("ES");


    #--------------------------------------------
    #
    # create node representing
    #            <apply>
    #              <times/>
    #              <ci> koff </ci>
    #              <ci> ES </ci>
    #            </apply>
    #
    #--------------------------------------------

    astTimes1 = ASTNode(AST_TIMES);
    astTimes1.addChild(astKoff);
    astTimes1.addChild(astES);

    #--------------------------------------------
    #
    # create node representing
    #            <apply>
    #              <times/>
    #              <ci> kon </ci>
    #              <ci> E </ci>
    #              <ci> S </ci>
    #            </apply>
    #
    #
    # (NOTES)
    #
    #  Since there is a restriction with an of "<times/>" operation
    #  such that the is a binary class and thus only two operands can
    #  be directly added, the following code in this comment block is invalid
    #  because the code directly adds three <ci> ASTNodes to <times/> ASTNode.
    #
    #    *astTimes = ASTNode(AST_TIMES);
    #    astTimes.addChild(astKon);
    #    astTimes.addChild(astE);
    #    astTimes.addChild(astS);
    #
    # The following valid code after this comment block creates the ASTNode
    # as a binary tree.
    #
    # Please see "Converting between ASTs and text strings" described
    # at http://sbml.org/Software/libSBML/docs/cpp-api/class_a_s_t_node.html
    # for the detailed information.
    #
    #--------------------------------------------

    astTimes2 = ASTNode(AST_TIMES);
    astTimes2.addChild(astE);
    astTimes2.addChild(astS);

    astTimes = ASTNode(AST_TIMES);
    astTimes.addChild(astKon);
    astTimes.addChild(astTimes2);

    #--------------------------------------------
    #
    # create node representing
    #          <apply>
    #            <minus/>
    #            <apply>
    #              <times/>
    #              <ci> kon </ci>
    #              <ci> E </ci>
    #              <ci> S </ci>
    #            </apply>
    #            <apply>
    #              <times/>
    #              <ci> koff </ci>
    #              <ci> ES </ci>
    #            </apply>
    #          </apply>
    #
    #--------------------------------------------

    astMinus = ASTNode(AST_MINUS);
    astMinus.addChild(astTimes);
    astMinus.addChild(astTimes1);


    #--------------------------------------------
    #
    # create node representing
    #        <apply>
    #          <times/>
    #          <ci> cytosol </ci>
    #          <apply>
    #            <minus/>
    #            <apply>
    #              <times/>
    #              <ci> kon </ci>
    #              <ci> E </ci>
    #              <ci> S </ci>
    #            </apply>
    #            <apply>
    #              <times/>
    #              <ci> koff </ci>
    #              <ci> ES </ci>
    #            </apply>
    #          </apply>
    #        </apply>
    #
    #--------------------------------------------

    astMath = ASTNode(AST_TIMES);
    astMath.addChild(astCytosol);
    astMath.addChild(astMinus);

    #---------------------------------------------
    #
    # set the Math element
    #
    #------------------------------------------------

    kl.setMath(astMath);


    #---------------------------------------------------------------------------
    # Creates local Parameter objects inside the KineticLaw object.
    #---------------------------------------------------------------------------

    # Creates a Parameter ("kon")

    para = kl.createParameter();
    para.setId("kon");
    para.setValue(1000000);
    para.setUnits("litre_per_mole_per_second");

    # Creates a Parameter ("koff")

    para = kl.createParameter();
    para.setId("koff");
    para.setValue(0.2);
    para.setUnits("per_second");


    #---------------------------------------------------------------------------
    # (Reaction2) Creates a Reaction object ("vcat") .
    #---------------------------------------------------------------------------

    reaction = model.createReaction();
    reaction.setId("vcat");
    reaction.setReversible(False);

    #---------------------------------------------------------------------------
    # Creates Reactant objects inside the Reaction object ("vcat"). 
    #---------------------------------------------------------------------------

    # (Reactant1) Creates a Reactant object that references Species "ES" in the
    # model.

    spr = reaction.createReactant();
    spr.setSpecies("ES");

    #---------------------------------------------------------------------------
    # Creates a Product object inside the Reaction object ("vcat"). 
    #---------------------------------------------------------------------------

    # (Product1) Creates a Product object that references Species "E" in the model.

    spr = reaction.createProduct();
    spr.setSpecies("E");

    # (Product2) Creates a Product object that references Species "P" in the model.

    spr = reaction.createProduct();
    spr.setSpecies("P");

    #---------------------------------------------------------------------------
    # Creates a KineticLaw object inside the Reaction object ("vcat"). 
    #---------------------------------------------------------------------------

    kl = reaction.createKineticLaw();

    #---------------------------------------------------------------------------
    # Sets a math (object) to the KineticLaw object.
    #---------------------------------------------------------------------------

    # To create mathematical expressions, one would typically construct
    # an tree as the above example code which creates a math of another
    # KineticLaw object.  Here, to save some space and illustrate another approach 
    # of doing it, we will write out the formula in MathML form and then use a 
    # libSBML convenience function to create the tree for us.  
    # (This is a bit dangerous; it's very easy to make mistakes when writing MathML 
    # by hand, so in a real program, we would not really want to do it this way.)

    mathXMLString = """<math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply>
        <times/>
        <ci> cytosol </ci>
        <ci> kcat </ci>
        <ci> ES </ci>
      </apply>
    </math>
	"""

    astMath = readMathMLFromString(mathXMLString);
    kl.setMath(astMath);


    #---------------------------------------------------------------------------
    # Creates local Parameter objects inside the KineticLaw object.
    #---------------------------------------------------------------------------

    # Creates a Parameter ("kcat")

    para = kl.createParameter();
    para.setId("kcat");
    para.setValue(0.1);
    para.setUnits("per_second");


    # Returns the created SBMLDocument object.
    # The returned object must be explicitly deleted by the caller,
    # otherwise a memory leak will happen.

    return sbmlDoc;

# 
# 
# Creates an SBML model represented in "7.2 Example involving units"
# in the SBML Level 2 Version 4 Specification.
# 
# 

def createExampleInvolvingUnits():
    level = Level;
    version = Version;

    #---------------------------------------------------------------------------
    #
    # Creates an SBMLDocument object 
    #
    #---------------------------------------------------------------------------

    sbmlDoc = SBMLDocument(level, version);

    # Adds the namespace for XHTML to the SBMLDocument object.  We need this
    # because we will add notes to the model.  (By default, the SBML document
    # created by SBMLDocument only declares the SBML XML namespace.)

    sbmlDoc.getNamespaces().add("http://www.w3.org/1999/xhtml", "xhtml");

    #---------------------------------------------------------------------------
    #
    # Creates a Model object inside the SBMLDocument object. 
    #
    #---------------------------------------------------------------------------

    model = sbmlDoc.createModel();
    model.setId("unitsExample");

    #---------------------------------------------------------------------------
    #
    # Creates UnitDefinition objects inside the Model object.
    #
    #---------------------------------------------------------------------------

    #---------------------------------------------------------------------------  
    # (UnitDefinition1) Creates an UnitDefinition object ("substance").
    #
    # This has the effect of redefining the default unit of subtance for the
    # whole model.
    #---------------------------------------------------------------------------

    unitdef = model.createUnitDefinition();
    unitdef.setId("substance");

    #  Creates an Unit inside the UnitDefinition object 

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_MOLE);
    unit.setScale(-3);

    #--------------------------------------------------------------------------------
    # (UnitDefinition2) Creates an UnitDefinition object ("mmls") 
    #--------------------------------------------------------------------------------

    # Note that we can reuse the pointers 'unitdef' and 'unit' because the
    # actual UnitDefinition object (along with the Unit objects within it)
    # is already attached to the Model object.

    unitdef = model.createUnitDefinition();
    unitdef.setId("mmls");

    #  Creates an Unit inside the UnitDefinition object ("mmls")

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_MOLE);
    unit.setScale(-3);

    #  Creates an Unit inside the UnitDefinition object ("mmls")

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_LITRE);
    unit.setExponent(-1);

    #  Creates an Unit inside the UnitDefinition object ("mmls")

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_SECOND);
    unit.setExponent(-1);

    #--------------------------------------------------------------------------------
    # (UnitDefinition3) Creates an UnitDefinition object ("mml") 
    #--------------------------------------------------------------------------------

    unitdef = model.createUnitDefinition();
    unitdef.setId("mml");

    #  Creates an Unit inside the UnitDefinition object ("mml")

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_MOLE);
    unit.setScale(-3);

    #  Creates an Unit inside the UnitDefinition object ("mml")

    unit = unitdef.createUnit();
    unit.setKind(UNIT_KIND_LITRE);
    unit.setExponent(-1);


    #---------------------------------------------------------------------------
    #
    # Creates a Compartment object inside the Model object. 
    #
    #---------------------------------------------------------------------------

    compName = "cell";

    # Creates a Compartment object ("cell")

    comp = model.createCompartment();
    comp.setId(compName);

    # Sets the "size" attribute of the Compartment object.
    #
    #   The units of this Compartment object is the default SBML 
    #   units of volume (litre), and thus we don't have to explicitly invoke 
    #   setUnits("litre") function to set the default units.
    #
    comp.setSize(1);


    #---------------------------------------------------------------------------
    #
    # Creates Species objects inside the Model object. 
    #
    #---------------------------------------------------------------------------

    
    #---------------------------------------------------------------------------
    # (Species1) Creates a Species object ("x0")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setId("x0");

    # Sets the "compartment" attribute of the Species object to identify the 
    # compartnet in which the Species object located.

    sp.setCompartment(compName);

    # Sets the "initialConcentration" attribute of the Species object.
    #
    #  The units of this Species object is determined by two attributes of this 
    #  Species object ("substanceUnits" and "hasOnlySubstanceUnits") and the
    #  "spatialDimensions" attribute of the Compartment object ("cytosol") in which 
    #  this species object is located.
    #  Since the default values are used for "substanceUnits" (substance (mole)) 
    #  and "hasOnlySubstanceUnits" (False) and the value of "spatialDimension" (3) 
    #  is greater than 0, the units of this Species object is  moles/liters . 
    #
    sp.setInitialConcentration(1);

    #---------------------------------------------------------------------------
    # (Species2) Creates a Species object ("x1")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setId("x1");
    sp.setCompartment(compName);
    sp.setInitialConcentration(1);

    #---------------------------------------------------------------------------
    # (Species3) Creates a Species object ("s1")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setCompartment(compName);
    sp.setId("s1");
    sp.setInitialConcentration(1);

    #---------------------------------------------------------------------------
    # (Species4) Creates a Species object ("s2")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setCompartment(compName);
    sp.setId("s2");
    sp.setInitialConcentration(1);

    #---------------------------------------------------------------------------
    #
    # Creates global Parameter objects inside the Model object. 
    #
    #---------------------------------------------------------------------------

    # Creates a Parameter ("vm")  

    para = model.createParameter();
    para.setId("vm");
    para.setValue(2);
    para.setUnits("mmls");

    # Creates a Parameter ("km")  

    para = model.createParameter();
    para.setId("km");
    para.setValue(2);
    para.setUnits("mml");


    #---------------------------------------------------------------------------
    #
    # Creates Reaction objects inside the Model object. 
    #
    #---------------------------------------------------------------------------

    #---------------------------------------------------------------------------
    # (Reaction1) Creates a Reaction object ("v1").
    #---------------------------------------------------------------------------

    reaction = model.createReaction();
    reaction.setId("v1");

    #---------------------------------------------------------------------------
    # Creates Reactant objects inside the Reaction object ("v1"). 
    #---------------------------------------------------------------------------

    # (Reactant1) Creates a Reactant object that references Species "x0"
    # in the model.

    spr = reaction.createReactant();
    spr.setSpecies("x0");

    #---------------------------------------------------------------------------
    # Creates a Product object inside the Reaction object ("v1"). 
    #---------------------------------------------------------------------------

    # Creates a Product object that references Species "s1" in the model. 

    spr = reaction.createProduct();
    spr.setSpecies("s1");

    #---------------------------------------------------------------------------
    # Creates a KineticLaw object inside the Reaction object ("v1"). 
    #---------------------------------------------------------------------------

    kl = reaction.createKineticLaw();

    # Creates a <notes> element in the KineticLaw object.
    # Here we illustrate how to do it using a literal string.  This requires
    # known the required syntax of XHTML and the requirements for SBML <notes>
    # elements.  Later below, we show how to create notes using objects instead
    # of strings.

    notesString = "<xhtml:p> ((vm * s1)/(km + s1)) * cell </xhtml:p>";
    kl.setNotes(notesString);

    #---------------------------------------------------------------------------
    # Creates an object which represents the following KineticLaw object.
    #
    #  <math xmlns="http://www.w3.org/1998/Math/MathML">
    #   <apply>
    #     <times/>
    #     <apply>
    #       <divide/>
    #       <apply>
    #         <times/>
    #           <ci> vm </ci>
    #           <ci> s1 </ci>
    #       </apply>
    #       <apply>
    #         <plus/>
    #           <ci> km </ci>
    #           <ci> s1 </ci>
    #       </apply>
    #     </apply>
    #     <ci> cell </ci>
    #    </apply>
    #  </math>
    #---------------------------------------------------------------------------

    #
    # In the following code, objects, which construct an tree 
    # of the above math, are created and added in the order of preorder traversal 
    # of the tree (i.e. the order corresponds to the nested structure of the above 
    # MathML elements), and thus the following code maybe a bit more efficient but 
    # maybe a bit difficult to read.
    #

    astMath = ASTNode(AST_TIMES);

    astMath.addChild(ASTNode(AST_DIVIDE));
    astDivide = astMath.getLeftChild();

    astDivide.addChild(ASTNode(AST_TIMES));
    astTimes = astDivide.getLeftChild();

    astTimes.addChild(ASTNode(AST_NAME));
    astTimes.getLeftChild().setName("vm");

    astTimes.addChild(ASTNode(AST_NAME));
    astTimes.getRightChild().setName("s1");

    astDivide.addChild(ASTNode(AST_PLUS));
    astPlus = astDivide.getRightChild();

    astPlus.addChild(ASTNode(AST_NAME));
    astPlus.getLeftChild().setName("km");

    astPlus.addChild(ASTNode(AST_NAME));
    astPlus.getRightChild().setName("s1");


    astMath.addChild(ASTNode(AST_NAME));
    astMath.getRightChild().setName("cell");

    #---------------------------------------------
    #
    # set the Math element
    #
    #------------------------------------------------

    kl.setMath(astMath);

    #---------------------------------------------------------------------------
    # (Reaction2) Creates a Reaction object ("v2").
    #---------------------------------------------------------------------------

    reaction = model.createReaction();
    reaction.setId("v2");

    #---------------------------------------------------------------------------
    # Creates Reactant objects inside the Reaction object ("v2"). 
    #---------------------------------------------------------------------------

    # (Reactant2) Creates a Reactant object that references Species "s1"
    # in the model.

    spr = reaction.createReactant();
    spr.setSpecies("s1");

    #---------------------------------------------------------------------------
    # Creates a Product object inside the Reaction object ("v2"). 
    #---------------------------------------------------------------------------

    # Creates a Product object that references Species "s2" in the model. 

    spr = reaction.createProduct();
    spr.setSpecies("s2");

    #---------------------------------------------------------------------------
    # Creates a KineticLaw object inside the Reaction object ("v2"). 
    #---------------------------------------------------------------------------

    kl = reaction.createKineticLaw();

    # Sets a notes (by XMLNode) to the KineticLaw object.
    #
    # The following code is an alternative to using setNotes(const string&).
    # The equivalent code would be like this:
    #   
    #     notesString = "<xhtml:p>((vm * s2)/(km + s2))*cell</xhtml:p>";
    #     kl.setNotes(notesString);

    # Creates an of start element (<xhtml:p>) without attributes.

    notesXMLNode = XMLNode(
        XMLTriple("p", "", "xhtml"),
        XMLAttributes());

    # Adds a text element to the start element.

    notesXMLNode.addChild(XMLNode(" ((vm * s2)/(km + s2)) * cell "));

    # Adds it to the kineticLaw object.

    kl.setNotes(notesXMLNode);

    #---------------------------------------------------------------------------
    # Sets a math (object) to the KineticLaw object.
    #---------------------------------------------------------------------------

    # To create mathematical expressions, one would typically construct
    # an tree as the above example code which creates a math of another
    # KineticLaw object.  Here, to save some space and illustrate another approach 
    # of doing it, we will write out the formula in MathML form and then use a 
    # libSBML convenience function to create the tree for us.  
    # (This is a bit dangerous; it's very easy to make mistakes when writing MathML 
    # by hand, so in a real program, we would not really want to do it this way.)

    mathXMLString = """<math xmlns="http://www.w3.org/1998/Math/MathML">
    <apply>
      <times/>
      <apply>
        <divide/>
        <apply>
          <times/>
          <ci> vm </ci>
          <ci> s2 </ci>
        </apply>
        <apply>
          <plus/>
            <ci> km </ci>
            <ci> s2 </ci>
        </apply>
      </apply>
      <ci> cell </ci>
    </apply>
    </math>
	"""
	
    astMath = readMathMLFromString(mathXMLString);
    kl.setMath(astMath);



    #---------------------------------------------------------------------------
    # (Reaction3) Creates a Reaction object ("v3").
    #---------------------------------------------------------------------------

    reaction = model.createReaction();
    reaction.setId("v3");

    #---------------------------------------------------------------------------
    # Creates Reactant objects inside the Reaction object ("v3"). 
    #---------------------------------------------------------------------------

    # (Reactant2) Creates a Reactant object that references Species "s2"
    # in the model.

    spr = reaction.createReactant();
    spr.setSpecies("s2");

    #---------------------------------------------------------------------------
    # Creates a Product object inside the Reaction object ("v3"). 
    #---------------------------------------------------------------------------

    # Creates a Product object that references Species "x1" in the model. 

    spr = reaction.createProduct();
    spr.setSpecies("x1");


    #---------------------------------------------------------------------------
    # Creates a KineticLaw object inside the Reaction object ("v3"). 
    #---------------------------------------------------------------------------

    kl = reaction.createKineticLaw();

    # Sets a notes (by string) to the KineticLaw object.

    notesString = "<xhtml:p> ((vm * x1)/(km + x1)) * cell </xhtml:p>";
    kl.setNotes(notesString);

    #---------------------------------------------------------------------------
    # Sets a math (object) to the KineticLaw object.
    #---------------------------------------------------------------------------

    mathXMLString = """<math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply>
        <times/>
        <apply>
          <divide/>
          <apply>
            <times/>
            <ci> vm </ci>
            <ci> x1 </ci>
          </apply>
          <apply>
            <plus/>
              <ci> km </ci>
              <ci> x1 </ci>
          </apply>
        </apply>
        <ci> cell </ci>
      </apply>
    </math>
	"""

    astMath = readMathMLFromString(mathXMLString);
    kl.setMath(astMath);

    # Returns the created SBMLDocument object.
    # The returned object must be explicitly deleted by the caller,
    # otherwise memory leak will happen.

    return sbmlDoc;



# 
# 
# Creates an SBML model represented in "7.8 Example involving function definitions"
# in the SBML Level 2 Version 4 Specification.
# 
# 

def createExampleInvolvingFunctionDefinitions():
    level = Level;
    version = Version;

    #---------------------------------------------------------------------------
    #
    # Creates an SBMLDocument object 
    #
    #---------------------------------------------------------------------------

    sbmlDoc = SBMLDocument(level, version);

    #---------------------------------------------------------------------------
    #
    # Creates a Model object inside the SBMLDocument object. 
    #
    #---------------------------------------------------------------------------

    model = sbmlDoc.createModel();
    model.setId("functionExample");

    #---------------------------------------------------------------------------
    #
    # Creates a FunctionDefinition object inside the Model object. 
    #
    #---------------------------------------------------------------------------

    fdef = model.createFunctionDefinition();
    fdef.setId("f");

    # Sets a math (object) to the FunctionDefinition object.

    mathXMLString = """<math xmlns="http://www.w3.org/1998/Math/MathML">
      <lambda>
        <bvar>
          <ci> x </ci>
        </bvar>
        <apply>
          <times/>
          <ci> x </ci>
          <cn> 2 </cn>
        </apply>
      </lambda>
    </math>
	"""

    astMath = readMathMLFromString(mathXMLString);
    fdef.setMath(astMath);

    #---------------------------------------------------------------------------
    #
    # Creates a Compartment object inside the Model object. 
    #
    #---------------------------------------------------------------------------

    compName = "compartmentOne";

    # Creates a Compartment object ("compartmentOne")

    comp = model.createCompartment();
    comp.setId(compName);

    # Sets the "size" attribute of the Compartment object.
    #
    #   The units of this Compartment object is the default SBML 
    #   units of volume (litre), and thus we don't have to explicitly invoke 
    #   setUnits("litre") function to set the default units.
    #
    comp.setSize(1);


    #---------------------------------------------------------------------------
    #
    # Creates Species objects inside the Model object. 
    #
    #---------------------------------------------------------------------------

    #---------------------------------------------------------------------------
    # (Species1) Creates a Species object ("S1")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setId("S1");

    # Sets the "compartment" attribute of the Species object to identify the 
    # compartnet in which the Species object located.

    sp.setCompartment(compName);

    # Sets the "initialConcentration" attribute of the Species object.
    #
    #  The units of this Species object is determined by two attributes of this 
    #  Species object ("substanceUnits" and "hasOnlySubstanceUnits") and the
    #  "spatialDimension" attribute of the Compartment object ("cytosol") in which 
    #  this species object located.
    #  Since the default values are used for "substanceUnits" (substance (mole)) 
    #  and "hasOnlySubstanceUnits" (False) and the value of "spatialDimension" (3) 
    #  is greater than 0, the units of this Species object is  mole/litre . 
    #

    sp.setInitialConcentration(1);

    #---------------------------------------------------------------------------
    # (Species2) Creates a Species object ("S2")
    #---------------------------------------------------------------------------

    sp = model.createSpecies();
    sp.setId("S2");
    sp.setCompartment(compName);
    sp.setInitialConcentration(0);


    #---------------------------------------------------------------------------
    #
    # Creates a global Parameter object inside the Model object. 
    #
    #---------------------------------------------------------------------------

    # Creates a Parameter ("t")  

    para = model.createParameter();
    para.setId("t");
    para.setValue(1);
    para.setUnits("second");


    #---------------------------------------------------------------------------
    #
    # Creates Reaction objects inside the Model object. 
    #
    #---------------------------------------------------------------------------

    #---------------------------------------------------------------------------
    # (Reaction1) Creates a Reaction object ("reaction_1").
    #---------------------------------------------------------------------------

    reaction = model.createReaction();
    reaction.setId("reaction_1");
    reaction.setReversible(False);

    #---------------------------------------------------------------------------
    # Creates Reactant objects inside the Reaction object ("reaction_1"). 
    #---------------------------------------------------------------------------

    # (Reactant1) Creates a Reactant object that references Species "S1"
    # in the model.

    spr = reaction.createReactant();
    spr.setSpecies("S1");

    #---------------------------------------------------------------------------
    # Creates a Product object inside the Reaction object ("reaction_1"). 
    #---------------------------------------------------------------------------

    # Creates a Product object that references Species "S2" in the model. 

    spr = reaction.createProduct();
    spr.setSpecies("S2");


    #---------------------------------------------------------------------------
    # Creates a KineticLaw object inside the Reaction object ("reaction_1"). 
    #---------------------------------------------------------------------------

    kl = reaction.createKineticLaw();

    #---------------------------------------------------------------------------
    # Sets a math (object) to the KineticLaw object.
    #---------------------------------------------------------------------------

    mathXMLString = """<math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply>
      <divide/>
        <apply>
          <times/>
          <apply>
            <ci> f </ci>
            <ci> S1 </ci>
          </apply>
          <ci> compartmentOne </ci>
        </apply>
        <ci> t </ci>
      </apply>
    </math>
	"""

    astMath = readMathMLFromString(mathXMLString);
    kl.setMath(astMath);

    # Returns the created SBMLDocument object.
    # The returned object must be explicitly deleted by the caller,
    # otherwise memory leak will happen.

    return sbmlDoc;

#===============================================================================
#
#
# Helper functions for writing/validating the given SBML documents.
# 
#
#===============================================================================

#
# 
# Validates the given SBMLDocument.
#
#  This function is based on validateSBML.py implemented by
#  Sarah Keating, Ben Bornstein, and Michael Hucka.
#
#

def validateExampleSBML(sbmlDoc):
    if (sbmlDoc == None):
        print("validateExampleSBML: given a None SBML Document");
        return False;

    consistencyMessages = "";
    validationMessages = "";
    noProblems = True;
    numCheckFailures = 0;
    numConsistencyErrors = 0;
    numConsistencyWarnings = 0;
    numValidationErrors = 0;
    numValidationWarnings = 0;

    # LibSBML 3.3 is lenient when generating models from scratch using the
    # API for creating objects.  Once the whole model is done and before it
    # gets written out, it's important to check that the whole model is in
    # fact complete, consistent and valid.

    numCheckFailures = sbmlDoc.checkInternalConsistency();
    if (numCheckFailures > 0):
        noProblems = False;
        for i in range(0, numCheckFailures):
            sbmlErr = sbmlDoc.getError(i);
            if (sbmlErr.isFatal() or sbmlErr.isError()):
                numConsistencyErrors = 1 + numConsistencyErrors;
            else:
                numConsistencyWarnings = 1+numConsistencyWarnings;
        sbmlDoc.printErrors();

    # If the internal checks fail, it makes little sense to attempt
    # further validation, because the model may be too compromised to
    # be properly interpreted.

    if (numConsistencyErrors > 0):
        consistencyMessages = consistencyMessages  + "Further validation aborted.";
    else:
        numCheckFailures = sbmlDoc.checkConsistency();
        if (numCheckFailures > 0):
            noProblems = False;
            for i in range(0, numCheckFailures):
                sbmlErr = sbmlDoc.getError(i);
                if (sbmlErr.isFatal() or sbmlErr.isError()):
                    numValidationErrors = 1+numValidationErrors;
                else:
                    numValidationWarnings = 1+numValidationWarnings;
            sbmlDoc.printErrors();

    if (noProblems):
        return True;
    else:
        if (numConsistencyErrors > 0):
			tmp = ""
			if (numConsistencyErrors > 1):
				tmp = "s";
			print("ERROR: encountered " + str(numConsistencyErrors) + " consistency error" + tmp + " in model '" + sbmlDoc.getModel().getId() + "'.");
		
        if (numConsistencyWarnings > 0):
			tmp = ""
			if (numConsistencyWarnings > 1):
				tmp = "s"
			print("Notice: encountered " + str(numConsistencyWarnings)
            + " consistency warning" + tmp
            + " in model '" + sbmlDoc.getModel().getId() + "'.");
        print(consistencyMessages);

        if (numValidationErrors > 0):
			tmp = ""
			if (numValidationErrors > 1):
				tmp = "s"
			print("ERROR: encountered " + str(numValidationErrors) + " validation error" + (tmp)
            + " in model '" + sbmlDoc.getModel().getId() + "'.");
        if (numValidationWarnings > 0):
			tmp = ""
			if (numValidationWarnings > 1):
				tmp = "s"
			print("Notice: encountered " + str(numValidationWarnings)
            + " validation warning" + (tmp)
            + " in model '" + sbmlDoc.getModel().getId() + "'.");
        print(validationMessages);

        return (numConsistencyErrors == 0 and numValidationErrors == 0);


# 
# 
# Writes the given SBMLDocument to the given file.
# 
# 
def writeExampleSBML(sbmlDoc, filename):
    result = writeSBML(sbmlDoc, filename);
    if (result == 1):
        print("Wrote file '" + filename + "'");
        return True;
    else:
        print("Failed to write '" + filename + "'");
        return False;


#===============================================================================
#
# Main routine
#
#  Creates SBML models represented in "Example models expressed in XML using
#  SBML" in Section 7 of the SBML Level 2 Version 4 specification(*). 
#
#   (*) The specification document is available at the following URL:
#       http://sbml.org/Documents/Specifications
#
#===============================================================================
#
def main (args):
    sbmlDoc = None;
    SBMLok = False;

    try:
      #-------------------------------------------------
      # 7.1 A Simple example application of SBML
      #-------------------------------------------------
      
      sbmlDoc = createExampleEnzymaticReaction();
      SBMLok = validateExampleSBML(sbmlDoc);
      if (SBMLok):
	  	writeExampleSBML(sbmlDoc, "enzymaticreaction.xml");
      if (not SBMLok):
	  	return 1;
      
      #-------------------------------------------------
      # 7.2 Example involving units
      #-------------------------------------------------
      
      sbmlDoc = createExampleInvolvingUnits();
      SBMLok = validateExampleSBML(sbmlDoc);
      if (SBMLok):
	  	writeExampleSBML(sbmlDoc, "units.xml");
      if (not SBMLok):
	  	return 1;
      
      #-------------------------------------------------
      # 7.8 Example involving function definitions
      #-------------------------------------------------
      
      sbmlDoc = createExampleInvolvingFunctionDefinitions();
      SBMLok = validateExampleSBML(sbmlDoc);
      if (SBMLok):
	  	writeExampleSBML(sbmlDoc, "functiondef.xml");
      if (not SBMLok):
	  	return 1;
    except:
      print("Unexpected exceptional condition encountered.");
      return 1;

    # A 0 return status is the standard Unix/Linux way to say "all ok".
    return 0;

  
if __name__ == '__main__':
  main(sys.argv)