Examples of org.sbml.jsbml.Reaction

org.sbml.jsbml.Reaction
Represents the reaction XML element of a SBML file. @author Andreas Dräger @author Nicolas Rodriguez @author Marine Dumousseau @since 0.8 @version $Rev: 1531 $

    Species s1 = m.createSpecies("s1", "species1", c);
    Species s2 = m.createSpecies("s2", "species2", c);
    Species s3 = m.createSpecies("s3", "species3", c);
    Species s4 = m.createSpecies("s4", "species4", c);
    
    Reaction r1 = m.createReaction("r1");
    r1.setName("reaction1");
    r1.setCompartment(c);
    SpeciesReference sr1 = r1.createReactant("sr1", s1);
    sr1.setName("reactant1");
    sr1.setStoichiometry(1d);
    SpeciesReference sr2 = r1.createProduct("sr2", s2);
    sr2.setName("product1");
    sr2.setStoichiometry(1d);
    ModifierSpeciesReference msr1 = r1.createModifier("msr1", s3);
    msr1.setName("modifier");
    
    Reaction r2 = m.createReaction("r2");
    r2.setName("reaction2");
    r2.setCompartment(c);
    SpeciesReference sr3 = r2.createReactant("sr3", s1);
    sr3.setName("reactant2");
    sr3.setStoichiometry(2d);
    SpeciesReference sr4 = r2.createProduct("sr4", s4);
    sr4.setName("product2");
    sr4.setStoichiometry(1d);
    ModifierSpeciesReference msr2 = r2.createModifier("msr2", s3);
    msr2.setName("modifier");
    
    SBMLWriter.write(doc, System.out, ' ', (short) 2);
    System.out.println('\n');
  }

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    Model m = doc.getModel();
    List<TreeNode> list = new LinkedList<TreeNode>();
    list.add(doc);
    list.add(m);
    list.add(m.getListOfReactions());
    Reaction r1 = m.getReaction(0);
    list.add(r1);
    list.add(r1.getListOfModifiers());
    list.add(r1.getModifier(0));
    Reaction r2 = m.getReaction(1);
    list.add(r2);
    list.add(r2.getListOfModifiers());
    list.add(r2.getModifier(0));
    List<? extends TreeNode> result = doc.filter(filter, true);
    System.out.println("filter result retain internals without pruning:\n  " + result);
    assertTrue(result.equals(list));
  }

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    Model m = doc.getModel();
    List<TreeNode> list = new LinkedList<TreeNode>();
    list.add(doc);
    list.add(m);
    list.add(m.getListOfReactions());
    Reaction r1 = m.getReaction(0);
    list.add(r1);
    list.add(r1.getListOfModifiers());
    list.add(r1.getModifier(0));
    List<? extends TreeNode> result = doc.filter(filter, true, true);
    System.out.println("filter result retain internals with pruning:\n  " + result);
    assertTrue(result.equals(list));
  }

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    SBMLDocument d;
    Model m;
    Compartment c;
    KineticLaw kl;
    LocalParameter p;
    Reaction r;
    Species s;
    SpeciesReference sr;
    UnitDefinition ud;
    String filename = DATA_FOLDER + "/libsbml-test-data/l1v1-branch.xml";
    d = new SBMLReader().readSBML(filename);
    if (d == null)
      ;
    {
    }
    assertTrue(d.getLevel() == 1);
    assertTrue(d.getVersion() == 1);
    m = d.getModel();
    assertTrue(m.getName().equals("Branch"));
    assertTrue(m.getCompartmentCount() == 1);
    c = m.getCompartment(0);
    assertTrue(c.getName().equals("compartmentOne"));
    assertTrue(c.getVolume() == 1);
    ud = c.getDerivedUnitDefinition();
    assertTrue(ud.getUnitCount() == 1);


    // assertTrue(ud.getUnit(0).getKind() == Unit.Kind.LITRE); // getDerivedUnitDefinition not working properly
    assertTrue(m.getSpeciesCount() == 4);
    s = m.getSpecies(0);
    assertTrue(s.getName().equals("S1"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == false);


    //    ud = s.getDerivedUnitDefinition(); // getDerivedUnitDefinition not working properly
//    assertTrue(ud.getUnitCount() == 2);
//    assertTrue(ud.getUnit(0).getKind() == Unit.Kind.MOLE);
//    assertTrue(ud.getUnit(0).getExponent() == 1);
//    assertTrue(ud.getUnit(1).getKind() == Unit.Kind.LITRE);
//    assertTrue(ud.getUnit(1).getExponent() == -1);
    
    s = m.getSpecies(1);
    assertTrue(s.getName().equals("X0"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    s = m.getSpecies(2);
    assertTrue(s.getName().equals("X1"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    s = m.getSpecies(3);
    assertTrue(s.getName().equals("X2"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    assertTrue(m.getReactionCount() == 3);
    r = m.getReaction(0);
    assertTrue(r.getName().equals("reaction_1"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    ud = r.getKineticLaw().getDerivedUnitDefinition();


    //    assertTrue(ud.getUnitCount() == 2);
//    assertTrue(ud.getUnit(0).getKind() == Unit.Kind.MOLE);
//    assertTrue(ud.getUnit(0).getExponent() == 1);
//    assertTrue(ud.getUnit(1).getKind() == Unit.Kind.LITRE);
//    assertTrue(ud.getUnit(1).getExponent() == -1);
    
    assertTrue(r.getKineticLaw().containsUndeclaredUnits() == true);
    r = m.getReaction(1);
    assertTrue(r.getName().equals("reaction_2"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    r = m.getReaction(2);
    assertTrue(r.getName().equals("reaction_3"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    r = m.getReaction(0);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("X0"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k1*X0")); // We are not putting the same space in the formula
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k1"));
    assertTrue(p.getValue() == 0);
    r = m.getReaction(1);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("X1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k2*S1")); // equals("k2 * S1")
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k2"));
    assertTrue(p.getValue() == 0);
    r = m.getReaction(2);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("X2"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k3*S1")); // equals("k3 * S1")
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k3"));
    assertTrue(p.getValue() == 0);

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  private Reaction R;


  @Before public void setUp() throws Exception
  {
    R = new  Reaction(2,4);
    if (R == null);
    {
    }
  }

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    assertTrue(dClkF != null);
    
    assertTrue(dClkF.getName().equals("free dClk"));
    
    Reaction rdClk = model.getReaction("rdClk");
    
    assertTrue(rdClk != null);
    
    assertTrue(rdClk.getName().equals("dClk production"));
    assertTrue(rdClk.getMetaId().equals("metaid_0000012"));
    assertTrue(rdClk.getListOfReactants().size() == 1);
    assertTrue(rdClk.getListOfProducts().size() == 1);
    assertTrue(rdClk.getListOfModifiers().size() == 1);
    
    assertTrue(rdClk.getListOfReactants().get(0).getSpecies().equals("EmptySet"));
    assertTrue(rdClk.getListOfProducts().get(0).getSpecies().equals("dClk"));
    assertTrue(rdClk.getListOfModifiers().get(0).getSpecies().equals("dClkF"));
    
    KineticLaw rdClkKL = rdClk.getKineticLaw();
    
    assertTrue(rdClkKL.getListOfParameters().size() == 3);
    assertTrue(rdClkKL.getListOfParameters().get(2).getId().equals("parameter_0000009"));
    assertTrue(rdClkKL.getListOfParameters().get(2).getName().equals("tau2"));
    assertTrue(rdClkKL.getListOfParameters().get(2).getValue() == 10);

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        // Reactions.
        //


        if (reactsIds != null) {
          for (int i = 0; i < reactsIds.length; i++) {
            Reaction relatedReaction = model.getReaction(reactsIds[i]);


            subModel.addReaction(relatedReaction.clone());


            if (relatedReaction.getKineticLaw() != null) {
              // TODO: Parameters!
              getRelatedFunctionsId(relatedFunctionsIdSet, allFunctionsIdSet, relatedReaction.getKineticLaw().getMath());
              processUnitsMap(unitsMap, model, relatedReaction.getKineticLaw());
            }
          }
        }

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    Parameter J18 = model.getParameter("J18");
    
    assertTrue(J18 != null);
    assertTrue(J18.getValue() == 0.6);
    
    Reaction pRB_synthesis = model.getReaction("pRB_synthesis");
    
    assertTrue(pRB_synthesis != null);
    System.out.println("pRB_synthesis additional annotation: " + pRB_synthesis.getAnnotation().getNonRDFannotation());


    assertTrue(pRB_synthesis.getAnnotation().getNonRDFannotation().trim().startsWith("<jigcell:ratelaw jigcell:name=\"Local\""));
    
    assertTrue(pRB_synthesis.getCVTerm(0).getResourceURI(0).equals("urn:miriam:obo.go:GO%3A0006412"));
    // GO:3A0006412
    
  }

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                    }
                }
                
                if (!thisSpeciesSelected && (reactsIds != null)) {
                    for (int j = 0; j < reactsIds.length; j++) {
                      Reaction reaction = model.getReaction(reactsIds[j]);
                        
                        thisSpeciesSelected = contains(reaction.getListOfReactants(), species);
                        
                        if (!thisSpeciesSelected) {
                            thisSpeciesSelected = contains(reaction.getListOfProducts(), species);
                        }
                        if (!thisSpeciesSelected) {
                            thisSpeciesSelected = contains(reaction.getListOfModifiers(), species);
                        }
                        
                        if (thisSpeciesSelected) {
                          break;
                        }

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    Compartment c;
    Species s;
    Parameter gp;
    LocalParameter lp;
    AssignmentRule ar;
    Reaction r;
    SpeciesReference sr;
    KineticLaw kl;
    UnitDefinition ud;
    Reaction r1;
    ListOf<Compartment> loc;
    Compartment c1;
    ListOf<Rule> lor;
    AssignmentRule ar1;
    ListOf<Parameter> lop;
    Parameter p1;
    ListOf<Species> los;
    Species s1;
    String filename = new String( DATA_FOLDER + "/libsbml-test-data/" );
    filename += "l2v1-assignment.xml";
    try {
    d = reader.readSBML(filename);
  } catch (IOException e) {
    e.printStackTrace();
    assert(false);
  } catch (XMLStreamException e) {
    e.printStackTrace();
    assert(false);
  }


  System.out.println(" TestReadFromFile 5: reading done.");
  
  assertTrue( d.getLevel() == 2 );
    assertTrue( d.getVersion() == 1 );
    m = d.getModel();
    assertTrue( m != null );
    assertTrue( m.getCompartmentCount() == 1 );
    c = m.getCompartment(0);
    assertTrue( c != null );
    assertTrue( c.getId().equals( "cell") );
/*    ud = c.getDerivedUnitDefinition();
    assertTrue( ud.getUnitCount() == 1 );
    assertTrue( ud.getUnit(0).getKind() == Kind.LITRE );
    */
    loc = m.getListOfCompartments();
    c1 = loc.get(0);
    assertTrue( c1.equals(c) );
    c1 = loc.get("cell");
    assertTrue( c1.equals(c) );
    assertTrue( m.getSpeciesCount() == 5 );
    s = m.getSpecies(0);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "X0"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 1.0 );
    los = m.getListOfSpecies();
    s1 = los.get(0);
    assertTrue( s1.equals(s) );
    s1 = los.get("X0");
    assertTrue( s1.equals(s) );
    s = m.getSpecies(1);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "X1"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(2);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "T"   ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(3);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "S1"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    s = m.getSpecies(4);
    assertTrue( s != null );
    assertTrue( s.getId().equals( "S2"  ) );
    assertTrue( s.getCompartment().equals( "cell") );
    assertTrue( s.getInitialConcentration() == 0.0 );
    assertTrue( m.getParameterCount() == 1 );
    gp = m.getParameter(0);
    assertTrue( gp != null );
    assertTrue( gp.getId().equals( "Keq") );
    assertTrue( gp.getValue() == 2.5 );
    lop = m.getListOfParameters();
    p1 = lop.get(0);
    assertTrue( p1.equals(gp) );
    p1 = lop.get("Keq");
    assertTrue( p1.equals(gp) );
    /*
    ud = gp.getDerivedUnitDefinition();
    assertTrue( ud.getUnitCount() == 0 );
    assertTrue( m.getRuleCount() == 2 );
    */
    ar = (AssignmentRule)  m.getRule(0);
    assertTrue( ar != null );
    assertTrue( ar.getVariable().equals( "S1"           ) );
    assertTrue( ar.getFormula().equals( "T/(1+Keq)") );
    /*
    ud = ar.getDerivedUnitDefinition();
    assertTrue( ud.getUnitCount() == 2 );
    assertTrue( ud.getUnit(0).getKind() == Kind.MOLE );
    assertTrue( ud.getUnit(0).getExponent() == 1 );
    assertTrue( ud.getUnit(1).getKind() == Kind.LITRE );
    assertTrue( ud.getUnit(1).getExponent() == -1 );
    */
    assertTrue( ar.containsUndeclaredUnits() == true );
    lor = m.getListOfRules();
    ar1 = (AssignmentRule) lor.get(0);
    assertTrue( ar1.equals(ar) );
    ar1 = (AssignmentRule) lor.get("S1");
    assertTrue( ar1.equals(ar) );
    ar = (AssignmentRule)  m.getRule(1);
    assertTrue( ar != null );
    assertTrue( ar.getVariable().equals( "S2"      ) );
    assertTrue( ar.getFormula().equals( "Keq*S1") );
    assertTrue( m.getReactionCount() == 2 );
    r = m.getReaction(0);
    assertTrue( r != null );
    assertTrue( r.getId().equals( "in") );
    assertTrue( r.getReactantCount() == 1 );
    assertTrue( r.getProductCount() == 1 );
    sr = r.getReactant(0);
    assertTrue( sr != null );
    assertTrue( sr.getSpecies().equals( "X0") );
    sr = r.getProduct(0);
    assertTrue( sr != null );
    assertTrue( sr.getSpecies().equals( "T" ) );
    kl = r.getKineticLaw();
    assertTrue( kl != null );
    assertTrue( kl.getFormula().equals( "k1*X0") );
    assertTrue( kl.getLocalParameterCount() == 1 );
    r1 = (Reaction) kl.getParentSBMLObject();
    assertTrue( r1 != null );
    assertTrue( r1.getId().equals( "in") );
    assertTrue( r1.getReactantCount() == 1 );
    assertTrue( r1.getProductCount() == 1 );
    lp = kl.getLocalParameter(0);
    assertTrue( lp != null );
    assertTrue( lp.getId().equals( "k1") );
    assertTrue( lp.getValue() == 0.1 );
    kl = (KineticLaw) lp.getParentSBMLObject().getParentSBMLObject();

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