List of addReactant() Examples

Examples of addReactant()

org.openscience.cdk.interfaces.IReaction.addReactant()
org.sbml.jsbml.Reaction.addReactant()
Adds a {@link SpeciesReference} instance to the listOfReactants of this {@link Reaction}. @param specref @return {@code true} if the {@link #listOfReactants} waschanged as a result of this call.
reaction.Reaction.addReactant()
add reactants from a pool at a certain stoichiometry and order @param pool @param name @param stoich @param order

Examples of org.sbml.jsbml.Reaction.addReactant()

              SpeciesReference speciesReference = (SpeciesReference) newContextObject;
              speciesReference.initDefaults();


              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);


                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

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Examples of org.sbml.jsbml.Reaction.addReactant()

            if (elementName.equals("specieReference")) {
              SpeciesReference speciesReference = (SpeciesReference) newContextObject;


              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);


                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

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Examples of org.sbml.jsbml.Reaction.addReactant()

    fd.setMath(math);
    System.out.println(math.toMathML());
    
    Species species = m.createSpecies("spec");
    Reaction r = m.createReaction("r");
    r.addReactant(new SpeciesReference(species));
    KineticLaw kl = new KineticLaw(level, version);
    math = new ASTNode(fd, kl);
    math.addChild(new ASTNode(species, kl));
    math = ASTNode.times(math, new ASTNode(3.7, 8, kl));
    kl.setMath(math);

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Examples of org.sbml.jsbml.Reaction.addReactant()

    SBMLDocument doc=new SBMLDocument(2,4);
    Model m=doc.createModel("model1");
    Reaction r = m.createReaction("id1");
    SpeciesReference s = new SpeciesReference();
    s.setMetaId("meta2");
    r.addReactant(s);
    r.setMetaId("meta");


    System.out.println("Reaction parent and model                    : " + r.getParent() + " " + r.getModel() + "\n");


    Reaction clonedReaction = r.clone();

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Examples of org.sbml.jsbml.Reaction.addReactant()

              SpeciesReference speciesReference = (SpeciesReference) newContextObject;
              speciesReference.initDefaults();


              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);


                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

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Examples of org.sbml.jsbml.Reaction.addReactant()

              SpeciesReference speciesReference = (SpeciesReference) newContextObject;
              speciesReference.initDefaults();


              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);


                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

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Examples of org.sbml.jsbml.Reaction.addReactant()

    fd.setMath(math);
    System.out.println(math.toMathML());
    
    Species species = m.createSpecies("spec");
    Reaction r = m.createReaction("r");
    r.addReactant(new SpeciesReference(species));
    KineticLaw kl = new KineticLaw(level, version);
    math = new ASTNode(fd, kl);
    math.addChild(new ASTNode(species, kl));
    math = ASTNode.times(math, new ASTNode(3.7, 8, kl));
    kl.setMath(math);

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Examples of org.sbml.jsbml.Reaction.addReactant()

            if (elementName.equals("specieReference")) {
              SpeciesReference speciesReference = (SpeciesReference) newContextObject;


              if (list.getSBaseListType().equals(
                  ListOf.Type.listOfReactants)) {
                reaction.addReactant(speciesReference);


                return speciesReference;
              } else if (list.getSBaseListType().equals(
                  ListOf.Type.listOfProducts)) {
                reaction.addProduct(speciesReference);

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Examples of reaction.Reaction.addReactant()

  public Reaction getTranscriptionRxn()
  {
    Reaction ret = new Reaction();
    
    // POL + TEMPLATE
    ret.addReactant(cell, POL, 1, 1);
    ret.addReactant(cell, TEMPLATE, 1, 1);
    
    // ---> POL + TEMPLATE + Nt
    ret.addProduct(cell, POL, (1 - alphaLtNt), tNt);
    ret.addProduct(cell, POL, alphaLtNt, tPOLt);

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Examples of reaction.Reaction.addReactant()

  {
    Reaction ret = new Reaction();
    
    // POL + TEMPLATE
    ret.addReactant(cell, POL, 1, 1);
    ret.addReactant(cell, TEMPLATE, 1, 1);
    
    // ---> POL + TEMPLATE + Nt
    ret.addProduct(cell, POL, (1 - alphaLtNt), tNt);
    ret.addProduct(cell, POL, alphaLtNt, tPOLt);
    ret.addProduct(cell, TEMPLATE, 1, polDelay);

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