Package reaction

Examples of reaction.Reaction.addReactant()

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  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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  {
    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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  public Reaction getNtRxn()
  {
    Reaction ret = new Reaction();
   
    // POL + TEMPLATE
    ret.addReactant(cell, RIB, 1, 1);
    ret.addReactant(cell, Nt, 1, 1);
   
    // ---> POL + TEMPLATE + Nt
    ret.addProduct(cell, RIB, 1, tNp);
    ret.addProduct(cell, Nt, 1, ribDelay);
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  {
    Reaction ret = new Reaction();
   
    // POL + TEMPLATE
    ret.addReactant(cell, RIB, 1, 1);
    ret.addReactant(cell, Nt, 1, 1);
   
    // ---> POL + TEMPLATE + Nt
    ret.addProduct(cell, RIB, 1, tNp);
    ret.addProduct(cell, Nt, 1, ribDelay);
    ret.addProduct(cell, N, 1, tNp);
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  public Reaction getPOLtRxn()
  {
    Reaction ret = new Reaction();
   
    // POL + TEMPLATE
    ret.addReactant(cell, RIB, 1, 1);
    ret.addReactant(cell, POLt, 1, 1);
   
    // ---> POL + TEMPLATE + Nt
    ret.addProduct(cell, RIB, 1, tPOLp);
    ret.addProduct(cell, POLt, 1, ribDelay);
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  {
    Reaction ret = new Reaction();
   
    // POL + TEMPLATE
    ret.addReactant(cell, RIB, 1, 1);
    ret.addReactant(cell, POLt, 1, 1);
   
    // ---> POL + TEMPLATE + Nt
    ret.addProduct(cell, RIB, 1, tPOLp);
    ret.addProduct(cell, POLt, 1, ribDelay);
    ret.addProduct(cell, POL, 1, tPOLp);
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  public Reaction getTemplateRxn()
  {
    Reaction ret = new Reaction();
   
    // POL + TEMPLATE
    ret.addReactant(cell, POL, 1, 1);
    ret.addReactant(cell, TEMPLATE, 1, 1);
    ret.addReactant(cell, N, 1258, 1);
   
    // ---> POL + TEMPLATE + NmRNA
    ret.addProduct(cell, POL, 1, tPOLt);
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  {
    Reaction ret = new Reaction();
   
    // POL + TEMPLATE
    ret.addReactant(cell, POL, 1, 1);
    ret.addReactant(cell, TEMPLATE, 1, 1);
    ret.addReactant(cell, N, 1258, 1);
   
    // ---> POL + TEMPLATE + NmRNA
    ret.addProduct(cell, POL, 1, tPOLt);
    ret.addProduct(cell, TEMPLATE, 1, polDelay);
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    Reaction ret = new Reaction();
   
    // POL + TEMPLATE
    ret.addReactant(cell, POL, 1, 1);
    ret.addReactant(cell, TEMPLATE, 1, 1);
    ret.addReactant(cell, N, 1258, 1);
   
    // ---> POL + TEMPLATE + NmRNA
    ret.addProduct(cell, POL, 1, tPOLt);
    ret.addProduct(cell, TEMPLATE, 1, polDelay);
    ret.addProduct(cell, rTEMPLATE, 1, tPOLt);
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  public Reaction getrTemplateRxn()
  {
    Reaction ret = new Reaction();
   
    // POL + TEMPLATE
    ret.addReactant(cell, POL, 1, 1);
    ret.addReactant(cell, rTEMPLATE, 1, 1);
    ret.addReactant(cell, N, 1258, 1);
   
    // ---> POL + TEMPLATE + NmRNA
    ret.addProduct(cell, POL, 1, tPOLt);
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