Exemplo n.º 1
0
void
createParameterAsRateRule(Model &m, SpeciesReference &sr, Rule &rr, 
                          unsigned int idCount)
{
  char newid[15];
  std::string id;

  // create parameter as variable of rate rule 
  // and use stoichiometryMath to point to this
  sprintf(newid, "parameterId_%u", idCount);
  id.assign(newid);

  Parameter *p = m.createParameter();
  p->setId(id);
  p->setConstant(false);

  rr.setVariable(id);
  
  StoichiometryMath *sm = sr.createStoichiometryMath();
  if (sm != NULL)
  {
    ASTNode *ast = SBML_parseFormula(id.c_str());
    sm->setMath(ast);
  }
}
Exemplo n.º 2
0
void
useStoichMath(Model & m, SpeciesReference &sr, bool isRule)
{
  // use stoichiometryMath instead
  StoichiometryMath *sm = sr.createStoichiometryMath();
  if (sm != NULL)
  {
    if (isRule == true)
    {
      sm->setMath(m.getRule(sr.getId())->getMath());
      m.removeRule(sr.getId());
    }
    else
    {
      sm->setMath(m.getInitialAssignment(sr.getId())->getMath());
      m.removeInitialAssignment(sr.getId());
    }
  }
}
Exemplo n.º 3
0
void
createNoValueStoichMath(Model & m, SpeciesReference & sr, unsigned int idCount)
{
  char newid[15];
  std::string id;

  // no stoichiometry and no id to set the stoichiometry
  // replace with stoichiometryMath using a parameter with no value

  sprintf(newid, "parameterId_%u", idCount);
  id.assign(newid);

  Parameter *p = m.createParameter();
  p->setId(id);
  p->setConstant(false);

  StoichiometryMath *sm = sr.createStoichiometryMath();
  if (sm != NULL)
  {
    ASTNode *ast = SBML_parseFormula(id.c_str());
    sm->setMath(ast);
  }
}
Exemplo n.º 4
0
void dealWithL1Stoichiometry(Model & m, bool l2)
{
  unsigned int idCount = 0;
  char newid[15];
  std::string id;

  for (unsigned int i = 0; i < m.getNumReactions(); i++)
  {
    Reaction *r = m.getReaction(i);
    unsigned int j;

    for (j = 0; j < r->getNumReactants(); j++)
    {
      SpeciesReference *sr = r->getReactant(j);
      if (sr->getDenominator() != 1)
      {
        long stoich = static_cast<long>(sr->getStoichiometry());
        int denom = sr->getDenominator();
        ASTNode *node = new ASTNode();
        node->setValue(stoich, denom);   
        if (l2 == true)
        {
          StoichiometryMath * sm = sr->createStoichiometryMath();
          sm->setMath(node);
        }
        else
        {
          sprintf(newid, "speciesRefId_%u", idCount);
          id.assign(newid);
          idCount++;
          sr->setId(id);
          InitialAssignment * ar = m.createInitialAssignment();
          ar->setSymbol(id);
          ar->setMath(node);
          sr->unsetStoichiometry();
        }
      }
    }
    for (j = 0; j < r->getNumProducts(); j++)
    {
      SpeciesReference *sr = r->getProduct(j);
      if (sr->getDenominator() != 1)
      {
        long stoich = static_cast<long>(sr->getStoichiometry());
        int denom = sr->getDenominator();
        ASTNode *node = new ASTNode();
        node->setValue(stoich, denom);   
        if (l2 == true)
        {
          StoichiometryMath * sm = sr->createStoichiometryMath();
          sm->setMath(node);
        }
        else
        {
          sprintf(newid, "speciesRefId_%u", idCount);
          id.assign(newid);
          idCount++;
          sr->setId(id);
          InitialAssignment * ar = m.createInitialAssignment();
          ar->setSymbol(id);
          ar->setMath(node);
          sr->unsetStoichiometry();
        }
      }
    }
  }
}