Esempio n. 1
0
bool CChemEq::addMetabolite(const std::string & key, const C_FLOAT64 multiplicity, const MetaboliteRole & role)
{
  CChemEqElement element;
  element.setMetabolite(key);
  element.setMultiplicity(multiplicity);

  switch (role)
    {
    case CChemEq::SUBSTRATE:
      addElement(mSubstrates, element);
      addElement(mBalances, element, CChemEq::SUBSTRATE);
      break;
    case CChemEq::PRODUCT:
      addElement(mProducts, element);
      addElement(mBalances, element);
      break;
    case CChemEq::MODIFIER:
      addElement(mModifiers, element);
      break;
    default:
      fatalError();
      break;
    }

  return true;
}
Esempio n. 2
0
void CModelExpansion::replaceInReaction(CReaction* pX, const ElementsMap & emap)
{
  //replace in the chemical equation
  size_t i;

  for (i = 0; i < pX->getChemEq().getSubstrates().size(); ++i)
    {
      CChemEqElement * sourceElement = pX->getChemEq().getSubstrates()[i];
      const CMetab* pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));

      if (pMetab)
        {
          sourceElement->setMetabolite(pMetab->getKey());
        }
    }

  for (i = 0; i < pX->getChemEq().getProducts().size(); ++i)
    {
      CChemEqElement * sourceElement = pX->getChemEq().getProducts()[i];
      const CMetab* pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));

      if (pMetab)
        {
          sourceElement->setMetabolite(pMetab->getKey());
        }
    }

  for (i = 0; i < pX->getChemEq().getModifiers().size(); ++i)
    {
      CChemEqElement * sourceElement = pX->getChemEq().getModifiers()[i];
      const CMetab* pMetab = dynamic_cast<const CMetab*>(emap.getDuplicatePtr(sourceElement->getMetabolite()));

      if (pMetab)
        {
          sourceElement->setMetabolite(pMetab->getKey());
        }
    }

  //mapping and local parameters
  for (i = 0; i < pX->getFunctionParameters().size(); ++i)
    {
      switch (pX->getFunctionParameters()[i]->getUsage())
        {
          case CFunctionParameter::SUBSTRATE:
          case CFunctionParameter::PRODUCT:
          case CFunctionParameter::MODIFIER:
          case CFunctionParameter::VOLUME:
          case CFunctionParameter::PARAMETER:
          {
            size_t k;

            for (k = 0; k < pX->getParameterMappings()[i].size(); ++k)
              {
                std::string targetKey = emap.getDuplicateKey(pX->getParameterMappings()[i][k]);

                if (targetKey != "")
                  pX->getParameterMappings()[i][k] = targetKey;
              }
          }
          break;

          case CFunctionParameter::TIME:
          default:
            break;
        }
    }
}
Esempio n. 3
0
bool CModelMerging::mergeMetabolites(std::string toKey, std::string  key)
{

  bool info = false;

  //merge in  the relevant reactions

  size_t i, imax = mpModel->getReactions().size();
  size_t j, jmax;

  for (i = 0; i < imax; ++i)
    {
      CReaction * reac = &mpModel->getReactions()[i];

      jmax = reac->getChemEq().getSubstrates().size();

      for (j = 0; j < jmax; ++j)
        {
          CChemEqElement * subst = const_cast< CChemEqElement * >(&reac->getChemEq().getSubstrates()[j]);

          if (subst->getMetabolite()->getKey() == key)
            subst->setMetabolite(toKey);
        }

      jmax = reac->getChemEq().getProducts().size();

      for (j = 0; j < jmax; ++j)
        {
          CChemEqElement * prod = const_cast< CChemEqElement * >(&reac->getChemEq().getProducts()[j]);

          if (prod->getMetabolite()->getKey() == key)
            prod->setMetabolite(toKey);
        }

      jmax = reac->getChemEq().getModifiers().size();

      for (j = 0; j < jmax; ++j)
        {
          CChemEqElement * modif = const_cast< CChemEqElement * >(&reac->getChemEq().getModifiers()[j]);

          if (modif->getMetabolite()->getKey() == key)
            modif->setMetabolite(toKey);
        }

      //change parameters of  the kinetic function

      for (j = 0; j < reac->getFunctionParameters().size(); ++j)
        {
          switch (reac->getFunctionParameters()[j]->getUsage())
            {
              case CFunctionParameter::SUBSTRATE:
              case CFunctionParameter::PRODUCT:
              case CFunctionParameter::MODIFIER:
                //translate the metab keys
              {

                //we assume that only SUBSTRATE, PRODUCT, MODIFIER can be vectors

                size_t k, kmax = reac->getParameterMappings()[j].size();

                for (k = 0; k < kmax; ++k)
                  if (reac->getParameterMappings()[j][k] == key)
                    reac->getParameterMappings()[j][k] = toKey;
              }
              break;

              case CFunctionParameter::TIME:
                break;

              case CFunctionParameter::VOLUME:
                // ??? TODO : have to ask
                break;

              case CFunctionParameter::PARAMETER:
                break;

              default:
                return info;
                break;
            }
        }
    }

  imax = mpModel->getEvents().size();

  for (i = 0; i < imax; ++i)
    {
      CEvent * event = &mpModel->getEvents()[i];

      if (!event) return info;

      /* merge in  trigger expressions */
      CExpression* pExpression = event->getTriggerExpressionPtr();

      if (pExpression == NULL) return info;

      if (!mergeInExpression(toKey, key, pExpression))  return info;

      pExpression = event->getDelayExpressionPtr();

      if (pExpression)
        if (!mergeInExpression(toKey, key, pExpression))
          return info;

      jmax = event->getAssignments().size();

      for (j = 0; j < jmax; ++j)
        {
          CEventAssignment* assignment = &event->getAssignments()[j];

          if (!assignment) return info;

          std::string assignmentKey = assignment->getTargetKey();

          if (assignmentKey == key) assignment->setTargetKey(toKey);

          pExpression = assignment->getExpressionPtr();

          if (pExpression == NULL) return info;

          if (!mergeInExpression(toKey, key, pExpression))    return info;
        }
    }

  imax = mpModel->getMetabolites().size();

  for (i = 0; i < imax; ++i)
    {
      CMetab* metab = &mpModel->getMetabolites()[i];

      if (!metab) return info;

      switch (metab->getStatus())
        {
          case CModelEntity::FIXED:
          case CModelEntity::REACTIONS:

            break;

          case CModelEntity::ASSIGNMENT:

            if (!mergeInExpression(toKey, key, metab->getExpressionPtr())) return info;

            break;

          case CModelEntity::ODE:

            if (!mergeInExpression(toKey, key, metab->getExpressionPtr())) return info;

            if (metab->getInitialExpression() != "")
              if (!mergeInExpression(toKey, key, metab->getInitialExpressionPtr())) return info;

            break;

          default:
            return info;
            break;
        }
    }

  imax = mpModel->getCompartments().size();

  for (i = 0; i < imax; ++i)
    {
      CCompartment* comp = &mpModel->getCompartments()[i];

      if (!comp) return info;

      switch (comp ->getStatus())
        {
          case CModelEntity::FIXED:

            break;

          case CModelEntity::ASSIGNMENT:

            if (!mergeInExpression(toKey, key, comp->getExpressionPtr())) return info;

            break;

          case CModelEntity::ODE:

            if (!mergeInExpression(toKey, key, comp->getExpressionPtr())) return info;

            if (comp->getInitialExpression() != "")
              if (!mergeInExpression(toKey, key, comp->getInitialExpressionPtr())) return info;

            break;

          default:
            return info;
            break;
        }
    }

  imax = mpModel->getModelValues().size();

  for (i = 0; i < imax; ++i)
    {
      CModelValue* modval = &mpModel->getModelValues()[i];

      if (!modval) return info;

      switch (modval ->getStatus())
        {
          case CModelEntity::FIXED:

            break;

          case CModelEntity::ASSIGNMENT:

            if (!mergeInExpression(toKey, key, modval->getExpressionPtr())) return info;

            break;

          case CModelEntity::ODE:

            if (!mergeInExpression(toKey, key, modval->getExpressionPtr())) return info;

            if (modval->getInitialExpression() != "")
              if (!mergeInExpression(toKey, key, modval->getInitialExpressionPtr())) return info;

            break;

          default:
            return info;
            break;
        }
    }

  return true;
}