C++ CCopasiDataModel::exportSBML方法代码示例

//.........这里部分代码省略.........
  assert(pModel->getReactions().size() == 1);
  // reaction converts S to P
  // we can set these on the chemical equation of the reaction
  CChemEq* pChemEq = &pReaction->getChemEq();
  // S is a substrate with stoichiometry 1
  pChemEq->addMetabolite(pS->getKey(), 1.0, CChemEq::SUBSTRATE);
  // P is a product with stoichiometry 1
  pChemEq->addMetabolite(pP->getKey(), 1.0, CChemEq::PRODUCT);
  assert(pChemEq->getSubstrates().size() == 1);
  assert(pChemEq->getProducts().size() == 1);
  // this reaction is to be irreversible
  pReaction->setReversible(false);
  assert(pReaction->isReversible() == false);

  CModelValue* pMV = pModel->createModelValue("K", 42.0);
  // set the status to FIXED
  pMV->setStatus(CModelValue::FIXED);
  assert(pMV != NULL);
  pObject = pMV->getInitialValueReference();
  assert(pObject != NULL);
  changedObjects.insert(pObject);
  assert(pModel->getModelValues().size() == 1);

  // now we ned to set a kinetic law on the reaction
  // for this we create a user defined function
  CFunctionDB* pFunDB = CCopasiRootContainer::getFunctionList();
  assert(pFunDB != NULL);

  CKinFunction* pFunction = new CKinFunction("My Rate Law");

  pFunDB->add(pFunction, true);
  CFunction* pRateLaw = dynamic_cast<CFunction*>(pFunDB->findFunction("My Rate Law"));

  assert(pRateLaw != NULL);

  // now we create the formula for the function and set it on the function
  std::string formula = "(1-0.4/(EXPONENTIALE^(temp-37)))*0.00001448471257*1.4^(temp-37)*substrate";

  bool result = pFunction->setInfix(formula);
  assert(result == true);
  // make the function irreversible
  pFunction->setReversible(TriFalse);
  // the formula string should have been parsed now
  // and COPASI should have determined that the formula string contained 2 parameters (temp and substrate)
  CFunctionParameters& variables = pFunction->getVariables();
  // per default the usage of those parameters will be set to VARIABLE
  size_t index = pFunction->getVariableIndex("temp");
  assert(index != C_INVALID_INDEX);
  CFunctionParameter* pParam = variables[index];
  assert(pParam->getUsage() == CFunctionParameter::VARIABLE);
  // This is correct for temp, but substrate should get the usage SUBSTRATE in order
  // for us to use the function with the reaction created above
  // So we need to set the usage for "substrate" manually
  index = pFunction->getVariableIndex("substrate");
  assert(index != C_INVALID_INDEX);
  pParam = variables[index];
  pParam->setUsage(CFunctionParameter::SUBSTRATE);

  // set the rate law for the reaction
  pReaction->setFunction(pFunction);
  assert(pReaction->getFunction() != NULL);

  // COPASI also needs to know what object it has to assocuiate with the individual function parameters
  // In our case we need to tell COPASI that substrate is to be replaced by the substrate of the reaction
  // and temp is to be replaced by the global parameter K
  pReaction->setParameterMapping("substrate", pS->getKey());
  pReaction->setParameterMapping("temp", pMV->getKey());

  // finally compile the model
  // compile needs to be done before updating all initial values for
  // the model with the refresh sequence
  pModel->compileIfNecessary(NULL);

  // now that we are done building the model, we have to make sure all
  // initial values are updated according to their dependencies
  std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
  std::vector<Refresh*>::iterator it2 = refreshes.begin(), endit2 = refreshes.end();

  while (it2 != endit2)
    {
      // call each refresh
      (**it2)();
      ++it2;
    }

  // save the model to a COPASI file
  // we save to a file named example1.cps, we don't want a progress report
  // and we want to overwrite any existing file with the same name
  // Default tasks are automatically generated and will always appear in cps
  // file unless they are explicitley deleted before saving.
  pDataModel->saveModel("example7.cps", NULL, true);

  // export the model to an SBML file
  // we save to a file named example1.xml, we want to overwrite any
  // existing file with the same name and we want SBML L2V3
  pDataModel->exportSBML("example7.xml", true, 2, 3);

  // destroy the root container once we are done
  CCopasiRootContainer::destroy();
}