// virtual
bool CModelParameter::refreshFromModel(const bool & modifyExistence)
{
bool success = true;
if (modifyExistence)
{
if (mCompareResult == CModelParameter::Obsolete)
{
delete this;
return true;
}
if (mCompareResult == CModelParameter::Missing)
{
mCompareResult = CModelParameter::Identical;
}
if (mType != ReactionParameter &&
mpObject != NULL)
{
mSimulationType = static_cast< CModelEntity * >(mpObject)->getStatus();
}
}
if (mpObject != NULL)
{
switch (mType)
{
case Model:
{
CModel * pModel = static_cast< CModel * >(mpObject);
if (!pModel->isAutonomous())
{
mValue = pModel->getInitialValue();
}
else
{
mValue = 0.0;
}
}
break;
case Compartment:
case Species:
case ModelValue:
{
CModelEntity * pEntity = static_cast< CModelEntity * >(mpObject);
mValue = pEntity->getInitialValue();
}
break;
case ReactionParameter:
{
CCopasiParameter * pParameter = static_cast< CCopasiParameter * >(mpObject);
mValue = * pParameter->getValue().pDOUBLE;
// We need to update the mapping
// Check whether this refers to a global quantity.
const CReaction * pReaction = static_cast< CModelParameterReactionParameter * >(this)->getReaction();
if (pReaction != NULL)
{
if (pReaction->isLocalParameter(getName()))
{
mSimulationType = CModelEntity::FIXED;
static_cast< CModelParameterReactionParameter * >(this)->setGlobalQuantityCN("");
}
else
{
mSimulationType = CModelEntity::ASSIGNMENT;
const std::vector<std::string> ModelValue = pReaction->getParameterMapping(getName());
assert(ModelValue.size() == 1);
CModelValue * pModelValue = static_cast< CModelValue * >(CCopasiRootContainer::getKeyFactory()->get(ModelValue[0]));
static_cast< CModelParameterReactionParameter * >(this)->setGlobalQuantityCN(pModelValue->getInitialValueReference()->getCN());
}
}
CCopasiObjectName GlobalQuantityCN = static_cast< CModelParameterReactionParameter * >(this)->getGlobalQuantityCN();
if (GlobalQuantityCN != "")
{
CModelParameter * pGlobalQuantity = getSet()->getModelParameter(GlobalQuantityCN);
if (pGlobalQuantity != NULL)
{
mValue = pGlobalQuantity->getValue(ParticleNumbers);
}
}
}
break;
default:
success = false;
break;
}
}
return success;
}
int main()
{
// initialize the backend library
// since we are not interested in the arguments
// that are passed to main, we pass 0 and NULL to
// init
CCopasiRootContainer::init(0, NULL);
assert(CCopasiRootContainer::getRoot() != NULL);
// create a new datamodel
CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
assert(CCopasiRootContainer::getDatamodelList()->size() == 1);
// get the model from the datamodel
CModel* pModel = pDataModel->getModel();
assert(pModel != NULL);
// set the units for the model
// we want seconds as the time unit
// microliter as the volume units
// and nanomole as the substance units
pModel->setTimeUnit(CModel::s);
pModel->setVolumeUnit(CModel::microl);
pModel->setQuantityUnit(CModel::nMol);
// we have to keep a set of all the initial values that are changed during
// the model building process
// They are needed after the model has been built to make sure all initial
// values are set to the correct initial value
std::set<const CCopasiObject*> changedObjects;
// create a compartment with the name cell and an initial volume of 5.0
// microliter
CCompartment* pCompartment = pModel->createCompartment("cell", 5.0);
const CCopasiObject* pObject = pCompartment->getValueReference();
assert(pObject != NULL);
changedObjects.insert(pObject);
assert(pCompartment != NULL);
assert(pModel->getCompartments().size() == 1);
// create a new metabolite with the name S and an inital
// concentration of 10 nanomol
// the metabolite belongs to the compartment we created and is is to be
// fixed
CMetab* pS = pModel->createMetabolite("S", pCompartment->getObjectName(), 10.0, CMetab::FIXED);
pObject = pS->getInitialConcentrationReference();
assert(pObject != NULL);
changedObjects.insert(pObject);
assert(pCompartment != NULL);
assert(pS != NULL);
assert(pModel->getMetabolites().size() == 1);
// create a second metabolite called P with an initial
// concentration of 0. This metabolite is to be changed by reactions
CMetab* pP = pModel->createMetabolite("P", pCompartment->getObjectName(), 0.0, CMetab::REACTIONS);
assert(pP != NULL);
pObject = pP->getInitialConcentrationReference();
assert(pObject != NULL);
changedObjects.insert(pObject);
assert(pModel->getMetabolites().size() == 2);
// now we create a reaction
CReaction* pReaction = pModel->createReaction("reaction");
assert(pReaction != NULL);
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();
}
