void test000087::test_simulate_reaction_flux_reference_1()
{
try
{
bool result = pCOPASIDATAMODEL->importSBMLFromString(test000087::MODEL_STRING5);
CPPUNIT_ASSERT(result = true);
}
catch (...)
{
// there should be no exception
CPPUNIT_ASSERT(false);
}
CModel* pModel = pCOPASIDATAMODEL->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 2);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 2);
CPPUNIT_ASSERT(pModel->getReactions().size() == 1);
const CReaction* pReaction = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction != NULL);
CModelValue* pConstParameter = NULL;
CModelValue* pNonConstParameter = NULL;
unsigned int i, iMax = pModel->getModelValues().size();
for (i = 0; i < iMax; ++i)
{
if (pModel->getModelValues()[i]->getStatus() == CModelEntity::FIXED)
{
pConstParameter = pModel->getModelValues()[i];
}
if (pModel->getModelValues()[i]->getStatus() == CModelEntity::ASSIGNMENT)
{
pNonConstParameter = pModel->getModelValues()[i];
}
}
CPPUNIT_ASSERT(pConstParameter != NULL);
CPPUNIT_ASSERT(pNonConstParameter != NULL);
// check if the kinetic law is mass action with const global parameter as the kinetic constant
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == false);
const CFunction* pKineticLaw = pReaction->getFunction();
CPPUNIT_ASSERT(pKineticLaw != NULL);
CPPUNIT_ASSERT(pKineticLaw->getType() == CEvaluationTree::MassAction);
const std::vector< std::vector<std::string> > & parameterMappings = pReaction->getParameterMappings();
CPPUNIT_ASSERT(parameterMappings.size() == 2);
CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
CPPUNIT_ASSERT(parameterMappings[0][0] == pConstParameter->getKey());
CPPUNIT_ASSERT(parameterMappings[1].size() == 1);
std::string substrateKey = parameterMappings[1][0];
const CCopasiObject* pTempObject = CCopasiRootContainer::getKeyFactory()->get(substrateKey);
CPPUNIT_ASSERT(pTempObject != NULL);
const CMetab* pSubstrate = dynamic_cast<const CMetab*>(pTempObject);
CPPUNIT_ASSERT(pSubstrate != NULL);
// check that the assignment consists of only one object node that is a reference to the reaction flux
const CExpression* pExpression = pNonConstParameter->getExpressionPtr();
CPPUNIT_ASSERT(pExpression != NULL);
const CEvaluationNode* pRoot = pExpression->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(CEvaluationNode::type(pRoot->getType()) == CEvaluationNode::OBJECT);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pRoot);
CPPUNIT_ASSERT(pObjectNode != NULL);
const CRegisteredObjectName cn = pObjectNode->getObjectCN();
std::vector<CCopasiContainer*> listOfContainers;
listOfContainers.push_back(pCOPASIDATAMODEL->getModel());
const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, cn);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isReference() == true);
CPPUNIT_ASSERT(pObject->getObjectName() == "Flux");
CPPUNIT_ASSERT(pObject->getObjectParent() == pReaction);
// Simulate the model (5 steps, stepsize 1 and check that at each step, the value of the variable parameter
// is the same as the flux through the reaction.
std::ostringstream result;
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector* pReports = pCOPASIDATAMODEL->getReportDefinitionList();
CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for simulation");
pReport->setTaskType(CCopasiTask::timeCourse);
pReport->setIsTable(false);
pReport->setSeparator(CCopasiReportSeparator(", "));
std::vector<CRegisteredObjectName>* pHeader = pReport->getHeaderAddr();
std::vector<CRegisteredObjectName>* pBody = pReport->getBodyAddr();
pHeader->push_back(CCopasiStaticString("time").getCN());
pHeader->push_back(pReport->getSeparator().getCN());
pHeader->push_back(CCopasiStaticString("substrate").getCN());
pHeader->push_back(pReport->getSeparator().getCN());
pHeader->push_back(CCopasiStaticString("reaction flux").getCN());
pHeader->push_back(pReport->getSeparator().getCN());
pHeader->push_back(CCopasiStaticString("variable model value").getCN());
pBody->push_back(CCopasiObjectName(pCOPASIDATAMODEL->getModel()->getCN() + ",Reference=Time"));
pBody->push_back(CRegisteredObjectName(pReport->getSeparator().getCN()));
pBody->push_back(CCopasiObjectName(pSubstrate->getCN() + ",Reference=Concentration"));
pBody->push_back(CRegisteredObjectName(pReport->getSeparator().getCN()));
pBody->push_back(CCopasiObjectName(pReaction->getCN() + ",Reference=Flux"));
pBody->push_back(CRegisteredObjectName(pReport->getSeparator().getCN()));
pBody->push_back(CCopasiObjectName(pNonConstParameter->getCN() + ",Reference=Value"));
//
// create a trajectory task
CTrajectoryTask* pTrajectoryTask = new CTrajectoryTask();
// use LSODAR from now on since we will have events pretty soon
pTrajectoryTask->setMethodType(CCopasiMethod::LSODAR);
pTrajectoryTask->getProblem()->setModel(pCOPASIDATAMODEL->getModel());
pTrajectoryTask->setScheduled(true);
pTrajectoryTask->getReport().setReportDefinition(pReport);
// the target needs to be set in order to get output on the stream
// object passed to the task in the call to initialize below
pTrajectoryTask->getReport().setTarget("test.tmp");
CTrajectoryProblem* pProblem = dynamic_cast<CTrajectoryProblem*>(pTrajectoryTask->getProblem());
pProblem->setStepNumber((const unsigned C_INT32)30);
pCOPASIDATAMODEL->getModel()->setInitialTime((const C_FLOAT64)0.0);
pProblem->setDuration((const C_FLOAT64)30);
pProblem->setTimeSeriesRequested(true);
CTrajectoryMethod* pMethod = dynamic_cast<CTrajectoryMethod*>(pTrajectoryTask->getMethod());
pMethod->getParameter("Absolute Tolerance")->setValue(1.0e-12);
CCopasiVectorN< CCopasiTask > & TaskList = * pCOPASIDATAMODEL->getTaskList();
TaskList.remove("Time-Course");
TaskList.add(pTrajectoryTask, true);
try
{
pTrajectoryTask->initialize(CCopasiTask::OUTPUT_UI, pCOPASIDATAMODEL, &result);
pTrajectoryTask->process(true);
pTrajectoryTask->restore();
}
catch (...)
{
// there should be no exception
CPPUNIT_ASSERT(false);
}
// analyse the result
CPPUNIT_ASSERT(!result.str().empty());
std::string result_string = result.str();
std::string delimiter = "\n";
std::string delimiter2 = ",";
std::size_t lastPos = result_string.find_first_not_of(delimiter);
std::size_t pos;
std::string line, number_string;
unsigned int index = 0;
unsigned int index2;
std::size_t lastPos2;
std::size_t pos2;
double last = std::numeric_limits<double>::max(), current = std::numeric_limits<double>::max();
while (lastPos != std::string::npos)
{
pos = result_string.find_first_of(delimiter, lastPos);
line = result_string.substr(lastPos, pos - lastPos);
lastPos = result_string.find_first_not_of(delimiter, pos);
lastPos2 = line.find_first_not_of(delimiter2);
// skip the header line
if (index != 0)
{
index2 = 0;
while (lastPos2 != std::string::npos)
{
pos2 = line.find_first_of(delimiter2, lastPos2);
number_string = line.substr(lastPos2, pos2 - lastPos2);
lastPos2 = line.find_first_not_of(delimiter2, pos2);
// skip the time column
if (index2 != 0)
{
//check that all values in the row (besides the time)
// are always the same
if (index2 == 1)
{
last = strToDouble(number_string.c_str(), NULL);
if (index == 1)
{
// just make sure that we don't compare all zeros
// The initial value of the substrate hould be higher than 1
CPPUNIT_ASSERT(fabs(pSubstrate->getInitialValue()) > 1);
// the first rwo should correspond the the initial value of the substrate
// We check this to make sure that the whole timeseries does not consist of zeros
CPPUNIT_ASSERT(fabs((last - pSubstrate->getInitialConcentration()) / pSubstrate->getInitialConcentration()) < 1e-20);
}
}
else
{
current = strToDouble(number_string.c_str(), NULL);
CPPUNIT_ASSERT(fabs((current - last) / last) < 1e-20);
last = current;
}
}
++index2;
}
}
++index;
}
// make sure there actually were datapoints
CPPUNIT_ASSERT(index > 1);
// the simulation is set to run until all substrate is depleted, so in the end
// last should be below the absolute tolerance for the simulation
CPPUNIT_ASSERT(last < *pMethod->getParameter("Absolute Tolerance")->getValue().pDOUBLE);
}
void CFixLocalReactionParameters::changeModel()
{
CCopasiParameter * pParameter = NULL;
CModelValue * pModelValue = NULL;
CReaction * pReaction = NULL;
std::stringstream NameStream;
std::stringstream Message;
std::string OldCN;
std::string NewCNBase;
std::string NewCN;
std::string Infix;
std::string::size_type Start;
// Loop through all changes.
std::multimap< CCopasiParameter *, const CExpression * >::const_iterator itChanges = mChanges.begin();
std::multimap< CCopasiParameter *, const CExpression * >::const_iterator endChanges = mChanges.end();
for (; itChanges != endChanges; ++itChanges)
{
if (pParameter != itChanges->first)
{
// We have a new parameter
pParameter = itChanges->first;
OldCN = "<" + pParameter->getCN() + ",Reference=";
// Create a global quantity of type FIXED.
std::string Name = pParameter->getObjectName();
pReaction = static_cast< CReaction * >(pParameter->getObjectAncestor("Reaction"));
Name += "{" + pReaction->getObjectName() + "}";
pModelValue = mpModel->createModelValue(Name, pParameter->getValue< C_FLOAT64 >());
// In case the created name is not unique we append _n with increasing n
// until we succeed;
C_INT32 index = 0;
while (pModelValue == NULL)
{
NameStream.str("");
NameStream << Name << "_" << index++;
pModelValue = mpModel->createModelValue(NameStream.str(), pParameter->getValue< C_FLOAT64 >());
}
NewCNBase = "<" + pModelValue->getCN() + ",Reference=";
// If the parameter is actually used in the reaction
// it is changed to the global quantity.
if (pReaction->isLocalParameter(pParameter->getObjectName()))
pReaction->setParameterMapping(pParameter->getObjectName(), pModelValue->getKey());
Message << " " << pParameter->getObjectName() << " in " << pReaction->getObjectName()
<< " is replaced by " << pModelValue->getObjectName() << std::endl;
}
// We need to distinguish between initial and other expressions.
if (itChanges->second->getObjectName().compare(0, 7, "Initial") == 0)
NewCN = NewCNBase + "Initial";
else
NewCN = NewCNBase;
// Replace the OldCN of the parameter with the NewCN of global quantity in all expressions.
Infix = itChanges->second->getInfix();
// There may be more than one occurrence.
Start = 0;
while ((Start = Infix.find(OldCN), Start) != std::string::npos)
Infix.replace(Start, OldCN.length(), NewCN);
const_cast< CExpression * >(itChanges->second)->setInfix(Infix);
}
CCopasiMessage(CCopasiMessage::WARNING, MCXML + 14, Message.str().c_str());
}
