public CModel createModel(CCopasiDataModel dataModel) {
try {
dataModel.newModel();
} catch (Exception e) {
return null;
}
CModel model = dataModel.getModel();
model.setVolumeUnit(CModel.fl);
model.setTimeUnit(CModel.s);
model.setQuantityUnit(CModel.fMol);
CCompartment comp = model.createCompartment("CompartmentA");
CMetab A = model.createMetabolite("A", comp.getObjectName());
A.setInitialConcentration(2.0e-4);
CMetab B = model.createMetabolite("B", comp.getObjectName());
B.setInitialConcentration(0.0);
CReaction react = model.createReaction("Decay_1");
react.addSubstrate(A.getKey());
react.addProduct(B.getKey());
react.setReversible(false);
react.setFunction("Mass action (irreversible)");
react.setParameterValue("k1", 0.5);
StringStdVector mapping = new StringStdVector();
mapping.add(react.getChemEq().getSubstrate(0).getMetabolite().getKey());
react.setParameterMappingVector(
react.getFunction().getVariables().getParameter(1).getObjectName(), mapping);
;
model.compileIfNecessary();
ObjectStdVector changedObjects = new ObjectStdVector();
changedObjects.add(comp.getObject(new CCopasiObjectName("Reference=InitialVolume")));
changedObjects.add(A.getObject(new CCopasiObjectName("Reference=InitialConcentration")));
changedObjects.add(B.getObject(new CCopasiObjectName("Reference=InitialConcentration")));
changedObjects.add(
react.getParameters().getParameter(0).getObject(new CCopasiObjectName("Reference=Value")));
model.updateInitialValues(changedObjects);
return model;
}
private void CompleteReaction(CReaction reaction, int numSubst, int numProd) {
reaction.setReversible(false);
// we need to get the function from the function database
CFunctionDB funcDB = CCopasiRootContainer.getFunctionList();
// it should be in the list of suitable functions
// lets get all suitable functions for an irreversible reaction with numSubst substrates and
// numProd products
CFunctionStdVector suitableFunctions =
funcDB.suitableFunctions(numSubst, numProd, COPASI.TriFalse);
int i;
int iMax = (int) suitableFunctions.size();
for (i = 0; i < iMax; ++i) {
// we just assume that the only suitable function with Constant in
// it's name is the one we want
// if (suitableFunctions.get(i).getObjectName().indexOf("Constant") != -1) {
if (suitableFunctions
.get(i)
.getObjectName()
.contains("Mass action (irreversible)")) { // "Mass action (irreversible)" //
// "Michaelis-Menten"
break;
}
}
System.out.println(" Function: " + i + "/" + iMax);
if (i < iMax) {
// we set the function.
// => the method should be smart enough to associate the reaction entities with the correct
// function parameters
reaction.setFunction(suitableFunctions.get(i));
// TaskVectorN taskVector = dataModel.getTaskList();
// dataModel.getTask(0).getProblem();
CCopasiParameterGroup parameterGroup = reaction.getParameters();
CCopasiParameter parameter;
// "Mass action (irreversible)" function has only one parameter k1
parameter = parameterGroup.getParameter("k1");
parameter.setDblValue(0.1);
// michaelis-Menten
/*
parameter= parameterGroup.getParameter("V"); // Michaelis-Menten has 2 parameters: V and Km
parameter.setDblValue(20);
parameter= parameterGroup.getParameter("Km"); // "Mass action (irreversible)" function has only one parameter k1
parameter.setDblValue(10);
*/
// for (i = 0; i < parameterGroup.size(); i++) {
//
// //System.out.println(parameterGroup.getParameter(i).getObjectName());
// parameterGroup.removeParameter(i);
// }
// String paramName;
// i=0;
// //for (i = 0; i < numSubst; i++) {
// paramName = "k"+(i+1); //metabolite_"+i+"_K";
// parameterGroup.addParameter(paramName, CCopasiParameter.DOUBLE);
// CCopasiParameter parameter=parameterGroup.getParameter(paramName);
// parameter.setDblValue(0.1);
// changedObjects.add(parameter.getValueReference());
// //}
} else {
System.err.println("Error. Could not find suitable function.");
System.exit(1);
}
}