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;
}
