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;
}
public static CSteadyStateTask runSteadyStateCalculation(
CCopasiDataModel dataModel,
HashMap<String, Object> problemParameters,
HashMap<String, Object> methodParameters) {
CSteadyStateTask steadyStateTask =
(CSteadyStateTask) dataModel.addTask(CCopasiTask.steadyState);
if (steadyStateTask == null) return null;
CSteadyStateProblem steadyStateProblem = (CSteadyStateProblem) steadyStateTask.getProblem();
if (steadyStateProblem == null) return null;
Set<String> keySet = problemParameters.keySet();
for (Iterator<String> it = keySet.iterator(); it.hasNext(); ) {
String key = (String) it.next();
CCopasiParameter param = steadyStateProblem.getParameter(key);
if (param == null) {
return null;
}
Object o = problemParameters.get(key);
if (o instanceof Double) {
param.setDblValue(((Double) o).doubleValue());
} else if (o instanceof Integer) {
param.setIntValue(((Integer) o).intValue());
} else if (o instanceof Boolean) {
param.setBoolValue(((Boolean) o).booleanValue());
} else if (o instanceof String) {
param.setStringValue(((String) o));
} else {
System.err.println("Error. Unknown parameter type.");
}
}
CNewtonMethod newtonMethod = (CNewtonMethod) steadyStateTask.getMethod();
if (newtonMethod == null) {
return null;
}
keySet = methodParameters.keySet();
for (Iterator<String> it = keySet.iterator(); it.hasNext(); ) {
String key = (String) it.next();
CCopasiParameter param = newtonMethod.getParameter(key);
if (param == null) {
return null;
}
Object o = methodParameters.get(key);
if (o instanceof Double) {
param.setDblValue(((Double) o).doubleValue());
} else if (o instanceof Integer) {
param.setIntValue(((Integer) o).intValue());
} else if (o instanceof Boolean) {
param.setBoolValue(((Boolean) o).booleanValue());
} else if (o instanceof String) {
param.setStringValue(((String) o));
} else {
System.err.println("Error. Unknown parameter type.");
}
}
boolean result = false;
try {
result = steadyStateTask.process(true);
} catch (Exception e) {
System.err.println("ERROR: " + e.getMessage());
}
if (!result) {
return null;
}
return steadyStateTask;
}
