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);
}
}
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;
}