// ## operation initGAGroupLibrary()
protected void initGAGroupLibrary() {
// #[ operation initGAGroupLibrary()
thermoLibrary = ThermoGAGroupLibrary.getINSTANCE();
// #]
}
public AbrahamGAValue getABGroup(ChemGraph p_chemGraph) {
// #[ operation getGAGroup(ChemGraph)
AbramData result_abram = new AbramData();
Graph g = p_chemGraph.getGraph();
HashMap oldCentralNode = (HashMap) (p_chemGraph.getCentralNode()).clone();
// satuate radical site
int max_radNum_molecule = ChemGraph.getMAX_RADICAL_NUM();
int max_radNum_atom = Math.min(8, max_radNum_molecule);
int[] idArray = new int[max_radNum_molecule];
Atom[] atomArray = new Atom[max_radNum_molecule];
Node[][] newnode = new Node[max_radNum_molecule][max_radNum_atom];
int radicalSite = 0;
Iterator iter = p_chemGraph.getNodeList();
FreeElectron satuated = FreeElectron.make("0");
while (iter.hasNext()) {
Node node = (Node) iter.next();
Atom atom = (Atom) node.getElement();
if (atom.isRadical()) {
radicalSite++;
// save the old radical atom
idArray[radicalSite - 1] = node.getID().intValue();
atomArray[radicalSite - 1] = atom;
// new a satuated atom and replace the old one
Atom newAtom = new Atom(atom.getChemElement(), satuated);
node.setElement(newAtom);
node.updateFeElement();
}
}
// add H to satuate chem graph
Atom H = Atom.make(ChemElement.make("H"), satuated);
Bond S = Bond.make("S");
for (int i = 0; i < radicalSite; i++) {
Node node = p_chemGraph.getNodeAt(idArray[i]);
Atom atom = atomArray[i];
int HNum = atom.getRadicalNumber();
for (int j = 0; j < HNum; j++) {
newnode[i][j] = g.addNode(H);
g.addArcBetween(node, S, newnode[i][j]);
}
node.updateFgElement();
}
// find all the thermo groups
iter = p_chemGraph.getNodeList();
while (iter.hasNext()) {
Node node = (Node) iter.next();
Atom atom = (Atom) node.getElement();
if (!(atom.getType().equals("H"))) {
if (!atom.isRadical()) {
p_chemGraph.resetThermoSite(node);
AbrahamGAValue thisAbrahamValue = thermoLibrary.findAbrahamGroup(p_chemGraph);
if (thisAbrahamValue == null) {
System.err.println("Abraham group not found: " + node.getID());
} else {
// System.out.println(node.getID() + " " + thisGAValue.getName()+ "
// "+thisGAValue.toString());
result_abram.plus(thisAbrahamValue);
}
} else {
System.err.println("Error: Radical detected after satuation!");
}
}
}
// // find the BDE for all radical groups
// for (int i=0; i<radicalSite; i++) {
// int id = idArray[i];
// Node node = g.getNodeAt(id);
// Atom old = (Atom)node.getElement();
// node.setElement(atomArray[i]);
// node.updateFeElement();
//
// // get rid of the extra H at ith site
// int HNum = atomArray[i].getRadicalNumber();
// for (int j=0;j<HNum;j++) {
// g.removeNode(newnode[i][j]);
// }
// node.updateFgElement();
//
// p_chemGraph.resetThermoSite(node);
// ThermoGAValue thisGAValue = thermoLibrary.findRadicalGroup(p_chemGraph);
// if (thisGAValue == null) {
// System.err.println("Radical group not found: " + node.getID());
// }
// else {
// //System.out.println(node.getID() + " radical correction: " +
// thisGAValue.getName() + " "+thisGAValue.toString());
// result.plus(thisGAValue);
// }
//
// //recover the satuated site for next radical site calculation
// node.setElement(old);
// node.updateFeElement();
// for (int j=0;j<HNum;j++) {
// newnode[i][j] = g.addNode(H);
// g.addArcBetween(node,S,newnode[i][j]);
// }
// node.updateFgElement();
//
// }
//
// // recover the chem graph structure
// // recover the radical
// for (int i=0; i<radicalSite; i++) {
// int id = idArray[i];
// Node node = g.getNodeAt(id);
// node.setElement(atomArray[i]);
// node.updateFeElement();
// int HNum = atomArray[i].getRadicalNumber();
// //get rid of extra H
// for (int j=0;j<HNum;j++) {
// g.removeNode(newnode[i][j]);
// }
// node.updateFgElement();
// }
//
// // substrate the enthalphy of H from the result
// int rad_number = p_chemGraph.getRadicalNumber();
// ThermoGAValue enthalpy_H = new ThermoGAValue(ENTHALPY_HYDROGEN * rad_number,
// 0,0,0,0,0,0,0,0,0,0,0,null);
// result.minus(enthalpy_H);
//
// // make the symmetric number correction to entropy
//
// if (p_chemGraph.isAcyclic()){
// int sigma = p_chemGraph.getSymmetryNumber();
// ThermoGAValue symmtryNumberCorrection = new
// ThermoGAValue(0,GasConstant.getCalMolK()*Math.log(sigma),0,0,0,0,0,0,0,0,0,0,null);
// result.minus(symmtryNumberCorrection);
// }
p_chemGraph.setCentralNode(oldCentralNode);
return result_abram;
// #]
}