private void processBondsBlock(int lineCount, IAtomContainer container) throws IOException {
for (int i = 0; i < lineCount; i++) {
String line = input.readLine();
int atom1 = Integer.parseInt(line.substring(10, 13).trim()) - 1;
int atom2 = Integer.parseInt(line.substring(16, 19).trim()) - 1;
if (container.getBond(container.getAtom(atom1), container.getAtom(atom2)) == null) {
IBond bond =
container.getBuilder().newBond(container.getAtom(atom1), container.getAtom(atom2));
int order = Integer.parseInt(line.substring(23).trim());
bond.setOrder(BondManipulator.createBondOrder((double) order));
container.addBond(bond);
} // else: bond already present; CTX store the bonds twice
}
}
/**
* Search if the setOfAtomContainer contains the atomContainer
*
* @param set ISetOfAtomContainer object where to search
* @param atomContainer IAtomContainer to search
* @return True, if the atomContainer is contained
*/
private boolean existAC(IAtomContainerSet set, IAtomContainer atomContainer) {
IAtomContainer acClone = null;
try {
acClone = (IMolecule) atomContainer.clone();
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
} catch (CloneNotSupportedException e1) {
e1.printStackTrace();
}
for (int i = 0; i < acClone.getAtomCount(); i++)
// if(acClone.getAtom(i).getID() == null)
acClone.getAtom(i).setID("" + acClone.getAtomNumber(acClone.getAtom(i)));
if (lookingSymmetry) {
try {
CDKHueckelAromaticityDetector.detectAromaticity(acClone);
} catch (CDKException e) {
e.printStackTrace();
}
} else {
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int i = 0; i < set.getAtomContainerCount(); i++) {
IAtomContainer ss = set.getAtomContainer(i);
for (int j = 0; j < ss.getAtomCount(); j++)
// if(ss.getAtom(j).getID() == null)
ss.getAtom(j).setID("" + ss.getAtomNumber(ss.getAtom(j)));
try {
if (!lookingSymmetry) {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) {
QueryAtomContainer qAC2 =
QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC2)) return true;
}
} else {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(acClone);
CDKHueckelAromaticityDetector.detectAromaticity(ss);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) return true;
}
} catch (CDKException e1) {
System.err.println(e1);
logger.error(e1.getMessage());
logger.debug(e1);
}
}
return false;
}
/**
* Get the container which is found resonance from a IMolecule. It is based on looking if the
* order of the bond changes.
*
* @param molecule The IMolecule to analyze
* @return The different containers
*/
@TestMethod("testGetContainers_IMolecule")
public IAtomContainerSet getContainers(IMolecule molecule) {
IAtomContainerSet setOfCont = molecule.getBuilder().newAtomContainerSet();
IMoleculeSet setOfMol = getStructures(molecule);
if (setOfMol.getMoleculeCount() == 0) return setOfCont;
/*extraction of all bonds which has been produced a changes of order*/
List<IBond> bondList = new ArrayList<IBond>();
for (int i = 1; i < setOfMol.getMoleculeCount(); i++) {
IMolecule mol = setOfMol.getMolecule(i);
for (int j = 0; j < mol.getBondCount(); j++) {
IBond bond = molecule.getBond(j);
if (!mol.getBond(j).getOrder().equals(bond.getOrder())) {
if (!bondList.contains(bond)) bondList.add(bond);
}
}
}
if (bondList.size() == 0) return null;
int[] flagBelonging = new int[bondList.size()];
for (int i = 0; i < flagBelonging.length; i++) flagBelonging[i] = 0;
int[] position = new int[bondList.size()];
int maxGroup = 1;
/*Analysis if the bond are linked together*/
List<IBond> newBondList = new ArrayList<IBond>();
newBondList.add(bondList.get(0));
int pos = 0;
for (int i = 0; i < newBondList.size(); i++) {
if (i == 0) flagBelonging[i] = maxGroup;
else {
if (flagBelonging[position[i]] == 0) {
maxGroup++;
flagBelonging[position[i]] = maxGroup;
}
}
IBond bondA = newBondList.get(i);
for (int ato = 0; ato < 2; ato++) {
IAtom atomA1 = bondA.getAtom(ato);
List<IBond> bondA1s = molecule.getConnectedBondsList(atomA1);
for (int j = 0; j < bondA1s.size(); j++) {
IBond bondB = bondA1s.get(j);
if (!newBondList.contains(bondB))
for (int k = 0; k < bondList.size(); k++)
if (bondList.get(k).equals(bondB))
if (flagBelonging[k] == 0) {
flagBelonging[k] = maxGroup;
pos++;
newBondList.add(bondB);
position[pos] = k;
}
}
}
// if it is final size and not all are added
if (newBondList.size() - 1 == i)
for (int k = 0; k < bondList.size(); k++)
if (!newBondList.contains(bondList.get(k))) {
newBondList.add(bondList.get(k));
position[i + 1] = k;
break;
}
}
/*creating containers according groups*/
for (int i = 0; i < maxGroup; i++) {
IAtomContainer container = molecule.getBuilder().newAtomContainer();
for (int j = 0; j < bondList.size(); j++) {
if (flagBelonging[j] != i + 1) continue;
IBond bond = bondList.get(j);
IAtom atomA1 = bond.getAtom(0);
IAtom atomA2 = bond.getAtom(1);
if (!container.contains(atomA1)) container.addAtom(atomA1);
if (!container.contains(atomA2)) container.addAtom(atomA2);
container.addBond(bond);
}
setOfCont.addAtomContainer(container);
}
return setOfCont;
}