public boolean checkIsomorphismAtPosition(IAtomContainer container, int atomNum) {
if ((atomNum < 0) || (atomNum >= container.getAtomCount())) return false;
target = container;
FlagStoreIsomorphismNode = false;
isomorphismNodes.clear();
if (query.getAtomCount() == 1) {
SMARTSAtom qa = (SMARTSAtom) query.getAtom(0);
return qa.matches(target.getAtom(atomNum));
}
TopLayer.setAtomTopLayers(target, TopLayer.TLProp);
executeSequenceAtPos(atomNum);
if (isomorphismFound) return true;
return false;
}
public List<Integer> getIsomorphismPositions(IAtomContainer container) {
target = container;
FlagStoreIsomorphismNode = false;
isomorphismNodes.clear();
List<Integer> v = new ArrayList<Integer>();
if (query.getAtomCount() == 1) {
SMARTSAtom qa = (SMARTSAtom) query.getAtom(0);
for (int i = 0; i < target.getAtomCount(); i++) {
if (qa.matches(target.getAtom(i))) v.add(new Integer(i));
}
return (v);
}
TopLayer.setAtomTopLayers(target, TopLayer.TLProp);
for (int i = 0; i < target.getAtomCount(); i++) {
executeSequenceAtPos(i);
if (isomorphismFound) v.add(new Integer(i));
}
return (v);
}