/**
* This function returns null if no isomorphism is found
*
* @param container
* @return
*/
public List<IAtom> getIsomorphismMapping(IAtomContainer container) {
if (query == null) return null;
target = container;
FlagStoreIsomorphismNode = true;
isomorphismNodes.clear();
if (query.getAtomCount() == 1) {
SMARTSAtom qa = (SMARTSAtom) query.getAtom(0);
for (int i = 0; i < target.getAtomCount(); i++) {
if (qa.matches(target.getAtom(i))) {
List<IAtom> v = new ArrayList<IAtom>();
v.add(target.getAtom(i));
return (v);
}
}
return null;
}
TopLayer.setAtomTopLayers(target, TopLayer.TLProp);
executeSequence(true);
if (isomorphismFound) {
// Getting the data from the Node
Node node = isomorphismNodes.get(0);
List<IAtom> v = new ArrayList<IAtom>();
for (int i = 0; i < node.atoms.length; i++) v.add(node.atoms[i]);
return (v);
} else return (null);
}
/**
* If no isomorphism is found the result is empty vector
*
* @param container
* @return
*/
public List<List<IAtom>> getAllIsomorphismMappings(IAtomContainer container) {
if (query == null) return null;
target = container;
FlagStoreIsomorphismNode = true;
isomorphismNodes.clear();
List<List<IAtom>> result = new ArrayList<List<IAtom>>();
if (query.getAtomCount() == 1) {
SMARTSAtom qa = (SMARTSAtom) query.getAtom(0);
for (int i = 0; i < target.getAtomCount(); i++) {
if (qa.matches(target.getAtom(i))) {
List<IAtom> v = new ArrayList<IAtom>();
v.add(target.getAtom(i));
result.add(v);
}
}
return result;
}
TopLayer.setAtomTopLayers(target, TopLayer.TLProp);
executeSequence(false);
if (isomorphismFound) {
// Getting the data from the all stored Nodes
for (int k = 0; k < isomorphismNodes.size(); k++) {
Node node = isomorphismNodes.get(k);
List<IAtom> v = new ArrayList<IAtom>();
for (int i = 0; i < node.atoms.length; i++) v.add(node.atoms[i]);
result.add(v);
}
}
return result;
}
public boolean hasIsomorphism(IAtomContainer container) {
target = container;
FlagStoreIsomorphismNode = false;
isomorphismNodes.clear();
if (query.getAtomCount() == 1) return (singleAtomIsomorphism());
TopLayer.setAtomTopLayers(target, TopLayer.TLProp);
executeSequence(true);
return (isomorphismFound);
}