void executeSequence(boolean stopAtFirstMapping) {
isomorphismFound = false;
stack.clear();
// Initial nodes
QuerySequenceElement el = sequence.get(0);
for (int k = 0; k < target.getAtomCount(); k++) {
IAtom at = target.getAtom(k);
if (el.center.matches(at)) {
Node node = new Node();
node.sequenceElNum = 0;
node.nullifyAtoms(query.getAtomCount());
node.atoms[el.centerNum] = at;
stack.push(node);
}
}
// Expanding the tree of all possible mappings
if (stopAtFirstMapping) {
while (!stack.isEmpty()) {
expandNode(stack.pop());
if (isomorphismFound) break;
}
} else {
while (!stack.isEmpty()) expandNode(stack.pop());
}
}
/**
* 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;
}
/**
* 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);
}
public void printDebugInfo() {
System.out.println("Query Atoms Topological Layers");
for (int i = 0; i < query.getAtomCount(); i++)
System.out.println("" + i + " " + query.getAtom(i).getProperty(TopLayer.TLProp).toString());
System.out.println();
System.out.println("Query Sequence");
for (int i = 0; i < sequence.size(); i++) System.out.println(sequence.get(i).toString(query));
}
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);
}
private boolean checkQuery(IQueryAtomContainer query) {
if (!(query instanceof PharmacophoreQuery)) return false;
HashMap<String, String> map = new HashMap<String, String>();
for (int i = 0; i < query.getAtomCount(); i++) {
IQueryAtom atom = (IQueryAtom) query.getAtom(i);
if (!(atom instanceof PharmacophoreQueryAtom)) return false;
PharmacophoreQueryAtom pqatom = (PharmacophoreQueryAtom) atom;
String label = pqatom.getSymbol();
String smarts = pqatom.getSmarts();
if (!map.containsKey(label)) map.put(label, smarts);
else {
if (!map.get(label).equals(smarts)) return false;
}
}
return true;
}
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;
}
void executeSequenceAtPos(int pos) {
isomorphismFound = false;
stack.clear();
// Initial node
QuerySequenceElement el = sequence.get(0);
IAtom at = target.getAtom(pos);
if (el.center.matches(at)) {
Node node = new Node();
node.sequenceElNum = 0;
node.nullifyAtoms(query.getAtomCount());
node.atoms[el.centerNum] = at;
stack.push(node);
}
// Expanding the tree of all possible mappings
while (!stack.isEmpty()) {
expandNode(stack.pop());
if (isomorphismFound) break;
}
}
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);
}