/**
* This function calculates all the possible combinations of MCS
*
* @param molecule1
* @param molecule2
* @param shouldMatchBonds
* @param shouldMatchRings
* @param matchAtomType
* @return
* @throws CDKException
*/
public synchronized List<Map<Integer, Integer>> calculateOverlapsAndReduce(
IAtomContainer molecule1,
IAtomContainer molecule2,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType)
throws CDKException {
setSource(molecule1);
setTarget(molecule2);
List<Map<Integer, Integer>> solution = new ArrayList<>();
setMappings(solution);
if ((getSource().getAtomCount() == 1) || (getTarget().getAtomCount() == 1)) {
List<CDKRMap> overlaps = CDKMCS.checkSingleAtomCases(getSource(), getTarget());
this.setTimeout(CDKMCS.isTimeout());
int nAtomsMatched = overlaps.size();
nAtomsMatched = (nAtomsMatched > 0) ? 1 : 0;
if (nAtomsMatched > 0) {
/*UnComment this to get one Unique Mapping*/
// List reducedList = removeRedundantMappingsForSingleAtomCase(overlaps);
// int counter = 0;
identifySingleAtomsMatchedParts(overlaps, getSource(), getTarget());
}
} else {
List<List<CDKRMap>> overlaps =
CDKMCS.search(
getSource(),
getTarget(),
new BitSet(),
new BitSet(),
true,
true,
shouldMatchBonds,
shouldMatchRings,
matchAtomType);
this.setTimeout(CDKMCS.isTimeout());
List<List<CDKRMap>> reducedList = removeSubGraph(overlaps);
Stack<List<CDKRMap>> allMaxOverlaps = getAllMaximum(reducedList);
while (!allMaxOverlaps.empty()) {
// System.out.println("source: " + source.getAtomCount() + ", target: " +
// target.getAtomCount() + ", overl: " + allMaxOverlaps.peek().size());
List<List<CDKRMap>> maxOverlapsAtoms =
makeAtomsMapOfBondsMap(allMaxOverlaps.peek(), getSource(), getTarget());
// System.out.println("size of maxOverlaps: " + maxOverlapsAtoms.size());
identifyMatchedParts(maxOverlapsAtoms, getSource(), getTarget());
// identifyMatchedParts(allMaxOverlaps.peek(), source, target);
allMaxOverlaps.pop();
}
}
return solution;
}
/**
* This function calculates only one solution (exact) because we are looking at the molecules
* which are exactly same in terms of the bonds and atoms determined by the Fingerprint
*
* @param Molecule1
* @param Molecule2
* @param shouldMatchBonds
* @param shouldMatchRings
* @param matchAtomType
* @throws CDKException
*/
public synchronized void calculateOverlapsAndReduceExactMatch(
IAtomContainer Molecule1,
IAtomContainer Molecule2,
boolean shouldMatchBonds,
boolean shouldMatchRings,
boolean matchAtomType)
throws CDKException {
setSource(Molecule1);
setTarget(Molecule2);
setMappings(new ArrayList<Map<Integer, Integer>>());
// System.out.println("Searching: ");
// List overlaps = UniversalIsomorphismTesterBondTypeInSensitive.getSubgraphAtomsMap(source,
// target);
if ((getSource().getAtomCount() == 1) || (getTarget().getAtomCount() == 1)) {
List<CDKRMap> overlaps = CDKMCS.checkSingleAtomCases(getSource(), getTarget());
this.setTimeout(CDKMCS.isTimeout());
int nAtomsMatched = overlaps.size();
nAtomsMatched = (nAtomsMatched > 0) ? 1 : 0;
if (nAtomsMatched > 0) {
identifySingleAtomsMatchedParts(overlaps, getSource(), getTarget());
}
} else {
List<List<CDKRMap>> overlaps =
CDKMCS.search(
getSource(),
getTarget(),
new BitSet(),
new BitSet(),
true,
true,
shouldMatchBonds,
shouldMatchRings,
matchAtomType);
this.setTimeout(CDKMCS.isTimeout());
List<List<CDKRMap>> reducedList = removeSubGraph(overlaps);
Stack<List<CDKRMap>> allMaxOverlaps = getAllMaximum(reducedList);
while (!allMaxOverlaps.empty()) {
List<List<CDKRMap>> maxOverlapsAtoms =
makeAtomsMapOfBondsMap(allMaxOverlaps.peek(), getSource(), getTarget());
identifyMatchedParts(maxOverlapsAtoms, getSource(), getTarget());
allMaxOverlaps.pop();
}
}
}