private synchronized void GenerateIsoMorphismMapping() throws Exception {
winner.searchWinners(educts, products, mh);
if (winner.getFlag()) {
// System.out.println("**********Updated Mapping**************");
UpdateMapping();
// System.out.println("**********Updated Matrix**************");
UpdateMatrix(mh, removeHydrogen);
// System.out.println("**********Generate Mapping**************");
GenerateMapping(false);
}
}
private synchronized void UpdateMapping() throws Exception {
boolean[][] FlagMatrix = winner.getFlagMatrix();
ReactionContainer reactionStructureInformationContainer = mh.getReactionContainer();
for (int iIndex = 0; iIndex < reactionStructureInformationContainer.getEductCount(); iIndex++) {
for (int jIndex = 0;
jIndex < reactionStructureInformationContainer.getProductCount();
jIndex++) {
int substrateIndex = iIndex;
int productIndex = jIndex;
IAtomContainer ac1 = reactionStructureInformationContainer.getEduct(substrateIndex);
IAtomContainer ac2 = reactionStructureInformationContainer.getProduct(productIndex);
if (FlagMatrix[substrateIndex][productIndex]) {
// updateFlag=true;
BitSet a_BitSet =
reactionStructureInformationContainer.getFingerPrintofEduct(
substrateIndex); // a_BitSet=EDUCT
BitSet b_BitSet =
reactionStructureInformationContainer.getFingerPrintofProduct(
productIndex); // b_BitSet=PRODUCT
/*
* Choose this function if you want JMCS to run
*/
ac1.setID(this.eductList.get(substrateIndex));
ac2.setID(this.productList.get(productIndex));
IGraphMatching graphMatching =
new GraphMatching(reactionName, ac1, ac2, _dirSuffix, removeHydrogen);
boolean mcsMatch =
graphMatching.mcsMatch(
mh, removeHydrogen, substrateIndex, productIndex, a_BitSet, b_BitSet);
if (DEBUG) {
out.println(
"Mol Size E: " + ac1.getAtomCount() + " , Mol Size P: " + ac2.getAtomCount());
}
if (mcsMatch) {
if (DEBUG) {
out.println(eductList.get(substrateIndex) + " <=> " + productList.get(productIndex));
}
delta += graphMatching.removeMatchedAtomsAndUpdateAAM(reaction);
List<MolMapping> rMap =
getReactionMolMapping()
.getMapping(
reactionName,
this.eductList.get(substrateIndex),
this.productList.get(productIndex));
for (MolMapping map : rMap) {
map.setReactionMapping(true);
IAtomContainer mol = graphMatching.getMatchedPart();
mol = canonLabeler.getCanonicalMolecule(mol);
CDKSMILES cdkSmiles = new CDKSMILES(mol, true, false);
map.setMatchedSMILES(cdkSmiles.getCanonicalSMILES(), ++stepIndex);
}
}
IAtomContainer remainingEduct = graphMatching.getRemainingEduct();
IAtomContainer remainingProduct = graphMatching.getRemainingProduct();
reactionStructureInformationContainer.putEduct(substrateIndex, remainingEduct);
reactionStructureInformationContainer.putProduct(productIndex, remainingProduct);
reactionStructureInformationContainer.setEductModified(substrateIndex, true);
reactionStructureInformationContainer.setProductModified(productIndex, true);
}
}
}
}
private synchronized void GenerateMapping(boolean flag) throws Exception {
boolean ruleMatchingFlag = flag;
if (DEBUG) {
// System.out.println("**********Orignal Matrix**************");
printMatrixAtomContainer(mh, eductList, productList);
printSimMatrix(mh, eductList, productList);
printCliqueMatrix(mh, eductList, productList);
// printStereoMatrix(mh, eductList, productList);
// printFragmentMatrix(mh, eductList, productList);
// printEnergyMatrix(mh, eductList, productList);
}
boolean conditionmet = false;
if (!ruleMatchingFlag) {
RuleBasedMappingHandler ruleBasedMappingHandler =
new RuleBasedMappingHandler(mh, eductList, productList);
if (ruleBasedMappingHandler.isMatchFound()) {
if (DEBUG) {
out.println("Rule Based Mapping Handler Match Found");
}
mh = Selector.modifyMatrix(ruleBasedMappingHandler.getMatrixHolder());
conditionmet = true;
}
ruleMatchingFlag = true;
}
if (!conditionmet) {
if (DEBUG) {
out.println("Subgraph/Exact Match Test");
}
IsomorphismMin omorphismMin = new IsomorphismMin(mh, eductList, productList);
if (omorphismMin.isSubAndCompleteMatchFlag()) {
if (DEBUG) {
out.println("Subgraph/Exact Match");
}
mh = omorphismMin.getUpdatedHolder();
}
}
if (DEBUG) {
out.println("**********Modified Matrix**************");
// printMatrixAtomContainer(mh, eductList, productList);
printSimMatrix(mh, eductList, productList);
printCliqueMatrix(mh, eductList, productList);
// printStereoMatrix(mh, eductList, productList);
// printFragmentMatrix(mh, eductList, productList);
// printEnergyMatrix(mh, eductList, productList);
}
winner.searchWinners(educts, products, mh);
if (DEBUG) {
printFlagMatrix(winner, eductList, productList);
}
if (winner.getFlag()) {
if (DEBUG) {
out.println("**********Updated Mapping**************");
}
UpdateMapping();
if (DEBUG) {
out.println("**********Updated Matrix**************");
}
UpdateMatrix(mh, removeHydrogen);
if (DEBUG) {
out.println("**********Generate Mapping**************");
}
GenerateMapping(ruleMatchingFlag);
}
}