Remove redundant perception + SMILES round-trip in hot path

MCSThread: removed redundant percieveAtomTypes + initializeMolecule
in getNewContainerWithIDs — already done in GraphMatcher (~25% waste).

Reactor.copyReferenceReaction: replaced SMILES serialize→parse round-trip
with direct clone + perceive (eliminates SmilesGenerator + SmilesParser).

All 135 tests pass. Speed: 3.5 rxn/sec.

Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>

Author: asad

src/main/java/com/bioinceptionlabs/reactionblast/mapping/Reactor.java

@@ -169,14 +169,16 @@ public String toString() {
                 + ", mapping=" + createReactionSMILES + '}';
     }
 
+    /**
+     * Copy reference reaction molecules into the stoichiometry reaction.
+     * Uses direct clone + perceive instead of expensive SMILES round-trip
+     * (serialize → parse → perceive was ~15% of total mapping time).
+     */
     private void copyReferenceReaction(IReaction referenceReaction) throws CDKException, IOException, Exception {
         try {
             for (int i = 0; i < referenceReaction.getReactantCount(); i++) {
                 IAtomContainer refMol = referenceReaction.getReactants().getAtomContainer(i);
-                IAtomContainer mol = cloneWithIDs(refMol);
-//                IAtomContainer mol = refMol.clone();
-                SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
-                IAtomContainer cloneMolecule = sp.parseSmiles(smiles.create(mol));
+                IAtomContainer cloneMolecule = cloneWithIDs(refMol);
                 ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(cloneMolecule);
                 cloneMolecule = prepareMol(cloneMolecule);
                 cloneMolecule.setID(refMol.getID());
@@ -190,10 +192,7 @@ private void copyReferenceReaction(IReaction referenceReaction) throws CDKExcept
         try {
             for (int i = 0; i < referenceReaction.getProductCount(); i++) {
                 IAtomContainer refMol = referenceReaction.getProducts().getAtomContainer(i);
-                IAtomContainer mol = cloneWithIDs(refMol);
-//                IAtomContainer mol = refMol.clone();
-                SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
-                IAtomContainer cloneMolecule = sp.parseSmiles(smiles.create(mol));
+                IAtomContainer cloneMolecule = cloneWithIDs(refMol);
                 ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(cloneMolecule);
                 cloneMolecule = prepareMol(cloneMolecule);
                 cloneMolecule.setID(refMol.getID());

src/main/java/com/bioinceptionlabs/reactionblast/mapping/graph/MCSThread.java

@@ -307,18 +307,15 @@ public MCSSolution call() throws Exception {
         return null;
     }
 
+    /**
+     * Clone molecule preserving IDs.
+     * Aromaticity and atom-type perception already done in GraphMatcher
+     * before MCSThread is created — do NOT repeat here (was ~25% of total time).
+     */
     private IAtomContainer getNewContainerWithIDs(IAtomContainer mol)
             throws CDKException, CloneNotSupportedException {
         if (mol != null && mol.getAtomCount() > 0) {
-            IAtomContainer ac;
-            ac = ExtAtomContainerManipulator.cloneWithIDs(mol);
-            // Aromaticity already applied in GraphMatcher — skip redundant computation
-            try {
-                ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
-                MoleculeInitializer.initializeMolecule(ac);
-            } catch (Exception ex) {
-                LOGGER.error(Level.SEVERE, "Error in Config. r.mol: ", ex.getMessage());
-            }
+            IAtomContainer ac = ExtAtomContainerManipulator.cloneWithIDs(mol);
 
             for (int i = 0; i < ac.getAtomCount(); i++) {
                 String atomID = mol.getAtom(i).getID() == null