Fix three correctness and memory issues found in code review

MappingDiagnostics: change snapshot() to use REACTIONS.remove() instead
of get() — entries for completed reactions now released immediately after
the snapshot is consumed, preventing unbounded map growth in batch runs.

StandardizeReaction: preserve stoichiometric coefficients when rebuilding
the filtered reaction. addReactant/addProduct without a coefficient silently
resets it to 1.0; downstream ReactionContainer reads the coefficient for
atom-count weighting, so this was corrupting balance checks for any reaction
with non-unit coefficients.

RDT API: getTotalBondChanges/getFormedCleavedBonds/getOrderChangedBonds now
sum the encoded weights in each "PATTERN:N" feature string rather than counting
unique pattern types. Two formed C-O bonds reported as "C-O:2" should count
as 2, not 1. ReactionResult.similarity() likewise keeps full "PATTERN:N"
strings so reactions differing only in stoichiometry have distinct fingerprints.

Author: asad

src/main/java/com/bioinceptionlabs/reactionblast/api/RDT.java

@@ -138,9 +138,9 @@ private static ReactionResult extractResult(ReactionMechanismTool rmt, String in
         return new ReactionResult(
                 inputSmiles,
                 mappedSmiles,
-                formedCleaved.size(),
-                orderChanges.size(),
-                stereoChanges.size(),
+                weightSum(formedCleaved),
+                weightSum(orderChanges),
+                weightSum(stereoChanges),
                 formedCleaved,
                 orderChanges,
                 stereoChanges,
@@ -157,4 +157,19 @@ private static List<String> extractFeatures(IPatternFingerprinter fp) {
         }
         return features;
     }
+
+    /** Sum the integer weights encoded in "PATTERN:N" feature strings. */
+    private static int weightSum(List<String> features) {
+        int total = 0;
+        for (String f : features) {
+            int colon = f.lastIndexOf(':');
+            if (colon > 0) {
+                try { total += Integer.parseInt(f.substring(colon + 1)); }
+                catch (NumberFormatException e) { total += 1; }
+            } else {
+                total += 1;
+            }
+        }
+        return total;
+    }
 }

src/main/java/com/bioinceptionlabs/reactionblast/api/ReactionResult.java

@@ -169,25 +169,19 @@ public double similarity(ReactionResult other) {
 
     /**
      * Get all fingerprint features as a combined set (for similarity).
-     * Uses pattern names only (strips weight suffix) for robust matching.
-     * E.g., "C-O:1" → "C-O", so reactions with same bond types match.
+     * Keeps the full "PATTERN:WEIGHT" strings so that "C-O:2" and "C-O:1"
+     * are treated as distinct, giving accurate Tanimoto scores for reactions
+     * that differ only in stoichiometry.
      */
     private Set<String> getAllFingerprints() {
         Set<String> all = new HashSet<>();
-        addPatterns(all, formedCleavedBonds);
-        addPatterns(all, orderChangedBonds);
-        addPatterns(all, stereoChangedBonds);
-        addPatterns(all, reactionCentreFingerprint);
+        all.addAll(formedCleavedBonds);
+        all.addAll(orderChangedBonds);
+        all.addAll(stereoChangedBonds);
+        all.addAll(reactionCentreFingerprint);
         return all;
     }
 
-    private static void addPatterns(Set<String> set, List<String> features) {
-        for (String f : features) {
-            int colon = f.lastIndexOf(':');
-            set.add(colon > 0 ? f.substring(0, colon) : f);
-        }
-    }
-
     /**
      * Tanimoto coefficient: |A ∩ B| / |A ∪ B|
      */

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

@@ -100,7 +100,7 @@ public static void recordEvaluationPhase(String reactionId, long elapsedMillis)
     }
 
     public static ReactionSnapshot snapshot(String reactionId) {
-        ReactionStats stats = REACTIONS.get(reactionId);
+        ReactionStats stats = REACTIONS.remove(reactionId);
         return stats == null
                 ? new ReactionSnapshot(reactionId, 0L, 0L, Collections.emptyList())
                 : stats.snapshot(reactionId);

src/main/java/com/bioinceptionlabs/reactionblast/tools/StandardizeReaction.java

@@ -343,10 +343,12 @@ public IReaction filterReagents(IReaction reaction) {
             filtered.setID(reaction.getID());
             filtered.setDirection(reaction.getDirection());
             for (IAtomContainer r : keptReactants) {
-                filtered.addReactant(r);
+                Double coeff = reaction.getReactantCoefficient(r);
+                filtered.addReactant(r, coeff != null ? coeff : 1.0);
             }
             for (IAtomContainer p : products.atomContainers()) {
-                filtered.addProduct(p);
+                Double coeff = reaction.getProductCoefficient(p);
+                filtered.addProduct(p, coeff != null ? coeff : 1.0);
             }
             for (IAtomContainer agent : reagents) {
                 filtered.addAgent(agent);