Align all docs, benchmarks, and jar references to v3.7.0

Author: asad

README.md

@@ -122,7 +122,7 @@ The package namespace has changed from `uk.ac.ebi` to `com.bioinceptionlabs` in
 <!-- Old (v2.x) -->
 <groupId>uk.ac.ebi.rdt</groupId>
 
-<!-- New (v3.6.0+) -->
+<!-- New (v3.7.0+) -->
 <groupId>com.bioinceptionlabs</groupId>
 ```
 
@@ -196,7 +196,7 @@ Sub-commands
 `AAM using SMILES`
 
   ```
-  java -jar rdt-3.6.0-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j AAM -f TEXT
+  java -jar rdt-3.7.0-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j AAM -f TEXT
   ```
 
 `Perform AAM` for Transporters
@@ -205,14 +205,14 @@ Sub-commands
 `AAM using SMILES` (accept mapping with no bond changes -b)
 
   ```
-  java -jar rdt-3.6.0-jar-with-dependencies.jar -Q SMI -q "O=C(O)C(N)CC(=O)N.O=C(O)C(N)CS>>C(N)(CC(=O)N)C(=O)O.O=C(O)C(N)CS" -b -g -c -j AAM -f TEXT
+  java -jar rdt-3.7.0-jar-with-dependencies.jar -Q SMI -q "O=C(O)C(N)CC(=O)N.O=C(O)C(N)CS>>C(N)(CC(=O)N)C(=O)O.O=C(O)C(N)CS" -b -g -c -j AAM -f TEXT
   ```
 
 `Annotate Reaction using SMILES`
 ---------------------------------
 
   ```
-  java -jar rdt-3.6.0-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j ANNOTATE -f XML
+  java -jar rdt-3.7.0-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j ANNOTATE -f XML
   ```
 
 
@@ -222,12 +222,12 @@ Sub-commands
 `Compare Reactions using SMILES with precomputed AAM mappings`
 
   ```
-  java -jar rdt-3.6.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u
+  java -jar rdt-3.7.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u
   ```
 
 
 `Compare Reactions using RXN files`
 
   ```
-  java -jar rdt-3.6.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH
+  java -jar rdt-3.7.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH
   ```

src/test/java/com/bioinceptionlabs/aamtool/GoldenDatasetBenchmarkTest.java

@@ -194,7 +194,7 @@ public void benchmarkGoldenDataset() throws Exception {
         // equivalentMatch includes exactAtomMatch cases, so true accuracy = equivalent/total
 
         System.out.println();
-        System.out.println("=== Golden Dataset Benchmark Results (RDT v3.6.1) ===");
+        System.out.println("=== Golden Dataset Benchmark Results (RDT v3.7.0) ===");
         System.out.println("Total reactions:        " + total);
         System.out.println();
         System.out.println("--- Core Metrics ---");
@@ -230,7 +230,7 @@ public void benchmarkGoldenDataset() throws Exception {
         System.out.println("| RXNMapper          | 83.74%      | -         | -         | Unsup.   | No            |");
         System.out.println("| RDTool (published) | 76.18%      | -         | -         | None     | Yes           |");
         System.out.println("| ChemAxon           | 70.45%      | -         | -         | Propr.   | Yes           |");
-        System.out.printf("| RDT v3.6.1         | %.1f%%      | %.1f%%    | %.1f%%    | None     | Yes           |%n",
+        System.out.printf("| RDT v3.7.0         | %.1f%%      | %.1f%%    | %.1f%%    | None     | Yes           |%n",
                 pct_d(exactAtomMatch, total), atomAccuracy, pct_d(bondChangeExact, total));
 
         assertTrue("Mapping success rate should be > 70%", success > total * 0.70);

src/test/java/com/bioinceptionlabs/aamtool/USPTO50KBenchmarkTest.java

@@ -149,7 +149,7 @@ public void benchmarkUSPTO50K() throws Exception {
 
         // Report
         System.out.println();
-        System.out.println("=== USPTO 50K Benchmark Results (RDT v3.1.0) ===");
+        System.out.println("=== USPTO 50K Benchmark Results (RDT v3.7.0) ===");
         System.out.println("Sample size:          " + total);
         System.out.println("Mapping success:      " + success + "/" + total
                 + " (" + pct(success, total) + "%)");
@@ -168,7 +168,7 @@ public void benchmarkUSPTO50K() throws Exception {
         System.out.println("| RXNMapper          | 98.1%     | Unsupervised   | No            |");
         System.out.println("| GraphormerMapper   | 82.7%     | Unsupervised   | No            |");
         System.out.println("| LocalMapper        | 98.5%     | 2% labeled     | No            |");
-        System.out.printf("| RDT v3.1.0 (auto)  | %s%%    | None           | Yes           |%n",
+        System.out.printf("| RDT v3.7.0 (auto)  | %s%%    | None           | Yes           |%n",
                 pct(success, total));
         System.out.println("| SynTemp (ensemble) | 99.5%     | 3 tools comb.  | No            |");