Release 3.8.1: SMSD 6.9.1, MolGraph canonical SMILES, benchmark refresh

Author: asad

README.md

@@ -7,7 +7,7 @@
 Introduction
 ============
 
-`Reaction Decoder Tool (RDT) v3.8.0`
+`Reaction Decoder Tool (RDT) v3.8.1`
 --------------------------------------
 
 **Toolkit-agnostic reaction mapping engine** with CDK adapter. Deterministic, no training data required.
@@ -18,7 +18,7 @@ Published tools are scored on **chemically equivalent** atom mapping — whether
 
 | Tool | Chemically Equivalent Atom-Map | Bond-Change Exact | Mol-Map Exact | Strict Atom-Index Exact | Deterministic |
 |------|-------------------------------|-------------------|---------------|------------------------|---------------|
-| **RDT v3.8.0** | **99.2%** | **99.2%** | **75.6%** | 22.8% | **Yes** |
+| **RDT v3.8.1** | **99.2%** | **99.2%** | **76.8%** | 19.6% | **Yes** |
 | RXNMapper | 83.74%† | - | - | - | No |
 | RDTool (published) | 76.18%† | - | - | - | Yes |
 | ChemAxon | 70.45%† | - | - | - | Yes |
@@ -133,7 +133,7 @@ The package namespace has changed from `uk.ac.ebi` to `com.bioinceptionlabs` in
 <!-- Old (v2.x) -->
 <groupId>uk.ac.ebi.rdt</groupId>
 
-<!-- New (v3.8.0+) -->
+<!-- New (v3.8.1+) -->
 <groupId>com.bioinceptionlabs</groupId>
 ```
 
@@ -207,7 +207,7 @@ Sub-commands
 `AAM using SMILES`
 
   ```
-  java -jar rdt-3.8.0-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-3.8.1-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
@@ -216,14 +216,14 @@ Sub-commands
 `AAM using SMILES` (accept mapping with no bond changes -b)
 
   ```
-  java -jar rdt-3.8.0-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-3.8.1-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-3.8.0-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-3.8.1-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
   ```
 
 
@@ -233,12 +233,12 @@ Sub-commands
 `Compare Reactions using SMILES with precomputed AAM mappings`
 
   ```
-  java -jar rdt-3.8.0-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-3.8.1-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-3.8.0-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-3.8.1-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH
   ```

pom.xml

@@ -4,7 +4,7 @@
     <groupId>com.bioinceptionlabs</groupId>
     <artifactId>rdt</artifactId>
     <description>Reaction Decoder Tool</description>
-    <version>3.8.0</version>
+    <version>3.8.1</version>
     <packaging>jar</packaging>
     <properties>
         <jdk.version>21</jdk.version>
@@ -185,7 +185,7 @@
         <dependency>
             <groupId>com.bioinceptionlabs</groupId>
             <artifactId>smsd</artifactId>
-            <version>6.9.0</version>
+            <version>6.9.1</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
@@ -226,7 +226,7 @@
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-assembly-plugin</artifactId>
-                        <version>3.8.0</version>
+                        <version>3.8.1</version>
                         <configuration>
                             <descriptorRefs>
                                 <descriptorRef>jar-with-dependencies</descriptorRef>

reports/golden-benchmark-report.md

@@ -1,8 +1,8 @@
 # Golden Benchmark Report
 
-Release: RDT v3.8.0
+Release: RDT v3.8.1
 
-Date: 2026-04-03
+Date: 2026-04-03 (v3.8.1)
 
 Dataset: Lin et al. 2022 golden dataset
 
@@ -34,7 +34,7 @@ mvn -q -Dtest=GoldenDatasetBenchmarkTest -Dgolden.max=250 test
 |------|-----------------|---------------|----------------|-------------------------------|-------------------|-------------------------|------------------------|-----------------------|----------------------|---------------------|-------|
 | `20` | `20/20 (100.0%)` | `11/20 (55.0%)` | `2/20 (10.0%)` | `20/20 (100.0%)` | `20/20 (100.0%)` | `20/20 (100.0%)` | `20/20 (100.0%)` | `20/20 (100.0%)` | `870/870 (100.0%)` | `0/20 (0.0%)` | `2.3 rxn/sec` |
 | `100` | `100/100 (100.0%)` | `71/100 (71.0%)` | `27/100 (27.0%)` | `100/100 (100.0%)` | `100/100 (100.0%)` | `100/100 (100.0%)` | `100/100 (100.0%)` | `100/100 (100.0%)` | `4509/4509 (100.0%)` | `0/100 (0.0%)` | `4.3 rxn/sec` |
-| `250` | `250/250 (100.0%)` | `189/250 (75.6%)` | `57/250 (22.8%)` | `248/250 (99.2%)` | `248/250 (99.2%)` | `248/250 (99.2%)` | `248/250 (99.2%)` | `248/250 (99.2%)` | `11747/11769 (99.8%)` | `2/250 (0.8%)` | `2.8 rxn/sec` |
+| `250` | `250/250 (100.0%)` | `192/250 (76.8%)` | `49/250 (19.6%)` | `248/250 (99.2%)` | `248/250 (99.2%)` | `248/250 (99.2%)` | `248/250 (99.2%)` | `248/250 (99.2%)` | `11747/11769 (99.8%)` | `2/250 (0.8%)` | `2.3 rxn/sec` |
 
 ## Interpretation
 

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

@@ -44,6 +44,7 @@
 import org.openscience.cdk.interfaces.IMapping;
 import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
+import com.bioinception.smsd.core.MolGraph;
 import org.openscience.cdk.smiles.SmiFlavor;
 import org.openscience.cdk.smiles.SmilesGenerator;
 import org.openscience.cdk.tools.ILoggingTool;
@@ -266,26 +267,25 @@ public static Collection<MCSSolution> matcher(Holder mh) throws Exception {
             }
 
             /*
-             * Pre-compute canonical SMILES for identity detection.
+             * Pre-compute canonical SMILES for identity detection using SMSD
+             * MolGraph (stereo-aware, independent of CDK SmilesGenerator).
              */
-            SmilesGenerator canonSmigen = new SmilesGenerator(
-                    SmiFlavor.Canonical | SmiFlavor.Stereo);
             Map<Integer, String> eductSmiles = new TreeMap<>();
             for (int i = 0; i < eductCount; i++) {
                 IAtomContainer e = reactionStructureInformation.getEduct(i);
                 if (e != null && e.getAtomCount() > 0) {
                     harmonizeForSmsd(e);
-                    try { eductSmiles.put(i, canonSmigen.create(e)); }
-                    catch (CDKException | RuntimeException ex) { eductSmiles.put(i, ""); }
+                    try { eductSmiles.put(i, new MolGraph(e).toCanonicalSmiles()); }
+                    catch (RuntimeException ex) { eductSmiles.put(i, ""); }
                 }
             }
             Map<Integer, String> productSmiles = new TreeMap<>();
             for (int j = 0; j < productCount; j++) {
                 IAtomContainer p = reactionStructureInformation.getProduct(j);
                 if (p != null && p.getAtomCount() > 0) {
                     harmonizeForSmsd(p);
-                    try { productSmiles.put(j, canonSmigen.create(p)); }
-                    catch (CDKException | RuntimeException ex) { productSmiles.put(j, ""); }
+                    try { productSmiles.put(j, new MolGraph(p).toCanonicalSmiles()); }
+                    catch (RuntimeException ex) { productSmiles.put(j, ""); }
                 }
             }