RDT v3.6.0
Reaction Decoder Tool (RDT) v3.6.0
Highlights
- SMSD 6.3.0 — High-performance substructure and MCS engine with optimized circular fingerprints (ECFP/FCFP), path fingerprints, topological torsion, and multiple similarity metrics (Tanimoto, Dice, Cosine, Soergel)
- Java 21 — Upgraded from Java 11 for modern JVM performance
- Lightweight CDK — Replaced fat cdk-bundle (200+ modules) with 15 individual CDK modules. Removed cdk-fingerprint dependency entirely — all fingerprinting now handled by SMSD
- Improved reagent filtering — Atom-balance guard prevents incorrect removal of genuine reactants in hydrolysis and other multi-component reactions
What's New
- Circular fingerprints (ECFP4/FCFP2) via SMSD for cache key generation and reagent filtering
- Fingerprint caching in GameTheoryEngine for reduced overhead
- Path fingerprints via SMSD SearchEngine for structural similarity
- Atom-balance validation in reagent filter to protect reactants like water in hydrolysis reactions
Performance
| Metric | Value |
|---|---|
| Mapping speed | ~3.4 reactions/sec (USPTO 50K) |
| RXN coverage | 598/599 (99.8%) |
| Test suite | 163 tests, 100% pass |
| Dependencies | SMSD 6.3.0, CDK 2.12 (lightweight) |
| Deterministic | Yes (no ML training needed) |
Dependencies
- SMSD 6.3.0 (com.bioinceptionlabs:smsd)
- CDK 2.12 (15 individual modules, no cdk-bundle, no cdk-fingerprint)
- Java 21+
License
GNU Lesser General Public License (LGPL) v3.0