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RDT v3.6.1

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@asad asad released this 31 Mar 05:37
v3.6.1
4df4734

Reaction Decoder Tool (RDT) v3.6.1

Security & Stability Fixes

  • XXE hardening: disabled DOCTYPE processing in all DocumentBuilderFactory/TransformerFactory instances
  • Path traversal protection in CLI file parsing via canonical path validation
  • FileWriter resource leak fix in BondChangeCalculator
  • ThreadSafeCache cleanup guaranteed via finally block (prevents memory retention across reactions)
  • Clone IAtomContainer before passing to parallel MCS threads (thread safety)

Performance Improvements

  • BitSet cloning reduced from 3x to 1x in Tanimoto/Cosine/Dice similarity methods (hot path optimization)
  • SMSD Isomorphism adapter: reuse single SMSD object for substructure check + MCS fallback (eliminates redundant object creation)
  • Substructure search limit reduced from 100 to 10 matches
  • 256-bit fingerprints for cache key generation (4x less memory, same accuracy)
  • RXNMappingTest: 176.9s (faster than v3.6.0's 195.8s, faster than CDK baseline 184.6s)

Dependencies

  • SMSD 6.3.0, CDK 2.12 (lightweight, no cdk-fingerprint)
  • Java 21+

Test Results

  • 163 tests, 0 failures, 100% pass rate

License

GNU Lesser General Public License (LGPL) v3.0

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