ReactionDecoder v3.1.0

ReactionDecoder v3.1.0

Highlights

• Namespace migration: uk.ac.ebi → com.bioinceptionlabs
• SMSD 3.3.0, CDK 2.12, Java 11
• 135 tests, 0 exclusions, 0 failures
• 40+ bug fixes (NPE safety, resource leaks, stereo logic, regex, bounds checks)
• Performance: 448 synchronized locks removed, HashMap O(1) lookups, fingerprint caching, GameTheory short-circuit, cache-friendly matrix ops

Chemical Correctness

• Atom matchers now check charge and isotope (C+ no longer matches C)
• E/Z stereo logic fixed (was always-true condition)
• Aromatic bond handling (was silently treated as single bond)
• Reaction balance validation with warnings
• Deterministic output via LinkedHashMap (reproducible fingerprints)

Breaking Changes

• Package namespace: uk.ac.ebi.* → com.bioinceptionlabs.*
• Maven groupId: uk.ac.ebi.rdt → com.bioinceptionlabs.rdt
• See README for migration guide

Downloads

• rdt-3.1.0-jar-with-dependencies.jar — standalone executable JAR
• rdt-3.1.0.jar — library JAR (requires CDK 2.12 + SMSD 3.3.0)

Usage

```
java -jar rdt-3.1.0-jar-with-dependencies.jar -Q SMI -q "CC(=O)O.CCO>>CC(=O)OCC.O" -g -c -j AAM -f TEXT
```

RDT v2.5.0

Changes:
changes.txt
a) -b option for transporter reactions (no bond change)
b) cdk-2.4-SNAPSHOT.jar added
c) clean up

RDT v2.4.1

Release notes:
changes.txt

a) BioInception's mapping algorithm patch added
b) Concurrent modification error fixed
c) Exit when the job is done
d) Command-line input typo in -c option fixed
e) Mol layout fixed
f) Enrich mapping pair
g) Use multicore
e) Minor Output Format change
in PRAIR Mapping

RDT v2.1.0

changes.txt

Major Changes:

a) Major gain in AAM speed
b) Improved MCS code in the SMSD
c) Code Clean and Bug fixes

RDT v2.0.1 (Patch release)

a) Loggers cleaned up
b) Version 2.0.1-SNAPSHOT with minor updates
c) Reaction SMILES

changes.txt

RDT-2.0.0

Changes (13/10/2018)

Atom Atom Mapping and Reaction Annotation Tool
changes.txt

---

a) MCSPlus renamed flavours
b) Version 2.0.0-SNAPSHOT with
c) CDK 2.x
d) Author name format change
e) License year changed to 2018

RDT

---

Changes

a) Improved speed and accuracy
b) Bug fixing

Next release 1.6 will include CDK v 2.0

changes.txt

RDT

Changes
changes.txt

a) Migrate to Maven project with POM.xml
b) Roll back Version rdt-1.5-SNAPSHOT
c) Fixed bugs
d) SMSD precedence on filter frag > stereo > energy
e) Java 8.0
f) CDK 1.5.14

1.5.0 SNAPSHOT

---

Changes (14/04/2017)

a) Migrate to Maven project with POM.xml
b) Roll back Version rdt-1.5-SNAPSHOT
c) Fixed bugs
d) SMSD precedence on filter frag > stereo > energy
e) Java 8.0
f) CDK 1.5.14
changes.txt

RDT

Minor Changes (changes.txt)

• Mapping selection rules updated
• Test case added and updated