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v2.6.0
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@dan2097 dan2097 released this 21 Dec 12:34
· 78 commits to master since this release
2.6.0
1a9fa6b
  • OPSIN now requires Java 8 (or higher)
  • OPSIN command-line functionality moved to opsin-cli module
  • OPSIN standalone jars are now built with mvn package
  • Updated from InChI 1.03 to InChI 1.06
  • Support for capturing relative/racemic stereochemistry (output via CxSmiles) [contributed by John Mayfield]
  • Support for deaza/dethia
  • Support nitrile as a suffix on amino acids [contributed by John Mayfield]
  • Support more glycero-n-phospho substituents
  • Support for chloroxime and other haloximes
  • Support cis/trans on rings where a stereocenter has two non-hydrogen substituents, using Cahn-Ingold-Prelog rules to determine which are relative
  • Multiple improvements to implicit bracketting logic
  • Corrected interpretation of methylselenopyruvate
  • Added group 1/2 nitrides e.g. magnesium nitride
  • Added molecular diatomics e.g. molecular hydrogen (or dihydrogen)
  • Fixed out of memory error if a fusion bracket referenced an interior atom instead of a peripheral atom
  • Fixed out of memory error while parsing very long ambiguous input, by switching parsing algorithm from breadth-first to depth-first

Dependency changes:

  • Updated logging from Log4J v1.2.17 to the latest Log4J2 (v2.17.0). Neither OPSIN 2.5.0 nor 2.6.0 are vulnerable to Log4Shell. The logging implementation is only included in the opsin-cli module
  • opsin-inchi now uses JNA-InChI rather than JNI-InChI. This supports the latest version of InChI and also support new Macs with ARM64 processors
  • Woodstox now uses groupid com.fasterxml.woodstox (the groupid change did not signify a break in API compatibility)
  • dk.brics.automaton now uses groupid dk.brics (the groupid change did not signify a break in API compatibility)
  • commons-cli is only used by the opsin-cli module
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