Published February 27, 2026 | Version Release_2025_09_6
Software Open

rdkit/rdkit: 2025_09_6 (Q3 2025) Release

Authors/Creators

  • 1. CozChemIx Limited
  • 2. Glysade LLC
  • 3. nil
  • 4. @schrodinger
  • 5. @DEShawResearch
  • 6. Google
  • 7. @merckgroup
  • 8. Schrodinger
  • 9. University of Alabama
  • 10. Wageningen University
  • 11. @treelinebio

Description

Release_2025.09.6

(Changes relative to Release_2025.09.5)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to see your contribution acknowledged with your name, please set your name in GitHub)

Jessica Braun, Jackson Burns, Sergey Fedorov, Lauriane Jacot-Descombes, Eisuke Kawashima, Brian Kelley, Joos Kiener, Yakov Pechersky, Paul Pillot, Ricardo Rodriguez, Matt Swain

New Features and Enhancements:

  • Exclude Zero order bonds from FindRingFamilies() and add arguments for includeDativeBonds, includeHydrogenBonds (github pull #9118 from ricrogz)

Bug Fixes:

  • Get things working with numpy 2.4 and pandas 3.0 (github pull #9072 from greglandrum)
  • Chemdraw build fails on Big-endian: cs_swapBytes.h: error: parse error in template argument list (github issue #9077 from barracuda156)
  • Another canonicalization fix (github pull #9082 from ricrogz)
  • CopyMolSubset silently rewires bonds when bondIndices reference atoms not in atomIndices (github issue #9084 from mcs07)
  • CopyMolSubset ignores bondIndices when all atoms are included (github issue #9088 from mcs07)
  • Fix SMARTS for the strict definition of rotatable bonds (github pull #9096 from brje01)
  • Cannot build JS bindings with MCS option enabled. (github pull #9110 from papillot)
  • DetermineBonds fails for thiolate (github issue #9114 from LaurianeJD)
  • when shifting double bonds in tautomerization, set double bond stereo to STEREOANY (github pull #9119 from pechersky)

Cleanup work:

  • style: apply readability-braces-around-statements (github pull #8136 from e-kwsm)
  • The precondition in Bond::getOtherAtomIdx() is redundant (github pull #9092 from ricrogz)
  • Modernize loops and clean up ring finding (github pull #9098 from ricrogz)
  • Further refactoring in SSSR finding (github pull #9104 from ricrogz)

Documentation:

  • fix the python docs for CanonicalRankAtomsInFragment (github pull #9087 from greglandrum)
  • Confusing Deprecation Warning regarding GetImplicitValence (github pull #9117 from kienerj)
  • Update The SSSR Problem GetSSSR Documentation (github pull #9121 from JacksonBurns)

Files

rdkit/rdkit-Release_2025_09_6.zip

Files (86.1 MB)

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md5:e2bf69ada2d8a088fa9bf02bb1907eeb
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Additional details

Related works

Is supplement to
Software: https://github.com/rdkit/rdkit/tree/Release_2025_09_6 (URL)

Software

Repository URL
https://github.com/rdkit/rdkit