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Published December 30, 2025 | Version Release_2025_09_4
Software Open

rdkit/rdkit: 2025_09_4 (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. Fraunhofer ITMP (Hamburg)

Description

Release_2025.09.4

(Changes relative to Release_2025.09.3)

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)

Kevin Boyd, Chi Cheng, David Cosgrove, Tad Hurst, Brian Kelley, Niels Maeder, Yakov Pechersky, Eliot Ragueneau, Pat Riley, Ricardo Rodriguez

New Features and Enhancements:

  • Add extract mol fragment api (github pull #8811 from bp-kelley)
  • Improve DetermineBonds and DetermineBondOrders performance (github pull #8888 from ChiCheng45)
  • Allow Hs to be ignored in the RMSD alignment functions (github pull #8976 from greglandrum)
  • Embed Parameters to JSON (github pull #8977 from nmaeder)
  • Allow spaces and special chars in SCSR fullname attrs (github pull #8982 from tadhurst-cdd)
  • Allow H removal to be skipped in ShowFeats.py (github pull #8986 from greglandrum)
  • some optimizations of AlignPoints() (github pull #8987 from greglandrum)
  • Allow adding custom atom and bond matcher functions for substructure searching (github pull #8994 from greglandrum)
  • Support serializing/deserializing FP generators to JSON (github pull #9000 from greglandrum)
  • Stop writing so many atom properties to cxsmiles (github pull #9002 from greglandrum)

Bug Fixes:

  • rdShapeAlign is sensitive to starting conformation (github issue #8513 from priley-vv)
  • SVG exports of bicolor solid wedge bound not working with stroke-width (github issue #8936 from EliotRagueneau)
  • Small fix in ring stereo/canonicalization (github pull #8962 from ricrogz)
  • Atropisomer bond is found in N-S(=O)C system (github issue #8973 from pechersky)
  • SynthonSpace Substructure search misses some hits (github issue #9007 from DavidACosgrove)
  • SynthonSpace Substructure search misses a hit - Mk2 (github issue #9009 from DavidACosgrove)
  • SDMolSupplier enters an infinite loop if number of SGroups is incorrect (github issue #9014 from ricrogz)
  • Invalid sulfonamide SMARTS in FragmentDescriptors.csv (github issue #9018 from scal444)

Cleanup work:

  • A bunch of modernization of the ShapeHelpers code (github pull #8954 from greglandrum)
  • Minor clean up in SMILES Writing double bond canonicalization (github pull #8971 from ricrogz)
  • Refactor atomVisitOrders and bondVisitOrders in SMILES Writer canonicalization (github pull #8972 from ricrogz)
  • Convert graphmolMolOpsTest to catch2 (github pull #8978 from ricrogz)
  • Some more cleaning up in SMILES Writing (github pull #8991 from ricrogz)
  • Converts testSubgraph2 to catch (github pull #9003 from ricrogz)
  • Convert smiTest1 to catch (github pull #9004 from ricrogz)
  • Last leak fixes for 2025! (github pull #9006 from ricrogz)
  • move molzip to its own file (github pull #9013 from greglandrum)
  • Convert testMolSupplier to catch2 (github pull #9015 from ricrogz)

Files

rdkit/rdkit-Release_2025_09_4.zip

Files (86.2 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/rdkit/rdkit/tree/Release_2025_09_4 (URL)

Software

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