Published January 30, 2026 | Version Release_2025_09_5
Software Open

rdkit/rdkit: 2025_09_5 (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_2025.09.5

(Changes relative to Release_2025.09.4)

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)

Chris Von Bargen, David Cosgrove, Tad Hurst, Eisuke Kawashima, Brian Kelley, Niels Maeder, Syed Zayyan Masud, Yakov Pechersky, Vandan Revanur, Ricardo Rodriguez, Raul Sofia, Philip Ullmann, kuzp, wszqkzqk, stephenting22, DrrDom, diogomart

New Features and Enhancements:

  • Performance improvement: Implement buffered reading for SDMolSupplier (github pull #9010 from RaulSofia)
  • Allow molzip to position fragments when joining them (github pull #9021 from greglandrum)
  • Improve POPCNT optimization flag handling to build on other arches like riscv64 and loong64 (github pull #9029 from wszqkzqk)
  • Read SD property names till the last '>' (github pull #9047 from ricrogz)
  • cleanup of stereogroups and wedges for non-chiral sites (github pull #9051 from tadhurst-cdd)
  • Store CIP-ranked anchors after CIP labeling. (github pull #9056 from ricrogz)

Bug Fixes:

  • Atom properties as SDF file data break if the array is too long (github issue #8918 from bp-kelley)
  • Handle chiral atoms with 2 hydrogens in SCSR parser (github pull #8939 from tadhurst-cdd)
  • Incorrect hydrogen bond acceptor count for N-heterocycles (github issue #8997 from stephenting22)
  • Hs labeled implicit or explicit depending on presence of 3D conformer. Chem.RemoveHs differs from MolFromMolBlock removeHs (github issue #9020 from diogomart)
  • Tversky for zero prototype string with alpha=1 and beta=0 returns incorrect output (github issue #9033 from DrrDom)
  • SIGSEGV in rdFMCS.FindMCS when params.StoreAll = True (github issue #9034 from kuzp)
  • BestAlignmentParams does not compile on macos due to clang issues (github issue #9041 from pechersky)
  • CXSMILES: do not add separators for unserializable Substance Groups (github pull #9048 from ricrogz)
  • Prevent CIP labels of bonds from being calculated twice. (github pull #9052 from ricrogz)
  • added FABS to test for issue #4364 (github pull #9053 from tadhurst-cdd)
  • Fix removing (non)redundant bond dir specs when exporting SMILES (github pull #9066 from ricrogz)

Cleanup work:

  • Fix deprecated literal operators and macro redefinition warnings for modern compilers (github pull #9055 from cdvonbargen)
  • Move some more tests over to catch2 (github pull #9058 from greglandrum)
  • Transform::SetRotationFromQuaternion takes const. (github pull #9063 from DavidACosgrove)

Documentation:

  • Update deprecation messages for valence methods (github pull #9050 from philipullmann)

Deprecated code (to be removed in a future release):

  • Chirality::StereoInfo::NOATOM (C++) and Chem.StereoInfo.NOATOM (Python) have been deprecated in favor of Atom::NOATOM and Chem.Atom.NOATOM.

Files

rdkit/rdkit-Release_2025_09_5.zip

Files (86.2 MB)

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md5:68912e04066a150c32b47f281bfd9a64
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Additional details

Related works

Is supplement to
Software: https://github.com/rdkit/rdkit/tree/Release_2025_09_5 (URL)

Software

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