Issues

• Synthon Space shape search doesn't test hits in similarity order

  bug
  rdkit/rdkit#9744 · Filter by author DavidACosgrove opened on Oct 24, 2026

• EmbedMultipleConfs with randomSeed=0 generates identical conformers

  bug
  rdkit/rdkit#9738 · Filter by author rjgildea opened on Oct 22, 2026

• ReactionToCXSmiles: incorrect enhanced-stereo atom index after canonical reactant reordering

  rdkit/rdkit#9732 · Filter by author NatalyLo opened on Oct 20, 2026

• CI: Windows_VS2022_x64_dll times out because the 1G ccache thrashes

  bug
  rdkit/rdkit#9729 · Filter by author Ardx19 opened on Oct 18, 2026

• postgres cartridge update from 4.7.0 to 4.8.0 fails

  bug
  rdkit/rdkit#9709 · Filter by author pechersky opened on Oct 13, 2026 · 2026_09_2
  2

  

• Read and write V3000 bond enhanced stereo collections (STEBABS, STEBRACn, STEBRELn)

  enhancement
  rdkit/rdkit#9705 · Filter by author jepdavidson opened on Oct 10, 2026

• Canonical SMILES not unique for rings with pseudoasymmetric centres with the new stereo perception (inositol)

  bug
  rdkit/rdkit#9701 · Filter by author jepdavidson opened on Oct 10, 2026
  2

• Reaction product E/Z stereo depends on reactant template order (_UnknownStereoRxnBond cleared during the first reactant's pass)

  bug
  rdkit/rdkit#9691 · Filter by author jpfeuffer opened on Oct 9, 2026
  2

• Allene stereochemistry lost upon SMILES -> mol -> SMILES round trip

  bug
  rdkit/rdkit#9678 · Filter by author SPlamondonTAI opened on Oct 6, 2026
  1

• Merging explicit hydrogens loses or inverts tetrahedral chirality

  bug
  rdkit/rdkit#9675 · Filter by author vdhaehnke opened on Oct 6, 2026

• 8 tests fail with SEGVs, precondition errors, Bost serialization registration, etc

  rdkit/rdkit#9666 · Filter by author yurivict opened on Oct 2, 2026
  3

• Possible missing stereo clean?

  rdkit/rdkit#9656 · Filter by author d-b-w opened on Sep 30, 2026
  1

• XyzParent functions are missing in the rdMolStandardize Python documentation

  bug
  rdkit/rdkit#9651 · Filter by author apahl opened on Sep 29, 2026

• Variant analysis: 3 unfixed sibling safety gaps in rdkit

  rdkit/rdkit#9647 · Filter by author x4evexnol opened on Sep 28, 2026
  1

• Bridgehead stereocenter with two ring-closure digits as first SMILES atom inverts CIP parity on MolToSmiles/MolFromSmiles round-trip (legacy stereo perception)

  bug
  rdkit/rdkit#9646 · Filter by author miglioremd-gh opened on Sep 27, 2026
  3

• Bridged bicyclic/polycyclic structures collapse when prefer_coordgen / CoordGen is enabled

  bug
  rdkit/rdkit#9638 · Filter by author m-lintolonappan opened on Sep 25, 2026

• CalcNumAtomStereoCenters() changes after identity RenumberAtoms() on bicyclic amines

  bug
  rdkit/rdkit#9629 · Filter by author braydonsprojects opened on Sep 19, 2026

• Clarify mol_from_smiles vs qmol_from_smarts for substruct_count queries in Postgresql cartridge

  enhancement
  rdkit/rdkit#9624 · Filter by author dpdoughe opened on Sep 18, 2026

• Improve depiction of RNA

  enhancement
  rdkit/rdkit#9617 · Filter by author rachelnwalker opened on Sep 18, 2026

• Tracking: nanobind wrapper improvements

  rdkit/rdkit#9601 · Filter by author skearnes opened on Sep 16, 2026
  1

• MolToInchi adds spurious /b stereo for symmetric ylidene with 2D coordinates

  bug
  rdkit/rdkit#9586 · Filter by author pechersky opened on Sep 15, 2026

• rdkit reports "Explicit valence for atom # 0 S, 7, is greater than permitted" for six-valent sulfur?

  rdkit/rdkit#9581 · Filter by author hrp1000 opened on Sep 11, 2026
  6

• Conflicting prototypes for function distdriver()

  bug
  rdkit/rdkit#9575 · Filter by author fxcoudert opened on Sep 9, 2026
  3

• Add context managers to handle config options in python tests

  enhancement
  rdkit/rdkit#9559 · Filter by author greglandrum opened on Sep 2, 2026

• Enable Link-Time-Optimization for production builds

  enhancement
  rdkit/rdkit#9554 · Filter by author scal444 opened on Aug 31, 2026
  3