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Published May 30, 2024 | Version Release_2024_03_3
Software Open

rdkit/rdkit: 2024_03_3 (Q1 2024) Release

Authors/Creators

  • 1. CozChemIx Limited
  • 2. Glysade LLC
  • 3. @schrodinger
  • 4. @DEShawResearch
  • 5. IBM Research
  • 6. @merckgroup
  • 7. University of Alabama
  • 8. Schrödinger
  • 9. MPI of Molecular Physiology (Dortmund)
  • 10. The University of Tokyo

Description

Release_2024.03.3

(Changes relative to Release_2024.03.2)

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)

Anna Brünisholz, David Cosgrove, Eloy Félix, Tad Hurst, Gareth Jones, Brian Kelley, Yuanyue Li, Mark Mackey, Syed Zayyan Masud, Ricardo Rodriguez, Philip
Ullmann, kekulai-fredchang,

New Features and Enhancements:

  • Update MinimalLib for Function Exposure: runReactants (github pull #7210 from syedzayyan)
  • Expose replaceAtomWithQueryAtom to Python (github pull #7380 from DavidACosgrove)
  • C sharp rascal mcs wrapper (github pull #7390 from jones-gareth)
  • No coords atropisomers - fix smiles output of atrop wedges after reordering (github pull #7418 from tadhurst-cdd)
  • Handle query atoms and bonds in SWIG wrappers (github pull #7431 from jones-gareth)
  • Expose a couple of additional functions to Python (github pull #7444 from greglandrum)
  • Expose the property pickle options to SWIG (github pull #7448 from greglandrum)

Bug Fixes:

  • Mistake in converting Phosphinic acid to InChI (github issue #5311 from YuanyueLi)
  • Rountripping through MaeWriter and MaeMolSupplier leaks stereo status property (github issue #7153 from ricrogz)
  • incorrect chiral carbon perception in Chem.FindMolChiralCenters new implementation (github issue #7300 from eloyfelix)
  • Wedge bond from atrop error (github pull #7355 from tadhurst-cdd)
  • RegistrationHash.GetMolLayers does not distinguish atropisomers (github issue #7367 from ricrogz)
  • Atropisomeric bond wedging should favor ring bonds (github issue #7371 from greglandrum)
  • DetectChemistryProblems fails with traceback when run on mols coming from aromatic SMARTS (github issue #7375 from ricrogz)
  • Allow disabling output of dative bonds to SMILES (github pull #7384 from greglandrum)
  • fix a lifetime bug in the fingerprint generator (github pull #7408 from greglandrum)
  • drawing mol with a non zero confID results in bad confID error (github issue #7409 from kekulai-fredchang)
  • CXSmiles writer does not use default conformer ID (github issue #7414 from greglandrum)
  • allow static builds to work with clang and no coordgen (github pull #7416 from greglandrum)
  • fixStructureCheckerBuildError - fix location of MolFileSterechem.h (github pull #7420 from tadhurst-cdd)
  • Planar amide nitrogen incorrectly flagged as _ChiralityPossible (github issue #7434 from mark-mackey-cresset)
  • MaeWriter: handle the R group label property and update the Maestro property prefixing (github pull #7454 from ricrogz)
  • Memory leakage in CachedSmilesMolHolder (github issue #7457 from philipullmann)
  • Remove unnecessary wrapped pointers (github pull #7465 from bp-kelley)

Cleanup work:

  • Cleanup: Force field (github pull #7406 from AnnaBruenisholz)

Files

rdkit/rdkit-Release_2024_03_3.zip

Files (83.4 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/rdkit/rdkit/tree/Release_2024_03_3 (URL)