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2023_09_3 (Q3 2023) Release
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@greglandrum greglandrum released this 06 Dec 03:51
· 66 commits to Release_2023_09 since this release
Release_2023_09_3
60fc5a5

Release_2023.09.3

(Changes relative to Release_2023.09.2)

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)

Jason Biggs, Hussein Faara, Brian Kelley, Yoshinobu Ogura, Yakov Pechersky,
Ricardo Rodriguez-Schmidt, Leonid Stolbov, Paolo Tosco, Ivan Tubert-Brohman,
dehaenw

New Features and Enhancements:

  • Support writing detailed SMARTS queries to CTABs using the SMARTSQ mechanism
    (github issue #5819 from greglandrum)
  • Support copying of GeneralizeQueryMolecules
    (github issue #6851 from greglandrum)
  • Enable chemist-friendly depiction of R-groups
    (github pull #6866 from ptosco)
  • Allow building DetermineBonds without YAeHMOP support
    (github pull #6885 from greglandrum)
  • Add multithreading to getBestRMS and new getAllConformerBestRMS
    (github pull #6896 from greglandrum)
  • switch to catch2 v3
    (github pull #6898 from greglandrum)
  • minilib functions exposure: mmpa
    (github pull #6902 from StLeonidas)
  • Add multi-threaded versions of some MolStandardize operations
    (github pull #6909 from greglandrum)
  • Add (multithreaded) functions to the fingerprint generators for calculating multiple fingeprints in one call
    (github pull #6910 from greglandrum)
  • Add Python modules to generate stubs and automatically patch docstrings
    (github pull #6919 from ptosco)

Bug Fixes:

  • MolEnumerator: use repeat counts for SRUs when present
    (github issue #6429 from greglandrum)
  • Double bonds should not be depicted as crossed bonds in the presence of wavy bonds
    (github issue #6816 from ptosco)
  • MurckoScaffold.MakeScaffoldGeneric() has issues with isotopes
    (github issue #6836 from dehaenw)
  • Wavy bonds in mol blocks can't be stereo enumerated
    (github issue #6876 from bp-kelley)
  • CDXML read of AND1 group (specifying racemic center) gets associated into an OR1 group
    (github issue #6887 from pechersky)
  • Segfault in JSONToMols when "commonchem" is an int
    (github issue #6890 from i-tub)
  • reapplyMolBlockWedging() should retain ENDDOWNRIGHT, ENDUPRIGHT dirs
    (github issue #6893 from ptosco)
  • MMPA FragmentMol segfaults when new stereo perception is turned on
    (github issue #6900 from jasondbiggs)
  • Obtaining descriptors via Descriptors.descList results in duplication of SPS.
    (github issue #6928 from wsuzume)
  • Some Clang-specific build instructions skip some clang compilers on mac
    (github issue #6941 from whosayn)
  • With new stereo, removing H from an Imine double bond does not remove bond stereo
    (github issue #6944 from ricrogz)
  • FindMolChiralCenters should honor RDK_USE_LEGACY_STEREO_PERCEPTION
    (github issue #6945 from ricrogz)
  • generateDepictionMatching2DStructure does not optimally align when refPatt!=None, allowRGroups=False, alignOnly=True
    (github issue #6952 from ptosco)
  • GetAtomPairFingerprint yields different rooted FP from generator
    (github issue #6958 from ptosco)

Cleanup work:

  • cmake cleanup
    (github pull #6814 from greglandrum)
  • Deprecate some of the ancient python-based ML code
    (github pull #6891 from greglandrum)
  • Remove boost::regex support #6817
    (github pull #6913 from whosayn)
  • Fix minimal build, allow building without boost::serialization
    (github pull #6932 from greglandrum)

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

  • The RDKit implementation of standard machine learning algorithms are
    deprecated and will be removed in the 2024.03 release. The affected packages
    include: rdkit.ML.Composite, rdkit.ML.DecTree, rdkit.ML.KNN,
    rdkit.ML.ModelPackage, rdkit.ML.NaiveBayes, rdkit.ML.Neural
    rdkit.ML.{Analyze,Screen,Grow,Build}Composite, rdkit.ML.CompositeRun,
    rdkit.ML.EnrichPlot
Assets 2