Release_2024.09.2

(Changes relative to Release_2024.09.1)

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, David Cosgrove, Tad Hurst, Brian Kelley, Zhen(Jack) Liu, Jeremy Monat, Dan Nealschneider, Timothy Palpant, Yakov Pechersky, Julianus Pfeuffer, Ricardo Rodriguez, Fio Ruggiu, Eva Snow, Paolo Tosco, Kollin Trujillo, UENO, M., bzoracler, esiaero

New Features and Enhancements:

• Fix canonicalization of stereogroups (github pull #7041 from tadhurst-cdd)
• Carry over enhanced stereochemistry groups from reaction product templates to products (github issue #7669 from jpfeuffer)
• Simple speed up for CIPLabeler (github pull #7826 from d-b-w)
• Additional compatibility updates for commutator/negator settings for … (github pull #7834 from esiaero)
• Support Writing CX Extensions for Reactions (github pull #7838 from KollinRT)
• Expose preset color palettes to MinimalLib through JSON (github pull #7853 from ptosco)
• Another 2x performance improvement in CIP labelling (github pull #7854 from d-b-w)
• Improve Morgan Fingerprint Performance (github pull #7862 from scal444)
• [IterateCIPRanks] Precompute neighbor indices and counts, sort them together for each atom (github pull #7889 from scal444)
• Optimize Butina Clustering for Performance and Expand API (github pull #7892 from evasnow1992)
• Expose three ROMol methods which were not previously exposed to SWIG wrappers (github pull #7895 from ptosco)
• Sort CIP entries in place using a lightweight wrapper, only sort tied entries (github pull #7911 from scal444)
• Only save the most recent CIP rank for sorting (github pull #7932 from scal444)
• Add to Cookbook "Include a Bond Index" recipe and image (github pull #7939 from bertiewooster)
• Updates to the Docs/Book directory (github pull #7942 from greglandrum)

Bug Fixes:

• Python SIGSEGV when calling rdkit.Chem.rdmolops.SplitMolByPDBResidues on some molecules (github issue #5599 from bzoracler)
• Tautomer canonicalizer invariant violation (github issue #7044 from fioruggiu)
• rdMolAlign.GetBestRMS gets stuck (github issue #7685 from LiuCMU)
• Fix 4.3.0--4.4.0 sql upgrade script (github pull #7774 from esiaero)
• RWMol::insertMol should not add an empty ABSOLUTE_STEREO group unnecessarily (github issue #7782 from ptosco)
• Setting an atom's pdb residue number with None segfaults (github issue #7873 from bp-kelley)
• Fix inversion of stereo with canonicalizeConformer (github pull #7878 from greglandrum)
• Restore "oops, exponential is a pain" code snippet in the RGD algorithm (github pull #7898 from ptosco)
• Fix some more mem errors in 2024.09.1 (github pull #7899 from ricrogz)
• AssignStereochemistry(cleanIt=True) does not clean _CIPCode property on bonds (github issue #7929 from ricrogz)

Cleanup work:

• Fix some mem errors in 2024.09.1 (github pull #7867 from ricrogz)
• FindPython Development.Module instead of Development (github pull #7881 from pechersky)
• Use smart pointer for buffer. (github pull #7883 from DavidACosgrove)
• Modernise ExplicitBitVect. (github pull #7884 from DavidACosgrove)
• Update PUBCHEMSHAPE_URL and remove patch code (github pull #7900 from eunos-1128)
• Fix misnamed test (github pull #7952 from ricrogz)