Release_2024.03.2

(Changes relative to Release_2024.03.1)

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)

Christoph Berg, Anna Brünisholz, Michael Cho, David Cosgrove, Andrew Dalke, Peter Eastman, Tad Hurst, Gareth Jones, Brian Kelley, Daniel Levine, Yakov Pechersky, Ricardo Rodriguez, Matt Swain, Paolo Tosco, Riccardo Vianello

Backwards incompatible changes

• The SMARTS for the unbranched alkanes in the fragment descriptors has been corrected. This descriptor will now frequently return different results.

New Features and Enhancements:

• Added JSON parameters to MinimalLib get_(cx)?sm(ile|art)s() functions (github pull #7194 from ptosco)
• Include macrocycles in atropisomer calculation by not sanitizing them away (github pull #7291 from pechersky)
• C# Build Net6 library and tests using cmake (github pull #7326 from jones-gareth)
• Add option for RASCAL to restrict atom matching to atoms of same degree (github pull #7344 from DavidACosgrove)
• Add MolStandardize to C# wrappers (github pull #7351 from jones-gareth)
• CDXML parser doesn't recognize any bonds (github issue #7357 from bp-kelley)
• Allow reapplyMolBlockWedging() to restore the original wedging regardless the bond type (github pull #7386 from rvianello)
• Add option for non-isomeric SMILES creation in the PostgreSQL cartridge (github pull #7395 from rvianello)

Bug Fixes:

• Correct unbranched alkane SMARTS to match the description given (github #7255 from levineds)
• restrict the application of 1,3- 1,5- conjugated cation normalization (github pull #7287 from rvianello)
• DetermineBondOrders() does not assign single bonds correctly (github issue #7299 from peastman)
• re-enable yaehmop support in DetermineBonds (github pull #7316 from greglandrum)
• AtomPairs.Utils.NumPiElectrons fails on atoms with dative bonds (github issue #7318 from ricrogz)
• Wedge bond from atrop error (github pull #7321 from tadhurst-cdd)
• Remove misleading walrus operators (github pull #7323 from mcs07)
• SaltRemover may clear computed properties even if no atoms are removed (github issue #7327 from ricrogz)
• DetermineBondOrders() makes incorrect assumptions about valence (github issue #7331 from peastman)
• remove some warnings with -Wextra (github pull #7339 from greglandrum)
• Fixes problem from discussion 7317 (github pull #7345 from DavidACosgrove)
• Trigonal Pyramid Carbon may or not have a parity depending on atom ordering (github issue #7346 from ricrogz)
• fixes bug with overly large count_bounds (github pull #7368 from greglandrum)
• Fix the Uncharger 'force' option w/ non-neutralizable negatively charged sites (github pull #7382 from rvianello)
• Do not apply the normalization of conjugated cations to the oxime oxygen (github pull #7403 from rvianello)

Cleanup work:

• Code/PgSQL: Fix Pointer vs Datum (Compatibility with PG16) (github pull #6733 from df7cb)
• switch to range-based for loops (github pull #7278 from AnnaBruenisholz)
• Cleaner forloops, deleting of empty header file (github pull #7320 from AnnaBruenisholz)
• Make ctest run installed tests if RDK_INSTALL_PYTHON_TESTS (github pull #7325 from mcs07)
• cleanup RDKit::MolOps::detectBondStereochemistry (github pull #7329 from rvianello)
• Cleanup of Code/DataStructs (github pull #7365 from AnnaBruenisholz)
• Fixes #7378, raw docstring to escape null chars (github pull #7379 from pechersky)
• Include header for boost::numeric_cast (github pull #7389 from cho-m)