2024_03_1 (Q1 2024) Release

[greglandrum]

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

Bug Fixes:

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

Cleanup work:

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

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This discussion was created from the release 2024_03_1 (Q1 2024) Release.