Release_2025.03.2

(Changes relative to Release_2025.03.1)

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)

Filip Chmielewski, David Cosgrove, Bryan Kelley, Niels Maeder, Dan Nealschneider, Axel Pahl, Lauren Reid, Ricardo Rodriguez, Paolo Tosco, stewu5, yuri@FreeBSD

Backwards incompatible changes:

• atom maps on dummy atoms are now always used in the calculation of canonical atom ranks.
• 2D coordinate generation may produce different results for some molecules due to a change in the way the atom ordering is computed in the depiction code.

New Features and Enhancements:

• switch to C++20 (github pull #8039 from greglandrum)
• Speed up GetProp Python keyerrors (github pull #8372 from d-b-w)
• add property to indicate when a CIP calculation has been done (github issue #8396 from greglandrum)
• Bump MaeParser version to 1.3.2 (github pull #8404 from ptosco)
• Moving towards getting all tests to pass when using the new stereo code (github pull #8409 from greglandrum)
• Enable the chiral flag on enumerated isomers (github pull #8410 from ricrogz)
• Support pickling Shape inputs (github pull #8434 from DavidACosgrove)
• add function to overwrite setattr to only accept valid arguments (github pull #8448 from nmaeder)
• add StereoGroup.getBonds() to Python wrapper (github pull #8451 from greglandrum)
• add quick H-H bond removal to connectTheDots (github pull #8452 from greglandrum)
• Protect Python DrawOptions from bad attributes. (github pull #8453 from DavidACosgrove)
• Add a custom CXSMILES feature to indicate Zero Order Bonds (github pull #8454 from ricrogz)
• Add the safeSetattr to the rdMolFiles param objects (github pull #8457 from nmaeder)

Bug Fixes:

• MHFP package error: all Bulk functions fail to execute in Python (github issue #3102 from stewu5)
• Possible Off-by-One Bug in the ERG Implementation (github issue #8201 from apahl)
• order dependence in tautomer hash (github issue #8205 from greglandrum)
• Missing bonds in MCES when singleLargestFrag = True (github issue #8360 from laurenreid1)
• RWMol::insertMol does not update _ringStereoOtherAtom (github issue #8379 from greglandrum)
• Fix SynthonSpace build when RDK_USE_BOOST_SERIALIZATION is not defined (github pull #8380 from ptosco)
• add correct export to SynthonSpace.h (github pull #8399 from greglandrum)
• Do not free sslib until patternFpArray is still needed by the test (github pull #8407 from ptosco)
• Avoid a segfault in CoordGen when a double bond has stereo spec but no stereo atoms (github pull #8415 from ptosco)
• Overwrite end of array in PubChemShape.cpp (github issue #8416 from DavidACosgrove)
• PR #8366 triggers range errors on imines with new stereo perception (github issue #8420 from ricrogz)
• update_pains.py script does not check for pains_c.in file existence (github issue #8430 from IridiumOxide)
• fix a logic error in needsHs (github pull #8442 from greglandrum)
• Pubchem Shape: make sure cutoff is set (github pull #8446 from DavidACosgrove)
• In pubchem-shape, overlaying onto a shape does an incorrect final translation (github issue #8462 from DavidACosgrove)

Cleanup work:

• find_package(better_enums) can never find better_enums (github issue #8438 from yurivict)