Release_2025.09.3

(Changes relative to Release_2025.09.2)

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)

David Cosgrove, Andrew Dirksen, Justin Gullingsrud, Tad Hurst, Brian Kelley, Phong Lam, Niels Maeder, Dan Nealschneider, Patrick Penner, Rachael Pirie, Max Rietmann, Ricardo Rodriguez, Anton Siomchen, Rachel Walker, dehaenw, paconius,

New Features and Enhancements:

• Incremental synthon search (github pull #8855 from jgullingsrud)
• [CONTRIB]: Freewilson now keeps the coordinates passed in (github pull #8868 from bp-kelley)
• add more benchmarking (github pull #8878 from bddap)
• added new attributes for scsr template as per BIOVIA doc 2023 (github pull #8911 from tadhurst-cdd)
• Allow using generators for similarity maps (github pull #8912 from greglandrum)
• Return original molecule from StereoisomerEnumerator when no unspecified stereocenters are available (github pull #8924 from phonglam3103)
• Add function to compute shape scores without overlay. (github pull #8950 from DavidACosgrove)
• expose Bond::invertChirality() to Python (github pull #8951 from paconius)
• Add a couple of utility functions for working with flat matrices (github pull #8955 from nmaeder)
• Add test to watch the state of canonicalization problems reported in #8775 (github pull #8958 from ricrogz)

Bug Fixes:

• Multiple absolute stereo groups shouldn't be allowed on a single mol (github issue #8873 from rachelnwalker)
• Unrecognized attachment points in synthon library results in broken molecules (github issue #8898 from jgullingsrud)
• CXSmiles strips away isotopes (github issue #8906 from bp-kelley)
• Unable to build any rdkit >= 2025.3.6, when RDK_BUILD_DESCRIPTORS3D=OFF (github issue #8922 from asiomchen)
• Ignore whitespace when patching RapidJSON (github pull #8927 from ricrogz)
• Fixes a bug with chirality perception of T-shaped centers in very large rings (github pull #8930 from greglandrum)
• Fixes for nontetrahedral stereo parsing from SMILES/SMARTS (github pull #8932 from greglandrum)
• Allow abbreviations without XBonds (github pull #8933 from greglandrum)
• Fix potential iterator invalidation (github pull #8944 from rietmann-nv)
• N#N=O and O=N#N parse to different mol (github issue #8945 from dehaenw)
• Valence error when parsing SCSR (github pull #8948 from tadhurst-cdd)
• Modern stereo perception: Smiles stereochemistry inversion at rings (github issue #8956 from d-b-w)
• stop ignoring confId in CalcMolDescriptors3D() (github pull #8967 from greglandrum)
• Valence error in scsr temlates for nitro and metal complexes (github pull #8969 from tadhurst-cdd)

Cleanup work:

• Switch from using RapidJSON to Boost::JSON for MolInterchange (github pull #8859 from greglandrum)
• Fix for issue with deprecated boost functions for MacOS build from source (github pull #8929 from RPirie96)
• Do not add a __computedProps property to molecules when initializing them (github pull #8931 from greglandrum)
• Do not reset the ringInfo information when adding bonds to RWMol (github pull #8934 from greglandrum)

Documentation:

• Extra documentation for EnumerateLibraries (github pull #8909 from DavidACosgrove)
• Update installation instructions for building RDKit from source for macOS (github pull #8928 from phonglam3103)
• Fixed Typo in Getting Started Docs (github pull #8947 from PatrickPenner)