Release_2024.09.5

(Changes relative to Release_2024.09.4)

Backwards incompatible changes

• Improvements have been made to the v2 tautomer hash. The hash will now be different for molecules with amides, esters, carboxylates, and related structures. There's more discussion of this in PR #8173 (https://github.com/rdkit/rdkit/pull/8173).

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)

Christopher Brown, Rubén Chaves, David Cosgrove, Oleksii Dukhno, Hussein Faara, Richard Gowers, Tad Hurst, Gareth Jones, Eisuke Kawashima, Brian Kelley, Niels Maeder, Jeremy Monat, Dan Nealschneider, Yechen Qiao, Nikitas Rontsis, Ricardo Rodriguez, Anton Siomchen, Inwan Yoo, bbu-imdea, EvaSnow, thomp-j, heng-yin, knalice

New Features and Enhancements:

• Update SMILES parsing syntax error to include bad token position (github issue #7980 from whosayn)
• SynthonSpace search timeout (github pull #8070 from DavidACosgrove)
• Conformer embedding timeout (github pull #8110 from nrontsis)
• efgs code (github pull #8145 from bbu-imdea)
• Optimisations to fingerprint search of Synthon Space (github pull #8152 from DavidACosgrove)
• Making SynthonSearch respond to Ctrl-C (github pull #8153 from DavidACosgrove)
• bump the inchi version to 1.07.2 (github pull #8176 from greglandrum)
• some optimizations of triangle smoothing and the bounds matrix code (github pull #8190 from greglandrum)
• support Ctrl-C in conformer generation (github pull #8197 from greglandrum)
• DistViolationContribs optimization (github pull #8208 from evasnow1992)
• Add option to omit brackets when drawing query atoms. (github pull #8212 from DavidACosgrove)
• Optimisation of fingerprint Synthon Search (github pull #8223 from DavidACosgrove)

Documentation:

• The Python type hint for GetMolLayers in RegistrationHash.py appears incorrect (github issue #7650 from yechenqiao)
• Add section How to Build RDKit Documentation Locally (github pull #8120 from bertiewooster)
• Expand on Explicit Valence Error - Partial Sanitization recipe (github pull #8131 from bertiewooster)
• GetAtomsMatchingQuery: Tell where to find query options for (github pull #8132 from bertiewooster)
• Explain how to run doctests locally (github pull #8135 from bertiewooster)
• Update KNIME section in GettingStartedWithContributing (github pull #8174 from knalice)
• Update InChi links (github pull #8187 from RubenChM)
• Fix typo in documentation (github pull #8220 from nmaeder)

Bug Fixes:

• rxn.RunReactants mismatch directional bonds in a heterocycle ring (github issue #7944 from m-hyin)
• Fix for removing bad stereo indications from Atropisomer parsing (github pull #7984 from tadhurst-cdd)
• HetAtomTautomerv2 detects tautomerism at carboxylate (github issue #8090 from d-b-w)
• Vulnerability fixes (github pull #8116 from thomp-j)
• symmetric ring finding not returning correct results for molecules with fragments (github issue #8121 from greglandrum)
• Fixes two out-of-bounds bugs in the InChI wrapper (github pull #8126 from greglandrum)
• Two out-of-bounds bugs in inchi interface (github issue #8129 from chbrown)
• Bad radical values are now ignored for MRV generation (github pull #8130 from tadhurst-cdd)
• INCHI-API: add_custom_command signature problem (github issue #8138 from e-kwsm)
• JavaWrappers: CMake add_custom_command has multiple comments (github issue #8139 from e-kwsm)
• Fix leaks in MIF wrappers (github pull #8143 from ricrogz)
• Fix division by zero in MIF descriptors (github pull #8144 from ricrogz)
• fix SetPositions when using strided numpy array (github pull #8150 from richardjgowers)
• Cyanamide incorrectly matches methyl-imidazole when aromaticMatchesConjugated is set (github issue #8162 from jones-gareth)
• Unify Mol rendering in IPython (github pull #8166 from asiomchen)
• improve handling of esters, amides, etc. in the v2 tautomer hash (github pull #8173 from greglandrum)
• bad conformer ID errors when drawing with unspecifiedStereoIsUnknown and prepareMolsBeforeDrawing drawoptions both set to false (github issue #8177 from oleksii-dukhno-bayer)
• Reaction Rendering Looks odd at small scales (github issue #8195 from bp-kelley)
• Rascal MCES missing an atom when ignoreAtomAromaticity is True (github issue #8198 from DavidACosgrove)
• RASCAL MCES gives duplicate results with singleLargestFrag = True (github issue #8200 from DavidACosgrove)
• Reaction products not being drawn with smooth corners (github issue #8209 from DavidACosgrove)
• Reaction drawing ignores panels, always draws across full canvas (github issue #8213 from DavidACosgrove)

Cleanup work:

• remove no-op macros and dead code (pt 2) (github pull #8035 from whosayn)
• remove no-op macros and dead code (pt 4) (github pull #8037 from whosayn)
• fix: apply modernize-use-nullptr (github pull #8134 from e-kwsm)
• relax two tolerances for ARM64 builds (github pull #8148 from tadhurst-cdd)