Release_2024.09.3

(Changes relative to Release_2024.09.2)

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)

François Bérenger, Eric Boittier, Jessica Braun, Michael Cho, David Cosgrove, Hussein Faara, Richard Gowers, Tad Hurst, Eisuke Kawashima, Brian Kelley, Alan Kerstjens, Daniel McNeela, Rocco Moretti, Dan Nealschneider, Jin Pan, Patrick Penner, Ricardo Rodriguez, Vincent F. Scalfani, Evan Senter, Julius Seumer, Efim Shats, Scott Smith, Paolo Tosco, Ivan Tubert-Brohman, Fabio Urbina, Franz Waibl, Nic Zonta, SPKorhonen, YOUNG-JAME, esiaero, Polydynamical, sirbiscuit, marcobICR, jasondbiggs, nbehrnd

New Features and Enhancements:

• Update reaction fingerprints to use generators (github issue #7521 from vfscalfani)
• Allow inclusion of molecule names in ScaffoldNetwork (github pull #7956 from PatrickPenner)
• SynthonSpace Search (github pull #7978 from DavidACosgrove)
• Update SMILES parsing syntax error to include bad token position (github pull #7979 from whosayn)
• Expose tautomer scoring functions to python (github pull #7994 from bp-kelley)
• Explicit valence for charged organic atoms when creating a MolBlock (github issue #8023 from greglandrum)
• improve defaults for the shape-based alignment (github pull #8029 from greglandrum)
• Synthon fingerprint search (github pull #8025 from greglandrum)

Documentation:

• expanded documentation in Chem and AllChem (github pull #8004 from greglandrum)
• Mol to smiles docs (github pull #8005 from DavidACosgrove)
• fixing the doc string in the shape alignment code (github pull #8040 from brje01)
• Improve doc string for ParseAbbreviations in python wrapper. (github pull #8049 from DavidACosgrove)

Bug Fixes:

• Online Documentation: Mol.GetAtoms and Mol.GetBonds miss signatures (github issue #7527 from e-kwsm)
• Chem.MolToSmiles(mol, rootedAtAtom=pos), when the parameter rootedAtAtom is greater than or equal to 20, the range error is reported. (github issue #7572 from YOUNG-JAME)
• MergeQueryHs fails to detect explicit H involved in OR queries where there's more than 2 options in the query (github issue #7687 from ricrogz)
• Fix 4.3.0--4.4.0 sql upgrade script (github pull #7774 from esiaero)
• Catch exceptions in MultithreadedMolSupplier callbacks (github pull #7810 from i-tub)
• HasPropWithValueQueryBase::getPair() may leak the value of RDValue. (github issue #7865 from ricrogz)
• Use .dylib on macOS for PostgreSQL 16+ (github pull #7869 from cho-m)
• Fix for trimethylcyclohexane error (github pull #7949 from tadhurst-cdd)
• Fix incorrect CIP values for some aromatic atropisomers (github pull #7957 from tadhurst-cdd)
• Need to reserve space before assignment (github pull #7964 from bp-kelley)
• Fixes a regression introduced in #7582 which made all SWIG enums become type-unsafe (github pull #7972 from ptosco)
• Morgan fingerprints with chirality distinguish chiral atoms too early (github pull #7972 from greglandrum)
• Wrong SMARTS pattern in O-benzyl deprotection reaction (github issue #7989 from marcobICR)
• Fix for kekuleAtrop wedge error (github pull #7992 from tadhurst-cdd)
• RMS pruning in conformer generation misses conformers above the threshold (github issue #8001 from fwaibl)
• Fix potential division by zero in UFF TorsionAngle (github pull #8007 from ricrogz)
• Fix probe molecule transformation for ShapeAlign (github pull #8016 from greglandrum)
• DistanceConstraintContrib is not exposed to SWIG wrappers anymore (github issue #8019 from ptosco)

Cleanup work:

• ... and more mem errors fixed (github pull #7924 from ricrogz)
• SA Score updates (github pull #7928 from DavidACosgrove)
• Remove deprecation warnings by switching MinimalLib to fingerprint generators (github pull #7938 from ptosco)
• One final round of mem errors (github pull #7943 from ricrogz)
• Make sure that FreeSASA can be built as DLL on Windows (github pull #7985 from ptosco)
• Remove unused code from GraphMol/SmilesParse (github pull #7996 from whosayn)
• Throw when attempting to normalize a Zero RDGeom::Point (github pull #8008 from ricrogz)
• Avoid division by zero in DrawMol (github pull #8011 from ricrogz)
• remove no-op macros and dead code (pt 1) (github pull #8012 from whosayn)
• Avoid division by zero in AlignPoints (github pull #8013 from ricrogz)
• Fix shifting of a potentially negative number (github pull #8014 from ricrogz)
• Fix some minor issues reported by ubsan and the compiler (github pull #8015 from ricrogz)
• Remove explicit default constructor from Compute2DCoordParameters (github pull #8046 from d-b-w)