Release_2025.09.2

(Changes relative to Release_2025.09.1)

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)

Jakub Adamczyk, Chris Von Bargen, David Cosgrove, Andrew Dirksen, Tad Hurst, Gareth Jones, Brian Kelley, Niels Maeder, Josh A. Mitchell, Rachael Pirie, Ricardo Rodriguez, Paolo Tosco, Ivan Tubert-Brohman, marlon2468morales-hue, spparel

Backwards incompatible changes:

• Simple AND queries are now merged into atoms. E.g. [C&+] now produces the the same result as [C+] when parsed as SMARTS.
• Molecules which do not have potential chiral centers or stereobonds will no longer have the "_CIPRank" atom property set by default. If you want to force the calculation of pseudo-CIP ranks, you can call Chem.ComputeAtomCIPRanks(). Note that if you just want a symmetry-aware canonical ranking of the atoms in a molecule, it is more efficient to use Chem.CanonicalRankAtoms(mol, breakTies=False).
• The behavior of H removal has changed slightly: hydrides will no longer removed by default, as this changes the global charge of the mol.
• MolToSmarts() no longer adds implicit hydrogens to atoms without queries. The one exception to this is for chiral atoms, which will still have an implicit H added if present.

New Features and Enhancements:

• MolFromSmiles scales quadratically with chain length (github issue #8776 from i-tub)
• Allow Multiple Core Hits in the Same Molecule in RGroupDecomposition (github pull #8813 from DavidACosgrove)
• Merge simple AND queries onto atoms. (github pull #8830 from ricrogz)
• Implement a mechanism to patch .pyi files as proposed in #8749 (github pull #8835 from ptosco)
• allow default radii in the DCLV calculation (github pull #8836 from greglandrum)
• Address #8840 by implementing dpi parameter in PandasTools.SaveXlsxFromFrame() (github pull #8841 from ptosco)
• Add safeSetattr to more params / options objects (github pull #8842 from nmaeder)
• add Reaction From Smiles python wrapper (github pull #8843 from RPirie96)
• Use properties in the MolDrawOptions python wrappers to make setting/getting colours easier (github pull #8857 from greglandrum)
• Minor docstring tweak. (github pull #8860 from DavidACosgrove)
• set up performance benchmarks (github pull #8865 from bddap)

Bug Fixes:

• Hydrides in organometallics removed when parsing (github issue #8726 from spparel)
• CSharp wrapper fails to build on Linux (github issue #8801 from jones-gareth)
• Setting maxAttempts vs maxIterations in EmbedMolecule (github issue #8807 from j-adamczyk)
• Allowed list atoms should be read as dummy atoms (github issue #8820 from cdvonbargen)
• Aromaticity perception with list queries depends on ordering of atoms (github issue #8823 from greglandrum)
• Install expat lib in static builds (github pull #8832 from ricrogz)
• Allow labeled atoms to have working queries (github pull #8849 from bp-kelley)
• A fix and some refactoring for substructure highlighting in notebooks (github pull #8851 from greglandrum)
• use bond labels in the ranking in MolFragmentToSmiles (github pull #8861 from greglandrum)
• Calling atom.SetQuery(None) segfaults (github issue #8877 from bp-kelley)
• Whitespace mangled in GetPropsAsDict() (github issue #8890 from Yoshanuikabundi)
• Partial fix to a problem with implicit Hs being written to SMARTS (github pull #8893 from greglandrum)
• Change docs in Python EmbedMultipleConfs. (github pull #8900 from DavidACosgrove)