Release_2025.03.3

(Changes relative to Release_2025.03.2)

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, Genevieve Evans, Tad Hurst, Kevin Keating, Brian Kelley, Jakub Klinkovský, Niels Maeder, Jeremy Monat, Yakov Pechersky, Ricardo Rodriguez, Paul Thiessen, Yi-Shu Tu, Paolo Tosco, Inwan Yoo, paconius, jdavies-nurix, InvincibleZZH, Forrest, rwalroth

New Features and Enhancements:

• Add SCSR parsing to RDKit (github pull #8147 from tadhurst-cdd)
• support clearPropertyCache() on ROMol and Atom (github issue #8241 from greglandrum)
• Change default ETversion. (github pull #8414 from DavidACosgrove)
• ShapeInput from subset of atoms in molecule (github pull #8449 from DavidACosgrove)
• Method to remove enhanced stereo from an atom (github issue #8467 from jdavies-nurix)
• Add Synthon space hit filters (github pull #8473 from DavidACosgrove)
• Set default Eigen3 version to 3.4.0 (github pull #8477 from pechersky)
• A couple optimizations to when the ring finding code is called (github pull #8482 from greglandrum)
• Allow single/double bonds to match aromatic in substructure search (github issue #8485 from PaulThiessen)
• improve operator<< for stereogroups (github pull #8489 from greglandrum)
• Print the version of InChI software being supported in RDKIt (github issue #8508 from glevans)
• Explain DrawArrow and rawCoords=True (github pull #8517 from bertiewooster)
• add support for allene- and cumulene-like structures to KDG (github pull #8518 from greglandrum)
• allow limiting the number of stereo groups to process (github pull #8541 from tadhurst-cdd)
• Replace incorrect Freetype cmake flags with correct ones (github pull #8543 from ptosco)
• Add missing default values to docker-compose configuration (github pull #8544 from ptosco)
• Avoid a large number of warnings when building MinimalLib with emscripten (github pull #8545 from ptosco)
• Add a "time out" to determineBondOrders (github pull #8548 from ricrogz)
• rdkit-targets.cmake now uses cmake package names for external libraries instead of absolute paths (github pull #8552 from KevKeating)
• Support Ctrl+C in determineBondOrders (github pull #8557 from ricrogz)

Documentation:

• Add documentation for SynthonSpaceSearch. (github pull #8293 from DavidACosgrove)
• Clarify Docstring of molzip when called with a Single mol object (github pull #8470 from badisa)

Bug Fixes:

• GetAtomConjGrpIdx documentation indicates it returns a signed int, but actually returns unsigned int (github issue #7112 from rwalroth)
• Chem.MolToSmiles: rootedAtAtom option not working properly with multiple fragments (github issue #8327 from iwyoo)
• Inconsistent SMARTS representation for stereochemical aromatic bonds (github issue #8424 from iwyoo)
• MolToJSON doesn't handle atropisomers (github issue #8460 from paconius)
• Postgres Cartridge Equality Shouldn't use coordinates (github issue #8465 from paconius)
• Build failure with GCC 15 (github issue #8491 from lahwaacz)
• TautomerQuery drops queries for some atoms (github issue #8492 from ricrogz)
• rdkit/rdkit/Chem/Features /ShowFeats.py TypeError: not all arguments converted during string formatting (github issue #8501 from InvincibleZZH)
• Synthon space substructure search failing for simple search (github issue #8502 from greglandrum)
• Fix arrowhead8500 (github pull #8504 from DavidACosgrove)
• Invalid read in moldraw2DTestCatch (github issue #8520 from ricrogz)
• Chem.GetMolFrags Destroys Stereogroups containing only bonds (github issue #8527 from paconius)
• Fix ETKDG double bond check from #8518 (github pull #8528 from nmaeder)
• SynthonSpaceSearch bad chiral atom count (github issue #8554 from DavidACosgrove)
• Explicitly wrap raw pointer into emscripten::val object with allow_raw_pointers() policy (github pull #8555 from ptosco)

Cleanup work:

• Consolidate MinimalLib Dockerfiles to avoid code duplication (github pull #8412 from ptosco)
• Modernization of some substructure code (github pull #8450 from greglandrum)
• A few mem fixes in tests (github pull #8521 from ricrogz)
• Fix irritating warning when DrawMolMCHLasso compiled. (github pull #8540 from DavidACosgrove)