Release_2025.09.1

(Changes relative to Release_2025.03.1)

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, Jason Biggs, Joshua Black, J.B. Brown, Anna Brünisholz, Kevin Boyd, Filip Chmielewski, Michael Cho, Brian Cole, David Cosgrove, Nia Dickson, Maria Dolotova, Genevieve Evans, Hussein Faara, Eloy Félix, Peter Gedeck, Noah Herrington, Tad Hurst, Eisuke Kawashima, Kevin Keating, Brian Kelley, Jakub Klinkovský, Patrick Kunzmann, Niels Maeder, Mark Mackey, Jeremy Monat, Dan Nealschneider, Axel Pahl, Yakov Pechersky, Rachael Pirie, Shashir Reddy, Vandan Revanur, Ricardo Rodriguez, Eric Taw, Paul Thiessen, Caleb Thomas, Paolo Tosco, Inwan Yoo, badisa, dehaenw, dpdoughe, getuem, InvincibleZZH, jdavies-nurix, Kacper-Kozubowski, paconius, rwalroth, Saul, Stephen, yuri@FreeBSD

Highlights

• We have added a parser for the self-contained sequence representation (SCSR) file format.
• There is an updated parser for the CDXML file format and a new parser for CDX files
• Multiple improvements to the shape-based alignment code have been made.

Backwards incompatible changes:

• atom maps on dummy atoms are now always used in the calculation of canonical atom ranks.
• 2D coordinate generation may produce different results for some molecules due to a change in the way the atom ordering is computed in the depiction code.
• The includeRingMembership argument to GetMorganAtomInvGen() is now mandatory. Previously, the default value was False.
• Default ET-version in ForceFields::CrystalFF::getExperimentalTorsions() is changed from 1 to 2.

New Features and Enhancements:

• switch to C++20 (github pull #8039 from greglandrum)
• Add SCSR parsing to RDKit (github pull #8147 from tadhurst-cdd)
• support clearPropertyCache() on ROMol and Atom (github issue #8241 from greglandrum)
• Speed up GetProp Python keyerrors (github pull #8372 from d-b-w)
• Expose reading/writing PNG metadata to CFFI and MinimalLib (github pull #8381 from ptosco)
• add property to indicate when a CIP calculation has been done (github issue #8396 from greglandrum)
• Bump MaeParser version to 1.3.2 (github pull #8404 from ptosco)
• Moving towards getting all tests to pass when using the new stereo code (github pull #8409 from greglandrum)
• Enable the chiral flag on enumerated isomers (github pull #8410 from ricrogz)
• Change default ETversion. (github pull #8414 from DavidACosgrove)
• Support pickling Shape inputs (github pull #8434 from DavidACosgrove)
• add function to overwrite setattr to only accept valid arguments (github pull #8448 from nmaeder)
• ShapeInput from subset of atoms in molecule (github pull #8449 from DavidACosgrove)
• add StereoGroup.getBonds() to Python wrapper (github pull #8451 from greglandrum)
• add quick H-H bond removal to connectTheDots (github pull #8452 from greglandrum)
• Protect Python DrawOptions from bad attributes. (github pull #8453 from DavidACosgrove)
• Add a custom CXSMILES feature to indicate Zero Order Bonds (github pull #8454 from ricrogz)
• Add the safeSetattr to the rdMolFiles param objects (github pull #8457 from nmaeder)
• 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)
• Cpp enumerate stereoisomers (github pull #8563 from DavidACosgrove)
• Bump maeparser to 1.3.3 (fixes #8525) (github pull #8580 from ricrogz)
• CIP labeler: attempt to resolve "easy" stereo centers first (github pull #8582 from ricrogz)
• Allow creation of bond-only stereogroups from Python (github issue #8584 from paconius)
• Make assignCIPLabels Ctrl+c interruptable (github pull #8589 from ricrogz)
• Expose the onlyWedgeFlags parameter to SWIG ClearSingleBondDirFlags (github pull #8600 from ptosco)
• Add option to draw all CIP codes in DrawMol.cpp (github pull #8609 from paconius)
• Update SMARTS parsing syntax error to include bad token position (github issue #8612 from whosayn)
• ChemDraw Document and read/write support for the RDKit (github pull #8620 from bp-kelley)
• Expose CDX support to FileParsers and ChemDraw to SWIG (github pull #8681 from bp-kelley)
• Add the useRingTemplates option to generateDepictionMatching2DStructure (github pull #8688 from ricrogz)
• Assign COST=100 to PgSQL functions during CREATE FUNCTION rather than leaving unspecified (github issue #8711 from dpdoughe)
• DCLV updates (github pull #8756 from RPirie96)
• Document Options in RGroupDcompose and other minor docs fixes (github pull #8757 from badisa)
• Fix non matchine if(x) end(x) statement (github pull #8769 from bp-kelley)
• support bond property lists in SDF (github pull #8778 from greglandrum)
• Implement new drawingExtentsInclude MolDrawOption (github pull #8783 from ptosco)
• Render all ROMol objects as images during export using PandasTools.SaveXlsxFromFrame (github issue #8793 from NoahHerrington)
• update default ET version to 2 in getExperimentalTorsions (github pull #8798 from nmaeder)
• allow custom shape points (github pull #8799 from greglandrum)
• Stop External/rapidjson-1.1.0 and Code/RDGeneral going to ${CMAKE_SOURCE_DIR} (github issue #8809 from jblack-mestre)
• Return draw coords (github pull #8815 from ptosco)
• Patch RapidJSON to make sure it builds on all platforms (github pull #8818 from ptosco)

Bug Fixes:

• MHFP package error: all Bulk functions fail to execute in Python (github issue #3102 from stewu5)
• Can't roundtrip CHEMBL4080644 through SMILES (github issue #5078 from greglandrum)
• SMILES canonicalization not idempotent (github issue #5124 from getuem)
• GetAtomConjGrpIdx documentation indicates it returns a signed int, but actually returns unsigned int (github issue #7112 from rwalroth)
• GETAWAY descriptors seem nondeterministic (github issue #7264 from j-adamczyk)
• Possible Off-by-One Bug in the ERG Implementation (github issue #8201 from apahl)
• order dependence in tautomer hash (github issue #8205 from greglandrum)
• Multithreaded mol reader can hang when not iterating through the whole file (github issue #8284 from bp-kelley)
• Chem.MolToSmiles: rootedAtAtom option not working properly with multiple fragments (github issue #8327 from iwyoo)
• RWMol::insertMol does not update _ringStereoOtherAtom (github issue #8379 from greglandrum)
• Fix SynthonSpace build when RDK_USE_BOOST_SERIALIZATION is not defined (github pull #8380 from ptosco)
• add correct export to SynthonSpace.h (github pull #8399 from greglandrum)
• Do not free sslib until patternFpArray is still needed by the test (github pull #8407 from ptosco)
• Avoid a segfault in CoordGen when a double bond has stereo spec but no stereo atoms (github pull #8415 from ptosco)
• Overwrite end of array in PubChemShape.cpp (github issue #8416 from DavidACosgrove)
• PR #8366 triggers range errors on imines with new stereo perception (github issue #8420 from ricrogz)
• Inconsistent SMARTS representation for stereochemical aromatic bonds (github issue #8424 from iwyoo)
• update_pains.py script does not check for pains_c.in file existence (github issue #8430 from IridiumOxide)
• fix a logic error in needsHs (github pull #8442 from greglandrum)
• Pubchem Shape: make sure cutoff is set (github pull #8446 from DavidACosgrove)
• MolToJSON doesn't handle atropisomers (github issue #8460 from paconius)
• In pubchem-shape, overlaying onto a shape does an incorrect final translation (github issue #8462 from DavidACosgrove)
• Postgres Cartridge Equality Shouldn't use coordinates (github issue #8465 from paconius)
• MolFromSmiles and MolFromSmarts accept strings containing invalid characters if they start with a valid character (github issue #8471 from jasondbiggs)
• 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)
• Issue reading .mae files (github issue #8525 from mark-mackey-cresset)
• Chem.GetMolFrags Destroys Stereogroups containing only bonds (github issue #8527 from paconius)
• Mol.GetDoubleProp() fails if any spaces in tag value (github issue #8546 from jbbrownlsi)
• SynthonSpaceSearch bad chiral atom count (github issue #8549 from DavidACosgrove)
• allow nested parentheses in tokens (github pull #8553 from tadhurst-cdd)
• Explicitly wrap raw pointer into emscripten::val object with allow_raw_pointers() policy (github pull #8555 from ptosco)
• Segmentation fault in AllChem.EmbedMolecule() (github issue #8559 from calebthomas259)
• RDKit minilib loses stereochemistry when breaking molecules to fragments (github issue #8569 from MariaDolotova)
• MolFromSmiles loses the information of "atom map number" property if cxsmiles is used (github issue #8586 from saultorre1995)
• Fixes the problems with wiggly bonds and EnumerateStereoisomers from #8506 (github pull #8598 from greglandrum)
• Fixed out of bounds vector access in GetGeodesicMatrix (github pull #8601 from ndickson-nvidia)
• Reading molecule from block gives None with no warning -- likely due to Cannot normalize a zero length vector in atropisomer code (github issue #8602 from pechersky)
• fix mrv parsing for Rgroups to make smiles work (github pull #8617 from tadhurst-cdd)
• Scsr sgroup error (github pull #8623 from tadhurst-cdd)
• ResonanceMolSupplier raises an error if Mol has no bonds (github issue #8638 from padix-key)
• Mem fixes (github pull #8640 from ricrogz)
• MultithreadedSDMolSupplier occasionally returns extra None entries (github issue #8644 from Kacper-Kozubowski)
• RascalMCES rapidly fills up memory on rdkit 2025.03 but not rdkit 2024.09 (github issue #8645 from dehaenw)
• Enhanced stereo synthons break SynthonSpace.ReadTextFile (github issue #8650 from coleb)
• RegistrationHash produces 2 separate hashes for 2636640-50-9 depending on input (github issue #8654 from jdavies-nurix)
• Incorrect canonicalization when generating CXSMILES without enhanced stereo (github issue #8655 from greglandrum)
• Incorrect MolHash when generating CXSMILES without enhanced stereo (github issue #8656 from greglandrum)
• Inconsistent default settings for Morgan atom invariant generator (github issue #8633 from gedeck)
• No Python class registered for C++ class ForceFields::PyForceField
• Canonical smiles can't be kekulized by MolFromSmiles (github issue #8670 from shashir)
• Fix parse error messages for bad characters (github pull #8675 from whosayn)
• DrawMoleculeWithHighlights doesn't use SetOffset (github issue #8679 from DavidACosgrove)
• modern stereo: canonicalization depends on bond iteration order (github issue #8689 from d-b-w)
• Fix build with Boost 1.89.0 (github pull #8694 from cho-m)
• Fix drawing of very short arcs in lasso. (github pull #8706 from DavidACosgrove)
• Forcefield Gradient Scaling misses large negative gradients (github issue #8716 from scal444)
• rdMolTransforms.CanonicalizeConformer inverts structure (github issue #8720 from DavidACosgrove)
• Two small MinimalLib RGD bug fixes (github pull #8729 from ptosco)
• Fixes a bug with bad H positions in output conformer (github pull #8731 from greglandrum)
• patch a memory allocation problem in the pubchem shape code (github pull #8733 from greglandrum) (github issue #8754 from tawe141)
• segmentation fault when parsing USPTO downloaded CDX file (github issue #8761 from eloyfelix)
• Avoid code duplication through a templated function and improve JSON parsing of Boolean flags (github pull #8773 from ptosco)
• Make InteractiveRenderer error reporting more robust and code cleanup (github pull #8774 from ptosco)
• Integer-valued list properties are not available from Python (github issue #8777 from greglandrum)
• EXCEEDED_TIMEOUT field in EmbedFailureCauses missing in Python (github issue #8806 from j-adamczyk)
• Fix leaking a PyObject in MetadataFromPNG file / string (github pull #8829 from ricrogz)

Cleanup work:

• style: apply modernize-use-override (github pull #8137 from e-kwsm)
• Consolidate MinimalLib Dockerfiles to avoid code duplication (github pull #8412 from ptosco)
• find_package(better_enums) can never find better_enums (github issue #8438 from yurivict)
• 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)
• Some cleanup of the xyz2mol code (github pull #8567 from greglandrum)
• Small cleanups of the MMFF94 code (github pull #8593 from greglandrum)
• Switch a bunch of C++ tests to use catch2 (github pull #8625 from greglandrum)
• Include <cstdint> for a couple of headers for windows compilation (github pull #8763 from cdvonbargen)

Code removed in this release:

Deprecated code (to be removed in a future release):

• The functions FileParserUtils::applyMolListPropToAtoms(), FileParserUtils::applyMolListPropsToAtoms(), and FileParserUtils::getAtomPropertyList() have been deprecated, please use FileParserUtils::applyMolListProp(), FileParserUtils::applyMolListProps(), and FileParserUtils::getPropertyList() instead.