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 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.