Release_2026.03.1b1 (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, Rody Arantes, Kevin Boyd, Jessica Braun, Katharina Buchthal, Jackson Burns, Chi Cheng, David Cosgrove, Andrew Dirksen, Sergey Fedorov, Justin Gullingsrud, Tad Hurst, Lauriane Jacot-Descombes, Gareth Jones, Eisuke Kawashima, Brian Kelley, Joos Kiener, Phong Lam, Niels Maeder, Josh A. Mitchell, Dan Nealschneider, Yakov Pechersky, PatrickPenner, Paul Pillot, Rachael Pirie, Eliot Ragueneau, Max Rietmann, Pat Riley, Ricardo Rodriguez, Lukas Sigmund, Anton Siomchen, Raul Sofia, Matt Swain, Paolo Tosco, Ivan Tubert-Brohman, Philip Ullmann, Chris Von Bargen, Rachel Walker, Nic Zonta, 空酱, Pavel, stephenting22, Paul, paconius, spparel, wszqkzqk, Diogo, dehaenw Highlights Backwards incompatible changes: The Dict class (and therefore all the properties interfaces) has been updated to std::string_view keys. This is transparent to the Python interfaces, but some C++ class might have to be updated. 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. Molecules no longer have a __computedProps property by default. The property is added whenever it's needed. The property is considered private (as indicated by the leading underscores) and shouldn't be used in client code, but if your code relies on its presence in molecules, you may need to check for it and add it yourself. RWMol::addBond() no longer removes RingInfo from the molecule, but it does clear the property cache of the begin and end atoms. This does not affect the general rule that molecules should be sanitized after adding/removing bonds. The algorithm to canonicalize double bonds in SMILES output has changed to address a potential issue that could alter stereo. As a result, SMILES of mols contaning stereo bonds may have changed. The Query infrastructure now uses std::function instead of function pointers for the DataFunc and MatchFunc. This does not affect Python. The results of the Kekulize() function are now, by default, no longer dependent on atom/bond ordering in the molecule. Additionally, the C++ API for MolOps::Kekulize(), MolOps::KekulizeIfPossible() and MolOps::KekulizeFragment() has been changed: these all now accept an optional argument toggling the canonical Kekulization. New Features and Enhancements: MolFromSmiles scales quadratically with chain length (github issue #8776 from i-tub) Add extract mol fragment api (github pull #8811 from bp-kelley) 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) Incremental synthon search (github pull #8855 from jgullingsrud) 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) Move some fields and methods from AtomPDBResidueInfo to base class (github pull #8863 from rachelnwalker) set up performance benchmarks (github pull #8865 from bddap) [CONTRIB]: Freewilson now keeps the coordinates passed in (github pull #8868 from bp-kelley) add more benchmarking (github pull #8878 from bddap) Improve DetermineBonds and DetermineBondOrders performance (github pull #8888 from ChiCheng45) added new attributes for scsr template as per BIOVIA doc 2023 (github pull #8911 from tadhurst-cdd) Allow using generators for similarity maps (github pull #8912 from greglandrum) Return original molecule from StereoisomerEnumerator when no unspecified stereocenters are available (github pull #8924 from phonglam3103) Add function to compute shape scores without overlay. (github pull #8950 from DavidACosgrove) expose Bond::invertChirality() to Python (github pull #8951 from paconius) Add a couple of utility functions for working with flat matrices (github pull #8955 from nmaeder) Add test to watch the state of canonicalization problems reported in #8775 (github pull #8958 from ricrogz) Allow Hs to be ignored in the RMSD alignment functions (github pull #8976 from greglandrum) Embed Parameters to JSON (github pull #8977 from nmaeder) Allow spaces and special chars in SCSR fullname attrs (github pull #8982 from tadhurst-cdd) Allow H removal to be skipped in ShowFeats.py (github pull #8986 from greglandrum) some optimizations of AlignPoints() (github pull #8987 from greglandrum) Allow adding custom atom and bond matcher functions for substructure searching (github pull #8994 from greglandrum) Support serializing/deserializing FP generators to JSON (github pull #9000 from greglandrum) Stop writing so many atom properties to cxsmiles (github pull #9002 from greglandrum) Performance improvement: Implement buffered reading for SDMolSupplier (github pull #9010 from RaulSofia) Allow molzip to position fragments when joining them (github pull #9021 from greglandrum) Improve POPCNT optimization flag handling to build on other arches like riscv64 and loong64 (github pull #9029 from wszqkzqk) Read SD property names till the last '>' (github pull #9047 from ricrogz) cleanup of stereogroups and wedges for non-chiral sites (github pull #9051 from tadhurst-cdd) Store CIP-ranked anchors after CIP labeling. (github pull #9056 from ricrogz) Exclude Zero order bonds from FindRingFamilies() and add arguments for includeDativeBonds, includeHydrogenBonds (github pull #9118 from ricrogz) Deterministic kekulize, independent of atom and bond order (github pull #9125 from pechersky) Add explicit operator= and copy c'tors to Transform3D and its base classes. (github pull #9133 from DavidACosgrove) Add RDLog::CaptureLog for capturing log messages (github pull #9138 from cdvonbargen) Add MolFromInchiAndAuxInfo to restore original atom order from AuxInfo (github pull #9158 from rodyarantes) Accept non-kekulisable molecules in drawMols3D. (github pull #9167 from DavidACosgrove) Follow up to PR #8968 (github pull #9168 from ricrogz) Add 'k' extension to SMARTS to support ringsize queries (github pull #9172 from greglandrum) Support double* in Transform3D::TransformPoint (github pull #9176 from DavidACosgrove) Switch to using SMARTS for 2D depiction templates (github pull #9179 from ZontaNicola) Adjust lower bounds to allow intramolecular H-Bonds (github pull #9188 from kabu00002) [bot] Update molecular templates header file (github pull #9193 from github-actions[bot]) Documentation: Extra documentation for EnumerateLibraries (github pull #8909 from DavidACosgrove) Update installation instructions for building RDKit from source for macOS (github pull #8928 from phonglam3103) Fixed Typo in Getting Started Docs (github pull #8947 from PatrickPenner) Update deprecation messages for valence methods (github pull #9050 from philipullmann) fix the python docs for CanonicalRankAtomsInFragment (github pull #9087 from greglandrum) Confusing Deprecation Warning regarding GetImplicitValence (github issue #9117 from kienerj) Update The SSSR Problem GetSSSR Documentation (github pull #9121 from JacksonBurns) Bug Fixes: rdShapeAlign is sensitive to starting conformation (github issue #8513 from priley-vv) 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) Multiple absolute stereo groups shouldn't be allowed on a single mol (github issue #8873 from rachelnwalker) 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) Unrecognized attachment points in synthon library results in broken molecules (github issue #8898 from jgullingsrud) Change docs in Python EmbedMultipleConfs. (github pull #8900 from DavidACosgrove) CXSmiles strips away isotopes (github issue #8906 from bp-kelley) Atom properties as SDF file data break if the array is too long (github issue #8918 from bp-kelley) Unable to build any rdkit >= 2025.3.6, when RDK_BUILD_DESCRIPTORS3D=OFF (github issue #8922 from asiomchen) Ignore whitespace when patching RapidJSON (github pull #8927 from ricrogz) Fixes a bug with chirality perception of T-shaped centers in very large rings (github pull #8930 from greglandrum) Fixes for nontetrahedral stereo parsing from SMILES/SMARTS (github pull #8932 from greglandrum) Allow abbreviations without XBonds (github pull #8933 from greglandrum) SVG exports of bicolor solid wedge bound not working with stroke-width (github issue #8936 from EliotRagueneau) Handle chiral atoms with 2 hydrogens in SCSR parser (github pull #8939 from tadhurst-cdd) Fix potential iterator invalidation (github pull #8944 from rietmann-nv) N#N=O and O=N#N parse to different mol (github issue #8945 from dehaenw) Valence error when parsing SCSR (github pull #8948 from tadhurst-cdd) Modern stereo perception: Smiles stereochemistry inversion at rings (github issue #8956 from d-b-w) Small fix in ring stereo/canonicalization (github pull #8962 from ricrogz) Stereo bond inversion in SMILES Writer canonicalization (github issue #8965 from ricrogz) stop ignoring confId in CalcMolDescriptors3D() (github pull #8967 from greglandrum) Valence error in scsr temlates for nitro and metal complexes (github pull #8969 from tadhurst-cdd) Atropisomer bond is found in N-S(=O)C system (github issue #8973 from pechersky) Incorrect hydrogen bond acceptor count for N-heterocycles (github issue #8997 from stephenting22) SynthonSpace Substructure search misses some hits (github issue #9007 from DavidACosgrove) SynthonSpace Substructure search misses a hit - Mk2 (github issue #9009 from DavidACosgrove) SDMolSupplier enters an infinite loop if number of SGroups is incorrect (github issue #9014 from ricrogz) Invalid sulfonamide SMARTS in FragmentDescriptors.csv (github issue #9018 from scal444) Hs labeled implicit or explicit depending on presence of 3D conformer. Chem.RemoveHs differs from MolFromMolBlock removeHs (github issue #9020 from diogomart) Tversky for zero prototype string with alpha=1 and beta=0 returns incorrect output (github issue #9033 from DrrDom) SIGSEGV in rdFMCS.FindMCS when params.StoreAll = True (github issue #9034 from kuzp) BestAlignmentParams does not compile on macos due to clang issues (github issue #9041 from pechersky) CXSMILES: do not add separators for unserializable Substance Groups (github pull #9048 from ricrogz) Prevent CIP labels of bonds from being calculated twice. (github pull #9052 from ricrogz) added FABS to test for issue #4364 (github pull #9053 from tadhurst-cdd) Fix removing (non)redundant bond dir specs when exporting SMILES (github pull #9066 from ricrogz) Get things working with numpy 2.4 and pandas 3.0 (github pull #9072 from greglandrum) Chemdraw build fails on Big-endian: cs_swapBytes.h: error: parse error in template argument list (github issue #9077 from barracuda156) Another canonicalization fix (github pull #9082 from ricrogz) CopyMolSubset silently rewires bonds when bondIndices reference atoms not in atomIndices (github issue #9084 from mcs07) CopyMolSubset ignores bondIndices when all atoms are included (github issue #9088 from mcs07) Fix SMARTS for the strict definition of rotatable bonds (github pull #9096 from brje01) SDMolSupplier length/indexing regression in 2025.09.5 when "$$$$\n" crosses 64KiB chunk boundary (github issue #9101 from kongexp) Cannot build JS bindings with MCS option enabled. (github pull #9110 from papillot) DetermineBonds fails for thiolate (github issue #9114 from LaurianeJD) when shifting double bonds in tautomerization, set double bond stereo to STEREOANY (github pull #9119 from pechersky) Fix link failure on macOS caused by AGL framework injection in Qt (github pull #9139 from cdvonbargen) Pyrrole molblock with explicit H is not read due to kekulization error (github issue #9140 from pechersky) PR #9082 breaks MolFragmentToSmarts() (github issue #9144 from ricrogz) PandasTools.SaveXlsxFromFrame is ignoring the remaining data in the dataframe when writing the .xlsx file (github issue #9151 from lmsigmund) DistGeom: disulfide pattern matches non-disulfide S-S (e.g., disulfite) (github issue #9165 from kabu00002) DistGeom: bounds get overwritten (github issue #9166 from kabu00002) Cleanup work: style: apply readability-braces-around-statements (github pull #8136 from e-kwsm) Change extern types to static consts (github pull #8765 from cdvonbargen) run clang-tidy and clang-format on the chemdraw files (github pull #8837 from greglandrum) Use std::string_view for property keys (github pull #8844 from ricrogz) Refactor iostreams includes (github pull #8846 from ricrogz) Minor refactor of the python wrappers (github pull #8847 from ricrogz) Propagate using string_view as property names (github pull #8858 from ricrogz) Switch from using RapidJSON to Boost::JSON for MolInterchange (github pull #8859 from greglandrum) Do not add explicit Hs in assignChiralTypesFromMolParity (github pull #8872 from ricrogz) make Point2D and Point3D constexpr (github pull #8882 from greglandrum) Fix for issue with deprecated boost functions for MacOS build from source (github pull #8929 from RPirie96) Do not add a __computedProps property to molecules when initializing them (github pull #8931 from greglandrum) Do not reset the ringInfo information when adding bonds to RWMol (github pull #8934 from greglandrum) A bunch of modernization of the ShapeHelpers code (github pull #8954 from greglandrum) Minor clean up in SMILES Writing double bond canonicalization (github pull #8971 from ricrogz) Refactor atomVisitOrders and bondVisitOrders in SMILES Writer canonicalization (github pull #8972 from ricrogz) Convert graphmolMolOpsTest to catch2 (github pull #8978 from ricrogz) Stop using raw pointers in the canonicalization interface (github pull #8990 from greglandrum) Some more cleaning up in SMILES Writing (github pull #8991 from ricrogz) Converts testSubgraph2 to catch (github pull #9003 from ricrogz) Convert smiTest1 to catch (github pull #9004 from ricrogz) Last leak fixes for 2025! (github pull #9006 from ricrogz) move molzip to its own file (github pull #9013 from greglandrum) Convert testMolSupplier to catch2 (github pull #9015 from ricrogz) Fix deprecated literal operators and macro redefinition warnings for modern compilers (github pull #9055 from cdvonbargen) Move some more tests over to catch2 (github pull #9058 from greglandrum) Transform::SetRotationFromQuaternion takes const. (github pull #9063 from DavidACosgrove) The precondition in Bond::getOtherAtomIdx() is redundant (github pull #9092 from ricrogz) Modernize loops and clean up ring finding (github pull #9098 from ricrogz) Further refactoring in SSSR finding (github pull #9104 from ricrogz) Hide data representation inside RDKit::Dict (github pull #9113 from bddap) Fix some minor annoyances in Python tests (github pull #9132 from ricrogz) Small refactor before PR #8968 follow up (github pull #9135 from ricrogz) Add suppresions for AppleClang and ChemDraw (github pull #9147 from bp-kelley) More refactoring in Canon.cpp (github pull #9155 from ricrogz) switch the Query infrastructure to use std::function instead of function pointers (github pull #9169 from greglandrum) Code removed in this release: Deprecated code (to be removed in a future release): The version of hanoiSort() that takes raw pointers has been deprecated. Please use the version that takes std::span and std::vector. Chirality::StereoInfo::NOATOM (C++) and Chem.StereoInfo.NOATOM (Python) have been deprecated in favor of Atom::NOATOM and Chem.Atom.NOATOM.