2026_03_1 (Q1 2026) Release

[greglandrum]

Release_2026.03.1

(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, Jimmy Kromann, Phong Lam, Niels Maeder,
Josh A. Mitchell, Dan Nealschneider, Yakov Pechersky, Patrick Penner, 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, dkranthi221, EvaSnow, Pavel, stephenting22, Paul, paconius, spparel,
wszqkzqk, Diogo, dehaenw

Highlights

• A significant number of known SMILES canonicalization problems were resolved.
• It's now possible to provide your own matching functions to supplement or
  replace the defaults when doing substructure matching.
• An experimental new implementation of shape-based alignment using Gaussians.
• Improvements to the molecular templates for 2D depiction and handling of
  macrocycles in the templates.

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 MolFromSmiles scales quadratically with chain length #8776 from i-tub)
• Add extract mol fragment api
  (github pull Add extract mol fragment api #8811 from bp-kelley)
• Allow Multiple Core Hits in the Same Molecule in RGroupDecomposition
  (github pull Allow Multiple Core Hits in the Same Molecule in RGroupDecomposition #8813 from DavidACosgrove)
• Merge simple AND queries onto atoms.
  (github pull Merge simple AND queries onto atoms. #8830 from ricrogz)
• Implement a mechanism to patch .pyi files as proposed in InChI module typehints #8749
  (github pull Implement a mechanism to patch .pyi files as proposed in #8749 #8835 from ptosco)
• allow default radii in the DCLV calculation
  (github pull allow default radii in the DCLV calculation #8836 from greglandrum)
• Address Any way to increase the resolution of Mol Object in PandasTools.SaveXlsxFromFrame() without changing the size? #8840 by implementing dpi parameter in PandasTools.SaveXlsxFromFrame()
  (github pull Address #8840 by implementing dpi parameter in PandasTools.SaveXlsxFromFrame() #8841 from ptosco)
• Add safeSetattr to more params / options objects
  (github pull Add safeSetattr to more params / options objects #8842 from nmaeder)
• add Reaction From Smiles python wrapper
  (github pull add Reaction From Smiles python wrapper #8843 from RPirie96)
• Incremental synthon search
  (github pull Incremental synthon search #8855 from jgullingsrud)
• Use properties in the MolDrawOptions python wrappers to make setting/getting colours easier
  (github pull Use properties in the MolDrawOptions python wrappers to make setting/getting colours easier #8857 from greglandrum)
• Minor docstring tweak.
  (github pull Minor docstring tweak. #8860 from DavidACosgrove)
• Move some fields and methods from AtomPDBResidueInfo to base class
  (github pull Move some fields and methods from AtomPDBResidueInfo to base class #8863 from rachelnwalker)
• set up performance benchmarks
  (github pull set up performance benchmarks #8865 from bddap)
• [CONTRIB]: Freewilson now keeps the coordinates passed in
  (github pull [CONTRIB]: Freewilson now keeps the coordinates passed in #8868 from bp-kelley)
• add more benchmarking
  (github pull add more benchmarking #8878 from bddap)
• Improve DetermineBonds and DetermineBondOrders performance
  (github pull Improve DetermineBonds and DetermineBondOrders performance #8888 from ChiCheng45)
• added new attributes for scsr template as per BIOVIA doc 2023
  (github pull added new attributes for scsr template as per BIOVIA doc 2023 #8911 from tadhurst-cdd)
• Allow using generators for similarity maps
  (github pull Allow using generators for similarity maps #8912 from greglandrum)
• Return original molecule from StereoisomerEnumerator when no unspecified stereocenters are available
  (github pull Return original molecule from StereoisomerEnumerator when no unspecified stereocenters are available #8924 from phonglam3103)
• Add function to compute shape scores without overlay.
  (github pull Add function to compute shape scores without overlay. #8950 from DavidACosgrove)
• expose Bond::invertChirality() to Python
  (github pull expose Bond::invertChirality() to Python #8951 from paconius)
• Add a couple of utility functions for working with flat matrices
  (github pull Add a couple of utility functions for working with flat matrices #8955 from nmaeder)
• Add test to watch the state of canonicalization problems reported in Smiles that can't be canonicalized - mega issue #8775
  (github pull Add test to watch the state of canonicalization problems reported in #8775 #8958 from ricrogz)
• Allow Hs to be ignored in the RMSD alignment functions
  (github pull Allow Hs to be ignored in the RMSD alignment functions #8976 from greglandrum)
• Embed Parameters to JSON
  (github pull Embed Parameters to JSON #8977 from nmaeder)
• Allow spaces and special chars in SCSR fullname attrs
  (github pull Allow spaces and special chars in SCSR fullname attrs #8982 from tadhurst-cdd)
• Allow H removal to be skipped in ShowFeats.py
  (github pull Allow H removal to be skipped in ShowFeats.py #8986 from greglandrum)
• some optimizations of AlignPoints()
  (github pull some optimizations of AlignPoints() #8987 from greglandrum)
• Allow adding custom atom and bond matcher functions for substructure searching
  (github pull Allow adding custom atom and bond matcher functions for substructure searching #8994 from greglandrum)
• Support serializing/deserializing FP generators to JSON
  (github pull Support serializing/deserializing FP generators to JSON #9000 from greglandrum)
• Stop writing so many atom properties to cxsmiles
  (github pull Stop writing so many atom properties to cxsmiles #9002 from greglandrum)
• Performance improvement: Implement buffered reading for SDMolSupplier
  (github pull Performance improvement: Implement buffered reading for SDMolSupplier #9010 from RaulSofia)
• Allow molzip to position fragments when joining them
  (github pull Allow molzip to position fragments when joining them #9021 from greglandrum)
• Improve POPCNT optimization flag handling to build on other arches like riscv64 and loong64
  (github pull Improve POPCNT optimization flag handling to build on other arches like riscv64 and loong64 #9029 from wszqkzqk)
• Read SD property names till the last '>'
  (github pull Read SD property names till the last '>' #9047 from ricrogz)
• cleanup of stereogroups and wedges for non-chiral sites
  (github pull cleanup of stereogroups and wedges for non-chiral sites #9051 from tadhurst-cdd)
• Store CIP-ranked anchors after CIP labeling.
  (github pull Store CIP-ranked anchors after CIP labeling. #9056 from ricrogz)
• Gaussian shape overlays
  (github pull Gaussian shape overlays #9095 from DavidACosgrove)
• Exclude Zero order bonds from FindRingFamilies() and add arguments for includeDativeBonds, includeHydrogenBonds
  (github pull Exclude Zero order bonds from FindRingFamilies() and add arguments for includeDativeBonds, includeHydrogenBonds #9118 from ricrogz)
• Deterministic kekulize, independent of atom and bond order
  (github pull Deterministic kekulize, independent of atom and bond order #9125 from pechersky)
• Add explicit operator= and copy c'tors to Transform3D and its base classes.
  (github pull Add explicit operator= and copy c'tors to Transform3D and its base classes. #9133 from DavidACosgrove)
• Add RDLog::CaptureLog for capturing log messages
  (github pull Add RDLog::CaptureLog for capturing log messages #9138 from cdvonbargen)
• Add MolFromInchiAndAuxInfo to restore original atom order from AuxInfo
  (github pull Add MolFromInchiAndAuxInfo to restore original atom order from AuxInfo #9158 from rodyarantes)
• Accept non-kekulisable molecules in drawMols3D.
  (github pull Accept non-kekulisable molecules in drawMols3D. #9167 from DavidACosgrove)
• Follow up to PR Fix for issue #8965 #8968
  (github pull Follow up to PR #8968 #9168 from ricrogz)
• Add 'k' extension to SMARTS to support ringsize queries
  (github pull Add 'k' extension to SMARTS to support ringsize queries #9172 from greglandrum)
• Support double* in Transform3D::TransformPoint
  (github pull Support double* in Transform3D::TransformPoint #9176 from DavidACosgrove)
• Switch to using SMARTS for 2D depiction templates
  (github pull Switch to using SMARTS for 2D depiction templates #9179 from ZontaNicola)
• Adjust lower bounds to allow intramolecular H-Bonds
  (github pull Adjust lower bounds to allow intramolecular H-Bonds #9188 from kabu00002)
• [bot] Update molecular templates header file
  (github pull [bot] Update molecular templates header file #9193 from github-actions[bot])
• useChirality support in MinimalLib (RDKit.js) on mol.get_substruct_matches
  (github pull Implement #9194 #9197 from ptosco)
• simple substructure search optimization
  (github pull simple substructure search optimization #9201 from greglandrum)
• Enable templating for macrocycles
  (github pull Enable templating for macrocycles #9203 from ZontaNicola)
• [bot] Update molecular templates header file
  (github pull [bot] Update molecular templates header file #9205 from github-actions[bot])

Documentation:

• Extra documentation for EnumerateLibraries
  (github pull Extra documentation for EnumerateLibraries #8909 from DavidACosgrove)
• Update installation instructions for building RDKit from source for macOS
  (github pull Update installation instructions for building RDKit from source for macOS  #8928 from phonglam3103)
• Fixed Typo in Getting Started Docs
  (github pull Fixed Typo in Getting Started Docs #8947 from PatrickPenner)
• Update deprecation messages for valence methods
  (github pull Update deprecation messages for valence methods #9050 from philipullmann)
• fix the python docs for CanonicalRankAtomsInFragment
  (github pull fix the python docs for CanonicalRankAtomsInFragment #9087 from greglandrum)
• Confusing Deprecation Warning regarding GetImplicitValence
  (github issue Confusing Deprecation Warning regarding GetImplicitValence #9117 from kienerj)
• Update The SSSR Problem GetSSSR Documentation
  (github pull Update The SSSR Problem GetSSSR Documentation #9121 from JacksonBurns)

Bug Fixes:

• rdShapeAlign is sensitive to starting conformation
  (github issue rdShapeAlign is sensitive to starting conformation #8513 from priley-vv)
• Hydrides in organometallics removed when parsing
  (github issue Hydrides in organometallics removed when parsing #8726 from spparel)
• CSharp wrapper fails to build on Linux
  (github issue CSharp wrapper fails to build on Linux #8801 from jones-gareth)
• Setting maxAttempts vs maxIterations in EmbedMolecule
  (github issue Setting maxAttempts vs maxIterations in EmbedMolecule #8807 from j-adamczyk)
• Allowed list atoms should be read as dummy atoms
  (github issue Allowed list atoms should be read as dummy atoms #8820 from cdvonbargen)
• Aromaticity perception with list queries depends on ordering of atoms
  (github issue Aromaticity perception with list queries depends on ordering of atoms #8823 from greglandrum)
• Install expat lib in static builds
  (github pull Install expat lib in static builds #8832 from ricrogz)
• Allow labeled atoms to have working queries
  (github pull Allow labeled atoms to have working queries #8849 from bp-kelley)
• A fix and some refactoring for substructure highlighting in notebooks
  (github pull A fix and some refactoring for substructure highlighting in notebooks #8851 from greglandrum)
• use bond labels in the ranking in MolFragmentToSmiles
  (github pull use bond labels in the ranking in MolFragmentToSmiles #8861 from greglandrum)
• Multiple absolute stereo groups shouldn't be allowed on a single mol
  (github issue Multiple absolute stereo groups shouldn't be allowed on a single mol #8873 from rachelnwalker)
• Calling atom.SetQuery(None) segfaults
  (github issue Calling atom.SetQuery(None) segfaults #8877 from bp-kelley)
• Whitespace mangled in GetPropsAsDict()
  (github issue Whitespace mangled in GetPropsAsDict() #8890 from Yoshanuikabundi)
• Partial fix to a problem with implicit Hs being written to SMARTS
  (github pull Partial fix to a problem with implicit Hs being written to SMARTS #8893 from greglandrum)
• Unrecognized attachment points in synthon library results in broken molecules
  (github issue Unrecognized attachment points in synthon library results in broken molecules #8898 from jgullingsrud)
• Change docs in Python EmbedMultipleConfs.
  (github pull Change docs in Python EmbedMultipleConfs. #8900 from DavidACosgrove)
• CXSmiles strips away isotopes
  (github issue CXSmiles strips away isotopes #8906 from bp-kelley)
• Atom properties as SDF file data break if the array is too long
  (github issue Atom properties as SDF file data break if the array is too long #8918 from bp-kelley)
• Unable to build any rdkit >= 2025.3.6, when RDK_BUILD_DESCRIPTORS3D=OFF
  (github issue Unable to build any rdkit >= 2025.3.6, when RDK_BUILD_DESCRIPTORS3D=OFF #8922 from asiomchen)
• Ignore whitespace when patching RapidJSON
  (github pull Ignore whitespace when patching RapidJSON #8927 from ricrogz)
• Fixes a bug with chirality perception of T-shaped centers in very large rings
  (github pull Fixes a bug with chirality perception of T-shaped centers in very large rings #8930 from greglandrum)
• Fixes for nontetrahedral stereo parsing from SMILES/SMARTS
  (github pull Fixes for nontetrahedral stereo parsing from SMILES/SMARTS #8932 from greglandrum)
• Allow abbreviations without XBonds
  (github pull Allow abbreviations without XBonds #8933 from greglandrum)
• SVG exports of bicolor solid wedge bound not working with stroke-width
  (github issue SVG exports of bicolor solid wedge bound not working with stroke-width #8936 from EliotRagueneau)
• Handle chiral atoms with 2 hydrogens in SCSR parser
  (github pull Handle chiral atoms with 2 hydrogens in SCSR parser #8939 from tadhurst-cdd)
• Fix potential iterator invalidation
  (github pull Fix potential iterator invalidation #8944 from rietmann-nv)
• N#N=O and O=N#N parse to different mol
  (github issue N#N=O and O=N#N parse to different mol #8945 from dehaenw)
• Valence error when parsing SCSR
  (github pull Valence error when parsing SCSR #8948 from tadhurst-cdd)
• Modern stereo perception: Smiles stereochemistry inversion at rings
  (github issue Modern stereo perception: Smiles stereochemistry inversion at rings #8956 from d-b-w)
• Small fix in ring stereo/canonicalization
  (github pull Small fix in ring stereo/canonicalization #8962 from ricrogz)
• Stereo bond inversion in SMILES Writer canonicalization
  (github issue Stereo bond inversion in SMILES Writer canonicalization #8965 from ricrogz)
• stop ignoring confId in CalcMolDescriptors3D()
  (github pull stop ignoring confId in CalcMolDescriptors3D() #8967 from greglandrum)
• Valence error in scsr temlates for nitro and metal complexes
  (github pull Valence error in scsr temlates for nitro and metal complexes #8969 from tadhurst-cdd)
• Atropisomer bond is found in N-S(=O)C system
  (github issue Atropisomer bond is found in N-S(=O)C system #8973 from pechersky)
• Incorrect hydrogen bond acceptor count for N-heterocycles
  (github issue Incorrect hydrogen bond acceptor count for N-heterocycles #8997 from stephenting22)
• SynthonSpace Substructure search misses some hits
  (github issue SynthonSpace Substructure search misses some hits #9007 from DavidACosgrove)
• SynthonSpace Substructure search misses a hit - Mk2
  (github issue SynthonSpace Substructure search misses a hit - Mk2 #9009 from DavidACosgrove)
• SDMolSupplier enters an infinite loop if number of SGroups is incorrect
  (github issue SDMolSupplier enters an infinite loop if number of SGroups is incorrect #9014 from ricrogz)
• Invalid sulfonamide SMARTS in FragmentDescriptors.csv
  (github issue Invalid sulfonamide SMARTS in FragmentDescriptors.csv #9018 from scal444)
• Hs labeled implicit or explicit depending on presence of 3D conformer. Chem.RemoveHs differs from MolFromMolBlock removeHs
  (github issue Hs labeled implicit or explicit depending on presence of 3D conformer. Chem.RemoveHs differs from MolFromMolBlock removeHs #9020 from diogomart)
• Tversky for zero prototype string with alpha=1 and beta=0 returns incorrect output
  (github issue Tversky for zero prototype string with alpha=1 and beta=0 returns incorrect output #9033 from DrrDom)
• SIGSEGV in rdFMCS.FindMCS when params.StoreAll = True
  (github issue SIGSEGV in rdFMCS.FindMCS when params.StoreAll = True #9034 from kuzp)
• BestAlignmentParams does not compile on macos due to clang issues
  (github issue BestAlignmentParams does not compile on macos due to clang issues #9041 from pechersky)
• CXSMILES: do not add separators for unserializable Substance Groups
  (github pull CXSMILES: do not add separators for unserializable Substance Groups #9048 from ricrogz)
• Prevent CIP labels of bonds from being calculated twice.
  (github pull Prevent CIP labels of bonds from being calculated twice. #9052 from ricrogz)
• added FABS to test for issue Specified grid spacing for ShapeTanimotoDistance is ignored. #4364
  (github pull added FABS to test for issue #4364 #9053 from tadhurst-cdd)
• Fix removing (non)redundant bond dir specs when exporting SMILES
  (github pull Fix removing (non)redundant bond dir specs when exporting SMILES #9066 from ricrogz)
• Get things working with numpy 2.4 and pandas 3.0
  (github pull Get things working with numpy 2.4 and pandas 3.0 #9072 from greglandrum)
• Chemdraw build fails on Big-endian: cs_swapBytes.h: error: parse error in template argument list
  (github issue Chemdraw build fails on Big-endian: cs_swapBytes.h: error: parse error in template argument list #9077 from barracuda156)
• Another canonicalization fix
  (github pull Another canonicalization fix #9082 from ricrogz)
• CopyMolSubset silently rewires bonds when bondIndices reference atoms not in atomIndices
  (github issue CopyMolSubset silently rewires bonds when bondIndices reference atoms not in atomIndices #9084 from mcs07)
• CopyMolSubset ignores bondIndices when all atoms are included
  (github issue CopyMolSubset ignores bondIndices when all atoms are included #9088 from mcs07)
• Fix SMARTS for the strict definition of rotatable bonds
  (github pull Fix SMARTS for the strict definition of rotatable bonds #9096 from brje01)
• SDMolSupplier length/indexing regression in 2025.09.5 when "$$$$\n" crosses 64KiB chunk boundary
  (github issue SDMolSupplier length/indexing regression in 2025.09.5 when "$$$$\n" crosses 64KiB chunk boundary #9101 from kongexp)
• Cannot build JS bindings with MCS option enabled.
  (github pull Cannot build JS bindings with MCS option enabled. #9110 from papillot)
• DetermineBonds fails for thiolate
  (github issue DetermineBonds fails for thiolate #9114 from LaurianeJD)
• when shifting double bonds in tautomerization, set double bond stereo to STEREOANY
  (github pull when shifting double bonds in tautomerization, set double bond stereo to STEREOANY #9119 from pechersky)
• Fix link failure on macOS caused by AGL framework injection in Qt
  (github pull Fix link failure on macOS caused by AGL framework injection in Qt #9139 from cdvonbargen)
• Pyrrole molblock with explicit H is not read due to kekulization error
  (github issue Pyrrole molblock with explicit H is not read due to kekulization error #9140 from pechersky)
• ETKDGv3 generating 90 degree twisted amides
  (github issue ETKDGv3 generating 90 degree twisted amides #9143 from dkranthi221)
• PR Another canonicalization fix #9082 breaks MolFragmentToSmarts()
  (github issue PR #9082 breaks MolFragmentToSmarts() #9144 from ricrogz)
• PandasTools.SaveXlsxFromFrame is ignoring the remaining data in the dataframe when writing the .xlsx file
  (github issue PandasTools.SaveXlsxFromFrame is ignoring the remaining data in the dataframe when writing the .xlsx file #9151 from lmsigmund)
• DistGeom: disulfide pattern matches non-disulfide S-S (e.g., disulfite)
  (github issue DistGeom: disulfide pattern matches non-disulfide *S-S* (e.g., disulfite) #9165 from kabu00002)
• DistGeom: bounds get overwritten
  (github issue DistGeom: bounds get overwritten #9166 from kabu00002)
• Fix typo in _calculateBeta: check nb1 instead of nb2 twice
  (github pull Fix typo in _calculateBeta: check nb1 instead of nb2 twice #9202 from evasnow1992)

Cleanup work:

• style: apply readability-braces-around-statements
  (github pull style: apply readability-braces-around-statements #8136 from e-kwsm)
• Change extern types to static consts
  (github pull Change extern types to static consts #8765 from cdvonbargen)
• run clang-tidy and clang-format on the chemdraw files
  (github pull run clang-tidy and clang-format on the chemdraw files #8837 from greglandrum)
• Use std::string_view for property keys
  (github pull Use std::string_view for property keys #8844 from ricrogz)
• Refactor iostreams includes
  (github pull Refactor iostreams includes #8846 from ricrogz)
• Minor refactor of the python wrappers
  (github pull Minor refactor of the python wrappers #8847 from ricrogz)
• Propagate using string_view as property names
  (github pull Propagate using string_view as property names #8858 from ricrogz)
• Switch from using RapidJSON to Boost::JSON for MolInterchange
  (github pull Switch from using RapidJSON to Boost::JSON for MolInterchange #8859 from greglandrum)
• Do not add explicit Hs in assignChiralTypesFromMolParity
  (github pull Do not add explicit Hs in assignChiralTypesFromMolParity #8872 from ricrogz)
• make Point2D and Point3D constexpr
  (github pull make Point2D and Point3D constexpr #8882 from greglandrum)
• Fix for issue with deprecated boost functions for MacOS build from source
  (github pull Fix for issue with deprecated boost functions for MacOS build from source #8929 from RPirie96)
• Do not add a __computedProps property to molecules when initializing them
  (github pull Do not add a __computedProps property to molecules when initializing them #8931 from greglandrum)
• Do not reset the ringInfo information when adding bonds to RWMol
  (github pull Do not reset the ringInfo information when adding bonds to RWMol #8934 from greglandrum)
• A bunch of modernization of the ShapeHelpers code
  (github pull A bunch of modernization of the ShapeHelpers code #8954 from greglandrum)
• Minor clean up in SMILES Writing double bond canonicalization
  (github pull Minor clean up in SMILES Writing double bond canonicalization #8971 from ricrogz)
• Refactor atomVisitOrders and bondVisitOrders in SMILES Writer canonicalization
  (github pull Refactor atomVisitOrders and bondVisitOrders in SMILES Writer canonicalization #8972 from ricrogz)
• Convert graphmolMolOpsTest to catch2
  (github pull Convert graphmolMolOpsTest to catch2 #8978 from ricrogz)
• Stop using raw pointers in the canonicalization interface
  (github pull Stop using raw pointers in the canonicalization interface #8990 from greglandrum)
• Some more cleaning up in SMILES Writing
  (github pull Some more cleaning up in SMILES Writing #8991 from ricrogz)
• Converts testSubgraph2 to catch
  (github pull Converts testSubgraph2 to catch #9003 from ricrogz)
• Convert smiTest1 to catch
  (github pull Convert smiTest1 to catch #9004 from ricrogz)
• Last leak fixes for 2025!
  (github pull Last leak fixes for 2025! #9006 from ricrogz)
• move molzip to its own file
  (github pull move molzip to its own file #9013 from greglandrum)
• Convert testMolSupplier to catch2
  (github pull Convert testMolSupplier to catch2 #9015 from ricrogz)
• Fix deprecated literal operators and macro redefinition warnings for modern compilers
  (github pull Fix deprecated literal operators and macro redefinition warnings for modern compilers #9055 from cdvonbargen)
• Move some more tests over to catch2
  (github pull Move some more tests over to catch2 #9058 from greglandrum)
• Transform::SetRotationFromQuaternion takes const.
  (github pull Transform::SetRotationFromQuaternion takes const. #9063 from DavidACosgrove)
• The precondition in Bond::getOtherAtomIdx() is redundant
  (github pull The precondition in Bond::getOtherAtomIdx() is redundant #9092 from ricrogz)
• Modernize loops and clean up ring finding
  (github pull Modernize loops and clean up ring finding #9098 from ricrogz)
• Further refactoring in SSSR finding
  (github pull Further refactoring in SSSR finding #9104 from ricrogz)
• Hide data representation inside RDKit::Dict
  (github pull Hide data representation inside RDKit::Dict #9113 from bddap)
• Fix some minor annoyances in Python tests
  (github pull Fix some minor annoyances in Python tests #9132 from ricrogz)
• Small refactor before PR Fix for issue #8965 #8968 follow up
  (github pull Small refactor before PR #8968 follow up #9135 from ricrogz)
• Add suppresions for AppleClang and ChemDraw
  (github pull Add suppresions for AppleClang and ChemDraw #9147 from bp-kelley)
• More refactoring in Canon.cpp
  (github pull More refactoring in Canon.cpp #9155 from ricrogz)
• switch the Query infrastructure to use std::function instead of function pointers
  (github pull switch the Query infrastructure to use std::function instead of function pointers #9169 from greglandrum)
• Leak fixes for 2026.03.1
  (github pull Leak fixes for 2026.03.1 #9198 from ricrogz)

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.

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This discussion was created from the release 2026_03_1 (Q1 2026) Release.