Bump rdkit from 2025.9.6 to 2026.3.3

[dependabot]

Bumps rdkit from 2025.9.6 to 2026.3.3.

Release notes

Sourced from rdkit's releases.

2026_03_3 (Q1 2026) Release

Release_2026.03.3

(Changes relative to Release_2026.03.2)

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)

Reza Bagheri Alashti, Marco Ballarotto, Kevin Boyd, David Cosgrove, Gareth Jones, Huw Jones, Steven Kearnes, Brian Kelley, Clay Moore, Dan Nealschneider, Emily Rhodes, Ricardo Rodriguez, Raul Sofia, Chris Von Bargen

New Features and Enhancements:

• CIP labeller performance: Don't calculate auxiliary descriptors unnecessarily (github pull #9171 from d-b-w)
• Add optional default value to Mol.GetProp() in Python (github issue #9241 from emilyrrhodes)
• CIPLabeler performance: Store vector of bonds (github pull #9250 from d-b-w)
• Pandastools improvements (github pull #9251 from marcobICR)
• Add MMFF Property Getter functions to python interface (github issue #9253 from scal444)
• [bot] Update molecular templates header file (github pull #9269 from github-actions[bot])
• Adds some features to the C# SWIG wrappers (github pull #9274 from jones-gareth)
• MolDrawOptions: Option for Uniform Bond Colour with Coloured Atom Labels (github issue #9282 from hdj-elixirsoftware)
• add checked atom and bond iterators (github pull #9290 from greglandrum)
• Adds MolToCDXMLBlock to FileParsers (github pull #9291 from bp-kelley)
• add ability to block atoms/bonds from participating in tautomer zones (github pull #9297 from greglandrum)
• Improve synthon substructure search performance ~20% (github pull #9305 from d-b-w)

Documentation:

• Docs: fix CosineSimilarity formula and clarify similarity metric names in BitOps.h (github pull #9264 from rezabagher)

Bug Fixes:

• Extended fix for #9101 (github pull #9255 from RaulSofia)
• Segfault when calling MolToSmiles on submol (github issue #9270 from ricrogz)
• DrawText::setFontScale Atom Font Scaling Issue (github issue #9280 from hdj-elixirsoftware)

... (truncated)

Changelog

Sourced from rdkit's changelog.

Release_2026.09.1

(Changes relative to Release_2026.03.1)

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)

Highlights

Backwards incompatible changes:

• Since #9208, atom rings are "normalized" so that the first atom in the ring definition is the one with the lowest index, and the second one is the neighbor to the first which also has the lowest index.

Code removed in this release:

• The version of hanoiSort() that takes raw pointers has been removed. Please use the version that takes std::span and std::vector.
• Chirality::StereoInfo::NOATOM (C++) and Chem.StereoInfo.NOATOM (Python) have been removed. Please use Atom::NOATOM and Chem.Atom.NOATOM.

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

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.

... (truncated)

Commits

• See full diff in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)