chore(deps): bump rdkit from 2026.3.4 to 2026.3.5 in the python-dependencies group

[dependabot]

Bumps the python-dependencies group with 1 update: rdkit.

Updates rdkit from 2026.3.4 to 2026.3.5

Release notes

Sourced from rdkit's releases.

2026_03_4 (Q1 2026) Release

Release_2026.03.4

(Changes relative to Release_2026.03.3)

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)

Rody Arantes, Katharina Buchthal, David Cosgrove, Tad Hurst, Steven Kearnes, Brian Kelley, Niels Maeder, John Mayfield, Dan Nealschneider, Yakov Pechersky, Ricardo Rodriguez, Jon Swain, Rachel Walker, Inwan Yoo, Nic Zonta, ankar-dav, ajeyabsf, thomp-j, vwe-ibm

Backwards incompatible changes:

• MolTransforms.h now includes <Eigen/Core> instead of <Eigen/Dense>. C++ code that included MolTransforms.h and relied on it to transitively pull in the Eigen dense modules (LU/QR/SVD/etc.) must now include <Eigen/Dense> directly.
• The DistGeomHelpers::EmbedParameters struct no longer has a constructor that takes arguments in C++. If you want to initialize data members to non-default values, use the designated initialization syntax. This change does not affect Python.

New Features and Enhancements:

• Add spiro flipping to 2D coord generation (github pull #9204 from ZontaNicola)
• Adds SVE to BFGSOpt (github pull #9216 from ajeyabsf)
• Multi conf gaussian shape (github pull #9265 from DavidACosgrove)
• All-In-One coordinate refinement for ETKDG (github pull #9292 from nmaeder)
• Synthon substructure search 2x performance (github pull #9307 from d-b-w)
• Configurable stereo labels in MolDraw2D (github pull #9311 from DavidACosgrove)
• Replace combineMols with RWMol::insertMol in SynthonSpaceSearch (github pull #9319 from DavidACosgrove)
• Add opt-in unity (jumbo) builds + fix latent missing include guards (github pull #9342 from skearnes)
• Make substructure search Ctrl+c interruptible (github pull #9349 from ricrogz)

Documentation:

• rdchem.pyi typing issue: non-default parameter following default parameter (github issue #9335 from ankar-dav)

Bug Fixes:

• Update RDKit_Book.rst (github pull #7946 from johnmay)

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