[scal444]

RDKit 2026.09 builds the ETKDG torsion terms after the topology bounds, which now record forced amide/ester 1-4 configurations that become torsion terms, and keeps one experimental torsion per central bond. nvMolKit used the legacy setTopolBounds overload before initETKDG, so those torsions were dropped and duplicate central-bond terms were kept.

• Set topology bounds through a version-aware helper that uses the EmbedParameters overload and records path14Configs on 2026.09.
• Run initETKDG after bounds setup on 2026.09.
• Keep the first experimental torsion per central bond on 2026.09.
• Reject parameters nvMolKit does not implement instead of ignoring them: all-in-one refinement, embedForceField=MMFF, onlyInitialEmbedding and internal-coordinate initial embedding. embedMolecules validates them before looking at the molecules.
• Treat initialEmbeddingMode=RANDOM_COORDINATE_EMBEDDING as useRandomCoords. RDKit 2026.09 deprecates the flag for the mode but still applies its random-coordinate basin threshold and 4D embedding only for the flag. As in RDKit, useRandomCoords also selects that mode, overriding internal-coordinate embedding.
• Tests: forced amide torsion and one term per central bond on 2026.09, experimental torsion energies against RDKit's construct3DForceField, 2026.09 hexane bounds, 2026.09 chiral dist-matrix failure count, each rejected setting in C++ and Python, embedding with only the random-coordinate mode set, and drop the positional EmbedParameters constructor removed in 2026.03.4.

[greptile-apps]

Confidence Score: 5/5

[Medium impact] The PR appears safe to merge; no actionable defects were established.

Summary

Updates ETKDG setup for RDKit 2026.09 while keeping the older setup behind version checks.

• RDKit 2026.09 bounds now feed forced amide and ester paths into ETKDG torsions.
• Each central bond contributes at most one experimental torsion on RDKit 2026.09.
• Embedding rejects unsupported settings and treats random-coordinate mode as random starts.

No actionable issues were established. Tests were not run.

_{Reviews (2) · Last reviewed commit: "Match RDKit 2026.09 standard ETKDG setup" · Reviewed by Greptile}

[scal444]

This is 1 of 4 for getting to parity with RDKit 2026.9 ETKDG

[evasnow1992]

Changes look good to me.