Add conformer RMSD docs and fix MMFF benchmark build after API change

[evasnow1992]

Add conformer RMSD to feature list (docs/index.rst) and API reference (docs/api/nvmolkit.rst) — missing since PR #105.

Fix mmff_multimol_bench.cpp build error: MMFFOptimizeMoleculesConfsBfgs now takes MMFFProperties instead of raw nonBondedThreshold (changed in PR #116).

[greptile-apps]

Greptile Summary

This PR makes two independent, targeted fixes: it adapts the MMFF benchmark to the MMFFProperties-based API introduced in PR #116, and it backfills the conformer RMSD feature (added in PR #105) into both the feature list (docs/index.rst) and the API reference (docs/api/nvmolkit.rst).

• benchmarks/mmff_multimol_bench.cpp: Replaces the now-removed raw nonBondedThreshold argument with an nvMolKit::MMFFProperties struct and sets properties.nonBondedThreshold = 100.0, matching the original value exactly. The fix is correct and minimal.
• docs/api/nvmolkit.rst: New "Conformer RMSD" autosummary section references conformerRmsd.GetConformerRMSMatrix and conformerRmsd.GetConformerRMSMatrixBatch — both names are verified to match nvmolkit/conformerRmsd.py's __all__ list.
• docs/index.rst: Single-line feature bullet added consistently with the surrounding list style.

No issues found across any of the three files.

Confidence Score: 5/5

• Safe to merge — all changes are correct, minimal, and well-scoped.
• Both the C++ build fix and the documentation additions are straightforward and accurate. No logic errors, no missing side-effects, and the documented API names match the actual Python module. No P0/P1 findings.
• No files require special attention.

Important Files Changed

Filename	Overview
benchmarks/mmff_multimol_bench.cpp	Adapts the BFGS benchmark call to pass MMFFProperties struct instead of a raw nonBondedThreshold float, matching the API change from PR #116. Correct fix — value preserved (100.0), no other logic changed.
docs/api/nvmolkit.rst	Adds a "Conformer RMSD" autosummary section listing GetConformerRMSMatrix and GetConformerRMSMatrixBatch. Both names match the actual module's all and public API exactly.
docs/index.rst	Adds a one-line Conformer RMSD bullet to the feature list, consistent in style with the surrounding entries.

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