feat: add protein folding stability benchmark

[lwalew]

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Summary

Adds the protein folding stability benchmark, migrated from the MLIP Audit suite. For a small set of proteins (chignolin, tryptophan cage, and an orexin/hypocretin fragment) an NVT molecular dynamics simulation is run at 300 K starting from the native folded reference conformation, and the model's ability to keep each protein folded is measured along the trajectory.

Reported metrics:

• RMSD — C-alpha RMSD from the native reference structure, averaged over the trajectory and across proteins (lower is better).
• TM score — TM score of each frame against the native reference, averaged over the trajectory and across proteins (closer to 1 is better).
• Rgyr deviation — maximum absolute deviation of the radius of gyration from the initial folded state, across proteins (lower is better).

The interactive app shows a line plot of the RMSD from the reference structure along the trajectory, averaged across proteins, for each model.

This benchmark introduces a new top-level biomolecules category (app tab, category YAML, and docs page). It also adds the shared mlipaudit wiring (optional extra, grace conflict entry, and [tool.uv.sources] git pin to the mlpeg-migration branch) plus the mlip_audit framework entry. This wiring is shared with other in-flight MLIP Audit migration PRs (e.g. ring planarity, water RDF, protein sampling), so overlap on pyproject.toml, frameworks.yml, and the biomolecules category files is expected and will be resolved at merge.

Linked issue

Resolves #725

Progress

• Calculations
• Analysis
• Application
• Documentation

Testing

End-to-end model runs are pending the upload of the input data to S3 (inputs/biomolecules/protein_folding_stability/protein_folding_stability.zip). All pre-commit hooks (ruff check, ruff format, numpydoc-validation, file checks) pass locally, and the new modules compile cleanly. The implementation follows the established MLIP Audit migration pattern (see the ring planarity and water RDF benchmarks).

New decorators/callbacks

None. The RMSD trajectory line plot reuses the existing @plot_scatter decorator (show_line=True, show_markers=False) and the plot_from_table_column callback.