This toolkit is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.

```bibtex theme={null} @article{kunzmann2023biotite, title={Biotite: new tools for a versatile {Python} bioinformatics library}, author={Kunzmann, Patrick and M{\"u}ller, Tom David and Greil, Maximilian and Krumbach, Jan Hendrik and Anter, Jacob Marcel and Bauer, Daniel and Islam, Faisal and Hamacher, Kay}, journal={BMC Bioinformatics}, volume={24}, number={1}, pages={236}, year={2023}, publisher={BioMed Central}, doi={10.1186/s12859-023-05345-6} } @article{labesse1997psea, title={{P-SEA}: a new efficient assignment of secondary structure from {C}$\alpha$ trace of proteins}, author={Labesse, Gilles and Colloc'h, Nathalie and Pothier, Joel and Mornon, Jean-Paul}, journal={Bioinformatics}, volume={13}, number={3}, pages={291--295}, year={1997}, publisher={Oxford University Press}, doi={10.1093/bioinformatics/13.3.291} } ```

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### Structure Quality Metrics (`structure-metrics`) Computes five quality metrics for each input structure: `helix_pct`, `sheet_pct`, `loop_pct` (secondary-structure composition on the 0 to 100 scale), `longest_alpha_helix` (residue count of the longest contiguous alpha-helical segment), and `gyration_radius` (radius of gyration in Å). Inputs are passed as a list of structures and results are returned in the same order. #### API Reference

Source Structures to analyze. Accepts file paths, raw PDB/CIF content strings, or `Structure` objects per item. Raw structure content in PDB or CIF format. Format of the content string (auto-detected if omitted). What the B-factor column represents. Optional source identifier (filepath or tool name). Associated metrics (e.g., pLDDT, pTM scores, per-chain lists, pairwise matrices). None values are stripped at construction.

Source Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Per-structure quality metrics, index-aligned with `inputs.structures`. Name of the metric that best summarizes the result overall (e.g. `"avg_plddt"` for AlphaFold2). Used by downstream UI and reporting to pick a headline value. Concrete Metrics subclass tag; enables typed reconstruction after a serialization round-trip. **Metrics** (one set per `metrics` item) | Metric | Type | Range | Availability | | --------------------- | ----- | ------------ | ------------ | | `longest_alpha_helix` | int | ≥ 0.0 | always | | `gyration_radius` | float | ≥ 0.0 | always | | `helix_pct` | float | 0.0 to 100.0 | always | | `sheet_pct` | float | 0.0 to 100.0 | always | | `loop_pct` | float | 0.0 to 100.0 | always |

#### Applications This tool is appropriate as a fast first-pass filter for batch screening of predicted protein structures. Representative applications include flagging predicted structures with unrealistically long alpha helices that often arise as artifacts on low-confidence regions, identifying extended or disordered conformations that fail to fold compactly, summarising the secondary-structure composition of a designed protein, and ranking generated structures by structural plausibility before more expensive downstream analyses. #### Usage Tips * **Inputs accept a list of `Structure` objects, file paths, or raw PDB or mmCIF content strings.** A single bare input is automatically wrapped in a list. Each item is coerced to a `Structure` before analysis. * **All five metrics are computed over every chain of the input structure.** There is no per-chain breakdown at the tool level. To analyse a specific chain, extract that chain into its own `Structure` using `Structure.select_chain()` before passing it in. * **Filter thresholds depend on the protein family.** A 50-residue alpha helix is a strong artifact signal for a typical globular protein but is normal for coiled-coil and fibrous proteins. A gyration radius above 45 Å indicates failed folding for a 1000-residue protein but is expected for naturally elongated proteins. Calibrate thresholds against known structures of the protein family being screened. * **The `secondary_structure_percentages` summary and `longest_alpha_helix` use the same P-SEA assignment.** The helix percentage and longest contiguous helix length are derived from the same per-residue annotation, so a structure with `helix_pct=80` and `longest_alpha_helix=200` indicates that nearly the entire structure is one continuous helix.