alphafold-skill

name: alphafold-skill description: Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups. Use when a user wants AlphaFold metadata or concise structure summaries

Operating rules

• Use scripts/rest_request.py for all AlphaFold API calls.
• Use base_url=https://alphafold.ebi.ac.uk/api.
• The script accepts max_items, but set it explicitly only when trimming array-heavy responses; single-entry lookups usually do not need it.
• For sequence/summary or annotations, start around max_items=3 to 5.
• Re-run the request if the conversation is long instead of trusting older tool output.
• Treat displayed ... in tool previews as UI truncation, not part of the real request.
• If the user asks for full JSON, set save_raw=true and report the saved file path instead of pasting the payload into chat.

Execution behavior

• Return concise markdown summaries from the script JSON by default.
• Return the script JSON verbatim only if the user explicitly asks for machine-readable output.
• Prefer these paths: prediction/<qualifier>, uniprot/summary/<qualifier>.json, sequence/summary, and annotations/<qualifier>.json.
• Keep sequence-style inputs compact and prefer rerunning instead of copying prior output back into context.

Input

• Read one JSON object from stdin.
• Required fields: base_url, path
• Optional fields: method, params, headers, json_body, form_body, record_path, response_format, max_items, max_depth, timeout_sec, save_raw, raw_output_path
• Common AlphaFold patterns:
  • {"base_url":"https://alphafold.ebi.ac.uk/api","path":"prediction/Q5VSL9"}
  • {"base_url":"https://alphafold.ebi.ac.uk/api","path":"uniprot/summary/Q5VSL9.json"}
  • {"base_url":"https://alphafold.ebi.ac.uk/api","path":"annotations/Q5VSL9.json","params":{"type":"MUTAGEN"},"max_items":3}

Output

• Success returns ok, source, path, method, status_code, warnings, and either compact records or a compact summary.
• Use raw_output_path when save_raw=true.
• Failure returns ok=false with error.code such as invalid_json, invalid_input, network_error, or invalid_response.

Execution

echo '{"base_url":"https://alphafold.ebi.ac.uk/api","path":"prediction/Q5VSL9"}' | python scripts/rest_request.py

References

• No additional runtime references are required; keep the import package limited to this file and scripts/rest_request.py.