alphafold-skill

## 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 ```bash 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`.