rcsb-pdb-skill - SKILL.md Agent Skill

name: rcsb-pdb-skill description: Submit compact RCSB PDB requests for core metadata, Search API queries, and FASTA downloads. Use when a user wants concise RCSB summaries; save raw JSON or FASTA only on request.

Use scripts/rest_request.py for all RCSB PDB and Search API calls.
Use base_url=https://data.rcsb.org/rest/v1 for core metadata, https://search.rcsb.org/rcsbsearch/v2 for Search API, and https://www.rcsb.org for FASTA downloads.
Core entry or assembly lookups usually do not need max_items; Search API results are better with query pager rows around 10 and max_items=10.
Re-run requests in long conversations instead of relying on older tool output.
Treat displayed ... in tool previews as UI truncation, not literal request content.

Return concise markdown summaries from the script JSON by default.
Prefer core metadata endpoints for focused lookups and Search API POST requests for discovery.
For FASTA downloads, use response_format=text so the script returns a short text_head unless raw output is requested.

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 RCSB patterns:
- {"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}
- {"base_url":"https://search.rcsb.org/rcsbsearch/v2","path":"query","method":"POST","json_body":{"query":{"type":"terminal","service":"full_text","parameters":{"value":"hemoglobin"}},"return_type":"entry","request_options":{"pager":{"start":0,"rows":10}}},"record_path":"result_set","max_items":10}
- {"base_url":"https://www.rcsb.org","path":"fasta/entry/4HHB/download","response_format":"text"}

Success returns ok, source, path, method, status_code, warnings, and either compact records, a compact summary, or text_head.
Use raw_output_path when save_raw=true.
Failure returns ok=false with error.code and error.message.

echo '{"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}' | python scripts/rest_request.py

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