Agent Skills
› openai/plugins
› rcsb-pdb-skill
rcsb-pdb-skill
GitHub用于向RCSB PDB提交核心元数据查询、搜索API请求及FASTA下载。支持通过脚本获取结构化摘要或原始数据，默认返回简洁Markdown格式，适用于蛋白质结构信息检索场景。
Trigger Scenarios
查询特定PDB条目详情
搜索蛋白质结构
下载FASTA序列
Install
npx skills add openai/plugins --skill rcsb-pdb-skill -g -y
SKILL.md
Frontmatter
{
"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."
}
Operating rules
- Use
scripts/rest_request.pyfor all RCSB PDB and Search API calls. - Use
base_url=https://data.rcsb.org/rest/v1for core metadata,https://search.rcsb.org/rcsbsearch/v2for Search API, andhttps://www.rcsb.orgfor FASTA downloads. - Core entry or assembly lookups usually do not need
max_items; Search API results are better with query pager rows around10andmax_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.
Execution behavior
- 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=textso the script returns a shorttext_headunless raw output is requested.
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 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"}
Output
- Success returns
ok,source,path,method,status_code,warnings, and either compactrecords, a compactsummary, ortext_head. - Use
raw_output_pathwhensave_raw=true. - Failure returns
ok=falsewitherror.codeanderror.message.
Execution
echo '{"base_url":"https://data.rcsb.org/rest/v1","path":"core/entry/4hhb"}' | 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.
Version History
- 11c74d6 Current 2026-07-19 09:39
