pdb-database

1# RCSB Protein Data Bank skill
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
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82.  **User Notification**: If .licenses/pdb_database_LICENSE.txt does not
9    already exist in the workspace root directory then (1) prominently notify
10    the user to check the terms at https://www.rcsb.org/pages/usage-policy, then
11    (2) create the file recording the notification text and timestamp.
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13 
14## Core Rules
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16-   **Always prefer to use the provided scripts**. Only as a last resort use
17    `curl`, `urllib`, raw HTTP requests, or any other method to access PDB APIs.
18    The scripts automatically enforce required rate limits.
19-   **Always redirect output to a file**. Parse output with e.g. `jq`, `grep`,
20    or a short Python snippet. Do NOT print large API responses to stdout to
21    avoid truncation.
22-   **Notification**: If this skill is used, ensure this is mentioned in the
23    output.
24-   **Explain your queries** On completing a task that used PDB JSON/GraphQL
25    queries, explain in clear language what your query did so the user can
26    correct any bad assumptions.
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28## Attribute-based search workflow
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301.  **Fetch the relevant schema** to discover searchable attribute names. For
31    structure attributes: `uv run scripts/fetch_schema.py --api search_structure
32    --output schema_structure.txt` For chemical attributes: `uv run
33    scripts/fetch_schema.py --api search_chemical --output schema_chemical.txt`
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