pdb-databaselisted

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