alphafold-database-fetch-and-analyzelisted

# AlphaFold Database: Fetch and Analyze ## 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/alphafold_database_fetch_and_analyze_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://alphafold.ebi.ac.uk/, then (2) create the file recording the notification text and timestamp. ## Overview Downloads AlphaFold predicted structures (mmCIF) and Predicted Aligned Error (PAE) matrices from the AlphaFold Database for a given UniProt ID, then performs automated heuristic analysis on structural confidence (pLDDT), intrinsically disordered regions, rigid domain boundaries, and inter-domain flexibility. **Do NOT use when:** - The user only has a protein name, gene name, or amino acid sequence (no UniProt ID) — ask them to look up the ID on [UniProt](https://www.uniprot.org). - The user wants to search for structural homologs (use **Foldseek**). - The user wants to run AlphaFold predictions on a custom sequence. - The user needs experimental PDB structures (use **RCSB PDB**). ## Core Rules - **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully. - Do not attempt to calculate domain boundaries or asse