foldseek-structural-search

1## Prerequisites
2 
31.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
4    `uv` is installed and on PATH.
52.  **User Notification**: If .licenses/foldseek_structural_search_LICENSE.txt
6    does not already exist in the workspace root directory then (1) prominently
7    notify the user to check the terms at https://search.foldseek.com/search and
8    https://github.com/steineggerlab/foldseek, then (2) create the file
9    recording the notification text and timestamp.
10 
11## Goal
12 
13Submit a user-provided 3D protein structure file (`.cif`, `.mmcif`, or `.pdb`)
14to the Foldseek web server API to find structurally similar proteins. Report the
15top structural hits, interpret key alignment metrics, summarize the inferred
16protein functions, save the Markdown-formatted table to a `.md` file, and save
17the full detailed results to a local JSON file.
18 
19## Core Rules
20 
21-   **File Requirement**: This tool absolutely cannot search by sequence, name,
22    or accession ID. It strictly requires a `.pdb`, `.cif`, or `.mmcif` file
23    path.
24-   **Strict Validation**: Never bypass the input validation or the database
25    allowlist check.
26-   **Do Not Parse the JSON**: Rely entirely on the generated `.md` file for
27    your immediate summary. The JSON is saved purely for subsequent, specialized
28    tool use.
29-   **No Raw Parsing**: Do not attempt to parse or read the raw 3D coordinates
30    yourself; always pass the file to the script.
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