molclaw-fpocket

name	molclaw-fpocket
description	Use fpocket to detect binding pockets and output their detailed properties for the input protein. This offers a more concise approach to pocket identification.
license	MIT license
metadata	{"skill-author":"PJLab"}

Pocket Detection

Note:

• Local files are not directly accessible by the server. Please upload them to the server using molclaw-file-transfer before execution.
• For PDB file inputs, it is recommended to preprocess them using molclaw-pdbfixer before execution.
• Please refer to skill molclaw-scp-server to complete tool invocation.

The description of tool fpocket_toolkit.

Detect binding pockets in a protein structure using fpocket_toolkit.
Args:
    pdb_file (str): Input PDB/mmCIF file path to scan for pockets (required)
    top_n (int): Limit returned pockets to the top N by druggability score; 0 means return all (default: 0)
    min_druggability (float | None): Filter out pockets below this druggability threshold (0.0~1.0); None means no filter (default: None)
    verbose (bool): Request verbose descriptor parsing during the run for detailed logging (default: False)
Return:
    status (str): 'success' or 'error'
    msg (str): Human-readable narrative about the run
    run_dir (str): Absolute directory storing this run's results
    output_dir (str): Path where fpocket preserved its raw outputs
    pockets (List[Dict[str, Any]]): Parsed pocket descriptors, including scores, centers, and residue contacts
    pocket_count (int): Number of pockets returned after filtering
    output_files (Dict[str, str]): Preserved fpocket output files such as info, pymol scripts, etc.
    exported (Dict[str, str] | None): Export metadata when export_path is provided
    files (Dict[str, str]): All files created under the run_dir