molclaw-fpocket-toolkit-base

name	molclaw-fpocket-toolkit-base
description	Detect binding pockets with fpocket_toolkit and return parsed pocket descriptors and run artifacts.
license	MIT license
metadata	{"skill-author":"PJLab"}

fpocket_toolkit Pocket Detection

Note:

• Local files are not directly accessible by the server. Please upload them to the server using drugsda-file-transfer before execution.
• For PDB file inputs, it is recommended to preprocess them using drugsda-fix_pdb before execution.

Usage

2. Pocket Detection

The description of tool fpocket_toolkit.

Detect pockets with fpocket_toolkit and store every run under the tool_result/fpocket_result directory.
Args:
    pdb_file (str): Input PDB/mmCIF file to scan (required).
    top_n (int): Limit returned pockets to the top N (0 = all). Default: 0.
    min_druggability (float|None): Filter out pockets below this threshold. Default: None.
    verbose (bool): Enable verbose descriptor parsing during the run. Default: False.
Return:
    status (str): 'success' or 'error'.
    msg (str): Human-readable narrative about the run.
    run_dir (str): Absolute directory storing this run.
    output_dir (str): Path where fpocket preserved its outputs.
    pockets (List[Dict[str, Any]]): Parsed pocket descriptors, including scores and centers.
    pocket_count (int): Number of pockets returned.
    output_files (Dict[str, str]): Preserved fpocket output files.
    exported (Dict[str, str]|None): Export metadata when requested.
    files (Dict[str, str]): All files created under the run_dir.

How to use tool fpocket_toolkit :

response = await client.session.call_tool(
    "fpocket_toolkit",
    arguments={
        "pdb_file": "/path/to/input.pdb",
        "top_n": 0,
        "min_druggability": None,
        "verbose": False,
    }
)
result = client.parse_result(response)
pockets = result.get("pockets")

Example parameter sets

# 1) Main mode: analyze full structure and return all pockets (README example)
{
    "pdb_file": "/path/to/input.pdb",
    "top_n": 0,
    "min_druggability": None,
    "verbose": False,
}

# 2) Variant mode: return top 3 pockets above a druggability threshold
{
    "pdb_file": "/path/to/input.pdb",
    "top_n": 3,
    "min_druggability": 0.5,
    "verbose": True,
}

---

⚠ Docking Box Size Enforcement (L3 Principle 18)

When fpocket pocket dimensions are used for downstream docking (QuickVina, etc.), enforce a minimum of 25.0 Å per dimension. If any pocket dimension returned by fpocket is less than 25 Å, override it to 25.0 Å before passing to the docking tool.

# After fpocket pocket detection:
size_x = max(25.0, pocket["size_x"])
size_y = max(25.0, pocket["size_y"])
size_z = max(25.0, pocket["size_z"])