molclaw-prolif-docking

name	molclaw-prolif-docking
description	ProLIF docking-pose analysis skill for batch interaction fingerprints and interaction count summaries.
license	MIT license
metadata	{"skill-author":"PJLab"}

ProLIF Docking Pose Analysis Skill

[!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.

Task Description

Batch-analyze multiple docking-generated binding poses and produce interaction fingerprints or interaction count summaries. Use this skill to screen binding modes and evaluate docking result quality.

Input Source Mapping

Parameter	Source Guidance
protein_path	Generated by structure retrieval/prediction tools (e.g., retrieve_protein_structure_by_*, pred_protein_structure_esmfold, chai1_predict) or a PDB fixed by fix_pdb
ligand_paths	Generated by docking tools (e.g., molecule_docking_quickvina, hdock_tool, run_karmadock_screening) as pose files (.sdf/.mol2/.pdbqt)
ligand_format	Must match the upstream docking output format: sdf, mol2, or pdbqt
template_smiles	Required when ligand_format is pdbqt to provide ligand chemistry reference

Usage

Tool: prolif_docking

Summarize docking poses with ProLIF and return a CSV of interaction fingerprints plus summary metrics.
Args:
    protein_path (str): Path to the receptor protein structure.
    ligand_paths (List[str]): List of ligand pose files.
    ligand_format (str): Ligand format identifier (e.g., 'sdf', 'mol2', 'pdbqt').
    template_smiles (str|None): Optional template SMILES; required when ligand_format is 'pdbqt'.
    interactions (List[str]|None): Optional interaction types to compute.
    count (bool): If True, compute interaction counts instead of fingerprints. Default: False.
    vicinity_cutoff (float|None): Optional distance cutoff for vicinity interactions.
    params_json (str|None): Optional JSON parameter file path for ProLIF interaction settings.
Return:
    status (str): 'success' or 'error'.
    msg (str): Human-readable summary or error message.
    command (str): The executed command label ('docking').
    output_dir (str|None): Run-specific directory under tool_result/prolif_result.
    output_file (str|None): Path to the produced CSV summary file.
    n_frames (int|None): Number of processed frames where applicable.
    n_interactions (int|None): Number of interaction columns in output.
    frequent_interactions (List[dict]|None): High-frequency interactions (>30%) with keys 'interaction' and 'frequency'.
    result_summary (dict|None): Full summary dictionary from the wrapper.

How To Use prolif_docking

response = await client.session.call_tool(
    "prolif_docking",
    arguments={
        "protein_path": "relative/path/to/receptor.pdb",
        "ligand_paths": [
            "relative/path/to/pose1.sdf",
            "relative/path/to/pose2.sdf"
        ],
        "ligand_format": "sdf",
        "interactions": ["Hydrophobic", "HBDonor"]
    }
)
result = client.parse_result(response)
key_output = result["output_file"]

Example Parameter Sets

# 1) Main mode
{
    "protein_path": "relative/path/to/receptor.pdb",
    "ligand_paths": [
        "relative/path/to/docking_poses.sdf"
    ],
    "ligand_format": "sdf"
}

# 2) Variant mode
{
    "protein_path": "relative/path/to/receptor.pdb",
    "ligand_paths": [
        "relative/path/to/pose1.pdbqt",
        "relative/path/to/pose2.pdbqt"
    ],
    "ligand_format": "pdbqt",
    "template_smiles": "CCO",
    "count": True,
    "vicinity_cutoff": 4.0
}

---

⚠ Residue Numbering Warning (L3 Principle 17 — CRITICAL)

ProLIF reports residue identifiers using the numbering of the input PDB file. If the PDB was generated by a prediction tool (ESMFold, Boltz-2, Chai-1), these numbers are tool-internal sequential numbers (1, 2, 3...) — NOT UniProt numbers.

Before interpreting ProLIF results when the task references specific residues (e.g., "confirm Met793 interaction"):

1. Determine which numbering scheme the input PDB uses.
2. If different from the task's reference scheme, run molclaw-residue-mapper to build a mapping table.
3. Translate ProLIF residue IDs to the task's reference scheme before drawing conclusions.

Common catastrophic error: ProLIF reports "HBDonor at MET76" from a Boltz-2 structure. Agent searches for "MET793" in ProLIF output, does not find it, and concludes "Met793 interaction is absent." In reality, MET76 (Boltz-2 internal) IS Met793 (UniProt). Use residue_mapper with query="tool:76" to verify.

⚠ Mandatory Image Download (L3 Principle 15)

After ProLIF analysis, download ALL visualization outputs (interaction heatmaps, frequency barplots, etc.) from the output directory using server_file_to_base64. These are Category A files essential for result communication and user verification.