molclaw-prolif-tool

ProLIF Multi-Scenario Analysis Toolkit

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.

[!IMPORTANT] Tool Priority: For single-structure interaction analysis (one complex, one pose), use molclaw-interaction-visualizer (local script) as the primary tool instead of prolif_pdb. ProLIF remains the primary tool for:

• prolif_docking — batch docking pose fingerprint comparison
• prolif_md — MD trajectory interaction dynamics
• prolif_protein_protein — protein-protein trajectory interface profiling

These capabilities are NOT available in interaction-visualizer.

[!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.

Usage

1. MD Trajectory Fingerprinting

The description of tool prolif_md.

Compute ProLIF fingerprints for an MD trajectory and return standardized summary metrics.
Args:
    topology_path (str): Path to the topology file (e.g., .psf, .pdb, .prmtop).
    trajectory_path (str): Path to the trajectory file to analyze.
    ligand_selection (str): Selection string identifying ligand atoms.
    protein_selection (str): Selection string for protein atoms. Default: 'protein'.
    interactions (List[str]|None): Optional interaction types to compute (e.g., Hydrophobic, HBDonor).
    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.
    start (int|None): Optional start frame index.
    stop (int|None): Optional stop frame index (exclusive).
    step (int|None): Optional frame stride.
    residues (List[str]|None): Optional explicit residue list to include.
    all_residues (bool): If True, include all residues in analysis. Default: False.
Return:
    status (str): 'success' or 'error'.
    msg (str): Human-readable summary or error message.
    command (str): The executed command label ('md').
    output_dir (str|None): Run-specific directory under tool_result/prolif_result.
    output_file (str|None): Path to the generated CSV file.
    n_frames (int|None): Number of processed frames.
    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.