molclaw-prolif-protein-protein

ProLIF Protein-Protein Interface Fingerprinting Skill

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.

[!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.

Task Description

Analyze protein-protein interaction trajectories and generate interface interaction fingerprints. Use this skill to evaluate interface stability and identify key residue contributions across simulation.

Routing note: This tool is the primary choice for protein-protein trajectory interface profiling (multi-frame analysis). For single-structure protein-protein interface analysis, use molclaw-interaction-visualizer in protein mode instead — it produces interface heatmaps, network diagrams, and decision-ready JSON.

Input Source Mapping

Parameter	Source Guidance
topology_path	System topology from MD tools: e.g., protein_openmm_md, prepare_protein_md, goca_pipeline
trajectory_path	Trajectory from the same MD tools, containing dynamic information for both protein chains
selection_a	User-defined selection string for protein chain A, for example segid A or protein and chainid A
selection_b	User-defined selection string for protein chain B, for example segid B or protein and chainid B

Usage

Tool: prolif_protein_protein

Analyze a protein-protein trajectory and return interaction fingerprints or counts with summary metrics.
Args:
    topology_path (str): Path to the system topology file.
    trajectory_path (str): Path to the trajectory file.
    selection_a (str): Selection string for partner A.
    selection_b (str): Selection string for partner B.
    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.
    start (int|None): Optional start frame index.
    stop (int|None): Optional stop frame index (exclusive).
    step (int|None): Optional frame stride.
Return:
    status (str): 'success' or 'error'.
    msg (str): Human-readable summary or error message.
    command (str): The executed command label ('protein-protein').
    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.