molclaw-prolif-protein-protein

name	molclaw-prolif-protein-protein
description	ProLIF protein-protein trajectory analysis skill for interface interaction fingerprints and stability profiling.
license	MIT license
metadata	{"skill-author":"PJLab"}

ProLIF Protein-Protein Interface Fingerprinting 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

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

Input Source Mapping

Parameter	Source Guidance
topology_path	System topology from MD tools: e.g., protein_openmm_md, prepare_protein_md, run_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.

How To Use prolif_protein_protein

response = await client.session.call_tool(
    "prolif_protein_protein",
    arguments={
        "topology_path": "relative/path/to/system.prmtop",
        "trajectory_path": "relative/path/to/md.nc",
        "selection_a": "segid A",
        "selection_b": "segid B",
        "start": 0,
        "step": 10
    }
)
result = client.parse_result(response)
key_output = result["output_file"]

Example Parameter Sets

# 1) Main mode
{
    "topology_path": "relative/path/to/system.prmtop",
    "trajectory_path": "relative/path/to/md.nc",
    "selection_a": "segid A",
    "selection_b": "segid B",
    "start": 0,
    "step": 10
}

# 2) Variant mode
{
    "topology_path": "relative/path/to/system.prmtop",
    "trajectory_path": "relative/path/to/md.nc",
    "selection_a": "protein and chainid A",
    "selection_b": "protein and chainid B",
    "count": True,
    "vicinity_cutoff": 3.5,
    "stop": 200
}

---

⚠ 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.