molclaw-prolif-pdb

name	molclaw-prolif-pdb
description	ProLIF static complex analysis skill for a single protein-ligand structure.
license	MIT license
metadata	{"skill-author":"PJLab"}

ProLIF Single-Structure PDB 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

Analyze interaction fingerprints from one static protein-ligand complex structure. Use this skill for fast assessment of crystal structures, top docking poses, or representative MD frames.

Input Source Mapping

Parameter	Source Guidance
structure_path	Can come from PDB retrieval tools, best docking poses, MD frame extraction (e.g., openmm_extract_frames), or complex preparation tools (e.g., prepare_complex) outputting complex PDB files
ligand_selection	User-defined ligand selection string that matches ligand identifiers in the structure file
protein_selection	Defaults to protein; can be customized to limit the analyzed region

Usage

Tool: prolif_pdb

Analyze a single complex structure and return ProLIF interaction fingerprints or counts with summary metrics.
Args:
    structure_path (str): Path to the complex structure file (commonly PDB).
    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.
    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 ('pdb').
    output_dir (str|None): Run-specific directory under tool_result/prolif_result.
    output_file (str|None): Path to the produced CSV file.
    n_frames (int|None): Number of processed frames (typically 1 for static structures).
    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_pdb

response = await client.session.call_tool(
    "prolif_pdb",
    arguments={
        "structure_path": "relative/path/to/complex.pdb",
        "ligand_selection": "resname LIG",
        "protein_selection": "protein",
        "interactions": ["Hydrophobic", "HBAcceptor"]
    }
)
result = client.parse_result(response)
key_output = result["output_file"]

Example Parameter Sets

# 1) Main mode
{
    "structure_path": "relative/path/to/complex.pdb",
    "ligand_selection": "resname LIG",
    "protein_selection": "protein",
    "interactions": ["Hydrophobic", "HBDonor"]
}

# 2) Variant mode
{
    "structure_path": "relative/path/to/complex.pdb",
    "ligand_selection": "resname LIG",
    "count": True,
    "params_json": "relative/path/to/prolif_override.json"
}

---

⚠ 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.