ProLIF Single-Structure PDB Analysis 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 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"
}

Tool Priority: interaction-visualizer is PRIMARY

Default: For all single-structure protein-ligand interaction analysis, use molclaw-interaction-visualizer (local script) as the primary tool. Use prolif_pdb (this tool) only when you specifically need ProLIF-format fingerprint data for downstream prolif_docking / prolif_md pipeline compatibility, or when the interaction-visualizer script is unavailable.

Need	Use interaction-visualizer (local, PRIMARY)	Use prolif_pdb (MCP, fallback)
Single-structure interaction analysis	✅ default	Only if visualizer unavailable
Schrödinger-style 2D interaction diagram	✅	❌
PyMOL 3D auto-rendering	✅	❌
Residue role annotations (Hinge/Gatekeeper/DFG)	✅	❌
Decision-ready JSON for agent loop	✅	❌
partner_site.csv for ligand atom modification diagnosis	✅	❌
Native --resid_offset for PDB→UniProt mapping	✅	❌ (manual mapping needed)
MCP server unavailable	✅ (local)	❌
ProLIF-format fingerprint for prolif_docking/prolif_md pipeline	❌	✅ use this
Interaction fingerprint CSV for cross-structure comparison	✅	✅