molclaw-run-bioemu

BioEmu Sampling and Structure Extraction

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.

Usage

1. BioEmu Sampling

The description of tool run_bioemu.

Generate BioEmu conformational samples for a sequence, store outputs under the shared result root, and return run metadata and key artifacts.
Args:
    sequence (str): Input sequence string or a path (FASTA/A3M) readable by BioEmu.
    num_samples (int): Number of conformational samples to generate.
    export_pdbs (bool): If True, export individual PDB files for each sample (default False).
    dry_run (bool): If True, validate inputs and create run directory without executing BioEmu.
Return:
    status (str): 'success' or 'error'.
    msg (str): Human-readable summary or error message.
    command (str): The invoked command ('run_bioemu').
    run_dir (str|None): Path to the run-specific output directory under tool_result/bioemu_result.
    output_dir (str|None): Same as `run_dir` for compatibility.
    files (List[str]|None): Sorted list of generated files under the run directory.
    pdb_path (str|None): First detected PDB file path if present.
    xtc_path (str|None): First detected XTC file path if present.
    sampling_statistics (dict|None): Parsed sampling statistics if available.
    sampling_statistics_path (str|None): Path to sampling_statistics.json if present.
    sequence_input (str|None): Resolved sequence or input path echoed by BioEmu.
    num_samples_requested (int|None): Number of requested samples echoed back.
    export_pdbs (bool|None): Whether PDB export was requested.

How to use tool run_bioemu :

response = await client.session.call_tool(
    "run_bioemu",
    arguments={
        "sequence": "GYDPETGTWG",
        "num_samples": 5,
        "export_pdbs": False,
        "dry_run": True
    }
)
result = client.parse_result(response)
key_output = result["run_dir"]