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Run BioEmu sequence sampling and extract ensemble structures for downstream conformation analysis.
license
MIT license
metadata
{"skill-author":"PJLab"}
BioEmu Sampling and Structure Extraction
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.
Usage
2. 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.
After calling this tool, you MUST download all output structure files from the MCP server to the local workspace using server_file_to_base64. A tool call is NOT considered complete until its output files have been downloaded and verified locally (ls -la <file> — size must be > 0).
import base64, os
response = await client.session.call_tool(
"server_file_to_base64",
arguments={"file_path": result["output_file"]} # or relevant output field
)
dl = client.parse_result(response)
local_path = "stepNN_descriptive_name.ext"withopen(local_path, "wb") as f:
f.write(base64.b64decode(dl["base64_string"]))
assert os.path.getsize(local_path) > 0, f"Download failed: {local_path}"
Download policy: All structure output files are Category A (user-critical) — essential for user verification, downstream analysis, and reproducibility. When in doubt, download. Over-collection is always preferred over under-collection.
Specific files to download from BioEmu output: All sampled PDB structures in the ensemble. Verify the count of downloaded structures matches the requested num_samples (L3 Principle 11).
