molclaw-extract-chains

name	molclaw-extract-chains
description	Extract protein sequence of each chain from the protein structure file (pdb format).
license	MIT license
metadata	{"skill-author":"PJLab"}

Extract Protein Chains

Use tool extract_pdb_chains to extract protein chains from the repaired pdb file

Tool description:

Extract the amino acid sequence of each chain from the PDB file.
Args:
    pdb_file_path (str): Path to input pdb file
Return:
    status (str): success/error
    msg (str): message
    chains (List[dict]): List of dict, each containing the keys 'chain' and 'sequence'.
        --chain (str): Chain ID
        --sequence (str): Sequence string

Tool usage:

response = await client.session.call_tool(
    "extract_pdb_chains",
    arguments={
        "pdb_file_path": fixed_pdb_path
    }
)
result = client.parse_result(response)
protein_chains = result['chains']

---

⚠ Mandatory Output File Download (L3 Principle 14)

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"
with open(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.