internscience/agents-a1/molclaw-extract-chains

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

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']

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}"