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

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.

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']