Molclaw Extract Chains
Documentsmolclaw-extract-chainsMolclaw Extract Chains is an Agent Skill for documents published in the InternScience/Agents-A1 repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.
Extract protein sequence of each chain from the protein structure file (pdb format).
How to use this skill
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Inspect the Agent Skill at https://github.com/InternScience/Agents-A1/blob/HEAD/evaluation/Tools/molbench/skills/L1_tools/molclaw-extract-chains/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/molclaw-extract-chains, but wait for my approval before writing files or running scripts.
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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.