molclaw-compound-retrieve

Retrieve Compound SMILES

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.

The description of tool retrieve_smiles_by_compoundname.

Retrieve SMILES strings by compound name. The service queries PubChem first and falls back to the NCI resolver when PubChem is busy or unavailable.
Args:
    compound_names (List[str]): List of input compound names (e.g., ["aspirin", "caffeine"])
Return:
    status (str): success/partial_success/error
    msg (str): message
    retrieve_smiles (List[dict]): List of dict, each containing the keys 'compound_name' and 'smiles'.
        --compound_name (str): A compound name of compound_names 
        --smiles (str): The retrieved SMILES string, if it exists; otherwise, None.

How to use tool retrieve_smiles_by_compoundname :

response = await client.session.call_tool(
    "retrieve_smiles_by_compoundname",
    arguments={
        "compound_names": compound_names
    }
)
result = client.parse_result(response)
retrieve_smiles = result["retrieve_smiles"]