Molclaw Protein Structure Retrieve

Retrieve Protein Structure

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.

Scene 1: If the gene name is provided, please use tool retrieveproteinstructurebygene_name.

The description of tool retrieveproteinstructurebygene_name.

Retrieve and download the protein structure (.pdb) file using standard gene name.
Args:
    gene_name (str): Input gene name (e.g., 'TP53')
    organism (str): Species NCBI Taxonomy ID (default: 9606 for human, 10090 for mouse)
    sort_by (str): The sorting strategy defaults ('length') to prioritizing sequence length for maximum coverage, with an alternative option ('resolution') to prioritize structural resolution. 
Return:
    status (str): success/error
    msg (str): message
    prot_structure_path (str): Path to the downloaded protein structure file (pdb format)

How to use tool retrieveproteinstructurebygene_name :

response = await client.session.call_tool(
    "retrieve_protein_structure_by_gene_name",
    arguments={
        "gene_name": gene_name,
        "organism": "9606",
        "sort_by": "length"
    }
)
result = client.parse_result(response)
prot_structure_path = result["prot_structure_path"]

Scene 2: If the UniProt ID is provided, please use tool retrieveproteinstructurebyuniprot_id.

The description of tool retrieveproteinstructurebyuniprot_id.

Retrieve and download the protein structure (.pdb) file using uniprot id.
Args:
    uniprot_id (str): Input uniprot id (e.g., 'P04637')
    sort_by (str): The sorting strategy defaults ('length') to prioritizing sequence length for maximum coverage, with an alternative option ('resolution') to prioritize structural resolution. 
Return:
    status (str): success/error
    msg (str): message
    prot_structure_path (str): Path to the downloaded protein structure file (pdb format)

How to use tool retrieveproteinstructurebyuniprot_id :

response = await client.session.call_tool(
    "retrieve_protein_structure_by_uniprot_id",
    arguments={
        "uniprot_id": uniprot_id,
        "sort_by": "length"
    }
)
result = client.parse_result(response)
prot_structure_path = result["prot_structure_path"]

Scene 3: If the PDB ID is provided, please use tool retrieveproteinstructurebypdb_id.

The description of tool retrieveproteinstructurebypdb_id.

Retrieve and download the protein structure (.pdb) file using pdb id.
Args:
    pdb_id (str): Input pdb id (e.g., "2l3r", "5XYF")
Return:
    status (str): success/error
    msg (str): message
    prot_structure_path (str): Path to the downloaded protein structure file (pdb format)

How to use tool retrieveproteinstructurebypdb_id :

response = await client.session.call_tool(
    "retrieve_protein_structure_by_uniprot_id",
    arguments={
        "pdb_id": pdb_id
    }
)
result = client.parse_result(response)
prot_structure_path = result["prot_structure_path"]

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: InternScience
• Source: InternScience/MolClaw
• License: MIT

Install and usage instructions live in the source repository linked above.