| name | drugsda-target-retrieve |
| description | Search the protein information from the input gene name and downloads the optimal PDB or AlphaFold structures. |
| license | MIT license |
| metadata | {"skill-author":"PJLab"} |
Target Protein Retrieve
Usage
1. MCP Server Definition
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession
class DrugSDAClient:
def __init__(self, server_url: str):
self.server_url = server_url
self.session = None
async def connect(self):
print(f"server url: {self.server_url}")
try:
self.transport = streamablehttp_client(
url=self.server_url,
headers={"SCP-HUB-API-KEY": "sk-a0033dde-b3cd-413b-adbe-980bc78d6126"}
)
self.read, self.write, self.get_session_id = await self.transport.__aenter__()
self.session_ctx = ClientSession(self.read, self.write)
self.session = await self.session_ctx.__aenter__()
await self.session.initialize()
session_id = self.get_session_id()
print(f"✓ connect success")
return True
except Exception as e:
print(f"✗ connect failure: {e}")
import traceback
traceback.print_exc()
return False
async def disconnect(self):
try:
if self.session:
await self.session_ctx.__aexit__(None, None, None)
if hasattr(self, 'transport'):
await self.transport.__aexit__(None, None, None)
print("✓ already disconnect")
except Exception as e:
print(f"✗ disconnect error: {e}")
def parse_result(self, result):
try:
if hasattr(result, 'content') and result.content:
content = result.content[0]
if hasattr(content, 'text'):
return json.loads(content.text)
return str(result)
except Exception as e:
return {"error": f"parse error: {e}", "raw": str(result)}
2. Retrieve Protein Structure
The description of tool retrieve_protein_structure_by_gene_name.
Search the protein information from the input gene name and downloads the optimal PDB or AlphaFold structures. Note that species support is limited to humans only.
Args:
gene_name (str): Input gene name (e.g., 'TP53')
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 retrieve_protein_structure_by_gene_name :
client = DrugSDAClient("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool")
if not await client.connect():
print("connection failed")
return
response = await client.session.call_tool(
"retrieve_protein_structure_by_gene_name",
arguments={
"gene_name": gene_name
}
)
result = client.parse_result(response)
prot_structure_path = result["prot_structure_path"]
await client.disconnect()
