Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names.
import asyncio
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession
class DrugSDAClient:
"""DrugSDA-Tool MCP Client"""
def __init__(self, server_url: str, api_key: str):
self.server_url = server_url
self.api_key = api_key
self.session = None
async def connect(self):
"""Establish connection and initialize session"""
try:
self.transport = streamablehttp_client(
url=self.server_url,
headers={"SCP-HUB-API-KEY": self.api_key}
)
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()
return True
except Exception as e:
print(f"✗ connect failure: {e}")
return False
async def disconnect(self):
"""Disconnect from server"""
try:
if self.session:
await self.session_ctx.__aexit__(None, None, None)
if hasattr(self, 'transport'):
await self.transport.__aexit__(None, None, None)
except Exception as e:
print(f"✗ disconnect error: {e}")
def parse_result(self, result):
"""Parse MCP tool call 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)}
This workflow retrieves SMILES strings from PubChem using common chemical names.
Workflow Steps:
Implementation:
## Initialize client
client = DrugSDAClient(
"https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool",
"<your-api-key>"
)
if not await client.connect():
print("connection failed")
exit()
## Input: List of compound names
compound_names = ["aspirin", "caffeine", "ibuprofen"]
## Retrieve SMILES from compound names
result = await client.session.call_tool(
"retrieve_smiles_from_name",
arguments={
"compound_names": compound_names
}
)
result_data = client.parse_result(result)
smiles_list = result_data["retrieve_smiles"]
## Display results
print("Retrieved SMILES strings:")
for item in smiles_list:
print(f"Name: {item['compound_name']}")
print(f"SMILES: {item['smiles']}\n")
await client.disconnect()
DrugSDA-Tool Server:
retrieve_smiles_from_name: Retrieve SMILES from PubChem by compound name
compound_names (list): List of chemical compound namesretrieve_smiles (list): List of name-SMILES pairs
compound_name (str): Input compound namesmiles (str): Canonical SMILES stringInput:
compound_names: List of chemical names (common names, IUPAC names, or synonyms)Output:
compound_name: Query compound namesmiles: Canonical SMILES representation