gabrielmoreira Protein or Molecule Data Check
Usage
1. MCP Server Definition
import json
from contextlib import AsyncExitStack
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._stack = AsyncExitStack()
await self._stack.__aenter__()
self.read, self.write, self.get_session_id = await self._stack.enter_async_context(self.transport)
self.session_ctx = ClientSession(self.read, self.write)
self.session = await self._stack.enter_async_context(self.session_ctx)
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):
"""Disconnect from server"""
try:
if hasattr(self, '_stack'):
await self._stack.aclose()
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. Protein Sequence Valid Check
The description of tool is_valid_protein_sequence.
Check if the input protein sequence string is valid.
Args:
sequences (List[str]): List of input protein sequences
Return:
status (str): success/partial_success/error
msg (str): message
valid_res (List[dict]): List of dict, each containing the keys 'sequence' and 'is_valid'.
--sequence (str): A protein sequence of the input sequences list
--is_valid (bool): Is the protein sequence valid or not
How to use tool is_valid_protein_sequence :
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(
"is_valid_protein_sequence",
arguments={
"sequences": sequence_list
}
)
result = client.parse_result(response)
valid_res = result["valid_res"]
await client.disconnect()
3. Molecule SMILCES Valid Check
The description of tool is_valid_smiles.
Check if the input SMILES string is valid
Args:
smiles_list (List[str]): List of input SMILES strings, (e.g., ["N[C@@H](Cc1ccc(O)cc1)C(=O)O", "CC(C)C1=CC=CC=C1"])
Return:
status (str): success/partial_success/error
msg (str): message
valid_res (List[dict]): List of dict, each containing the keys 'smiles' and 'is_valid'.
--smiles (str): A SMILES string of smiles_list
--is_valid (bool): Is the SMILES valid or not
How to use tool is_valid_smiles :
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(
"is_valid_smiles",
arguments={
"smiles_list": smiles_list
}
)
result = client.parse_result(response)
valid_res = result["valid_res"]
await client.disconnect()