chemical-structure-comparison

name	chemical_structure_comparison
description	Chemical Structure Comparison - Compare chemical structures: get SMILES, analyze structures, compute similarity, and check PubChem records. Use this skill for cheminformatics tasks involving NameToSMILES ChemicalStructureAnalyzer calculate smiles similarity get compound by name. Combines 4 tools from 4 SCP server(s).
i18n	{"zh":{"description":"化学结构对比与相似度计算。"}}

Chemical Structure Comparison

Discipline: Cheminformatics | Tools Used: 4 | Servers: 4

Description

Compare chemical structures: get SMILES, analyze structures, compute similarity, and check PubChem records.

Tools Used

• NameToSMILES from server-31 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/31/SciToolAgent-Chem
• ChemicalStructureAnalyzer from server-28 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/28/InternAgent
• calculate_smiles_similarity from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool
• get_compound_by_name from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem

Workflow

1. Convert names to SMILES
2. Analyze both structures
3. Compute similarity
4. Get PubChem compound data

Test Case

Input

{
    "compound_a": "aspirin",
    "compound_b": "ibuprofen"
}

Expected Steps

1. Convert names to SMILES
2. Analyze both structures
3. Compute similarity
4. Get PubChem compound data

Usage Example

Note: Replace <YOUR_SCP_HUB_API_KEY> with your own SCP Hub API Key. You can obtain one from the SCP Platform.

import asyncio
import json
from mcp import ClientSession
from mcp.client.streamable_http import streamablehttp_client
from mcp.client.sse import sse_client

SERVERS = {
    "server-31": "https://scp.intern-ai.org.cn/api/v1/mcp/31/SciToolAgent-Chem",
    "server-28": "https://scp.intern-ai.org.cn/api/v1/mcp/28/InternAgent",
    "server-2": "https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool",
    "pubchem-server": "https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem"
}

async def connect(url, transport_type):
    transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "<YOUR_SCP_HUB_API_KEY>"})
    read, write, _ = await transport.__aenter__()
    ctx = ClientSession(read, write)
    session = await ctx.__aenter__()
    await session.initialize()
    return session, ctx, transport

def parse(result):
    try:
        if hasattr(result, 'content') and result.content:
            c = result.content[0]
            if hasattr(c, 'text'):
                try: return json.loads(c.text)
                except: return c.text
        return str(result)
    :  (result)

  ():
    
    sessions = {}
    sessions[], _, _ =  connect(, )
    sessions[], _, _ =  connect(, )
    sessions[], _, _ =  connect(, )
    sessions[], _, _ =  connect(, )

    
    
    result_1 =  sessions[].call_tool(, arguments={})
    data_1 = parse(result_1)
    ()

    
    result_2 =  sessions[].call_tool(, arguments={})
    data_2 = parse(result_2)
    ()

    
    result_3 =  sessions[].call_tool(, arguments={})
    data_3 = parse(result_3)
    ()

    
    result_4 =  sessions[].call_tool(, arguments={})
    data_4 = parse(result_4)
    ()

    
    ()

 __name__ == :
    asyncio.run(main())