pubchem-deep-dive

name: pubchem_deep_dive description: "PubChem Deep Dive Analysis - Deep dive into PubChem: compound info, bioassay summary, 3D conformers, synonyms, and general description. Use this skill for chemical databases tasks involving get pubchem compound by cid get assay summary by cid get conformers by cid get compound synonyms by name get general info by compound name. Combines 5 tools from 1 SCP server(s)."

PubChem Deep Dive Analysis

Discipline: Chemical Databases | Tools Used: 5 | Servers: 1

Description

Deep dive into PubChem: compound info, bioassay summary, 3D conformers, synonyms, and general description.

Tools Used

• get_pubchem_compound_by_cid from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem
• get_assay_summary_by_cid from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem
• get_conformers_by_cid from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem
• get_compound_synonyms_by_name from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem
• get_general_info_by_compound_name from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem

Workflow

1. Get full compound info
2. Get bioassay summary
3. Get 3D conformers
4. Get all synonyms
5. Get general description

Test Case

Input

{
    "compound_name": "aspirin",
    "cid": 2244
}

Expected Steps

1. Get full compound info
2. Get bioassay summary
3. Get 3D conformers
4. Get all synonyms
5. Get general description

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 = {
    "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)
    except: return str(result)

async def main():
    # Connect to required servers
    sessions = {}
    sessions["pubchem-server"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem", "streamable-http")

    # Execute workflow steps
    # Step 1: Get full compound info
    result_1 = await sessions["pubchem-server"].call_tool("get_pubchem_compound_by_cid", arguments={})
    data_1 = parse(result_1)
    print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

    # Step 2: Get bioassay summary
    result_2 = await sessions["pubchem-server"].call_tool("get_assay_summary_by_cid", arguments={})
    data_2 = parse(result_2)
    print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

    # Step 3: Get 3D conformers
    result_3 = await sessions["pubchem-server"].call_tool("get_conformers_by_cid", arguments={})
    data_3 = parse(result_3)
    print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

    # Step 4: Get all synonyms
    result_4 = await sessions["pubchem-server"].call_tool("get_compound_synonyms_by_name", arguments={})
    data_4 = parse(result_4)
    print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")

    # Step 5: Get general description
    result_5 = await sessions["pubchem-server"].call_tool("get_general_info_by_compound_name", arguments={})
    data_5 = parse(result_5)
    print(f"Step 5 result: {json.dumps(data_5, indent=2, ensure_ascii=False)[:500]}")

    # Cleanup
    print("Workflow complete!")

if __name__ == "__main__":
    asyncio.run(main())