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chemical_patent_analysis

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Chemical Patent & Novelty Analysis - Analyze chemical novelty: PubChem substructure CAS search, ChEMBL similarity search, compound synonyms, and literature. Use this skill for patent chemistry tasks involving get substructure cas get similarity by smiles get compound synonyms by name search literature. Combines 4 tools from 3 SCP server(s).

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Chemical Patent & Novelty Analysis

Discipline: Patent Chemistry | Tools Used: 4 | Servers: 3

Description

Analyze chemical novelty: PubChem substructure CAS search, ChEMBL similarity search, compound synonyms, and literature.

Tools Used

  • get_substructure_cas from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem
  • get_similarity_by_smiles from chembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL
  • get_compound_synonyms_by_name from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem
  • search_literature from server-1 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory

Workflow

  1. Search CAS by substructure
  2. Search ChEMBL by similarity
  3. Get compound synonyms
  4. Search patent literature

Test Case

Input

{
    "smiles": "c1ccc(-c2ccccc2)cc1",
    "compound_name": "biphenyl"
}

Expected Steps

  1. Search CAS by substructure
  2. Search ChEMBL by similarity
  3. Get compound synonyms
  4. Search patent literature

Usage Example

Note: Replace sk-b04409a1-b32b-4511-9aeb-22980abdc05c with your own SCP Hub API Key. You can obtain one from the SCP Platform.

import asyncio
import json
from contextlib import AsyncExitStack
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",
    "chembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL",
    "server-1": "https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory"
}

async def connect(url, stack):
    transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "sk-b04409a1-b32b-4511-9aeb-22980abdc05c"})
    read, write, _ = await stack.enter_async_context(transport)
    ctx = ClientSession(read, write)
    session = await stack.enter_async_context(ctx)
    await session.initialize()
    return session

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():
    async with AsyncExitStack() as stack:
        # Connect to required servers
        sessions = {}
        sessions["pubchem-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem", stack)
        sessions["chembl-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL", stack)
        sessions["server-1"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory", stack)

        # Execute workflow steps
        # Step 1: Search CAS by substructure
        result_1 = await sessions["pubchem-server"].call_tool("get_substructure_cas", arguments={})
        data_1 = parse(result_1)
        print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

        # Step 2: Search ChEMBL by similarity
        result_2 = await sessions["chembl-server"].call_tool("get_similarity_by_smiles", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

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

        # Step 4: Search patent literature
        result_4 = await sessions["server-1"].call_tool("search_literature", arguments={})
        data_4 = parse(result_4)
        print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")

        # Cleanup
        print("Workflow complete!")

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