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currentAutomated scan100/100internscience/scp/pubchem-deep-dive
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version: "1.0.1" 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
- Get full compound info
- Get bioassay summary
- Get 3D conformers
- Get all synonyms
- Get general description
Test Case
Input
json
{"compound_name": "aspirin","cid": 2244}
Expected Steps
- Get full compound info
- Get bioassay summary
- Get 3D conformers
- Get all synonyms
- 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.
python
import asyncioimport jsonfrom mcp import ClientSessionfrom mcp.client.streamable_http import streamablehttp_clientfrom mcp.client.sse import sse_clientSERVERS = {"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, transportdef 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.textreturn str(result)except: return str(result)async def main():# Connect to required serverssessions = {}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 inforesult_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 summaryresult_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 conformersresult_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 synonymsresult_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 descriptionresult_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]}")# Cleanupprint("Workflow complete!")if __name__ == "__main__":asyncio.run(main())