molecular-visualization-suite

name: molecular_visualization_suite description: "Molecular Visualization Suite - Visualize molecules: convert SMILES to formats, visualize molecule, visualize protein, visualize complex. Use this skill for chemical visualization tasks involving convert smiles to format visualize molecule visualize protein visualize complex. Combines 4 tools from 1 SCP server(s)."

Molecular Visualization Suite

Discipline: Chemical Visualization | Tools Used: 4 | Servers: 1

Description

Visualize molecules: convert SMILES to formats, visualize molecule, visualize protein, visualize complex.

Tools Used

• convert_smiles_to_format from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool
• visualize_molecule from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool
• visualize_protein from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool
• visualize_complex from server-2 (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool

Workflow

1. Convert SMILES to SDF
2. Visualize small molecule
3. Visualize protein
4. Visualize protein-ligand complex

Test Case

Input

{
    "smiles": "CC(=O)Oc1ccccc1C(=O)O",
    "pdb_code": "1AKE"
}

Expected Steps

1. Convert SMILES to SDF
2. Visualize small molecule
3. Visualize protein
4. Visualize protein-ligand complex

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-2": "https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool"
}

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["server-2"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", "streamable-http")

    # Execute workflow steps
    # Step 1: Convert SMILES to SDF
    result_1 = await sessions["server-2"].call_tool("convert_smiles_to_format", arguments={})
    data_1 = parse(result_1)
    print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

    # Step 2: Visualize small molecule
    result_2 = await sessions["server-2"].call_tool("visualize_molecule", arguments={})
    data_2 = parse(result_2)
    print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

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

    # Step 4: Visualize protein-ligand complex
    result_4 = await sessions["server-2"].call_tool("visualize_complex", 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())