Molecule MCP

🚀 Molecular Visualization Tool Documentation

This tool aims to provide visualization support for common molecules, including molecular structure analysis and chemical calculation functions. Users can interact with the server through the command-line interface to generate molecular images, query properties, and access databases.

🚀 Quick Start

✨ Features

• Support for visualizing molecular structures.
• Integration with a common molecule database.
• Tools for calculating chemical properties.
• Scalability to support new molecule types and extend chemical analysis algorithms.
• A unified logging system.
• High performance in molecular rendering, database query response, and concurrent processing.

📦 Installation

Project Dependencies

The third-party libraries required for the project are listed in the requirements.txt file:

mcp[cli]>=0.1.0
rdkit>=2023.3.1
pillow>=10.0.0

It is recommended to use Python 3.8 or higher for installation and operation.

Running the Server

To start the molecular visualization server, execute the following command:

python molecule_server.py

💻 Usage Examples

Basic Usage

# Example 1: Visualize the aspirin molecule
from mcp import ClientSession, StdioServerParameters
from mcp.client.stdio import stdio_client

async def visualize_aspirin():
    server_params = StdioServerParameters(
        command="python",
        args=["aspirin_visualizer.py"],
        env=None
    )
    
    async with stdio_client(server_params) as (stdin, stdout):
        client = ClientSession(stdin, stdout)
        await client.initialize()
        
        # Call the visualization tool
        result = await client.call_tool("visualize_molecule", {"query": "aspirin"})
        
        # Save the image file
        with open("aspirin_visualization.png", "wb") as f:
            f.write(result.content[0].image.data)

Advanced Usage

# Example 2: Get the molecular properties of caffeine
async def get_caffeine_properties():
    server_params = StdioServerParameters(
        command="python",
        args=["caffeine_analyzer.py"],
        env=None
    )
    
    async with stdio_client(server_params) as (stdin, stdout):
        client = ClientSession(stdin, stdout)
        await client.initialize()
        
        # Query the molecular properties
        result = await client.call_tool("get_molecule_properties", {"query": "caffeine"})
        print(result.content[0].text)

📚 Documentation

Tool Interfaces

Molecular Visualization Tool

1. Display Molecular Structure

visualize_molecule --query <Molecule Name or SMILES String>

2. Export as Base64 Encoded Image

visualize_molecule_base64 --query <Molecule Name or SMILES String>

3. Get Molecular Property Information

get_molecule_properties --query <Molecule Name or SMILES String>

Molecular Database Query

1. List All Supported Molecules

list_common_molecules

2. Get the SMILES Encoding of a Specific Molecule

get_smiles_for --name <Molecule Name>

Resource Interfaces

1. Get Basic Molecular Information

molecule://{name}/info

2. Get Molecular Structure Data

molecule://{name}/structure

3. View Molecular Properties

molecule://{name}/properties

🔧 Technical Details

Functional Requirements

1. Core Functions
   • Support for visualizing molecular structures.
   • Integration with a common molecule database.
   • Tools for calculating chemical properties.
2. Scalability Requirements
   • Support for new molecule types.
   • Extension of chemical analysis algorithms.
   • Maintenance of a unified logging system.
3. Performance Metrics
   • Molecular rendering efficiency: The rendering time for a single molecule should not exceed 5 seconds.
   • Database query response: The average response time should be less than 200 milliseconds.
   • Concurrent processing capacity: Support for handling at least 10 client requests simultaneously.

📄 License

This project is licensed under the MIT License. Please refer to the LICENSE file for specific terms.

Related Links

• RDKit Official Documentation
• Python Imaging Library Pillow Tutorial
• MCP Protocol Technical Specification

Project Maintainers

• Zhang San
• Li Si

Contribution Guidelines

Community contributions are welcome! If you want to submit code or report issues, please visit our GitHub repository to submit Pull Requests or Issues.