Rdkit Chemical Informatics

by s20ss

3 stars

267 downloads

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GitHub

Developer Tools

Description

[![MseeP.ai Security Assessment Badge](https://mseep.net/pr/s20ss-mcp-rdkit-badge.png)](https://mseep.ai/app/s20ss-mcp-rdkit) # MCP RDKit Project ## Overview The `mcp_rdkit` project integrates the RDKit library with the MCP (Model Context Protocol) framework to provide advanced…

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Details

Author: s20ss
GitHub stars: 3
Downloads: 267
Categories: Developer Tools

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below

Plugin Name Rdkit Chemical Informatics

Command (node, npx, python, etc.)

Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

From the repository

Install the package via pip install mcp-rdkit, then run python -m mcp_rdkit to start the MCP server in stdio mode. Add the provided JSON configuration to your MCP config file to connect the server.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "rdkit chemical informatics": {
            "rdkit": {
                "command": "python",
                "args": [
                    "-m",
                    "mcp_rdkit"
                ]
            }
        }
    }
}

McpServers

{
    "rdkit": {
        "command": "python",
        "args": [
            "-m",
            "mcp_rdkit"
        ]
    }
}

MCP RDKit Project

Overview

The mcp_rdkit project integrates the RDKit library with the MCP (Model Context Protocol) framework to provide advanced chemical informatics tools. It includes functionalities for molecular visualization, descriptor calculation, and interaction with an MCP server.

Features

- Molecular Visualization: Generate images of molecules using RDKit.
- Descriptor Calculation: Compute molecular descriptors such as molecular weight, logP, and more.
- MCP Server Integration: Communicate with an MCP server for advanced chemical informatics tasks.

Project Structure

- mcp_rdkit/
- __main__.py: Entry point for the application. It initializes the MCP server and runs it in "stdio" mode.
- rdkit_helper.py: Contains helper functions for RDKit operations, including:
- Converting PIL images to base64.
- Interfacing with the MCP server.
- Utilizing RDKit for chemical computations.

- setup.py: Configuration for packaging and distribution.

Requirements

- Python 3.8 or higher
- RDKit library
- MCP framework

Installation

1. Install the package using pip:

   pip install mcp-rdkit

2. Run the application:

   python -m mcp_rdkit

Demo

You can integrate this directly into Claude App:

Demo 1
Demo 2 .png?raw=true)
Demo 3 .png?raw=true)

Usage

- Run the MCP server:
The application starts an MCP server that can process chemical informatics tasks.

- Generate molecular images:
Use the RDKit helper functions to visualize molecules.

- Calculate descriptors:
Leverage RDKit's descriptor calculation tools for chemical analysis.

MCP Configuration Example

To use the RDKit server with MCP, add the following configuration to your mcp config file:

"rdkit-server": {
  "type": "stdio",
  "command": "python",
  "args": [
    "-m",
    "mcp_rdkit"
  ]
}

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Description

About

Details

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Setting up with Highlight

From the repository

Claude Desktop / Cursor

McpServers

MCP RDKit Project

Overview

Features

Project Structure

Requirements

Installation

Demo

Usage

MCP Configuration Example

Install

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