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RDKit Chemistry

v1.0.0•Data Science & ML•stable

MCP server that enables language models to interact with RDKit through natural language

cheminformaticschemistrydrug-discoveryllmmcp
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What is RDKit Chemistry?

RDKit Chemistry is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to mcp server that enables language models to interact with rdkit through natural language

MCP server that enables language models to interact with RDKit through natural language

This server falls under the Data Science & ML category on MCPgee, the world's largest MCP server directory with 33,000+ servers.

Features

  • MCP server that enables language models to interact with RDK

Use Cases

Cheminformatics via natural language
Drug discovery automation
Molecular analysis
tandemai-inc

Maintainer

LicenseMIT
Languagepython
Versionv1.0.0
UpdatedMay 18, 2026
Statushealthy
Maintenanceactive

Works with

ClaudeOpenAIwindowsmacoslinux
View SourceBrowse All Servers

Installation

Manual Installation

npx rdkit

Configuration

Configuration Details

Config File

claude_desktop_config.json

Performance

Response Metrics

Response Time< 200ms
ThroughputMedium

Resource Usage

Memory UsageLow
CPU UsageLow

How to Set Up and Use RDKit Chemistry

The RDKit MCP Server exposes RDKit's cheminformatics functions to any MCP-compatible language model through natural language, covering the full RDKit 2025.3.1 API without requiring the user to write code. Researchers in drug discovery, cheminformatics, and molecular analysis can ask questions about SMILES strings, compute molecular properties, generate fingerprints, perform substructure searches, and more — all conversationally. It is built by TandemAI and is designed for agent-level, code-free access to a mature scientific computing library.

Prerequisites

  • Python 3.8 or higher installed
  • RDKit installed (conda install -c conda-forge rdkit or pip install rdkit)
  • The rdkit-mcp-server repository cloned locally
  • An MCP-compatible client such as Claude Desktop
  • Optionally an OpenAI API key if using the built-in CLI client
1

Clone the repository and install dependencies

Clone the rdkit-mcp-server repository and install it with pip. RDKit must already be available in your Python environment.

git clone https://github.com/tandemai-inc/rdkit-mcp-server.git
cd rdkit-mcp-server
pip install .
2

Review available settings

Copy the example settings file to configure which RDKit tools are exposed and any server options.

cp settings.example.yaml settings.yaml
# Edit settings.yaml as needed
3

Start the MCP server

Run the server script. By default it listens for MCP connections and exposes the full set of RDKit tools.

python run_server.py --settings settings.yaml
4

List available tools (optional)

Use the list_tools script to see all RDKit functions exposed by the server before connecting your AI client.

python list_tools.py --settings settings.yaml
5

Add the server to your MCP client configuration

Register the server in your Claude Desktop config or equivalent MCP client so the AI can call RDKit tools.

{
  "mcpServers": {
    "rdkit": {
      "command": "python",
      "args": ["/path/to/rdkit-mcp-server/run_server.py", "--settings", "/path/to/rdkit-mcp-server/settings.yaml"]
    }
  }
}

RDKit Chemistry Examples

Client configuration

Claude Desktop configuration for the RDKit MCP server using the run_server.py entry point.

{
  "mcpServers": {
    "rdkit": {
      "command": "python",
      "args": [
        "/home/user/rdkit-mcp-server/run_server.py",
        "--settings",
        "/home/user/rdkit-mcp-server/settings.yaml"
      ]
    }
  }
}

Prompts to try

Ask RDKit questions in natural language once the server is connected to your MCP client.

- "What is the molecular weight of aspirin? Its SMILES is CC(=O)Oc1ccccc1C(=O)O"
- "Generate a Morgan fingerprint with radius 2 for caffeine (SMILES: Cn1cnc2c1c(=O)n(c(=O)n2C)C)"
- "Does the molecule CC(=O)Nc1ccc(O)cc1 contain a phenol substructure?"
- "Calculate the LogP and TPSA for ibuprofen: CC(C)Cc1ccc(cc1)C(C)C(=O)O"
- "Find the Murcko scaffold for the molecule C1CCN(CC1)c1ncnc2[nH]cnc12"

Troubleshooting RDKit Chemistry

ImportError: No module named 'rdkit'

RDKit must be installed separately before installing the server. Use conda: `conda install -c conda-forge rdkit`, or pip: `pip install rdkit`. Confirm with `python -c 'from rdkit import Chem; print(Chem.__version__)'`.

Server starts but no tools appear in the MCP client

Check the settings.yaml to ensure tools are not disabled. Restart the MCP client after updating the config. Run `python list_tools.py` to confirm the server itself is exposing tools.

Invalid SMILES errors when querying molecules

RDKit will return an error for malformed SMILES strings. Validate your SMILES input using a tool like https://www.cheminfo.org/Chemistry_-_Cheminformatics/Mole_cule/SMILES_validator/ before passing it to the server.

Frequently Asked Questions about RDKit Chemistry

What is RDKit Chemistry?

RDKit Chemistry is a Model Context Protocol (MCP) server that mcp server that enables language models to interact with rdkit through natural language It connects AI assistants to external tools and data sources through a standardized interface.

How do I install RDKit Chemistry?

Follow the installation instructions on the RDKit Chemistry GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.

Which AI clients work with RDKit Chemistry?

RDKit Chemistry works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.

Is RDKit Chemistry free to use?

Yes, RDKit Chemistry is open source and available under the MIT license. You can use it freely in both personal and commercial projects.

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Quick Config Preview

{ "mcpServers": { "rdkit": { "command": "npx", "args": ["-y", "rdkit"] } } }

Add this to your claude_desktop_config.json or .cursor/mcp.json

Read the full setup guide →

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