# Rdkit Mcp Server

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

- **Type:** MCP server
- **Install:** `agentstack add mcp-tandemai-inc-rdkit-mcp-server`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [tandemai-inc](https://agentstack.voostack.com/s/tandemai-inc)
- **Installs:** 0
- **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [tandemai-inc](https://github.com/tandemai-inc)
- **Source:** https://github.com/tandemai-inc/rdkit-mcp-server
- **Website:** https://tandemai.com

## Install

```sh
agentstack add mcp-tandemai-inc-rdkit-mcp-server
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# RDKit MCP Server: Agentic Access to RDKit for LLMs

RDKit MCP Server is an open-source MCP server that enables language models to interact with RDKit through natural language. The goal is to provide agent-level access to every function in RDKit 2025.3.1 without writing any code.

## Features

* **Seamless Integration**: Exposes RDKit functions via the Model Context Protocol (MCP).
* **Language Model Support**: Connect any LLM that supports the MCP protocol.
* **CLI Client**: Includes a command-line client powered by OpenAI for quick experimentation.

## Table of Contents

* [Installation](#installation)
* [Usage](#usage)

  * [Start the Server](#start-the-server)
  * [CLI Client](#cli-client)
* [Available Tools](#available-tools)
* [Evaluations](#evaluations)
* [Contributing](#contributing)

## Installation

Install the package:

```bash
pip install .
```

## Usage

### Start the Server

```bash
python run_server.py [--settings settings.yaml]
```

See `settings.example.yaml` for setting options

Once the server is running, any MCP-compliant LLM can connect. For example, see the [Claude Desktop quickstart](https://modelcontextprotocol.io/quickstart/user).

### CLI Client

A CLI client is included for rapid prototyping with OpenAI:

```bash
export OPENAI_API_KEY="sk-proj-xxx"
python run_client.py
```

## Available Tools

List all available RDKit tools exposed by the server:

```bash
python list_tools.py [--settings settings.yaml]
```

## Evaluations

The `evals` directory contains a test suite for evaluating RDKit MCP tool outputs and agent responses using [pydantic-evals](https://ai.pydantic.dev/evals/).

### Install Dependencies

```bash
pip install ".[evals]"
```

### Start the MCP Server

In one terminal, start the server:

```bash
python run_server.py
```

### Run Evaluations

In another terminal, run the evaluation suite:

```bash
python evals/run_evals.py
```

Options:
- `--verbose` - Show detailed output including inputs and outputs
- `--filter ` - Run only cases matching the name
- `--output-json results.json` - Export results to JSON

Each test uses LLM-based evaluation (LLMJudge) to assess whether the agent correctly used the RDKit tools and produced accurate results.

## Contributing

We welcome contributions, feature requests, and bug reports:

See `CONTRIB.md` for guidelines on how to get started.

Together, we can make RDKit accessible to a wider range of applications through natural language interfaces.

## Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [tandemai-inc](https://github.com/tandemai-inc)
- **Source:** [tandemai-inc/rdkit-mcp-server](https://github.com/tandemai-inc/rdkit-mcp-server)
- **License:** MIT
- **Homepage:** https://tandemai.com

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/mcp-tandemai-inc-rdkit-mcp-server
- Seller: https://agentstack.voostack.com/s/tandemai-inc
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.