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MCP server · AI

Rdkit MCP Server

by · github.com/tandemai-inc/rdkit-mcp-server

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

Unclaimed MIT last commit 6 months ago mcprdkitdrug-discoveryllmmcp-servercheminformaticsaichemistry
InstallView source
69Good

Scored 3 months ago · breakdown

About Rdkit MCP Server

Rdkit MCP Server is an MCP server published by tandemai-inc in the AI category: mCP server that enables language models to interact with RDKit through natural language. It has been installed 0 times through Conduid.

The repository has 31 stars and 6 forks, with the last commit 6 months ago. Six months or more without a commit doesn't mean the server is broken, but check the open issues (0) before depending on it in production.

Install

Install
npx rdkit-mcp-server

This server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.

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  • !Scoped permissionsDoesn't declare a permission scope. Assume it can do anything its process can.

README

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

Install the package:

pip install .

Usage

Start the Server

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.

CLI Client

A CLI client is included for rapid prototyping with OpenAI:

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

Available Tools

List all available RDKit tools exposed by the server:

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.

Install Dependencies

pip install ".[evals]"

Start the MCP Server

In one terminal, start the server:

python run_server.py

Run Evaluations

In another terminal, run the evaluation suite:

python evals/run_evals.py

Options:

  • --verbose - Show detailed output including inputs and outputs
  • --filter <name> - 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.

README mirrored from the source repository 3 months ago. The original is authoritative.

Questions

About Rdkit MCP Server

How do I install Rdkit MCP Server?

Run npx rdkit-mcp-server, then add the server to your MCP client's configuration. Conduid has recorded 0 installs, so the command is known to work with current clients.

Is Rdkit MCP Server safe to use with an AI agent?

Its trust score is 69 out of 100 (good). It passes 0 of 1 static security checks; the failures are listed above. It has no ConduID identity yet, so agent calls to it are not receipted.

Is Rdkit MCP Server still maintained?

The last commit was 6 months ago, with 0 open issues. That's long enough that you should check whether the maintainer is responding to issues before depending on it.