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Molecule Visualizer MCP Server

@leelasd

Repository

Basic information

Category

Other

License

Apache-2.0

Transports

stdio

Author

leelasd

About Molecule Visualizer MCP Server

MCP server for visualizing molecules in Claude Desktop :)

#molecule-visualizer#chemistry#molecular-properties

Molecule Visualizer MCP Server config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "molecule_mcp": {
      "command": "uv",
      "args": [
        "venv"
      ]
    }
  }
}

Molecule Visualizer MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is Molecule Visualizer MCP Server?

A Model Context Protocol server that provides tools for visualizing molecules and retrieving molecular properties using SMILES codes. It integrates with LLM applications like Claude Desktop for chemistry‑focused capabilities such as exploring structures, analyzing properties, and generating visualizations.

How to use Molecule Visualizer MCP Server?

Install Python 3.10+, RDKit, the MCP Python SDK, and Pillow. Run the setup script or use uv to install dependencies, then configure Claude Desktop by adding the server to claude_desktop_config.json. You can also run the server directly with python molecule_server.py.

Key features of Molecule Visualizer MCP Server

  • Generate 2D visualizations from SMILES strings or common names.
  • Return MCP Image objects for direct LLM integration.
  • Markdown‑compatible output with base64‑encoded images.
  • Customizable image dimensions and optional atom indices.
  • Calculate molecular properties including Lipinski’s Rule of Five.
  • Access a built‑in database of common molecules by name.

Use cases of Molecule Visualizer MCP Server

  • Exploring molecular structures and analyzing chemical properties.
  • Generating molecule visualizations for educational content or research assistance.
  • Integrating reliable chemistry capabilities into LLM‑based applications.

Frequently asked questions

1

What dependencies does Molecule Visualizer MCP Server require?

Python 3.10+, RDKit 2023.3.1+, the MCP Python SDK, and Pillow 10.0.0+.

2

Where are common molecules stored?

The server includes a built‑in database of common molecules accessible by name.

3

How does it compare to using web access for molecule visualization?

The

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