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Hydroxyl

Hydroxyl

Local
hydroxyl.appScience & Education0Updated 1w ago
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About Hydroxyl

Hydroxyl is a local MCP server for researchers and AI assistants working with chemical structures. It creates publication figures, checks structures, reports molecular properties, and converts formats without making network calls from the server.

Key features

  1. 01Render structure figures as PNG or SVG
  2. 02Check valence and drawing issues
  3. 03Describe formula, mass, charge, and CIP labels
  4. 04Convert structures to molfile or canonical SMILES
  5. 05Create editor links

Use cases

  1. 01Prepare a chemical structure figure for a journal
  2. 02Review structure warnings and suggested fixes
  3. 03Retrieve molecular properties for a structure
  4. 04Convert a structure between supported formats

MCP support

The local stdio MCP server exposes five tools for rendering, checking, describing, converting, and opening chemical structures in the editor.

Configuration

Local server config is the same for every client. Copy it into your client’s MCP config file.

mcp.json · Universal config
{
  "mcpServers": {
    "trebeljahr-hydroxyl": {
      "command": "npx",
      "args": [
        "-y",
        "hydroxyl-mcp"
      ],
      "env": {
        "HYDROXYL_EDITOR_URL": "<HYDROXYL_EDITOR_URL>"
      }
    }
  }
}
Run commandnpx -y hydroxyl-mcp
Environment variables to set
HYDROXYL_EDITOR_URLEditor that editor_link points at (default https://hydroxyl.app/editor/)

Local servers need a runtime on your machine (e.g. Node.js 18+). Config file locations differ by client; see your client’s docs.

Packages
npmhydroxyl-mcp0.1.0

Tools

5

Saved tool list · updated 2w ago

ParameterTypeRequiredDescription
dpianyNoPNG resolution, 300 (default) or 600.
namestringNoA common name from the editor's structure dictionary, e.g. "benzene", "glycine", "DMSO". Not a full name-to-structure parser: unknown names are refused.
styleenumNopublication (ACS 1996 settings, default), nature (Nature Portfolio), or screen.publication | nature | screen
viewsarrayNoOne panel per view, in order. skeletal (default), kekule, explicitH, lewis, condensed, sumFormula.
widthanyNoMaximum width: "single" or "double" journal column (default single), or a width in cm.
formatenumNopng (default) or svg.png | svg
smilesstringNoA SMILES string, e.g. "c1ccccc1".
molfilestringNoAn MDL molfile (V2000 or V3000), the whole text including the header lines.
backgroundenumNoPNG background, white (default) or transparent. The SVG is always transparent.white | transparent

Details

From the project README

hydroxyl-mcp

hydroxyl-mcp is a local Model Context Protocol server. An assistant such as Claude Desktop can use it to draw a structure as a journal figure, check it, and convert it. It runs on your machine over stdio and makes no network calls. Structures you send go to your assistant's provider, never to us.

It has five tools:

ToolInputOutput
render_figurea structure; views; width (single, double or cm); png or svgthe figure, its printed size, its label size, and a warning for text under 8 pt
check_structurea structurethe valence and drawing issues the editor flags, each with its one-click fixes
describea structureformula, molecular weight, exact mass, net charge, CIP labels
converta structurea molfile or a canonical SMILES
editor_linka structurea link that opens the structure in the editor

A structure is one of smiles, molfile, or name (a compound from the editor's insert box, such as caffeine).

Add it to your MCP client; npx fetches the hydroxyl-mcp package from npm (Node.js 22 or newer). For Claude Desktop, edit claude_desktop_config.json (Settings → Developer → Edit Config) and restart the app:

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

Other clients that start stdio servers take the same command and arguments. For Claude Code:

claude mcp add hydroxyl -- npx -y hydroxyl-mcp

editor_link points at https://hydroxyl.app/editor/. Set HYDROXYL_EDITOR_URL in the server's environment to link to a local or self-hosted editor instead.

The editor itself is at hydroxyl.app; source at github.com/trebeljahr/hydroxyl.app.

Licence

MIT. The package depends on RDKit (BSD-3-Clause) and resvg-wasm (MPL-2.0), and ships the Arimo font (OFL-1.1, text in dist/arimo-OFL.txt).

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New to MCP?

From what the protocol is to installing your first server, these answers cover most first questions.

An open protocol that defines how AI applications connect to external tools and data in a uniform way. Clients talk to the model; MCP servers provide tools, resources and prompt templates. They exchange standard messages, so one server can be reused by many clients.