Hydroxyl

Lets an assistant render chemical structures as journal figures, check them for valence and drawing issues, and convert them between formats.

What it does

A local stdio MCP server with five tools for chemical structures. render_figure draws a structure as a figure at single, double or custom width in PNG or SVG, reporting printed size, label size and a warning for text under 8 pt. check_structure returns valence and drawing issues with one-click fixes, describe returns formula, molecular weight, exact mass, net charge and CIP labels, convert returns a molfile or canonical SMILES, and editor_link returns a link that opens the structure in the editor. Structures can be given as SMILES, molfile, or a compound name such as caffeine.

When to use it

Useful when an assistant works with chemistry: preparing publication figures, sanity-checking a structure before use, or converting between SMILES, molfile and names. It suits desktop clients that start local stdio servers.

Requirements

Runs locally over stdio; no network calls. Needs Node.js 22 or newer, since npx fetches the hydroxyl-mcp package from npm. Add the command and arguments to the MCP client configuration. The optional HYDROXYL_EDITOR_URL environment variable changes the editor that editor_link points at; it defaults to the hosted editor.