Hydroxyl

Local stdio MCP server: publication figures, structure checks and conversions for AI assistants

Connector by trebeljahr · GitHub account verified by the MCP Registry

IndexedMITLocal (stdio)

Install

Works with Claude Code, Codex, VS Code, Cursor, Windsurf, Claude Desktop. Read the repository before you give any tool access to your data.

npx agentmarket install connector/trebeljahr-hydroxyl

Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.

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About

Local stdio MCP server: publication figures, structure checks and conversions for AI assistants

Reviews

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Permissions

What this server can do and what it asks for, from its tool list and install config. Checked Oct 25, 2026.

Tools: 3 read · 0 write · 0 delete · 2 not yet classified
Secrets: None asked for
Install scripts: Not scanned yet
Runs as: Node.js package

Tools by what they do 5

Read from the source code; the running server may list different tools.

Read 3 · Look things up without changing anything.

check_structure
convert
describe

Not yet classified 2 · We could not tell from the name and description.

editor_link
render_figure

Secrets and settings it asks for

Other settings (environment variables or headers).

HYDROXYL_EDITOR_URL

Tools (5)

Read from the source code; the running server may differ. Descriptions are the server’s own words; hidden characters are shown as [U+…].

check_structureCheck a structure
Report every valence and drawing problem the editor would flag (over-valent atoms, misplaced wedges), each with the obvious one-click fixes as corrected molfiles, plus RDKit's refusal if it would refuse it. Atoms are numbered 1-based in molfile order.
convertConvert between SMILES and molfile
Convert a structure to a molfile (as the editor saves it) or to RDKit's canonical SMILES. By default a SMILES becomes a molfile and anything else becomes a SMILES.
describeDescribe a structure
Sum formula (Hill order), average molecular weight, monoisotopic exact mass, net charge, and the CIP label of every stereocentre and stereogenic double bond. Atoms are numbered 1-based in molfile order.
editor_linkLink to the structure in the editor
A link that opens the structure in the Hydroxyl editor as a new, unsaved sketch. The structure travels in the URL fragment, which the browser does not send to the server.
render_figureRender a publication figure
Draw a structure as a journal figure: one bond prints at the style's standard length (5.08 mm for ACS-style Publication), and the width is a maximum the figure is scaled down to fit. Returns the figure (PNG or SVG), its printed size, its label size, and a warning for any text that prints below the style's minimum (8 pt for Publication).

Signals

Stars: 0
Forks: 0
Open issues: 0
Last commit (this folder): Oct 8, 2026 (21 days ago)
Last release: Oct 8, 2026 (21 days ago)

From GitHub (fetched Oct 24, 2026).

Details

Registry name: io.github.trebeljahr/hydroxyl
Version: 0.1.0
Auth: No auth
Packages: npm hydroxyl-mcp
License: MIT
Repository: github.com/trebeljahr/hydroxyl.app
Website: hydroxyl.app
First seen: Oct 24, 2026
Last checked: Oct 24, 2026
Source: Official MCP Registry github-graphql