Hydroxyl MCP

A local stdio MCP server for AI assistants that enables chemical structure editing, validation, and conversion. It allows agents to draw molecules, check structures, and export figures in various representations such as skeletal, Kekulé, Lewis dot, and condensed formulas, leveraging a pure TypeScript chemistry core.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Community listingLocal stdioSource reviewed; not executedPublished by trebeljahr

Vendor documentation

What you can do with it

Draw and edit 2D chemical structures
Export molecular figures in multiple representations
Validate chemical formulas and valence
Convert structures to skeletal or Lewis dot formats

Source and maintenance

Community listingRegistry 0.1.0

mcp-registry: io.github.trebeljahr/hydroxyl@0.1.0 Source repository Project website

Maintenance checked: Oct 31, 2026, 10:27 PM UTC

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

hydroxyl-mcp 0.1.0

npm

hydroxyl-mcp package definition

{
  "version": "0.1.0",
  "transport": "stdio",
  "identifier": "hydroxyl-mcp",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "HYDROXYL_EDITOR_URL",
      "format": "string",
      "description": "Editor that editor_link points at (default https://hydroxyl.app/editor/)"
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.

Cursor configuration

{
  "mcpServers": {
    "hydroxyl-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "hydroxyl-mcp@0.1.0"
      ],
      "env": {
        "HYDROXYL_EDITOR_URL": "<YOUR_HYDROXYL_EDITOR_URL>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.

Cline configuration

{
  "mcpServers": {
    "hydroxyl-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "hydroxyl-mcp@0.1.0"
      ],
      "env": {
        "HYDROXYL_EDITOR_URL": "<YOUR_HYDROXYL_EDITOR_URL>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.

VS Code configuration

{
  "servers": {
    "hydroxyl-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "hydroxyl-mcp@0.1.0"
      ],
      "env": {
        "HYDROXYL_EDITOR_URL": "<YOUR_HYDROXYL_EDITOR_URL>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.

Claude Desktop configuration

{
  "mcpServers": {
    "hydroxyl-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "hydroxyl-mcp@0.1.0"
      ],
      "env": {
        "HYDROXYL_EDITOR_URL": "<YOUR_HYDROXYL_EDITOR_URL>"
      }
    }
  }
}

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