# Hydroxyl (npm · hydroxyl-mcp)

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

- Trust score: 78/100 (medium)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- npm · `hydroxyl-mcp`: 78/100 (this document), [markdown](https://verifymcp.io/servers/trebeljahr-hydroxyl/hydroxyl-mcp.md), [page](https://verifymcp.io/servers/trebeljahr-hydroxyl/hydroxyl-mcp)

## Channel facts

- Registry: `npm`
- Package: `hydroxyl-mcp`
- Version: `0.1.0`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 98/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - 30 of 94 dependencies flagged as unhealthy.
- **Provenance & Transparency**: 45/100
  - Source repository is publicly reachable at the declared URL.
  - Provenance check failed: no build-provenance attestation is published.
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 28 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 65/100
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 920 tokens (~184/item across 5 items; 5 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 73/100
  - Stability observed for 22 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 5 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 5 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Hydroxyl MCP server?

Hydroxyl runs locally as an npm package, launched with npx -y hydroxyl-mcp. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add trebeljahr-hydroxyl -- npx -y hydroxyl-mcp
```

### Cursor

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

### VS Code

```json
{
  "servers": {
    "trebeljahr-hydroxyl": {
      "command": "npx",
      "args": [
        "-y",
        "hydroxyl-mcp"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add trebeljahr-hydroxyl -- npx -y hydroxyl-mcp
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "trebeljahr-hydroxyl": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "hydroxyl-mcp"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add trebeljahr-hydroxyl --command npx --arg -y --arg hydroxyl-mcp
```

### Hermes

```yaml
mcp_servers:
  trebeljahr-hydroxyl:
    command: "npx"
    args: ["-y", "hydroxyl-mcp"]
```

### Netclaw

```json
{
  "McpServers": {
    "trebeljahr-hydroxyl": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "hydroxyl-mcp"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add trebeljahr-hydroxyl -t stdio -c npx -a -y hydroxyl-mcp
```

### Other

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

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-04 (score 78, +1)

No change was recorded against any check on this day. Stability & Change Management went from 67 to 70. That category is still filling its 30-day observation window: 20 days of observed history at the previous scan, 21 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-01 (score 77, +1)

No change was recorded against any check on this day. Stability & Change Management went from 57 to 60. That category is still filling its 30-day observation window: 17 days of observed history at the previous scan, 18 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-30 (score 76, +1)

No change was recorded against any check on this day. Stability & Change Management went from 50 to 53. That category is still filling its 30-day observation window: 15 days of observed history at the previous scan, 16 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-28 (score 75, +1)

No change was recorded against any check on this day. Stability & Change Management went from 43 to 47. That category is still filling its 30-day observation window: 13 days of observed history at the previous scan, 14 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-26 (score 74, +1)

No change was recorded against any check on this day. Stability & Change Management went from 37 to 40. That category is still filling its 30-day observation window: 11 days of observed history at the previous scan, 12 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-24 (score 73, +1)

No change was recorded against any check on this day. Stability & Change Management went from 30 to 33. That category is still filling its 30-day observation window: 9 days of observed history at the previous scan, 10 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-22 (score 72, +4)

- [functional improvement] Stability: unverified → 0.27

### 2026-10-14 (score 68, +30)

- [security improvement] Injection markers: unverified → pass
- [security] First check of Judged manipulation: pass
- [security] Stability: Stability not yet verified: not enough scan history yet (needs a 30-day window).
- [functional improvement] Tool coverage: unverified → 100
- [functional improvement] MCP protocol: unverified → pass
- [functional] First check of Schema quality: fail
- [functional] First check of Destructive annotations: pass
- [functional] First check of Schema quality: fail
- [functional] First check of Schema quality: good
- [functional] First check of Tool coverage: 100

## MCP tools (5)

### `render_figure` (~314 tokens)

Render 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).

Input parameters:

- `background` (string): PNG background, white (default) or transparent. The SVG is always transparent.
- `dpi`: PNG resolution, 300 (default) or 600.
- `format` (string): png (default) or svg.
- `molfile` (string): An MDL molfile (V2000 or V3000), the whole text including the header lines.
- `name` (string): A common name from the editor's structure dictionary, e.g. "benzene", "glycine", "DMSO". Not a full name-to-structure parser: unknown names are refused.
- `smiles` (string): A SMILES string, e.g. "c1ccccc1".
- `style` (string): publication (ACS 1996 settings, default), nature (Nature Portfolio), or screen.
- `views` (array): One panel per view, in order. skeletal (default), kekule, explicitH, lewis, condensed, sumFormula.
- `width`: Maximum width: "single" or "double" journal column (default single), or a width in cm.

### `check_structure` (~160 tokens)

Check 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.

Input parameters:

- `molfile` (string): An MDL molfile (V2000 or V3000), the whole text including the header lines.
- `name` (string): A common name from the editor's structure dictionary, e.g. "benzene", "glycine", "DMSO". Not a full name-to-structure parser: unknown names are refused.
- `smiles` (string): A SMILES string, e.g. "c1ccccc1".

### `describe` (~150 tokens)

Describe 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.

Input parameters:

- `molfile` (string): An MDL molfile (V2000 or V3000), the whole text including the header lines.
- `name` (string): A common name from the editor's structure dictionary, e.g. "benzene", "glycine", "DMSO". Not a full name-to-structure parser: unknown names are refused.
- `smiles` (string): A SMILES string, e.g. "c1ccccc1".

### `convert` (~154 tokens)

Convert 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.

Input parameters:

- `molfile` (string): An MDL molfile (V2000 or V3000), the whole text including the header lines.
- `name` (string): A common name from the editor's structure dictionary, e.g. "benzene", "glycine", "DMSO". Not a full name-to-structure parser: unknown names are refused.
- `smiles` (string): A SMILES string, e.g. "c1ccccc1".
- `to` (string): The format to produce.

### `editor_link` (~142 tokens)

Link 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.

Input parameters:

- `molfile` (string): An MDL molfile (V2000 or V3000), the whole text including the header lines.
- `name` (string): A common name from the editor's structure dictionary, e.g. "benzene", "glycine", "DMSO". Not a full name-to-structure parser: unknown names are refused.
- `smiles` (string): A SMILES string, e.g. "c1ccccc1".

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/trebeljahr-hydroxyl/hydroxyl-mcp#diagnostics

## Score history

- 2026-11-05: 78
- 2026-11-04: 78
- 2026-11-03: 77
- 2026-11-02: 77
- 2026-11-01: 77
- 2026-10-31: 76
- 2026-10-30: 76
- 2026-10-29: 75
- 2026-10-28: 75
- 2026-10-27: 74
- 2026-10-26: 74
- 2026-10-25: 73
- 2026-10-24: 73
- 2026-10-23: 72
- 2026-10-22: 72
- 2026-10-21: 68
- 2026-10-20: 68
- 2026-10-19: 68
- 2026-10-18: 68
- 2026-10-17: 68
- 2026-10-16: 68
- 2026-10-15: 68
- 2026-10-14: 68
- 2026-10-13: 38
- 2026-10-12: 38
- 2026-10-11: 23

## Common questions

### What is the Hydroxyl MCP server?

Hydroxyl is an MCP server listed in the public MCP registry as io.github.trebeljahr/hydroxyl. Local stdio MCP server: publication figures, structure checks and conversions for AI assistants. This page covers its npm package (hydroxyl-mcp).

### Is the Hydroxyl MCP server safe to use?

Hydroxyl scores 78 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Hydroxyl MCP server expose?

Hydroxyl exposes 5 tools: render_figure, check_structure, describe, convert, editor_link. Their descriptions and schemas cost roughly 920 tokens of context every time the server is loaded.

### Is the Hydroxyl MCP server still maintained?

Hydroxyl is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Hydroxyl MCP server under?

Hydroxyl declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

## Links

- npm package: https://www.npmjs.com/package/hydroxyl-mcp
- Socket report: https://socket.dev/npm/package/hydroxyl-mcp
- Repository: https://github.com/trebeljahr/hydroxyl.app
- Website: https://hydroxyl.app/
- Changelog RSS feed: https://verifymcp.io/servers/trebeljahr-hydroxyl/hydroxyl-mcp.xml
- Changelog JSON feed: https://verifymcp.io/servers/trebeljahr-hydroxyl/hydroxyl-mcp.json
- HTML version of this page: https://verifymcp.io/servers/trebeljahr-hydroxyl/hydroxyl-mcp