Hydroxyl
NPM · HYDROXYL-MCP
Local stdio MCP server: publication figures, structure checks and conversions for AI assistants
Available components
Last scanned (6 hours ago)
Scores higher than 58% of npm servers
Category Health and Science
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. How we score → Why this is hard to score →
Supply Chain Security98
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- 30 of 94 dependencies flagged as unhealthy. View diagnostics → Partial
Provenance & Transparency45
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Provenance check failed: no build-provenance attestation is published. See how to fix → View diagnostics → Fail
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 28 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability65
- AI-judged instruction clarity (good).Pass
- 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. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management73
- Stability observed for 22 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 5 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 5 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 4 Nov 26 +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.
- 1 Nov 26 +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.
- 30 Oct 26 +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.
- 28 Oct 26 +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.
- 26 Oct 26 +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.
- 24 Oct 26 +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.
- 22 Oct 26 +4
- Stability: unverified → 0.27 ▲ functional
- 14 Oct 26 +30
- 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). security
- Tool coverage: unverified → 100 ▲ functional
- 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 functional
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed npm/hydroxyl-mcp@0.1.0
Provenance No attestation
The registry publishes no build provenance for this version, so there is nothing to verify.
| Result | No attestation |
|---|---|
| Ecosystem | npm |
Background: How many MCP packages publish verified provenance →
Dependencies 94 packages
| Packages resolved | 94 |
|---|---|
| Stale | 30 |
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
check_structure Check a structure ~160
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.
| Name | Type | Req | Description |
|---|---|---|---|
| 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". |
No output schema declared.
No examples provided.
convert Convert between SMILES and molfile ~154
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.
| Name | Type | Req | Description |
|---|---|---|---|
| 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. |
No output schema declared.
No examples provided.
describe Describe a structure ~150
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.
| Name | Type | Req | Description |
|---|---|---|---|
| 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". |
No output schema declared.
No examples provided.
editor_link Link to the structure in the editor ~142
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.
| Name | Type | Req | Description |
|---|---|---|---|
| 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". |
No output schema declared.
No examples provided.
render_figure Render a publication figure ~314
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).
| Name | Type | Req | Description |
|---|---|---|---|
| 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. |
No output schema declared.
No examples provided.
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.
npm · hydroxyl-mcp
claude mcp add trebeljahr-hydroxyl -- npx -y hydroxyl-mcp
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.