Admetlab Mcp

[](https://github.com/ToxMCP/admetlab-mcp/actions/workflows/ci.yml)

Architecture

[](https://doi.org/10.64898/2026.02.06.703989) [](./LICENSE) [](https://github.com/ToxMCP/admetlab-mcp/releases) [](https://www.python.org/)

ADMETlab MCP (ADMETlab 3.0 MCP Server)

> Part of ToxMCP Suite → https://github.com/ToxMCP/toxmcp

Public MCP endpoint for the ADMETlab 3.0 API. Expose molecule washing, SVG rendering, ADMET prediction, and CSV retrieval to any MCP-aware agent (Codex CLI, Gemini CLI, Claude Code, etc.).

Why this project exists

ADMETlab 3.0 provides ADMET property calculations, washing, and visualization. Researchers often script against the API or copy/paste results; MCP packaging makes these workflows discoverable and callable by LLM copilots with guardrails and structured schemas.

---

Feature snapshot

| Capability | Description | | --- | --- | | 🌐 MCP over HTTP | JSON-RPC /mcp endpoint with lifecycle + tool catalog. | | 🧪 ADMET Tools | Wash molecules, render SVGs, run ADMET predictions, fetch CSV outputs. | | 🛡️ Client-side Guardrails | Rate limit ( Note: ADMET predictions try /api/admet then fall back to /api/single/admet. The official site currently reports instability; expect occasional 5xx/404 responses from upstream.

---

Configuration

Settings use pydantic-settings with .env support (prefix ADMETLAB_):

| Variable | Default | Description | | --- | --- | --- | | ADMETLAB_BASE_URL | https://admetlab3.scbdd.com | Base URL for all requests. | | ADMETLAB_TIMEOUT_SECONDS | 30 | HTTP timeout. | | ADMETLAB_RETRY_ATTEMPTS | 3 | Retry attempts on 5xx/429. | | ADMETLAB_RETRY_BACKOFF | 0.5 | Initial backoff seconds (exponential). | | ADMETLAB_RPS_LIMIT | 5 | Client-side requests per second cap. | | ADMETLAB_BATCH_SIZE | 1000 | SMILES per request before chunking. | | ADMETLAB_FEATURE_DEFAULT | false | Default feature flag for ADMET. | | ADMETLAB_UNCERTAIN_DEFAULT | false | Default uncertain flag for ADMET. | | ADMETLAB_ADMET_ENDPOINT | /api/admet | Primary ADMET endpoint. | | ADMETLAB_ADMET_FALLBACK_ENDPOINTS | /api/single/admet | Fallback endpoints. Accepts comma-separated paths or JSON array string. | | ADMETLAB_API_KEY | empty | Reserved for future auth. | | ADMETLAB_LOG_LEVEL | INFO | Log level. |

---

Tool catalog

| Tool | Upstream | Description | | --- | --- | --- | | wash_molecule | POST /api/washmol | Standardize molecules; returns cleaned SMILES list. | | render_molecule_svg | POST /api/molsvg | Render molecule SVG; optional figsize [w,h]. | | predict_admet | POST /api/admet (fallback /api/single/admet) | ADMET panel with decision codes, probabilities, SVG highlights; returns batch aggregation and taskid from upstream payload. | | fetch_admet_csv | POST /api/admetCSV | Fetch CSV results by taskId; response includes headers and content. |

Lifecycle: initialize, initialized, shutdown, exit exposed via /mcp. Tool schemas are discoverable via tools/list.

---

Running the server

uvicorn admetlab_mcp.transport.http:app --host 0.0.0.0 --port 8200

Sample MCP calls (HTTP):

# initialize
curl -s http://localhost:8200/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{}}'

# list tools
curl -s http://localhost:8200/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/list","params":{}}'

# wash molecule
curl -s http://localhost:8200/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":3,"method":"tools/call","params":{"name":"wash_molecule","arguments":{"SMILES":"CCO"}}}'

---

Output artifacts

• Tool results are returned as JSON under result.content in MCP JSON-RPC responses.
• CSV fetch includes raw text plus headers for client-side saving.
• SVGs are returned inline as strings from render_molecule_svg.

---

Security checklist

• Client-side rate limiting honors service guidance (<=5 rps).
• Input validation and batch caps to avoid oversize requests.
• Optional API key header placeholder for future auth.
• Prefer running behind TLS-terminating proxy; restrict exposure to trusted clients.

---

Development notes

• Tests: pytest
• Lint/format: black . && isort .
• Known upstream issues: ADMET endpoints may return 404/500 due to service instability (per official notice). The client retries and falls back but cannot guarantee success.

---

Contributing

See [CONTRIBUTING.md](CONTRIBUTING.md) for development setup and pull request guidance.

Community and governance

• Code of Conduct: [CODE_OF_CONDUCT.md](CODEOFCONDUCT.md)
• Security policy: [SECURITY.md](SECURITY.md)
• Release checklist: [RELEASE_CHECKLIST.md](RELEASE_CHECKLIST.md)
• Changelog: [CHANGELOG.md](CHANGELOG.md)

License

MIT. See [LICENSE](LICENSE).

Acknowledgements / Origins

ToxMCP was developed in the context of the VHP4Safety project (see: https://github.com/VHP4Safety) and related research/engineering efforts.

Funding: Dutch Research Council (NWO) — NWA.1292.19.272 (NWA programme)

This suite integrates with third-party data sources and services (e.g., EPA CompTox, ADMETlab, AOP resources, OECD QSAR Toolbox, Open Systems Pharmacology). Those upstream resources are owned and governed by their respective providers; users are responsible for meeting any access, API key, rate limit, and license/EULA requirements described in each module.

✅ Citation

Djidrovski, I. ToxMCP: Guardrailed, Auditable Agentic Workflows for Computational Toxicology via the Model Context Protocol. bioRxiv (2026). https://doi.org/10.64898/2026.02.06.703989

@article{djidrovski2026toxmcp,
  title   = {ToxMCP: Guardrailed, Auditable Agentic Workflows for Computational Toxicology via the Model Context Protocol},
  author  = {Djidrovski, Ivo},
  journal = {bioRxiv},
  year    = {2026},
  doi     = {10.64898/2026.02.06.703989},
  url     = {https://doi.org/10.64898/2026.02.06.703989}
}

Citation metadata: [CITATION.cff](./CITATION.cff)

Verification (smoke test)

Once the server is running:

# health
curl -s http://localhost:8200/health | jq .

# list MCP tools
curl -s http://localhost:8200/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list","params":{}}' | jq .

Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: ToxMCP
• Source: ToxMCP/admetlab-mcp
• License: Apache-2.0
• Homepage: https://github.com/ToxMCP/toxmcp

Install and usage instructions live in the source repository linked above.