Cmxflow MCP Server

Build cheminformatics and computational chemistry pipelines with composable blocks. Tune end-to-end with Bayesian Optimization. Or ask an LLM agent to do it. It runs locally over stdio via the published package.

People who work with bayesian optimization, cheminformatics and drug discovery and want it reachable from Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

VERIFIED ACTIVE

LAST COMMIT 2026-08-31 · ★ 2 · #165 OF 241 MAINTAINED AUTOMATION · VERIFIED 2026-09-30

MIT · Python servers · how we verify → /methodology

01 · Install Cmxflow

Claude Code

claude mcp add b-shields-cmxflow -- uvx cmxflow

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "b-shields-cmxflow": {
      "command": "uvx",
      "args": [
        "cmxflow"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license MIT - declared in the repository

pypi package cmxflow - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.b-shields is GitHub-verified and matches the repo owner

03 · What Cmxflow can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

Latest releases

v0.4.0 · 2026-06-15

Add Cloudflare Web Analytics to docs site · Rewrite README around three quick examples and an LLM agent pitch · Add improved docking engine with ILS search, scaffold indexing, and template docking [minor]

v0.3.1 · 2026-05-16

[patch] Add MCP registry manifest

v0.3.0 · 2026-05-16

[minor] Simplify README description of cmxflow

04 · Who maintains Cmxflow

cmxflow is maintained by b-shields. It's the only MCP server we track from this author; the repo dates to Jan 2026.

05 · Facts

repository: github.com/b-shields/cmxflow
website: https://b-shields.github.io/cmxflow/
category: automation - ranked #165 of 241 actively-maintained automation servers as of 2026-09-30.
registry: io.github.b-shields/cmxflow (active, first published 2026-05-16 · 2 versions)
packages: pypi:cmxflow

06 · Cmxflow FAQ

What is Cmxflow?

Is Cmxflow still maintained?

Yes - as of 2026-09-30, its last commit was 2026-08-31. We re-verify nightly.

How do I install Cmxflow?

Run `uvx cmxflow`. You can also paste the ready-made client config above.

Does Cmxflow run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Cmxflow

Alternatives to Cmxflow

Maintained automation servers if Cmxflow isn't the fit.

More automation MCP servers · Bridge MCP · Godot Agent Loop · Rvt MCP · KiCad Copilot · Agent Lsp

More Python MCP servers · Beget Hosting · Kr Crypto Intelligence · Tool API · Plesk Dev Docs · see all