cmxflow MCP Server

by b-shields Your server? Claim it

local only

cmxflow runs on your own machine — the client starts it, so there is no endpoint to ping. 106 installs a week from pypi. Last commit 31 Aug 2026.

Composable, tunable cheminformatics workflows: library preparation, clustering, docking, and more.

Installs per day peak 25 · avg 10 · +159% w/w

a month agotoday

106

Installs / week

pypi · cmxflow

Stars

3 open issues

31 Aug 2026

Last commit

from GitHub

MIT

License

Python

What the code does

We read the source, 5 d ago · rules 995398eba69f

Capabilities

What this server is able to do. For an MCP server this is often the job itself — a terminal server runs commands because that is what it is for. Listed so you know what you are plugging in, not as an accusation.

Runs an external command src/cmxflow/utils/pymol.py:60, [пакет] src/cmxflow/utils/pymol.py:60

    process = subprocess.Popen(

Unsafe deserialization src/cmxflow/utils/serial.py:66, [пакет] src/cmxflow/utils/serial.py:66

            workflow: Workflow = pickle.load(f)

Is this your server and something here is wrong? Tell us — corrections are free and do not require a plan.

This code can reach further than it looks

We found places where it runs commands, builds paths or queries from values it is given. None of that is a flaw by itself — it becomes one when the code changes, and code changes quietly between releases. We re-read it on every one.

Connect this server

This server runs on your own machine — install it with the package manager and the client starts it for you. Package name taken from the official registry entry.

Claude Code Claude Desktop Codex Cursor VS Code

run in your terminal

claude mcp add cmxflow -- uvx cmxflow

~/Library/Application Support/Claude/claude_desktop_config.json

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

~/.codex/config.toml

[mcp_servers.cmxflow]
command = "uvx"
args = ["cmxflow"]

.cursor/mcp.json

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

.vscode/mcp.json

{
  "servers": {
    "cmxflow": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "cmxflow"
      ]
    }
  }
}

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cmxflow — questions

Answers built from our own checks of this server.

Why is there no uptime for cmxflow?

cmxflow runs on your own machine over stdio — there is no network address to reach, so uptime cannot be measured for it by anyone. What can be measured is adoption: the pypi package cmxflow was installed 106 times last week.

How do I connect cmxflow?

Copy the ready config from this page. We generate it for Claude Code, Claude Desktop, Codex, Cursor and VS Code, each in the form that client actually reads. It runs locally, so the command pulls cmxflow straight from pypi; nothing to host, nothing to sign up for.

How many people use cmxflow?

The pypi package cmxflow was installed 106 times in the last week. Week over week that is +159%. We show installs rather than GitHub stars on purpose: a star is a bookmark, an install is someone actually running it.

Is cmxflow open source?

Yes — it is published under the MIT licence, written in Python, 2 stars on GitHub and 3 open issues. The source link is on this page, so you can read exactly what it does with your data before you connect it.