Molecule AI MCP Server

MCP server that exposes Molecule AI platform operations as tools for AI coding agents.

87 Tools Available

See the full tool registry for all tools. Highlights:

Category	Tools
Workspace	list, create, get, update, delete, restart, pause, resume
Agent	chat_with, assign, replace, remove, move, get_model
Delegation	async_delegate, check_delegations, record_delegation, notify_user, list_activity
Secrets	set, list, delete (workspace + global variants)
Files	list, read, write, delete, replace_all, get_config, update_config
Memory	commit, search, delete (HMA scopes) + memory_set/get/list/delete (K/V)
Plugins	list registry, list installed, install, uninstall, list sources, check compatibility
Channels	list adapters, list, add, update, remove, send, test, discover chats
Schedules	list, create, update, delete, run, get history
Discovery	list peers, discover, check_access, list events, import/export, canvas viewport
Approvals	list pending, decide, create, get workspace approvals
Remote Agents	list (runtime=external), get state, setup command, check freshness

Setup

Claude Code

Add to your project's .mcp.json:

{
  "mcpServers": {
    "molecule": {
      "command": "node",
      "args": ["./mcp-server/dist/index.js"],
      "env": {
        "MOLECULE_API_URL": "http://localhost:8080"
      }
    }
  }
}

Cursor

Add to .cursor/mcp.json:

{
  "mcpServers": {
    "molecule": {
      "command": "node",
      "args": ["./mcp-server/dist/index.js"],
      "env": {
        "MOLECULE_API_URL": "http://localhost:8080"
      }
    }
  }
}

Codex / OpenCode

MOLECULE_API_URL=http://localhost:8080 node mcp-server/dist/index.js

Environment Variables

Variable	Default	Description
MOLECULE_API_URL	http://localhost:8080	Platform API base URL
MOLECULE_API_KEY	—	API key for platform authentication
MCP_SERVER_PORT	3000	Port (for HTTP/SSE transport)

Quick Start

1. npm install && npm run build
2. Set MOLECULE_API_URL and MOLECULE_API_KEY
3. npm start (stdio mode) or use an MCP host config

Examples

You: "Create an SEO agent workspace using the seo-agent template"
Agent: [calls create_workspace with template="seo-agent"]

You: "Set the OpenRouter API key for the SEO workspace"
Agent: [calls set_secret with key="OPENROUTER_API_KEY"]

You: "Ask the SEO agent to audit my homepage"
Agent: [calls chat_with_agent with message="Audit https://example.com for SEO"]

You: "What skills does the coding agent have?"
Agent: [calls get_workspace, reads agent_card.skills]

Remote Agents (Phase 30)

For agents running outside the platform's Docker network, the get_remote_agent_setup_command tool generates a bash one-liner:

pip install molecule-ai-sdk
WORKSPACE_ID=... PLATFORM_URL=... python3 -c "from molecule_agent import RemoteAgentClient; ..."

See the full tool registry in CLAUDE.md for all 87 tools.