Molecule AI MCP Server

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

20 Tools Available

Tool	Description
list_workspaces	List all workspaces with status and skills
create_workspace	Create a new workspace (with optional template)
get_workspace	Get workspace details
delete_workspace	Delete workspace (cascades to children)
restart_workspace	Restart offline/failed workspace
chat_with_agent	Send message and get AI response
assign_agent	Assign model to workspace
set_secret	Set API key or env var
list_secrets	List secret keys (no values)
list_files	List workspace config files
read_file	Read a config file
write_file	Create or update a file
delete_file	Delete file or folder
commit_memory	Store fact (LOCAL/TEAM/GLOBAL)
search_memory	Search workspace memories
list_templates	List available templates
expand_team	Expand workspace to team
collapse_team	Collapse team to single workspace
list_pending_approvals	List pending approval requests
decide_approval	Approve or deny a request

Phase 30 — Remote agent (SaaS) management

Tools that surface workspaces with runtime='external' (agents that run on machines outside this platform's Docker network and join via HTTP).

Tool	Description
list_remote_agents	Filter the workspace list to remote agents only — id / status / url / heartbeat
get_remote_agent_state	Lightweight {status, paused, deleted} projection — faster than get_workspace when you only need lifecycle
get_remote_agent_setup_command	Emit a WORKSPACE_ID=… PLATFORM_URL=… python3 … bash one-liner an operator can paste into a remote shell
check_remote_agent_freshness	Compare last_heartbeat_at against a threshold (default 90s) — returns {fresh, seconds_since_heartbeat}

Setup

Claude Code

Add to your project's .mcp.json:

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

Cursor

Add to .cursor/mcp.json:

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

Codex / OpenCode

# Run directly
MOLECULE_URL=http://localhost:8080 node mcp-server/dist/index.js

Environment Variables

Variable	Default	Description
MOLECULE_URL	http://localhost:8080	Platform API URL

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]