MCP Server Setup

Paramus exposes computational chemistry tools to AI assistants through the Model Context Protocol (MCP). The tray application runs locally — no cloud services, no API keys, no manual configuration files.

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Quick Start

Make sure the Paramus tray application is running (system tray icon visible).

VS Code (Copilot)

Add .vscode/mcp.json to your workspace:

{
  "servers": {
    "paramus-chemistry": {
      "type": "http",
      "url": "http://localhost:8765/mcp"
    }
  }
}

VS Code detects the server and asks to start it:

On first run, select Always Allow Tools from paramus-chemistry-os:

Tools are now available. Ask any question and the AI calls them automatically:

Claude Desktop

Edit %APPDATA%\Claude\claude_desktop_config.json:

{
  "mcpServers": {
    "Paramus Chemistry": {
      "command": "C:\\Users\\<user>\\AppData\\Local\\Paramus\\Server\\paramus-client\\paramus-client.exe"
    }
  }
}

Restart Claude Desktop after saving.

Windsurf

Edit ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "Paramus Chemistry": {
      "command": "C:\\Users\\<user>\\AppData\\Local\\Paramus\\Server\\paramus-client\\paramus-client.exe"
    }
  }
}

Troubleshooting

Problem	Solution
VS Code shows no tools	Check .vscode/mcp.json points to http://localhost:8765/mcp and tray icon is visible
Claude Desktop shows no tools	Check claude_desktop_config.json path. Restart Claude after config changes
“Tray App not reachable”	Start the tray application (paramus-app.exe or run.bat)
Tools missing after update	Restart the tray app (it auto-discovers tools on startup)
BRAIN/WORLD tools not showing	Check network connectivity to backend hosts. Unreachable services are hidden automatically

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Details

Architecture

The tray application starts an HTTP server on localhost:8765. AI clients connect to this endpoint and receive access to 10 gateway meta-tools that route to the full tool catalog across 15 categories.

Tool Categories

Molecular Chemistry, Analytical Chemistry, Chemical Kinetics, Thermodynamics, Quantum Chemistry, Polymer Science, Materials Science, Electrochemistry, Drug Discovery, Data Science, Engineering, BRAIN Platform, WORLD Platform, OPERATE Platform, INTENT Core.

The visible count depends on which backend services (BRAIN, WORLD, OPERATE) are reachable.

Transport Modes

Client	Transport	Subprocess?
VS Code	HTTP direct to :8765	No
Claude Desktop	STDIO gateway -> HTTP proxy to :8765	Yes
Windsurf	STDIO gateway -> HTTP proxy to :8765	Yes

VS Code connects directly via HTTP. Claude Desktop and Windsurf use STDIO, so the paramus-client.exe (1.7 MB, stdlib-only, < 0.3s startup) bridges STDIO to HTTP. When running from source, use python -m paramus.intent.gateway instead.

Island Mode

When BRAIN or WORLD backends are unreachable, their tools are automatically hidden. They reappear when connectivity is restored. Local tools (RDKit, CoolProp, Cantera) always work.

Ports

Port	Service
8765	Tray app MCP endpoint
8766	Settings UI (browser)

Frequently Asked Questions