Add Model Context Protocol (MCP) server for molecular database access

[Copilot]

Adds a lightweight MCP server to expose molecular interaction rules database functionality to AI assistants via JSON-RPC 2.0 protocol.

Implementation

• mcp_server.py: STDIO-based MCP server with 5 tools:

  • list_molecules: Enumerate all molecules in database
  • get_molecule_fg_family: Retrieve functional group family
  • get_atom_names: Get interaction site names
  • get_monomer_coordinates: Return z-matrix for monomer
  • form_dimer_coordinates: Generate dimer z-matrix from two monomers

• mcp_cli.py: Console script entry point for server invocation

• Configuration: Sample mcp-config.json and documentation in MCP_README.md

Usage

# Install and run
pip install molecular-interaction-rules
molecular-interaction-rules-mcp

// MCP client configuration
{
  "mcpServers": {
    "molecular-interaction-rules": {
      "command": "molecular-interaction-rules-mcp"
    }
  }
}

# Direct Python usage
from molecular_interaction_rules import MCPServer

server = MCPServer()
response = server.handle_request({
    'jsonrpc': '2.0',
    'id': 1,
    'method': 'tools/call',
    'params': {
        'name': 'form_dimer_coordinates',
        'arguments': {
            'molecule_1': 'benzene',
            'site_1': 'RC1',
            'molecule_2': 'benzene',
            'site_2': 'H1'
        }
    }
})

Changes

• Added console script entry point in setup.py
• Exported MCPServer in package __init__.py
• Removed non-existent dithiolane import
• Updated README with MCP quick start

Original prompt

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This section details on the original issue you should resolve

<issue_title>SS-1: Add a Model Context Protocol on top of the package</issue_title>
<issue_description>Hi Copilot,

I need this package for the automatic generation of monomers and dimers of z-matrices at any given distance to have a model context protocol layer on top. We are going to register this with the MCP, I want this minimal code and lightweight.

Follow my style of code I put in the package.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes SS-1: Add a Model Context Protocol on top of the package #4

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