# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
#
# Provenance: Authenticated by MD BABU MIA

import json
from typing import Dict, Any

# BioMCP Server
# Implements the Model Context Protocol (MCP) for Biomedical Tools.
# Allows Claude Desktop to "see" and "use" these python functions directly.

class BioMCPServer:
    def __init__(self):
        self.tools = [
            {
                "name": "reverse_complement",
                "description": "Calculates the reverse complement of a DNA sequence.",
                "input_schema": {
                    "type": "object",
                    "properties": {
                        "sequence": {"type": "string"}
                    },
                    "required": ["sequence"]
                }
            },
            {
                "name": "calculate_mw",
                "description": "Calculates molecular weight from a SMILES string.",
                "input_schema": {
                    "type": "object",
                    "properties": {
                        "smiles": {"type": "string"}
                    },
                    "required": ["smiles"]
                }
            }
        ]

    def list_tools(self) -> List[Dict]:
        """MCP Endpoint: List available tools."""
        return self.tools

    def call_tool(self, name: str, arguments: Dict) -> Any:
        """MCP Endpoint: Execute a tool."""
        if name == "reverse_complement":
            return self._reverse_complement(arguments["sequence"])
        elif name == "calculate_mw":
            return self._calculate_mw(arguments["smiles"])
        else:
            raise ValueError(f"Tool {name} not found")

    def _reverse_complement(self, seq: str) -> str:
        complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
        return "".join(complement.get(base, base) for base in reversed(seq.upper()))

    def _calculate_mw(self, smiles: str) -> float:
        # Mock RDKit calculation
        return len(smiles) * 12.01 # Dummy math

# Integration Adapter for stdio (Standard Input/Output)
if __name__ == "__main__":
    # This loop simulates how an MCP client (like Claude) talks to the server
    # In production, this reads JSON-RPC from stdin
    server = BioMCPServer()
    print("BioMCP Server Ready. Available Tools:", [t["name"] for t in server.list_tools()])
    
    # Test execution
    res = server.call_tool("reverse_complement", {"sequence": "ATGC"})
    print(f"Test Execution (ATGC -> {res})")
__AUTHOR_SIGNATURE__ = "9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE"
