SpectrAI-Initiative/molecular-properties-calculation

Molecular Properties Calculation

Usage

1. MCP Server Definition

import asyncio
import json
from contextlib import AsyncExitStack
from fastmcp import Client
from fastmcp.client.transports import StreamableHttpTransport

class ChemicalToolsClient:
    """Chemical Tools MCP Client using FastMCP"""

    def __init__(self, server_url: str, headers: dict = None):
        self.server_url = server_url
        self.headers = headers or {}
        self.client = None

    async def connect(self):
        """Establish connection and initialize session"""
        print(f"Connecting to: {self.server_url}")
        try:
            transport = StreamableHttpTransport(
                url=self.server_url,
                headers=self.headers
            )

            self._stack = AsyncExitStack()
            await self._stack.__aenter__()
            self.client = Client(transport)
            await self._stack.enter_async_context(self.client)

            print(f"✓ connect success")
            return True

        except Exception as e:
            print(f"✗ connect failure: {e}")
            import traceback
            traceback.print_exc()
            return False

    async def disconnect(self):
        """Disconnect from server"""
        try:
            if hasattr(self, '_stack'):
                await self._stack.aclose()
            print("✓ already disconnect")
        except Exception as e:
            print(f"✗ disconnect error: {e}")
    def parse_result(self, result):
        """Parse MCP tool call result"""
        try:
            if hasattr(result, 'content') and result.content:
                content = result.content[0]
                if hasattr(content, 'text'):
                    try:
                        return json.loads(content.text)
                    except:
                        return content.text
            return str(result)
        except Exception as e:
            return {"error": f"parse error: {e}", "raw": str(result)}

2. Molecular Properties Calculation Workflow

This workflow calculates fundamental molecular properties from SMILES strings, useful for drug discovery, chemical analysis, and computational chemistry.

Workflow Steps:

1. Calculate Molecular Weight - Compute average molecular weight
2. Calculate Molecular Formula - Determine elemental composition
3. Calculate Exact Molecular Weight - Compute monoisotopic mass
4. Count Atoms - Determine total and heavy atom counts

Implementation:

## Initialize client
HEADERS = {"SCP-HUB-API-KEY": "<your-api-key>"}

client = ChemicalToolsClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/31/SciToolAgent-Chem",
    HEADERS
)

if not await client.connect():
    print("connection failed")
    exit()

## Input: SMILES string to analyze
smiles = "CCO"  # Ethanol
print(f"=== Molecular Properties for {smiles} ===\n")

## Step 1: Calculate molecular weight
print("Step 1: Molecular Weight")
result = await client.client.call_tool(
    "SMILESToWeight",
    arguments={"smiles": smiles}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")

## Step 2: Calculate molecular formula
print("Step 2: Molecular Formula")
result = await client.client.call_tool(
    "GetMolFormula",
    arguments={"smiles": smiles}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")

## Step 3: Calculate exact molecular weight
print("Step 3: Exact Molecular Weight")
result = await client.client.call_tool(
    "GetExactMolceularWeight",
    arguments={"smiles": smiles}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")

## Step 4: Count atoms
print("Step 4: Atom Count")
result = await client.client.call_tool(
    "GetAtomsNum",
    arguments={"smiles": smiles}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")

## Step 5: Count heavy atoms
print("Step 5: Heavy Atom Count")
result = await client.client.call_tool(
    "GetHeavyAtomsNum",
    arguments={"smiles": smiles}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")

await client.disconnect()

Tool Descriptions

SciToolAgent-Chem Server:

• SMILESToWeight: Calculate average molecular weight

  • Args: smiles (str) - SMILES string
  • Returns: Molecular weight in g/mol

• GetMolFormula: Calculate molecular formula

  • Args: smiles (str) - SMILES string
  • Returns: Molecular formula (e.g., C₂H₆O)

• GetExactMolceularWeight: Calculate exact (monoisotopic) molecular weight

  • Args: smiles (str) - SMILES string
  • Returns: Exact mass (most abundant isotope composition)

• GetAtomsNum: Count total number of atoms

  • Args: smiles (str) - SMILES string
  • Returns: Total atom count (excluding hydrogens in implicit SMILES)

• GetHeavyAtomsNum: Count heavy atoms (non-hydrogen)

  • Args: smiles (str) - SMILES string
  • Returns: Heavy atom count

Input/Output

Input:

• smiles: Molecule in SMILES format (e.g., "CCO", "c1ccccc1", "CC(=O)O")

Output:

• Molecular Weight: Average mass based on natural isotope abundances (g/mol or Da)
• Molecular Formula: Elemental composition (CₓHᵧNᵢOⱼ...)
• Exact Molecular Weight: Monoisotopic mass (most abundant isotope for each element)
• Atom Count: Total number of atoms in the molecule
• Heavy Atom Count: Number of non-hydrogen atoms

Use Cases

• Drug-likeness assessment (molecular weight screening)
• Mass spectrometry data interpretation
• Stoichiometry calculations
• Chemical database queries
• Lipinski's Rule of Five evaluation
• Compound library characterization
• Quality control for chemical synthesis

Molecular Weight Types

• Average MW: Used for general calculations, based on natural isotope distribution
• Exact MW: Used for mass spectrometry, based on most abundant isotopes
• Difference: Minimal for small molecules, can be significant for large biomolecules

Example:

• Ethanol (C₂H₆O): Average MW = 46.07 Da, Exact MW = 46.0418 Da

Additional Molecular Property Tools

The SciToolAgent-Chem server provides 160+ additional tools including:

• GetRotatableBondsNum: Count rotatable bonds
• GetHBDNum/GetHBANum: Hydrogen bond donors/acceptors
• GetRingsNum: Count ring systems
• GetTPSA: Calculate topological polar surface area (TPSA)
• GetCrippenDescriptors: Calculate logP and molar refractivity
• GetLipinskiHBDNum/GetLipinskiHBANum: Lipinski rule parameters
• GetAromaticRingsNum: Count aromatic rings
• GetFractionCSP3: Calculate fraction of sp³ carbons

Lipinski's Rule of Five

For drug-likeness, molecules should satisfy:

1. Molecular weight ≤ 500 Da
2. LogP ≤ 5
3. Hydrogen bond donors ≤ 5
4. Hydrogen bond acceptors ≤ 10

Use the property calculation tools to assess these criteria.