Calculate comprehensive protein sequence properties including isoelectric point, molecular weight, hydrophobicity, and physicochemical parameters.
import asyncio
import json
from contextlib import AsyncExitStack
from fastmcp import Client
from fastmcp.client.transports import StreamableHttpTransport
class BiologyToolsClient:
"""Biology 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)}
This workflow calculates comprehensive physicochemical properties of protein sequences including molecular weight, isoelectric point, hydrophobicity, and other parameters useful for protein characterization.
Workflow Steps:
Implementation:
## Initialize client
HEADERS = {"SCP-HUB-API-KEY": "<your-api-key>"}
client = BiologyToolsClient(
"https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio",
HEADERS
)
if not await client.connect():
print("connection failed")
exit()
## Input: Protein sequence to analyze
protein_sequence = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL"
print("=== Protein Properties Calculation ===\n")
## Step 1: Calculate isoelectric point and molecular weight
print("Step 1: Isoelectric Point and Molecular Weight")
result = await client.client.call_tool(
"ComputePiMw",
arguments={"protein": protein_sequence}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")
## Step 2: Calculate comprehensive protein parameters
print("Step 2: Protein Sequence Parameters")
result = await client.client.call_tool(
"ComputeProtPara",
arguments={"protein": protein_sequence}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")
## Step 3: Calculate hydrophobicity scale
print("Step 3: Hydrophobicity Profile")
result = await client.client.call_tool(
"ComputeProtScale",
arguments={"protein": protein_sequence}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")
## Step 4: Calculate extinction coefficient
print("Step 4: Extinction Coefficient")
result = await client.client.call_tool(
"ComputeExtinctionCoefficient",
arguments={"protein": protein_sequence}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")
await client.disconnect()
SciToolAgent-Bio Server:
ComputePiMw: Calculate protein isoelectric point and molecular weight
protein (str) - Protein sequenceComputeProtPara: Calculate comprehensive protein parameters
protein (str) - Protein sequenceComputeProtScale: Calculate hydrophobicity scale
protein (str) - Protein sequenceComputeExtinctionCoefficient: Calculate extinction coefficient at 280nm
protein (str) - Protein sequenceInput:
protein: Protein sequence in single-letter amino acid codeOutput:
The SciToolAgent-Bio server provides 50+ additional tools including:
ProteinCodonOptimization)PeptideWeightCalculator)ProteinSolubilityPredictor)InherentDisorderedRegionsPredictor)ProteinNuclearLocalizationSequencePrediction)