Calculate comprehensive protein sequence properties including isoelectric point, molecular weight, hydrophobicity, and physicochemical parameters.
import asyncio
import json
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.client = Client(transport)
await self.client.__aenter__()
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 self.client:
await self.client.__aexit__(None, None, None)
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)