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Skill v1.0.0
currentAutomated scan100/100internscience/scp/drugsda-mol2mol-sampling
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PublishedJune 16, 2026 at 11:17 PM
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version: "1.0.0" name: drugsda-mol2mol-sampling description: Generate new molecules sampling from the input molecule. license: MIT license metadata: skill-author: PJLab
Molecule Generation
Usage
1. MCP Server Definition
python
import jsonfrom mcp.client.streamable_http import streamablehttp_clientfrom mcp import ClientSessionclass DrugSDAClient:def __init__(self, server_url: str):self.server_url = server_urlself.session = Noneasync def connect(self):print(f"server url: {self.server_url}")try:self.transport = streamablehttp_client(url=self.server_url,headers={"SCP-HUB-API-KEY": "sk-a0033dde-b3cd-413b-adbe-980bc78d6126"})self.read, self.write, self.get_session_id = await self.transport.__aenter__()self.session_ctx = ClientSession(self.read, self.write)self.session = await self.session_ctx.__aenter__()await self.session.initialize()session_id = self.get_session_id()print(f"✓ connect success")return Trueexcept Exception as e:print(f"✗ connect failure: {e}")import tracebacktraceback.print_exc()return Falseasync def disconnect(self):try:if self.session:await self.session_ctx.__aexit__(None, None, None)if hasattr(self, 'transport'):await self.transport.__aexit__(None, None, None)print("✓ already disconnect")except Exception as e:print(f"✗ disconnect error: {e}")def parse_result(self, result):try:if hasattr(result, 'content') and result.content:content = result.content[0]if hasattr(content, 'text'):return json.loads(content.text)return str(result)except Exception as e:return {"error": f"parse error: {e}", "raw": str(result)}
2. Mol2Mol Sampling
The description of tool reinvent_mol2mol_sampling.
tex
Generate new molecules sampling from the input molecule using different priors ('similarity': broad exploration, 'medium_similarity': balanced exploration, 'high_similarity': conservative optimization, 'scaffold': strict scaffold preservation, 'scaffold_generic': generic scaffold preservation, 'mmp': MMP-style local modifications).Args:smiles (str): Input SMILES stringn (int): Number of molecules for samplingmin_similarity (float): Minimum similarity threshold, default is 0.6prior_type (str): Prior type for generation, options: ['scaffold_generic', 'scaffold', 'mmp', 'similarity', 'high_similarity', 'medium_similarity'], default is 'similarity'lipinski (bool): Whether to apply Lipinski's rule of five filtering, default is Truefilter_preset (str): Filter preset, options: ['none', 'minimal', 'default', 'strict'], default is 'default'Return:status (str): success/errormsg (str): messagesave_smiles_file (str): Path to the saved SMILES fileoutput_smiles_list (List[str]): List of generated SMILES strings
How to use tool reinvent_denovo_sampling :
python
client = DrugSDAClient("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool")if not await client.connect():print("connection failed")returnresponse = await client.session.call_tool("reinvent_mol2mol_sampling",arguments={"smiles": smiles,"n": n,"min_similarity": min_similarity,"prior_type": prior_type,"lipinski": True,"filter_preset": filter_type})result = client.parse_result(response)output_smiles_list = result["output_smiles_list"]await client.disconnect()