Pharmaclaw Tox Agent

该Skill接收SMILES，使用RDKit计算MW、logP、TPSA、HBD、HBA、可旋转键、环与芳香环数及QED，并执行Lipinski Rule of Five、Veber规则和简化PAINS子结构筛查，输出低/中/高风险分级与属性报告；依赖rdkit-pypi，可对接Chemistry Query与IP Expansion。

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热度 84.87

最近更新 2026-05-11 17:30:39

分类：数据依赖：代码执行应用场景：数据处理 / 研究 / 报告撰写

安装技能

复制下面的话术发给你的 Agent，它会通过 secure-skills 检索并安装该技能。

执行命令安装此 skill： npx secure-skills-cli add pharmaclaw-tox-agent

Metadata

name: pharmaclaw-tox-agent
description: Toxicology Agent for pharma drug safety profiling from SMILES. Computes RDKit ADMET descriptors (logP, TPSA, MW, HBD, HBA, rotatable bonds), Lipinski Rule of Five violations, Veber rule checks, QED drug-likeness score, and PAINS substructure alerts. Outputs risk classification (Low/Medium/High) with full property report. Chains from Chemistry Query (receives SMILES) and feeds into IP Expansion for safer derivative suggestions. Triggers on tox, toxicology, safety, ADMET, hepatotox, carcinogen, risk, PAINS, drug safety, Lipinski, Veber, QED.

PharmaClaw Toxicology Agent

Overview

Predictive toxicology and drug safety profiling agent for the PharmaClaw pipeline. Screens drug candidates via RDKit descriptors, rule-based filters (Lipinski Ro5, Veber), QED scoring, and PAINS alerts to flag safety risks early in the discovery process.

Quick Start

# Analyze a compound
python scripts/tox_agent.py "CC(=O)Nc1ccc(O)cc1"

# Default (ethanol)
python scripts/tox_agent.py

Capabilities

Check	Method	Threshold
Lipinski Ro5	MW, LogP, HBD, HBA	MW>500, LogP>5, HBD>5, HBA>10
Veber Rules	TPSA, Rotatable Bonds	TPSA>140, RotB>10
QED Score	RDKit QED module	0-1 (higher = more drug-like)
PAINS Alerts	Substructure matching	Known assay interference patterns
Ring Analysis	Aromatic/total ring count	Complexity indicator

Decision Tree

SMILES input → RDKit descriptor calculation → Rule-based screening
Lipinski violations = 0 AND PAINS = 0 → Risk: Low
Any violations or PAINS hits → Risk: Medium/High
High risk flagged → Recommend analogs via Chemistry Query / IP Expansion

Output Format

{
  "lipinski_viol": 0,
  "veber_viol": 0,
  "qed": 0.737,
  "pains": 0,
  "risk": "Low",
  "props": {
    "mw": 151.2,
    "logp": 1.02,
    "tpsa": 49.3,
    "hbd": 2,
    "hba": 2,
    "rotb": 1,
    "rings": 1,
    "arom": 1
  }
}

Risk Classification

Low: No Lipinski violations, no PAINS alerts, QED > 0.5
Medium: 1-2 Lipinski violations OR low QED
High: 3+ Lipinski violations, PAINS hits, or multiple Veber violations

Chain Integration

Receives from: Chemistry Query (SMILES), Pharmacology (ADME flags)
Feeds into: IP Expansion (safer derivative suggestions), Synthesis (avoid toxic intermediates)
Cross-references: Market Intel (FAERS adverse events for similar structures)

Dependencies

rdkit-pypi — Molecular descriptors, QED, substructure matching

Scripts

scripts/tox_agent.py — Main agent: ToxAgent class with analyze(smiles) method

Limitations

PAINS screening uses simplified substructure set (production should use full PAINS catalog)
No Ames mutagenicity or hERG channel prediction (descriptor-based proxies planned)
LD50 estimation not yet implemented (QSAR model planned for future version)