Agent Skills
› synthetic-sciences/openscience
› smiles-validation
smiles-validation
GitHub用于严格验证LLM生成的SMILES有效性，检查结构相似性、骨架保留及修改真实性。支持单分子解析校验、原改对比及批量质检，确保分子设计可复现且符合化学逻辑。
Trigger Scenarios
LLM生成SMILES后需验证有效性
确认分子优化或修改是否符合描述
批量检查生成的分子库质量
Install
npx skills add synthetic-sciences/openscience --skill smiles-validation -g -y
SKILL.md
Frontmatter
{
"name": "smiles-validation",
"tags": [
"cheminformatics",
"validation",
"SMILES",
"quality-control"
],
"license": "MIT",
"version": "1.0.0",
"category": "chemistry",
"metadata": {
"skill-author": "Synthetic Sciences"
},
"description": "Strict SMILES validation, structural comparison, and modification verification. Catches invalid LLM-generated molecules.",
"dependencies": [
"rdkit-pypi"
]
}
SMILES Validation
Overview
LLMs frequently generate invalid SMILES or produce molecules that don't match their stated reasoning. This skill provides strict validation, structural comparison, and modification verification.
Key checks:
- Parse validation: RDKit sanitization, valence checking, parenthesis/bracket balance
- Structural comparison: Tanimoto similarity, scaffold preservation, MCS analysis
- Modification verification: Confirm claimed structural changes exist in the actual molecule
- Classification: Categorize changes as optimization (>0.6 similarity), significant modification (0.4-0.6), or de novo design (<0.4)
When to Use This Skill
- After molecule generation: Validate every SMILES before reporting results
- Optimization verification: Confirm proposed modifications match the actual structure
- Batch validation: Check a library of generated molecules for validity
- Quality control: Ensure reproducibility of molecular designs
Installation
pip install rdkit-pypi
Core Workflows
1. Validate a Single SMILES
python scripts/validate.py --smiles "c1ccccc1"
2. Compare Original vs Modified
python scripts/validate.py --original "c1ccccc1" --proposed "c1ccc(O)cc1" --check-modification "Added hydroxyl group"
3. Batch Validation
python scripts/validate.py --input generated_molecules.csv --output validation_report.json
Script Reference
| Script | Purpose | Key Outputs |
|---|---|---|
validate.py |
SMILES validation, comparison, and modification checking | JSON report with validity, similarity, scaffold match, modification verification |
Version History
- e9844a4 Current 2026-07-11 17:22
Dependencies
-
required
rdkit-pypi
