fadrienne/apps/smiles-validation

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Strict SMILES validation, structural comparison, and modification verification. Catches invalid LLM-generated molecules.

Install

npx vskill@latest install fadrienne/apps/smiles-validation

SKILL.md

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

bash
pip install rdkit-pypi

Core Workflows

1. Validate a Single SMILES
bash
python scripts/validate.py --smiles "c1ccccc1"
2. Compare Original vs Modified
bash
python scripts/validate.py --original "c1ccccc1" --proposed "c1ccc(O)cc1" --check-modification "Added hydroxyl group"
3. Batch Validation
bash
python scripts/validate.py --input generated_molecules.csv --output validation_report.json

Script Reference

ScriptPurposeKey Outputs
validate.pySMILES validation, comparison, and modification checkingJSON report with validity, similarity, scaffold match, modification verification

Security

  • Security scanPassed, 95 of 100Pattern checks on the skill's files.
  • Model reviewPassed

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Source

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