Individual skill
smiles-validation
Strict SMILES validation, structural comparison, and modification verification. Catches invalid LLM-generated molecules.
backend/cli/skills/chemistry/smiles-validation/SKILL.md
Source commit a08e0ad0ad3d6448123039ee4659163eb2e35d99
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- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 2, 2026
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Repository context
- Repository stars (not skill ratings)
- 4,351
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
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- agent Repository topic
- ai Repository topic
- bun Repository topic
- cli Repository topic
- llm Repository topic
- ml Repository topic
- open-source Repository topic
- research Repository topic
- science Repository topic
- ai-agent Repository topic
- cheminformatics Declared skill tag
- validation Declared skill tag
- smiles Declared skill tag
- quality-control Declared skill tag
- engineering Derived category
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# 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
