Lipinski Rule Filter

Filter small molecule compound libraries based on Lipinski's Rule of Five to identify compounds with poor absorption.

Usage

python scripts/main.py --input compounds.smi --output filtered.smi
python scripts/main.py --smiles "CC(=O)Oc1ccccc1C(=O)O" --check

Parameters

Parameter	Type	Required	Default	Description
--input	str	No	-	Input SMILES/SDF file path
--smiles	str	No	-	Single SMILES string to check
--output	str	No	-	Output file path for passing compounds
--violations	int	No	1	Maximum allowed Lipinski rule violations

Lipinski's Rules

• MW < 500 Da
• LogP < 5
• H-bond donors < 5
• H-bond acceptors < 10

Output

• Filtered compound list
• Rule violation report
• Drug-likeness score

Risk Assessment

Risk Indicator	Assessment	Level
Code Execution	Python/R scripts executed locally	Medium
Network Access	No external API calls	Low
File System Access	Read input files, write output files	Medium
Instruction Tampering	Standard prompt guidelines	Low
Data Exposure	Output files saved to workspace	Low

Security Checklist

• No hardcoded credentials or API keys
• No unauthorized file system access (../)
• Output does not expose sensitive information
• Prompt injection protections in place
• Input file paths validated (no ../ traversal)
• Output directory restricted to workspace
• Script execution in sandboxed environment
• Error messages sanitized (no stack traces exposed)
• Dependencies audited

Prerequisites

No additional Python packages required.

Evaluation Criteria

Success Metrics

• Successfully executes main functionality
• Output meets quality standards
• Handles edge cases gracefully
• Performance is acceptable

Test Cases

1. Basic Functionality: Standard input → Expected output
2. Edge Case: Invalid input → Graceful error handling
3. Performance: Large dataset → Acceptable processing time

Lifecycle Status

• Current Stage: Draft
• Next Review Date: 2026-03-06
• Known Issues: None
• Planned Improvements:
  • Performance optimization
  • Additional feature support