medchem

npx skills add LeonChaoX/qinyan-academic-skills --skill medchem --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Medchem ## Overview Medchem is a Python library for molecular filtering and prioritization in drug discovery workflows. Apply hundreds of well-established and novel molecular filters, structural alerts, and medicinal chemistry rules to efficiently triage and prioritize compound libraries at scale. Rules and filters are context-specific—use as guidelines combined with domain expertise. ## When to Use This Skill This skill should be used when: - Applying drug-likeness rules (Lipinski, Veber, etc.) to compound libraries - Filtering molecules by structural alerts or PAINS patterns - Prioritizing compounds for lead optimization - Assessing compound quality and medicinal chemistry properties - Detecting reactive or problematic functional groups - Calculating molecular complexity metrics ## Installation ```bash uv pip install medchem ``` ## Core Capabilities ### 1. Medicinal Chemistry Rules Apply established drug-likeness rules to molecules using the `medchem.rules` module. **Available Rules:** - Rule of Five (Lipinski) - Rule of Oprea - Rule of CNS - Rule of leadlike (soft and strict) - Rule of three - Rule of Reos - Rule of drug - Rule of Veber - Golden triangle - PAINS filters **Sing

uv pip install medchem
python scripts/filter_molecules.py input.csv --rules rule_of_five,rule_of_cns --alerts nibr --output filtered.csv