# Medchem

Medicinal chemistry filters.

- Repository: https://github.com/LeonChaoX/qinyan-academic-skills (996 stars)
- Category: Engineering
- License: Apache-2.0 license
- Last updated: 2026-07-20
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add LeonChaoX/qinyan-academic-skills --skill medchem -g -a claude-code -y`
Codex: `npx skills add LeonChaoX/qinyan-academic-skills --skill medchem -g -a codex -y`
Cursor: `npx skills add LeonChaoX/qinyan-academic-skills --skill medchem -g -a cursor -y`
Gemini CLI: `npx skills add LeonChaoX/qinyan-academic-skills --skill medchem -g -a gemini-cli -y`

## Description

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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

**Single Rule Application:**

```python
import medchem as mc

# Apply Rule of Five to a SMILES string
smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"  # Aspirin
passes = mc.rules.basic_rules.rule_of_five(smiles)
# Returns: True

# Check specific rules
passes_oprea = mc.rules.basic_rules.rule_of_oprea(smiles)
passes_cns = mc.rules.basic_rules.rule_of_cns(smiles)
```

**Multiple Rules with RuleFilters:**

```python
import datamol as dm
import medchem as mc

# Load molecules
mols = [dm.to_mol(smiles) for smiles in smiles_list]

# Create filter with multiple rules
rfilter = mc.rules.RuleFilters(
    rule_list=[
        "rule_of_five",
        "rule_of_oprea",
        "rule_of_cns",
        "rule_of_leadlike_soft"
    ]
)

The rest: https://github.com/LeonChaoX/qinyan-academic-skills/blob/HEAD/skills/06-化学信息与药物发现/medchem/SKILL.md