medchem

name	medchem
description	Apply Lipinski Rule of Five (Ro5) to molecules: check MW, LogP, HBD, HBA. Use when users ask about drug-likeness, Lipinski rules, or oral bioavailability filters.

Medchem: Lipinski Rule of Five

Overview

Medchem is a Python library for molecular filtering. This skill covers applying the Lipinski Rule of Five (Ro5) to assess oral drug-likeness.

Rule of Five (Lipinski)

Reference: Lipinski et al., Adv Drug Deliv Rev (1997) 23:3-25

Purpose: Predict oral bioavailability

Criteria:

• Molecular Weight ≤ 500 Da
• LogP ≤ 5
• Hydrogen Bond Donors ≤ 5
• Hydrogen Bond Acceptors ≤ 10

Usage:

import medchem as mc
from rdkit import Chem

# Apply to SMILES string
passes = mc.rules.basic_rules.rule_of_five("CC(=O)OC1=CC=CC=C1C(=O)O")
# Returns: True or False

# Get individual properties
from rdkit.Chem import Descriptors
mol = Chem.MolFromSmiles("CC(=O)OC1=CC=CC=C1C(=O)O")
mw = Descriptors.MolWt(mol)
logp = Descriptors.MolLogP(mol)
hbd = Descriptors.NumHDonors(mol)
hba = Descriptors.NumHAcceptors(mol)

Rule Filters for Multiple Molecules:

import datamol as dm
import medchem as mc

# Load molecules from SMILES list
mols = [dm.to_mol(smi) for smi in smiles_list]

# Apply Rule of Five
rfilter = mc.rules.RuleFilters(rule_list=["rule_of_five"])
results = rfilter(mols=mols, n_jobs=-1)
# Returns list of dicts with 'rule_of_five' key per molecule

Result Format:

# Single molecule
mc.rules.basic_rules.rule_of_five(smiles)  # Returns bool

# Multiple molecules via RuleFilters
results = rfilter(mols=mols)
# Each result: {"rule_of_five": True/False}

Key Reference

• mc.rules.basic_rules.rule_of_five(mol) — Check single molecule, returns bool
• mc.rules.RuleFilters(rule_list=["rule_of_five"]) — Batch filter multiple molecules
• Descriptors.MolWt(mol) — Get molecular weight
• Descriptors.MolLogP(mol) — Get LogP value
• Descriptors.NumHDonors(mol) — Get H-bond donor count
• Descriptors.NumHAcceptors(mol) — Get H-bond acceptor count