rdkit

name	rdkit
description	Cheminformatics with RDKit. Use for molecular analysis, drug-likeness, fingerprints, and similarity.

RDKit — Cheminformatics

When to Use

• Analyzing molecules from SMILES strings
• Computing physicochemical properties (MW, LogP, TPSA, etc.)
• Drug-likeness assessment (Lipinski, Veber, etc.)
• Molecular similarity (Tanimoto with Morgan fingerprints)
• Molecular fingerprint generation

Available Tools

• analyze_molecule(smiles) — Full property profile
• lipinski_filter(smiles) — Rule of Five check
• molecular_similarity(smiles1, smiles2) — Tanimoto similarity

SMILES Reference

SMILES (Simplified Molecular Input Line Entry System) is a line notation for molecular structures:

• CC(=O)OC1=CC=CC=C1C(=O)O — Aspirin
• CC(C)CC1=CC=C(C=C1)C(C)C(=O)O — Ibuprofen
• CN1C=NC2=C1C(=O)N(C(=O)N2C)C — Caffeine

Drug-Likeness Rules

• Lipinski's Rule of Five: MW≤500, LogP≤5, HBD≤5, HBA≤10 (≤1 violation)
• Veber: RotBonds≤10, TPSA≤140
• Lead-like: MW 250-350, LogP -1 to 3, RotBonds≤7

Similarity Interpretation

• Tanimoto > 0.85 — Very similar, likely same scaffold
• Tanimoto 0.7-0.85 — Similar, may share target activity
• Tanimoto 0.4-0.7 — Moderate, may share pharmacophore features
• Tanimoto < 0.4 — Dissimilar