Smile Format

The same chemical compound can be represented in multiple ways — by its structural diagram, its full chemical name, or in a format interpretable by machine learning models. The SMILES format (Simplified Molecular Input Line Entry System) is a line notation that encodes molecular structures as strings, allowing computers to process chemical information efficiently.

In the example shown above, 2-thiobarbituric acid is displayed in three forms:

• Chemical name: 2-thioxodihydropyrimidine-4,6(1H,5H)-dione
• SMILES string: O=C1CC(=O)NC(=S)N1
• Structural diagram

When preparing data for training models, it’s important to split the dataset meaningfully based on chemical properties. Instead of random splits, a scaffold-based split groups compounds by their core structure, which provides a more realistic and chemically meaningful distribution for testing model performance.