SMILES (Simplified Molecular-Input Line-Entry System)

Cheminformatics Tutorials - Herong's Tutorial Examples

∟SMILES (Simplified Molecular-Input Line-Entry System)

This chapter provides introductions and tutorial examples on SMILES (Simplified Molecular-Input Line-Entry System). Topics include SMILES representations for atoms, bonds, rings, disconnected structures, charges, directional bonds, isotopes, chiral centers.

What Is SMILES

What Is Canonical SMILES

Atom Represenations in SMILES

Bond Represenations in SMILES

Branch Represenations in SMILES

Ring Represenations in SMILES

Disconnected Structures in SMILES

Charge Represenations in SMILES

Isotope Represenations in SMILES

Directional Bonds in SMILES

Tetrahedral Centers in SMILES

Chirality Representations in SMILES

Hydrogen Representations in SMILES

Takeaways:

SMILES (Simplified Molecular-Input Line-Entry System) is a specification in the form of a line notation for describing molecule structures using short ASCII strings.
Canonical SMILES is a special version of SMILES where each SMILES string uniquely identifies a single molecule structure.
Each non-hydrogen atom is represented by its atomic symbol followed by H or Hn for bonded hydrogens in square brackets [].
Organic atoms, B, C, N, O, P, S, F, Cl, Br, and I, may be represented without brackets if the number of bonded hydrogens conforms to the lowest normal valence consistent with explicit bonds.
Single, double, triple, and aromatic bonds are represented by the symbols -, =, #, and :, respectively.
Single bonds may be omitted.
Aromatic bonds may be omitted, if atoms are represented by lower case letters.
An extra bond and its connected branch of atoms is represented in round brackets (...) inserted after the bonding atom and before any existing bonds.
A ring is represented by appending a numeric digit to the starting atom of a ring and close it with the numeric digit as the start atom.
Disconnected structures are separated by the '.' symbol.
Positive/negative charges are represented by repeating '+'/'-' symbols or '+n'/'-n'.
Isotopes are represented by prefixing the mass count of the atom in square brackets [].
Directional bonds, '/' and '\', are used to identify different configurations on additional atoms connected a pair of double-bond connected atoms.
'@' is appended to a tetrahedral center atom in square brackets [] to indicate that the next 3 branches are in anticlockwise order when looking at them from the preceding bond direction.
Different types of chirality are represented in as different chiral class codes in an format of [x@ccn].
Hydrogens are represented explicitly as atoms 'O([H])[H]', explicitly as counts '[OH2]', or implicitly like 'O'.