Simplified Molecular Input Line Entry Specification

The Simplified Molecular Input Line Entry Specification, or SMILES for short, is a specification for unambiguously describing the structure of chemicals using ASCII character strings. With a little bit of practice, these strings can be written, read, and understood directly; several molecular software packages can read or generate SMILES strings.

Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as [Au] for gold. Hydroxide anion[?] is [OH-]. If the brackets are omitted, the proper number of implicit hydrogen atoms is assumed; for instance the SMILES for water is simply O and that for ethanol is CCO. The double-bonded carbon dioxide is represented as O=C=O and the triple-bonded hydrogen cyanide as C#N. Cyclohexane[?] is represented as C1CCCCC1, the idea being that the two ones label the same position in the molecule, thus forming a ring with six carbons. Branches are described with parentheses, as in CCC(=O)O for propionic acid[?] and FC(F)F, or alternatively C(F)(F)F, for fluoroform[?].

The SMILES specification was developed by David Weininger in the late 1980s.

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External links:

• SMILES tutorial, http://www.daylight.com/dayhtml/smiles/smiles-intro
• Web-based applications capable of rendering SMILES strings into 2D figures, http://www.daylight.com/daycgi/depict
• Molecule editor applet that can create SMILES, http://www.molinspiration.com/jme/index