SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. Some examples are:
| SMILES | Name |
| C1CCCCC1 | Cyclohexane |
SMILES contains the same information as might be found in an extended connection table. The primary reason SMILES is more useful than a connection table is that it is a linguistic construct, rather than a computer data structure. SMILES is a true language, albeit with a simple vocabulary (atom and bond symbols) and only a few grammar rules. SMILES representations of structure can in turn be used as "words" in the vocabulary of other languages designed for storage of chemical information (information about chemicals) and chemical intelligence (information about chemistry).
These properties open many doors to the chemical information programmer. Examples of uses for SMILES are:
- Keys for database access
- Mechanism for researchers to exchange chemical information
- Entry system for chemical data
- Part of languages for artificial intelligence or expert systems in chemistry
1. Branches
Branches are specified by enclosing them in parentheses, and can be nested or stacked. In all cases, the implicit connection to a parenthesized expression (a "branch") is to the left.
2. Cyclic Structures
Cyclic structures are represented by breaking one bond in each ring. The bonds are numbered in any order, designating ring opening (or ring closure) bonds by a digit immediately following the atomic symbol at each ring closure. This leaves a connected non-cyclic graph which is written as a non-cyclic structure using the three rules described above.
