Molecules from SMILES Strings
SMILES strings are a compact way of representing a molecule, instead of using systematic chemical names. The notation allows you to quickly and easily generate novel chemical structures.
The basic unit of a SMILES string is the atomic symbol wrapped in brackets. For example, "[Xe]" represents a free atom.
Two atomic symbols together with nothing between them represent a single bond.
Charge or isotope values can be included within the atom symbol.
For the common organic elements, it is not necessary to add brackets around the atomic symbol, and hydrogen atoms are added to fill out the normal atomic valence. Hence methane is represented simply as "C".
When converted to a Molecule, the hydrogens are added in automatically.
To make a linear chain of atoms connected by single bonds, just combine their symbols in order.
Double and triple bonds are indicated with "=" and "#" symbols, respectively, and rings are denoted by adding a numeric label to two adjacent atoms.
The following illustrates a linear chain and a ring variant. The only difference in the notation is marking the first and last atoms with the same number.