Table Of Contents

Previous topic

Common cheminformatics formats

Next topic

Chemical Markup Language (cml, mrv)

This Page

Canonical SMILES format (can)

A canonical form of the SMILES linear text format

The SMILES format is a linear text format which can describe the connectivity and chirality of a molecule. Canonical SMILES gives a single ‘canonical’ form for any particular molecule.

Write Options

a Output atomclass like [C:2], if available
h Output explicit hydrogens as such
i Do not include isotopic or chiral markings
n No molecule name
r Radicals lower case eg ethyl is Cc
t Molecule name only

Comments

See also, the “regular” SMILES format, which results in faster output, since no canonical numbering is performed.