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Common cheminformatics formats

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Chemical Markup Language (cml, mrv)

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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


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