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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.

See also

The “regular” SMILES format (smi, smiles) gives faster output, since no canonical numbering is performed.

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
f <atomno>

Specify the first atom

This atom will be used to begin the SMILES string.

l <atomno>

Specify the last atom

The output will be rearranged so that any additional SMILES added to the end will be attached to this atom. See the SMILES format (smi, smiles) for more information.