Table Of Contents

Previous topic

Protein Data Bank format (pdb, ent)

Next topic

Sybyl Mol2 format (ml2, sy2, mol2)

This Page

SMILES format (smi, smiles)

A linear text format which can describe the connectivity and chirality of a molecule

Open Babel implements the OpenSMILES specification.

It also implements an extension to this specification for radicals.

Note that the l <atomno> option, used to specify a “last” atom, is intended for the generation of SMILES strings to which additional atoms will be concatenated. If the atom specified has an explicit H within a bracket (e.g. [nH] or [C@@H]) the output will have the H removed along with any associated stereo symbols.

See also

The Canonical SMILES format (can) produces a canonical representation of the molecule in SMILES format. This is the same as the c option below but may be more convenient to use.

Write Options

a Output atomclass like [C:2], if available
c Output in canonical form
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
x append X/Y coordinates in canonical-SMILES order
C ‘anti-canonical’ random order (mostly for testing)
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.