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
-U Universal SMILES
-I Inchified SMILES
-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)
-o <ordering>

Output in user-specified order

Ordering should be specified like 4-2-1-3 for a 4-atom molecule. This gives canonical labels 1,2,3,4 to atoms 4,2,1,3 respectively, so that atom 4 will be visited first and the remaining atoms visited in a depth-first manner following the lowest canonical labels.

-F <atom numbers>
 

Generate SMILES for a fragment

The atom numbers should be specified like “1 2 4 7”.

-R Do not reuse bond closure symbols
-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.