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
[C@@H]) the output will have the H removed along with any
associated stereo symbols.
The Canonical SMILES format (can) produces a canonical representation
of the molecule in SMILES format. This is the same as the
below but may be more convenient to use.
|-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)|
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|
Specify the first atom
This atom will be used to begin the SMILES string.
Specify the last atom
The output will be rearranged so that any additional SMILES added to the end will be attached to this atom.