26.1 Daylight SMILES
Unfortunately, there are a number of ambiguities in the original paper
describing the Daylight SMILES syntax, that have led to different
SMILES being accepted or rejected by independent SMILES parser
implementations.
Table 26.1:
Differences between various SMILES parser implementations
| |
Daylight |
Corina |
Corina |
Concord |
COBRA |
Synopsis |
OEChem |
| SMILES |
4.41 |
1.6 |
WWW |
3.2.1 |
3.21A |
4.0 |
1.5 |
| C1.C1 |
Y |
Y |
Y |
N |
N |
Y |
Y |
| C%00CC%00 |
Y |
Y |
Y |
N |
N |
N |
Y |
| C(C.C)C |
Y |
Y |
Y |
N |
N |
Y |
Y |
| C(C)1CC1 |
Y |
N |
N |
N |
Y |
N |
Y |
| C(.C) |
Y |
Y |
Y |
N |
N |
Y |
Y |
| C() |
Y |
Y |
N |
Y |
Y |
Y |
Y |
| (CO)=O |
N |
N |
N |
N |
N |
Y |
N |
| (C) |
N |
N |
N |
N |
N |
Y |
Y |
| .C |
N |
N |
N |
Y |
Y |
N |
Y |
| C..C |
N |
Y |
N |
Y |
Y |
N |
Y |
| C. |
N |
Y |
Y |
Y |
Y |
Y |
Y |
| C=(O)C |
N |
Y |
N |
N |
Y |
N |
N |
| C((C)) |
N |
Y |
N |
Y |
N |
Y |
Y |
| C.(C) |
N |
Y |
N |
Y |
N |
N |
Y |
| C1CC(=1) |
N |
Y |
N |
N |
N |
N |
Y |
| C1CC(1) |
N |
N |
N |
N |
N |
N |
Y |
| C(C.) |
N |
Y |
N |
N |
N |
N |
Y |
| C==C |
N |
Y |
N |
N |
N |
N |
Y |
| C(1CC1) |
N |
N |
N |
N |
N |
N |
Y |
| C(1)CC1 |
N |
N |
N |
N |
N |
N |
Y |
|
The OEChem SMILES parser actually has two modes. The default is
relaxed which produces the results above and enables the SMILES
extensions described in the next section. It also has a strict mode
that may be used for validating SMILES strings that is far less
forgiving about dubious SMILES strings.
