Table 4 Jmol SMILES directives
From: Jmol SMILES and Jmol SMARTS: specifications and applications
Prefix | Meaning | Jmol example |
|---|---|---|
/open/ | Use the OpenSMILES aromaticity model; required for Jmol SMILES matching of atom class | LOAD $quinone SELECT smiles(“/open/c1ccccc1”) (will return “0 atoms selected” because OpenSMILES does not consider quinone to be aromatic) |
/strict/ | Use electron counting to define aromatic ring using the Hückel rule (Jmol application default) | LOAD :cyclobutadiene SELECT smiles(“/strict/c1ccc1”) will return “0 atoms selected” |
/noAromatic/ | Ignore upper/lower case indicators of aromaticity; indicated double bonds must match exactly | /noAromatic/C1CCCCC1 |
/noStereo/ | Ignore differences in stereochemistry at chirality centers and double bonds | /nostereo/C{[C@H]}(O)CC=C |
/invertStereo/ | Reverse stereochemistry match result (chirality centers only, not double bonds) | /invertstereo/C{[C@@H]}(O)CC=C |
/noAtomClass/ | Disregard atom class designations when matching | /noAtomClass/C[C:1]CC |