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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