Skip to main content

Table 1 Basic Jmol SMILES additions

From: Jmol SMILES and Jmol SMARTS: specifications and applications

Note Notation Meaning Example Explanation
a+ //*….*// Comment //* prod. by Jmol *// Optional; application-dependent; no general function; removal does not affect processing
a+ <whitespace> Allowed for formatting   Optional use of whitespace; removal does not affect processing of Jmol SMILES (however there may be aspects of Jmol SMARTS that require whitespace, these are application-dependent).
a+ /…../ Processing directive /strict/c1cccccc1 Optional; if present, must precede molecule description; see discussion and Table 3
+ [Xx] Dummy atom [Xx] The atomic symbol “Xx” represents a “dummy” atom that is present but not part of the actual chemical structure
+ <lower-case symbol> Aromatic atoms c1cocc1 Furan
Any atom other than hydrogen may be indicated as aromatic. Note that only b, c, n, o, p, si, and se are allowed to be aromatic using the processing directives/open/or/strict/(see below).
+ %(n) Unlimited connectivity C%(102)CCC%(102) Any non-negative number
+ a=a Aromatic double bond c1cc(O)=c(O)cc1 A specific double bond Kekulization, but still aromatic
  1. In the first column, a indicates result may depend upon application; + indicates additions to OpenSMILES