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Table 7 Jmol SMARTS non-primitives

From: Jmol SMILES and Jmol SMARTS: specifications and applications

Notes Notation Meaning Example Explanation
+ {…} Selection set; include only these atoms in the final atom selection {[#6]}C=O Select all alpha carbons
+ A(.d:x-y)B Distance from connected atoms A and B within range x–y C(.d:1.5-1.6)C All aliphatic carbon–carbon bonds that are between 1.5 and 1.6 Å long
+ A(.d:!x-y)B Optional “!” indicates “not in this range” C(.d:!1.5-1.6)C Select all CC bonds not in the range 1.5-1.6
+ A(.a:x-y)BC Angle A–B–C within range x–y C(.a:115-125)CC All CCC with angle between 115 and 125 degrees
+ A(.t:x-y)BCD Dihedral A–B–C–D within range x–y, where x and y are in the range −180 to 180 {[CH3]}(.t:50,70)CC{[CH3]} ||{[CH3]}(.t:-50,-70)CC{[CH3]} Find gauche methyl groups and select just them
+ $R1=“xxx”; Replacement variables .$R1=“C=O”; $(*[$R1]) Same as $(*C=O)
component-level grouping (with definition of a component determined by/groupByModel/and/groupByMolecule/directives in Jmol) (F.O) Unconnected F and O in the same component
(F).(O) F and O in different components
(*).(*) Only select atoms if there are multiple components
  1. D indicates same as Daylight SMARTS; + indicates additions to OpenSMARTS