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Table 8 Jmol application-specific directives

From: Jmol SMILES and Jmol SMARTS: specifications and applications

Note Directive Meaning Jmol example
G /atomComments/ Add comments when generating SMILES strings that indicate the correlation between SMILES atoms and Jmol atoms PRINT {*}.find(“SMILES/atomComments/”)
SHOW SMILES/atomComments
G /hydrogens/ Makes all hydrogens explicit in generating a SMILES string LOAD $benzene
PRINT {*}.find(“SMILES/hydrogens/”)
c1([H])c([H])c([H])c([H])c([H])c1[H]
G /topology/ Generate SMILES strings that represent all atoms as “*”, thus allowing SMARTS pattern matches without regard to specific elements LOAD $indane
SHOW SMILES/topology
*1*2*****2**1
P /firstMatchOnly/ Return only the first match, not all occurrences of a match LOAD $heptane SELECT ON search(“/firstMatchOnly/C”) 1 atom selected
P /groupByMolecule/ 3D components are grouped by covalently-bonded sets (Jmol default) LOAD “$carbetapentane citrate”
SELECT on search(“/groupByMolecule/(C=O.C=O)”)
(highlights the carbonyl groups of the citrate ion only, because carbetapentane has only one carbonyl group, and the indicated grouping requires that both be in the same component)
P /groupByModel/ Consider each model in Jmol to be one component, regardless of how many covalently disjoint sets it contains x = search(“/groupByModel, firstMatchOnly/(C).(C)”)
(returns an atom set containing the first nonaromatic carbon of each model when there are two, or no atoms if there is only one model)
GSP /aromaticDouble/ Double bonds between aromatic atoms must match explicitly for 3D molecule comparison—SMILES strings and SMARTS patterns with = between aromatic atoms will set this flag automatically during processing LOAD files “$1,2-dihydroxybenzene” “:1,2-dihyroxybenzene”
PRINT {1.1}.find(“SMILES”,{2.1}) == {1.1}
true (because both NCI and PubChem have structures for these two compounds)
PRINT {1.1}.find(“SMILES/aromaticDouble/”,{2.1}) == {1.1}
false (because the two structures have different double-bonding patterns)
GSP /aromaticPlanar/ Carry out a 3D analysis to define aromatic atoms LOAD $quinone
SELECT smiles(“/aromaticPlanar/c1ccccc1”)
(will return “6 atoms selected” because Jmol’s default is to consider the planar ring of quinone to be aromatic)
GSP /aromaticDefined/ Bonds to be matched as aromatic are already marked as such; make no attempt to determine aromaticity in the structure LOAD :benzene
CONNECT {*} {*} aromatic modify
CALCULATE aromatic
SELECT smiles(“/aromaticDefined/c1ccccc1”)
(aromatic atoms have been pre-calculated)
  1. G for Jmol SMILES generation; S for Jmol SMILES (full molecule) matching; P for Jmol SMARTS pattern matching