Table 8 Jmol application-specific directives

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)