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ParameterMeaningDefault
atomSet0.1 ... atomSet0.63
atomSet1.1 ... atomSet1.63
...
Atom sets. Comma separated list of atom indices (0, ..., n-1). An atom in molecule cell number N will be in set M if its number appears in the atomSetN.M list. By default, all atoms are in set 0. 
atomSetColor0
...
atomSetColor63
Atom set color in hexa. 
bondSet0.1 ... bondSet0.63
bondSet1.1 ... bondSet1.63
...
Bond sets. Comma separated list of atom index pairs in i-j format, where i, j = 0, ..., n-1. A bond in molecule cell number N will be in set M if the corresponding atom pair appears in the bondSetN.M list. By default, all bonds are in set 0. 
bondSetColor1
...
bondSetColor63
Bond set color in hexa. 
clean2dOptsOptions for 2D cleaning (0D->2D) See base 2D cleaning options 
clean3dOptsOptions for 3D cleaning (0D->3D) See base 3D cleaning options 
cleanDimNumber of space dimensions for cleaning.
  • 2 - two-dimensional cleaning
  • 3 - three-dimensional cleaning
See also: cleanOpts, importConv options
2
cleanOptsOptions for 2D or 3D cleaning.
cleanOpts accepts the same parameter values as clean2dOpts or clean3dOpts depending on the cleaning dimension (cleanDim).
 
importConv

Conversion(s) after molecule loading. Currently the following options are implemented:

"a" or "+a"    General aromatization
"a_bas" or "+a_bas"    Basic aromatization
"-a"dearomatization
"H" or "+H"    add explicit H atoms
"-H"remove explicit H atoms
"c"automatic cleaning
 
setColoringEnabledAtom/bond set coloring.true