MarvinView Structure Parameters

Parameter

Meaning

Default

atomSet0.1 ... atomSet0.63atomSet1.1 ... atomSet1.63...

Atom sets. A 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

The atom set color in hex.

bondSet0.1 ... bondSet0.63bondSet1.1 ... bondSet1.63...

Bond sets. A 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

The bond set color in hex.

clean2dOpts

Options for 2D cleaning (0D->2D) See base 2D cleaning options

clean3dOpts

Options for 3D cleaning (0D->3D) See base 3D cleaning options

cleanDim

The number of space dimensions for cleaning.

  • 2 - two-dimensional cleaning

  • 3 - three-dimensional cleaning

See also: cleanOpts, importConv options

2

cleanOpts

Options 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

setColoringEnabled

Atom/bond set coloring.

true