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 atomSet N . M list. By default, all atoms are in set 0. N/A
    atomSetColor0...atomSetColor63 The atom set color in hex. N/A
    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 bondSet N . M list. By default, all bonds are in set 0. N/A
    bondSetColor1...bondSetColor63 The bond set color in hex. N/A
    clean2dOpts Options for 2D cleaning (0D->2D) See base 2D cleaning options N/A
    clean3dOpts Options for 3D cleaning (0D->3D) See base 3D cleaning options N/A
    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). N/A
    importConv Conversion(s) after molecule loading. Currently, the following options are implemented:
    • General aromatization ("a" or "+a")
    • Basic aromatization ("a_bas" or "+a_bas")
    • Dearomatization ("-a")
    • Add explicit H atoms ("H" or "+H")
    • Remove explicit H atoms ("-H")
    • Automatic cleaning ("c")
    N/A
    setColoringEnabled Atom/bond set coloring. true