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.
    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 bondSet N . M list. By default, all bonds are in set 0.
    bondSetColor1...bondSetColor63 The bond set color in hex.
    <a name="src-1803642-marvinviewstructureparameters-2d"></a>clean2dOpts Options for 2D cleaning (0D->2D) See base 2D cleaning options
    <a name="src-1803642-marvinviewstructureparameters-3d"></a>clean3dOpts Options for 3D cleaning (0D->3D) See base 3D cleaning options
    <a name="src-1803642-marvinviewstructureparameters-dim"></a>cleanDim The number of space dimensions for cleaning. 2 - two-dimensional cleaning 3 - three-dimensional cleaningSee also: cleanOpts, importConv options 2
    <a name="src-1803642-marvinviewstructureparameters-opts"></a>cleanOpts Options for 2D or 3D cleaning. cleanOpts accepts the same parameter values as clean2dOpts or clean3dOpts depending on the cleaning dimension (cleanDim).
    <a name="src-1803642-marvinviewstructureparameters-imp"></a>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