Image export in Marvin

Contents

• Image formats
• Export options

Image formats

1. These are binary file formats, so the applet.getMol(...) function does not work.
2. Instead of the molecule.toFormat(...) function, the molecule.toBinFormat(...) method should be used.
3. Command line creation of image files using MolConverter works only in Java 1.2 or later JVMs.

Export options

...	Basic aromatization and H atom adding/removal options.
H_off	Do not show implicit Hydrogen labels.
H_hetero	Implicit Hydrogen labels on heteroatoms only.
H_heteroterm	Implicit Hydrogen labels on hetero- and terminal atoms (default).
H_all	Implicit Hydrogen labels on all atoms.
chiral_off	Switch off chirality support, do not show R/S labels (default).
chiral_selected	Show R/S if the chiral flag is set for the molecule.
chiral_all	Show R/S for any molecule.
w... h...	Image width and height in pixels. If only one from w and h is specified, then the other will have the same value. If none of them is specified, then their values are calculated from scale. If scale is not specified, then the default size is 200x200.
scale...	Magnification. 1.54Å (C-C bond length) is scale pixels.
maxscale...	Maximizes the magnification to prevent overscaling of small molecules. It is usually set to 28, which is the scale factor for 100% magnification.
atsiz...	Atom label font size in C-C bond length units. Default: 0.4 atsiz*1.54 Å = atsiz*scale points
bondw...	Width of double bond in C-C bond length units. Default: 0.18 bondw*1.54 Å = bondw*scale pixels
wireThickness...	Bond thickness in wireframe mode. Default: 0.064
stickThickness...	The stick diameter for ball and stick mode. Default: 0.1
ballRadius...	Ball radius for ball and stick mode. Default: 0.5
#rrggbb	Background color. It also determines the brightness of the CPK palette (for atoms and bonds); lighter colors are choosen automatically for dark background and conversely. Default: "#ffffff"
#aarrggbb	Background color with alpha value. Use alpha=0 for transparent background, e.g. #00ffffff. Note that the alpha channel is not supported by all image formats. Default: "#ffffffff"
mono	Black & white.
cpk	Use CPK colors (default).
shapely	Use the shapely color scheme.
group	Use coloring based on residue sequence numbers.
setcolors setcolors:...	Use atom/bond set colors. Colors can be specified as a colon separated list of values. Use "ak:#rrggbb" for atom set k, "bk:#rrggbb" for bond set k. The hashmark "#" can be omitted. Human-readable color names like "red", "green", "blue" can also be used.
wireframe	Wireframe rendering style (default for 2D).
wireknobs	Wireframe with knobs.
ballstick	"Ball & stick" rendering style (default for 3D).
spacefill	Spacefill rendering style.
noantialias	Switch off antialiasing.
amap	Displays atom mapping.
anum	Displays atom numbers.
lp	Displays lone pairs.
lpexpl	Display the explicit lone pairs instead of the implicit lone pairs if lone pair displaying is switched on. See the lp parameter.
downwedge_mdl	Down wedge orientation points downward (MDL). (default)
downwedge_daylight	Down wedge orientation points upward (Daylight).
anybond_auto	Draw any bonds with dashed lines in most cases. If all bonds are generated from atom coordinates, any bonds are displayed with solid lines. (default)
anybond_dashed	Draw any bonds with dashed lines.
anybond_solid	Draw any bond with solid lines.
noatsym	Hide atom symbols in 3D mode.
ez	Show E/Z.
cv_on	Always show the atom labels of carbon atoms.
cv_off	Never show the atom labels of carbon atoms.
cv_inChain	Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.
grinvVisible	Displays graph invariants.
bondLengthVisible	Displays the length of bonds in Angstroms.
valenceErrorVisible	Displays valence errors.
absLabelVisible	Sets the Abolute label visibility to true.

3D defaults: H_heteroterm,w200,h200,#ff000000,cpk,ballstick

Examples:

jpeg	Default settings: 200x200 pixels, white background (or black in 3D).
jpeg:w100,#ffff00	100x100 JPEG with yellow background.
jpeg:w100,h150	100x150 JPEG with default background.