Image export in Marvin

Contents

Image formats

Marvin is able to export bitmap image files like JPEG, MS BMP, PNG, PPM and vector graphics files like SVG, PDF and EMF. Restrictions:
  1. These are binary file formats, so the applet.getMol(...) function does not work.
  2. The molecule.toFormat(...) function do not work, use molecule.toBinFormat(...) instead.
  3. Command line creation of image files using MolConverter works only in Java 1.2 or later JVMs

Export options

Image export options are separated by colons in format descriptor strings.
The following common options are recognized by all image export modules:
... 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.
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. Default: "#ffffff"
#aarrggbb Background color with alpha value. 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.
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.
2D defaults: H_heteroterm,w200,h200,#ffffffff,cpk,wireframe

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.