Image export in Marvin

Contents

• Image formats
• Export options

Image formats

Restrictions:

1. These are binary file formats, so the applet.getMol(...) function does not work.
2. Instead of the molecule.toFormat(...) function, the MolExporter.exportToBinFormat(...) 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"
transbg	Sets the image background to transparent.
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.
atomNumberingType...	Sets the type of atom numbering. Implies anum parameter. Possible values: 1 (Atom numbers) 2 (IUPAC numbering)
disableAminoAcidBondColoring	Disables peptide bridge coloring.
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.
lonePairsAsLine	Display lone pairs as a line instead of the default two dots. This parameter has effect only if the lp parameter is also specified.
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.
valprop	Show valence property on atoms that have the valence property explicitly set.
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.
ligandOrderVisibility_withDef	Active by default. Show ligand order on images only when the R-group definition is present.
ligandOrderVisibility_on	Show all ligand order on images for R-groups.
ligandOrderVisibility_off	Never show ligand order on images for R-groups.
aprop	Show explicitly set properties on atoms.
liganderr	Show ligand errors on R-groups.
coordBondStyle_solid	Display coordinate bond as a single bond.
coordBondStyle_arrow	Display coordinate bond as an arrow.
coordBondStyleAtMulticenter_dashed	Display coordinate bond as a dashed bond when it connects to a multicenter atom.
coordBondStyleAtMulticenter_solid	Display coordinate bond as a single bond when it connects to a multicenter atom.
chargeWithCircle	Display charge symbols in a circle.
oneLetterPeptideDisplay	Display peptides with their one letter abbreviation instead of the three letter abbreviation which is the default.

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.
png:aprop -s "C1-C10 alkyl" -o alkyl.png	PNG showing "C1-C10 alkyl".