Image Export in Marvin

Image formats

Marvin is able to export bitmap image files like JPEG, MS BMP, PNG, TIFF and vector graphics files like EPS, SVG, PDF and EMF.

Restrictions:

These are binary file formats, so the applet.getMol(...) function does not work.

Instead of the molecule.toFormat(...) function, the MolExporter.exportToBinFormat(...) method should be used.

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 commas in format descriptor strings.
The following common options are recognized by all image export modules:

a, +a, +a_gen

General aromatization

XXX:a
a_loose 

Loose aromatization

XXX:a_loose
a_ambig

Ambiguous aromatization

XXX:a_ambig
-a, -a_gen

General Dearomatization

XXX:-a
-a_huckel

Huckel dearomatization

XXX:-a_huckel
-a_huckel_ex

Huckel dearomatization, throwing exception in case of failure

XXX:-a_huckel_ex
H, +H

Add explicit Hydrogen atoms

XXX:H
-H

Remove explicit Hydrogen atoms

XXX:-H
+numbering

assigns atom numberings corresponding to the IUPAC name

XXX:+numbering

H_off

Do not show implicit Hydrogen labels.

XXX:H_off

H_hetero

Implicit Hydrogen labels on heteroatoms only.

XXX:H_hetero

H_heteroterm

Implicit Hydrogen labels on hetero- and terminal atoms (default).

XXX:H_heteroterm

H_all

Implicit Hydrogen labels on all atoms.

XXX:H_all

chiral_off

Switch off chirality support, do not show R/S labels (default).

XXX:chiral_off

chiral_selected

Show R/S if the chiral flag is set for the molecule.

XXX:chiral_selected

chiral_all

Show R/S for any molecule.

XXX:chiral_all
MP_LABEL_VISIBLE

Show M/P for any molecule.

XXX:mp

noRGroups

Do not show R-groups.

XXX:noRgroups

noRLogic

Do not show R-logic.

XXX:noRLogic

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.

XXX:w200,h200

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

Note: atsiz*1.54 Å = atsiz*scale points

atomFont...

Atom label font type and size in pt.

atomFont:SansSerif-ITALIC-10
atomFont:Times New Roman-PLAIN-10

bondl...

Bond length in pt. Default: 28

bondl42.0

bondw...

Bond spacing in C-C bond length units. Default: 0.18

Note: bondw*1.54 Å = bondw*scale pixels

boldbondw...

Width of bold bond in pt. Default: 6

bondHashSpacing...

The spacing of the hash in hashed bonds in C-C bond length units.

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).

group

Use coloring based on residue sequence numbers.

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 - used til version 17.9. Later versions fall back to wireframe

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)

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 labels.

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.

bondLengthVisible

Display the length of bonds in Angstroms.

valenceErrorVisible

Display valence errors.

absLabelVisible

Set the Absolute 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_hashed

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.

disableAminoAcidBondColoring

Disable the amino acid bond coloring.

fogFactor...

Set the fog factor scale value (integer). Default value: 0, range: 0..100.

marginSize...

Set the margin width in pt. Default: 10

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.

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

PNG showing "C1-C10 alkyl".