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Image formats

Marvin is able to export bitmap image files like  JPEGMS BMPPNGTIFF  and vector graphics files like  EPSSVGPDF  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_offDo not show implicit Hydrogen labels.
XXX:H_off
H_heteroImplicit Hydrogen labels on heteroatoms only.
XXX:H_hetero
H_heterotermImplicit Hydrogen labels on hetero- and terminal atoms (default).
XXX:H_heteroterm
H_allImplicit Hydrogen labels on all atoms.
XXX:H_all
chiral_offSwitch off chirality support, do not show R/S labels (default).
XXX:chiral_off
chiral_selectedShow R/S if the chiral flag is set for the molecule.
XXX:chiral_selected
chiral_allShow R/S for any molecule.
XXX:chiral_all
MP_LABEL_VISIBLE
Show M/P for any molecule.
XXX:mp
noRGroupsDo not show R-groups.
XXX:noRgroups
noRLogicDo 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
#rrggbbBackground 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"
#aarrggbbBackground 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"
transbgSets the image background to transparent.
monoBlack & white.
cpkUse CPK colors (default).
shapelyUse the shapely color scheme.
groupUse 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.
wireframeWireframe rendering style (default for 2D).
wireknobsWireframe with knobs - used til version 17.9. Later versions fall back to wireframe
ballstick"Ball & stick" rendering style (default for 3D).
spacefillSpacefill rendering style.
noantialiasSwitch off antialiasing.
amapDisplays atom mapping.
anumDisplays atom numbers.
atomNumberingType...Sets the type of atom numbering. Implies anum parameter.
Possible values:
  • 1 (Atom numbers)
  • 2 (IUPAC numbering)

lpDisplays lone pairs.
lpexplDisplay the explicit lone pairs instead of the implicit lone pairs if lone pair displaying is switched on. See the lp parameter.
lonePairsAsLineDisplay lone pairs as a line instead of the default two dots. This parameter has effect only if the lp parameter is also specified.
downwedge_mdlDown wedge orientation points downward (MDL). (default)
downwedge_daylightDown wedge orientation points upward (Daylight).
anybond_autoDraw 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_dashedDraw any bonds with dashed lines.
anybond_solidDraw any bond with solid lines.
noatsymHide atom symbols in 3D mode.
valpropShow valence property on atoms that have the valence property explicitly set.
ezShow E/Z labels.
cv_onAlways show the atom labels of carbon atoms.
cv_offNever show the atom labels of carbon atoms.
cv_inChainShow the atom labels of carbon atoms at straight angles and at implicit Hydrogens.
bondLengthVisibleDisplay the length of bonds in Angstroms.
valenceErrorVisibleDisplay valence errors.
absLabelVisibleSet the Absolute label visibility to true.
ligandOrderVisibility_withDefActive by default. Show ligand order on images only when the R-group definition is present.
ligandOrderVisibility_onShow all ligand order on images for R-groups.
ligandOrderVisibility_offNever show ligand order on images for R-groups.
apropShow explicitly set properties on atoms.
liganderrShow ligand errors on R-groups.
coordBondStyle_solidDisplay coordinate bond as a single bond.
coordBondStyle_arrowDisplay coordinate bond as an arrow.
coordBondStyleAtMulticenter_hashedDisplay coordinate bond as a dashed bond when it connects to a multicenter atom.
coordBondStyleAtMulticenter_solidDisplay coordinate bond as a single bond when it connects to a multicenter atom.
chargeWithCircleDisplay charge symbols in a circle.
oneLetterPeptideDisplayDisplay 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:

jpegDefault 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.pngPNG showing "C1-C10 alkyl".