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.

Export options

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

Basic aromatization and H atom adding/removal options:

a, +a, +a_gen: General aromatization.
a_bas: Basic aromatization.
a_loose: Loose aromatization.
a_ambig: Ambiguous aromatization.
-a, -a_gen: General Dearomatization.
-a_huckel: Huckel dearomatization.
-a_huckel_ex: Huckel dearomatization, throwing exception in case of failure.
H or +H: Add explicit Hydrogen atoms.
-H: Remove explicit Hydrogen atoms.

Code	Explanation
`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.
`MP_LABEL_VISIBLE`	Show M/P for any molecule.
`noRGroups`	Do not show R-groups.
`noRLogic`	Do not show R-logic.
`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. 1.54 Å (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: 0.4Note: *atsiz1.54 Å = atsizscale* points
`atomFont...`	Atom label font type and size in pt.
`bondl...`	Bond length in pt. Default: 28
`bondw...`	Bond spacing in C-C bond length units. Default: 0.18Note: *bondw1.54 Å = bondwscale* 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

Code	Explanation
`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".