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.


    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: atsiz*1.54 Å = atsiz*scale 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: 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


    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".