Package chemaxon.marvin

Class MolPrinter

  • @PublicAPI
public class MolPrinter
extends Object
    Molecule renderer that can draw a molecule to a graphics context using various display settings.

    Example of usage: 

     import chemaxon.marvin.MolPrinter;
 import chemaxon.struc.Molecule;
 import chemaxon.formats.MolImporter;
 import java.awt.Color;
 import java.awt.Rectangle;
 import java.awt.Graphics2D;
 import java.awt.image.BufferedImage;
 import java.io.File;
 import java.io.IOException;
 import javax.imageio.ImageIO;
 
 public class MolPrinterTest {
     static BufferedImage createTestImage() throws IOException {
        // Create a molecule
        Molecule mol = MolImporter.importMol("CN1C=NC2=C1C(=O)N(C)C(=O)N2C");
        // Create a writable image
        BufferedImage im = new BufferedImage(400, 400, BufferedImage.TYPE_INT_ARGB);
        Graphics2D g = im.createGraphics();
        // Clear background
        g.setColor(Color.white);
        g.fillRect(0, 0, im.getWidth(), im.getHeight());
        // Draw the bounding rectangle
        g.setColor(Color.red);
        Rectangle rect = new Rectangle(20, 20, 360, 200);
        g.draw(rect);
        // Paint the molecule
        MolPrinter molPrinter = new MolPrinter(mol);
        molPrinter.setScale(molPrinter.maxScale(rect)); // fit image in the rectangle
        molPrinter.setBackgroundColor(Color.white);
        molPrinter.paint(g, rect);
        return im;
     }
 
     public static void main(String[] args) throws Exception {
        BufferedImage im = createTestImage();
        ImageIO.write(im, "png", new File("test.png"));
     }
 }

    • Constructor Detail

      • MolPrinter

        public MolPrinter()
        Constructs a molecule renderer for an empty molecule.

      • MolPrinter

        public MolPrinter​(MoleculeGraph m)
        Constructs a molecule renderer for the specified molecule.
        Parameters:
        m - a molecule graph
        Since:
        Marvin 4.1.8, 04/20/2007

      • MolPrinter

        public MolPrinter​(MDocument d)
        Constructs a molecule renderer for the specified document.
        Parameters:
        d - the document
        Since:
        Marvin 4.1.8, 04/20/2007

    • Method Detail

      • getDispopts

        public int getDispopts()
        Returns the actual display options. Note that this is an advanced way of handling display options. It may be easier to see specific methods that provides information on each display options individually.
        Example with explicit hydrogen atom display:
        1. boolean explicitHVisible = (molPrinter.getDispopts() & DispOptConsts.EXPLICITH_FLAG) != 0;
        2. boolean explicitHVisible = molPrinter.isExplicitHVisible();
        Returns:
        display options
        Since:
        Marvin 2.6
        See Also:
        DispOptConsts

      • setDispopts

        public void setDispopts​(int f)
        Modifies the display options in the advanced way of handling display options.
        Parameters:
        f - display options to set
        Since:
        Marvin 2.6
        See Also:
        DispOptConsts

      • setDispopts

        public void setDispopts​(int f,
                        int mask)
        Modifies the display options as in setDispopts(int), but affects only limited display options using a mask.
        Parameters:
        f - display options
        mask - the bits of the mask determine the specific display options to set
        Since:
        Marvin 4.1.9, 06/05/2007
        See Also:
        DispOptConsts

      • setDispoptsExt

        public void setDispoptsExt​(int f,
                           int mask)
        Modifies the extended display options as in setDispoptsExt(int), but affects only limited display options using a mask.
        Parameters:
        f - display options
        mask - the bits of the mask determine the specific display options to set
        Since:
        Marvin 5.5
        See Also:
        DispOptConsts, getDispoptsExt()

      • getScale

        public double getScale()
        Returns the scale factor in units of regular bond length.
        Returns:
        displayed length of a C-C bond in pixels
        Since:
        Marvin 2.9.11

      • setScale

        public void setScale​(double m)
        Sets the scale factor in units of regular bond length.
        Parameters:
        m - displayed length of a C-C bond in pixels
        Since:
        Marvin 2.9.11

      • maxScale

        public double maxScale​(Rectangle r)
        Calculates the maximum scaling factor for fitting the image in the specified rectangle.
        Parameters:
        r - the rectangle to fit
        Returns:
        calculated maximum scale factor
        Since:
        Marvin 4.1.8, 04/20/2007

      • maxScale

        public double maxScale​(Dimension d)
        Calculates the maximum scaling factor for fitting the image in a rectangle of the specified size.
        Parameters:
        d - the size of the rectangle to fit
        Returns:
        calculated maximum scale factor

      • getBoundingRectangle

        public Rectangle getBoundingRectangle​(MoleculeGraph[] mols)
        Returns the bounding rectangle of the specified molecules using the current scale factor. This method is useful to determine what the minimum size of the rectangle should be in paint(java.awt.Graphics2D, java.awt.Rectangle) to draw the molecules using a certain scale factor. Example: 
         molPrinter.setScale(28);
 Rectangle r = molPrinter.getBoundingRectangle(mols);
 BufferedImage im = new BufferedImage(r.x, r.y, BufferedImage.TYPE_INT_ARGB);
 Graphics2D g = im.createGraphics();
 molPrinter.paint(g, r);
        Note that having an MDocument object, one can call getBoundingRectangle(mDocument.getAllMolecules()).
        Parameters:
        mols - the molecules
        Returns:
        the bounding rectangle

      • getAtomsize

        @Deprecated
public double getAtomsize()
        Deprecated.
        As of Marvin 5.2.2, replaced by getAtomSize().
        Returns the atom size in units of regular bond length.
        Returns:
        the size of displayed atom labels

      • getAtomSize

        public double getAtomSize()
        Returns the atom size in units of regular bond length.
        Returns:
        the size of displayed atom labels
        Since:
        Marvin 5.2.2 04/15/2009

      • setAtomsize

        @Deprecated
public void setAtomsize​(double l)
        Deprecated.
        As of Marvin 5.2.2, replaced by setAtomSize(double).
        Sets the size of displayed atoms in units of regular bond length.
        Parameters:
        l - size of the displayed atom labels

      • setAtomSize

        public void setAtomSize​(double s)
        Sets the size of displayed atoms in units of regular bond length.
        Parameters:
        s - size of the displayed atom labels
        Since:
        Marvin 5.2.2 04/15/2009

      • getBondSpacing

        public double getBondSpacing()
        Returns the double bond spacing that is the distance of the two lines representing a double bond.
        Returns:
        the bond spacing in regular bond length units.
        Since:
        Marvin 4.1, 10/19/2005

      • getBondHashSpacing

        public double getBondHashSpacing()
        Returns the bond hash spacing that is the distance hashes in a hashed bond.
        Returns:
        the bond hash spacing in regular bond length units.

      • getBallRadius

        public double getBallRadius()
        Gets the ball radius for "ball and stick" mode.
        Returns:
        the ball radius
        Since:
        Marvin 5.2.5

      • setBallRadius

        public void setBallRadius​(double r)
        Sets the ball radius for "ball and stick" mode.
        Parameters:
        r - the ball radius
        Since:
        Marvin 5.2.5

      • getStickThickness

        public double getStickThickness()
        Gets the 3D stick's diameter.
        Returns:
        the stick thickness
        Since:
        Marvin 5.2.5

      • setStickThickness

        public void setStickThickness​(double w)
        Sets the 3D stick's diameter.
        Parameters:
        w - the stick thickness
        Since:
        Marvin 5.2.5

      • isAminoAcidBondColoringEnabled

        public boolean isAminoAcidBondColoringEnabled()
        Is peptide bridge coloring enabled?
        Returns:
        true if enabled
        Since:
        Marvin 6.3.1

      • setAminoAcidBondColoringEnabled

        public void setAminoAcidBondColoringEnabled​(boolean v)
        Sets peptide bridge coloring enabled.
        Parameters:
        v - true for enabled
        Since:
        Marvin 6.3.1

      • isAbsoluteLabelsVisible

        public boolean isAbsoluteLabelsVisible()
        Is 'Absolute' label visible?.
        Returns:
        true if visible, false if invisible
        Since:
        Marvin 4.1

      • setAbsoluteLabelsVisible

        public void setAbsoluteLabelsVisible​(boolean v)
        Set 'Absolute' label visibility.
        Parameters:
        v - true to visible, false to invisible
        Since:
        Marvin 4.1

      • setPeptideDisplay

        public void setPeptideDisplay​(String type)
        Sets the Peptide display settings.
        Parameters:
        type - "1-letter" to One Letter Peptide Display anything else to Three Letter Peptide Display
        Since:
        Marvin 4.1

      • isOneLetterPeptideDisplay

        public boolean isOneLetterPeptideDisplay()
        Decides whether the Peptide display settings set to one letter.
        Returns:
        true if the Peptide display settings are set to one letter.

      • isThreeLetterPeptideDisplay

        public boolean isThreeLetterPeptideDisplay()
        Decides whether the Peptide display settings set to three letter.
        Returns:
        true if the Peptide display settings are set to three letter.

      • setRgroupsVisible

        public void setRgroupsVisible​(boolean v)
        Sets whether the R-group definitions are visible.
        Parameters:
        v - true to visible, false to invisible

      • isRgroupsVisible

        public boolean isRgroupsVisible()
        Decides whether the R-group definitions are visible.
        Returns:
        true if the R-group definitions are visible, false otherwise.

      • setAnyBondStyles

        public void setAnyBondStyles​(String s)
        Sets the any bond style.
        Parameters:
        s - the style

      • getAnyBondStyles

        public String getAnyBondStyles()
        Gets the any bond style.
        Returns:
        the style

      • setLonePairAsLine

        public void setLonePairAsLine​(boolean v)
        Sets the visibility of Lone Pairs

      • isLonePairAsLine

        public boolean isLonePairAsLine()
        Get the visibility of Lone Pairs: dots/line

      • setChargeWithCircle

        public void setChargeWithCircle​(boolean v)
        Sets the visibility of Charge with Circle

      • isChargeWithCircle

        public boolean isChargeWithCircle()
        Get the visibility of Charge with Circle

      • getChargeFont

        public Font getChargeFont()
        Gets the charge's font.
        Returns:
        the font
        Since:
        Marvin 5.12

      • setChargeFont

        @Deprecated
public void setChargeFont​(Font f)
        Deprecated.
        in Marvin 15.5.18
        Sets the circled charge's font.
        Parameters:
        f - the font
        Since:
        Marvin 5.12

      • getChargeFontSize

        public double getChargeFontSize()
        Gets the circled charge's font's size.
        Returns:
        the chargeFontSize
        Since:
        Marvin 5.12

      • getWireThickness

        public double getWireThickness()
        Gets the line thickness for wireframe mode.
        Returns:
        the line thickness in Angstroms
        Since:
        Marvin 5.2.5

      • setWireThickness

        public void setWireThickness​(double w)
        Sets the line thickness for wireframe mode.
        Parameters:
        w - the line thickness in Angstroms
        Since:
        Marvin 5.2.5

      • setBondSpacing

        public void setBondSpacing​(double s)
        Sets the double bond spacing that is the distance of the two lines representing a double bond.

        spacing = s * 1.54 Å = s * scale pixels

        Parameters:
        s - the bond spacing in regular bond length units.
        Since:
        Marvin 4.1, 10/19/2005

      • setBondHashSpacing

        public void setBondHashSpacing​(double s)
        Sets the bond hash spacing that is the distance the hashes in a hashed bond.

        spacing = s * 1.54 Å = s * scale pixels

        Parameters:
        s - the bond hash spacing in regular bond length units.

      • getColorScheme

        public String getColorScheme()
        Returns the current color scheme.
        • Displays all atoms with the default drawing color: MONO_SCHEME_S
        • Displays all atoms with Corey-Pauling-Kultun colors: CPK_SCHEME_S
        • Coloring atoms based on RasMol's shapely color scheme for nucleic and amino acids: SHAPELY_SCHEME_S
        • Coloring atoms based on PDB residue numbers: GROUP_SCHEME_S
        Returns:
        the color scheme as String
        Since:
        Marvin 2.9.11
        See Also:
        DispOptConsts.COLOR_SCHEMES

      • setColorScheme

        public void setColorScheme​(String s)
        Sets the color scheme.
        • Displays all atoms with the default drawing color: MONO_SCHEME_S
        • Displays all atoms with Corey-Pauling-Kultun colors: CPK_SCHEME_S
        • Coloring atoms based on RasMol's shapely color scheme for nucleic and amino acids: SHAPELY_SCHEME_S
        • Coloring atoms based on PDB residue numbers: GROUP_SCHEME_S
        Parameters:
        s - the color scheme as String
        Since:
        Marvin 2.9.11
        See Also:
        DispOptConsts.COLOR_SCHEMES

      • isSetColoringEnabled

        public boolean isSetColoringEnabled()
        Returns true if atoms and bonds are colored according to the color of the pre-defined set they belong to. For more information, see http://www.chemaxon.com/marvin/help/developer/core/sets.html
        Returns:
        true if atom/bond set coloring is enabled
        Since:
        Marvin 3.3

      • setSetColoringEnabled

        public void setSetColoringEnabled​(boolean v)
        Colors atoms and bonds according to the color of the pre-defined set they belong to. For more information, see http://www.chemaxon.com/marvin/help/developer/core/sets.html
        Parameters:
        v - true to enable atom/bond set coloring
        Since:
        Marvin 3.3

      • getRendering

        public String getRendering()
        Returns the rendering style of atoms and bonds.
        • Displays bonds as thin lines, and atoms (except Carbon) as symbols: WIREFRAME_RENDERING_S
        • Displays bonds as thin lines, Carbon atoms as knobs, and other atoms as symbols:
        • Displays bonds as thick lines, and atoms (except Carbon) as symbols: STICKS_RENDERING_S
        • Displays bonds as thick lines, atoms as shaded balls, and atoms (except Carbon and Hydrogen) as symbols on balls: BALLSTICK_RENDERING_S
        • Displays atoms as large shaded balls, and atoms (except Carbon and Hydrogen) as symbols on the balls: SPACEFILL_RENDERING_S
        Returns:
        the rendering style as String
        Since:
        Marvin 2.9.11
        See Also:
        DispOptConsts.RENDERING_STYLES

      • setRendering

        public void setRendering​(String s)
        Sets the rendering style of atoms and bonds.
        • Displays bonds as thin lines, and atoms (except Carbon) as symbols: WIREFRAME_RENDERING_S
        • Displays bonds as thin lines, Carbon atoms as knobs, and other atoms as symbols:
        • Displays bonds as thick lines, and atoms (except Carbon) as symbols: STICKS_RENDERING_S
        • Displays bonds as thick lines, atoms as shaded balls, and atoms (except Carbon and Hydrogen) as symbols on balls: BALLSTICK_RENDERING_S
        • Displays atoms as large shaded balls, and atoms (except Carbon and Hydrogen) as symbols on the balls: SPACEFILL_RENDERING_S
        Parameters:
        s - the rendering style as String
        Since:
        Marvin 2.9.11
        See Also:
        DispOptConsts.RENDERING_STYLES

      • getBackgroundColor

        public Color getBackgroundColor()
        Returns the current background color.
        Returns:
        the background color
        Since:
        Marvin 5.2.2

      • setBackgroundColor

        public void setBackgroundColor​(Color color)
        Sets the background color.
        Parameters:
        color - the desired bakcground Color
        Since:
        Marvin 4.1.13

      • isAtomSymbolsVisible

        public boolean isAtomSymbolsVisible()
        Returns the atom symbol visibility of 3D mode.
        Returns:
        true if atom symbols are visible in 3D mode
        Since:
        Marvin 3.3.3

      • setAtomSymbolsVisible

        public void setAtomSymbolsVisible​(boolean v)
        Sets atom symbol visibility in 3D mode. Note that in 3D mode, atoms may become invisible in Wireframe and Stick mode by hiding atom symbols.
        Parameters:
        v - show (true) or hide (false) atom symbols in 3D mode
        Since:
        Marvin 3.3.3

      • setAtomNumbersVisible

        @Deprecated
public void setAtomNumbersVisible​(boolean v)
        Deprecated.
        in 6.2.0. Use setAtomNumberingType() instead.
        Sets the atom number visibility. Please note that atom numbers are numbered from 0 in molecule structures, but displayed from 1.
        Parameters:
        v - true to show, false to hide
        Since:
        Marvin 5.7

      • isAtomNumbersVisible

        @Deprecated
public boolean isAtomNumbersVisible()
        Deprecated.
        in 6.2.0. Use getAtomNumberingType instead.
        Returns true if atom numbers are visible.
        Returns:
        true if visible, false if not
        Since:
        Marvin 5.7

      • setAtomNumberingType

        public void setAtomNumberingType​(int t)
        sets atom numbering type.
        Parameters:
        t - (0) for off, (1) for atom numbers and (2) for IUPAC numbering
        Since:
        Marvin 6.1

      • getAtomNumberingType

        public int getAtomNumberingType()
        Returns atom numbering type.
        Returns:
        (0) for off, (1) for atom numbers and (2) for IUPAC numbering
        Since:
        Marvin 6.1

      • setAtomMappingVisible

        public void setAtomMappingVisible​(boolean v)
        Sets the atom mapping visibility.
        Parameters:
        v - true to show, false to hide
        Since:
        Marvin 5.7

      • isAtomMappingVisible

        public boolean isAtomMappingVisible()
        Returns true if atom mapping is visible.
        Returns:
        true if visible, false if not
        Since:
        Marvin 5.7

      • isEzVisible

        @Deprecated
public boolean isEzVisible()
        Deprecated.
        As of Marvin 5.2.2, replaced by isEZLabelsVisible()
        Returns the E/Z labels display option.
        Returns:
        show (true) or hide (false)
        Since:
        Marvin 3.3.3

      • setEzVisible

        @Deprecated
public void setEzVisible​(boolean v)
        Deprecated.
        As of Marvin 5.2.2, replaced by setEZLabelsVisible(boolean)
        Sets the E/Z labels display option.
        Parameters:
        v - show (true) or hide (false) E/Z
        Since:
        Marvin 3.3.3

      • isEZLabelsVisible

        public boolean isEZLabelsVisible()
        Returns the visibility state of absolute double bond stereo configuration labels.
        Returns:
        true if E/Z labels are visible
        Since:
        Marvin 3.3.3

      • setEZLabelsVisible

        public void setEZLabelsVisible​(boolean v)
        Sets the visibility state of absolute double bond stereo configuration labels. Bonds known to have an (E) or (Z) configuration will be marked as such.
        Parameters:
        v - show (true) or hide (false) E/Z labels
        Since:
        Marvin 3.3.3

      • isMPLabelsVisible

        public boolean isMPLabelsVisible()
        Returns the visibility state of M/P labels.
        Returns:
        true if M/P labels are visible
        Since:
        Marvin 3.3.3

      • setMPLabelsVisible

        public void setMPLabelsVisible​(boolean v)
        Sets the visibility state of M/P labels.
        Parameters:
        v - show (true) or hide (false) M/P labels
        Since:
        Marvin 3.3.3

      • isLonePairsVisible

        public boolean isLonePairsVisible()
        Returns the visibility state of lone pairs.
        Returns:
        true if lone pairs are visible
        Since:
        Marvin 5.2.2

      • setLonePairsVisible

        public void setLonePairsVisible​(boolean v)
        Sets the visibility state of lone pairs. In case the molecule does not contain explicit lone pairs this method may not display lone pairs. To display lone pairs in this case, use the setLonePairsAutoCalculated(boolean) method too.
        Parameters:
        v - show (true) or hide (false) lone pairs
        Since:
        Marvin 5.2.2

      • isLonePairsAutoCalculated

        public boolean isLonePairsAutoCalculated()
        Returns the state of the automatic calculation of lone pairs.
        Returns:
        true if lone pairs are calculated automatically.
        Since:
        Marvin 5.2.5

      • setLonePairsAutoCalculated

        public void setLonePairsAutoCalculated​(boolean v)
        Sets the state of the automatic calculation of lone pairs.
        Parameters:
        v - true if lone pairs should be calculated automatically
        Since:
        Marvin 5.2.5

      • isTransparent

        public boolean isTransparent()
        Returns the transparency state of the painting.
        Returns:
        true if the painter is in transparent drawing mode.
        Since:
        Marvin 5.2.5

      • setTransparent

        public void setTransparent​(boolean transparency)
        Sets the transparency state of the painting.
        Parameters:
        transparency - if true then the painting is in transparent mode.
        Since:
        Marvin 5.2.5

      • isValenceErrorvisible

        public boolean isValenceErrorvisible()
        Returns the visibility state of valence errors. If valence errors are set to visible, they are indicated by a red underline under the atom labels. The default value is false.
        Returns:
        true if valence errors are shown.

      • setValenceErrorVisible

        public void setValenceErrorVisible​(boolean b)
        Sets the visibility state of valence errors.
        Parameters:
        b - true if the valence errors are drawn

      • isAtomPropertiesVisible

        public boolean isAtomPropertiesVisible()
        Get the atom properties visibility
        Returns:
        true if atom properties has to be drawn.
        Since:
        Marvin 5.5

      • setAtomPropertiesVisible

        public void setAtomPropertiesVisible​(boolean v)
        Set the atom properties visibility
        Parameters:
        v - true to draw atom properties.
        Since:
        Marvin 5.5

      • isRLogicVisible

        public boolean isRLogicVisible()
        Is R-logic visible?.
        Returns:
        true if visible, false if invisible
        Since:
        Marvin 5.5

      • setRLogicVisible

        public void setRLogicVisible​(boolean v)
        Set R-logic visibility.
        Parameters:
        v - true to visible, false to invisible
        Since:
        Marvin 5.5

      • isValencePropertyVisible

        public boolean isValencePropertyVisible()
        Gets the atom valence property visibility
        Returns:
        true if the valence property is visibile
        Since:
        Marvin 5.5

      • setValencePropertyVisible

        public void setValencePropertyVisible​(boolean v)
        Sets the atom valence propertiy visibility
        Parameters:
        v - the valence property visibility
        Since:
        Marvin 5.5

      • areAttachmentPointsVisible

        public boolean areAttachmentPointsVisible()
        Gets the attachment points visibility.
        Returns:

      • setAttachmentPointsVisible

        public void setAttachmentPointsVisible​(boolean v)
        Sets the attachment points visibility.

      • isLigandErrorVisible

        public boolean isLigandErrorVisible()
        Gets the bond's ligand error visibility
        Returns:
        true if the ligand error is visibile
        Since:
        Marvin 5.6

      • setLigandErrorVisible

        public void setLigandErrorVisible​(boolean v)
        Sets the bond's ligand error visibility
        Parameters:
        v - the ligand error visibility
        Since:
        Marvin 5.6

      • getCoordinateBondStyle

        public String getCoordinateBondStyle()
        Gets the coordinate bond line style when both atoms are single.
        Returns:
        the coordinative bond line style "solid"/"arrow"

      • setCoordinateBondStyle

        public void setCoordinateBondStyle​(String s)
        Set the coordinate bond line style when both atoms are single.
        Parameters:
        s - "solid"/"arrow"

      • getCoordinateBondStyleAtMulticenter

        public String getCoordinateBondStyleAtMulticenter()
        Gets the coordinate bond line style.
        Returns:
        the coordinate bond line style "solid"/"hashed"

      • setCoordinateBondStyleAtMulticenter

        public void setCoordinateBondStyleAtMulticenter​(String s)
        Set the coordinate bond line style.
        Parameters:
        s - "solid"/"hashed"

      • setMol

        public void setMol​(Molecule m)
        Sets the current molecule and calculate its bounds.
        Parameters:
        m - the molecule

      • setMolTemplate

        public void setMolTemplate​(Molecule m)

      • setMol

        public void setMol​(String s)
            throws MolFormatException
        Sets the current molecule and calculate its bounds.
        Parameters:
        s - string containing the molecule file in some known format
        Throws:
        MolFormatException - if the molecule string cannot be imported

      • setDoc

        public void setDoc​(MDocument d)
        Sets the current document and calculates its bounds.
        Parameters:
        d - the document
        Since:
        Marvin 4.1.8, 04/20/2007

      • paint

        public void paint​(Graphics g,
                  Rectangle r)
        Paints the molecule into the center of the specified rectangle.
        Parameters:
        g - the graphics context to paint on
        r - the rectangle in which the molecule is painted

      • paint

        public void paint​(Graphics2D g,
                  Rectangle r)
        Paints the molecule into the center of the specified rectangle.
        Parameters:
        g - the graphics context to paint on
        r - the rectangle in which the molecule is painted
        Since:
        Marvin 5.2.2 04/15/2009

      • paint

        public void paint​(Graphics2D g,
                  Dimension d)
        Paints the molecule on the specified graphics context in the given size.
        Parameters:
        g - the graphics context to paint on
        d - the dimension of the painted molecule
        Since:
        Marvin 5.3 12/01/2009

      • getBondWidth

        @Deprecated
public double getBondWidth()
        Deprecated.
        as of Marvin 4.1, replaced by getBondSpacing()
        Returns the double bond spacing that is the distance of the two lines representing a double bond.
        Returns:
        the bond spacing in regular bond length units.

      • setBondWidth

        @Deprecated
public void setBondWidth​(double w)
        Deprecated.
        as of Marvin 4.1, replaced by setBondSpacing(double)
        Sets the double bond spacing that is the distance of the two lines representing a double bond.
        Parameters:
        w - the bond spacing in regular bond length units.

      • molToScreenCoords

        public void molToScreenCoords​(DPoint3 molcoords,
                              Point2D scrcoords)
        Converts molecular coordinates to 2D screen coordinates.
        Parameters:
        molcoords - molecular coordinates in Angstroms (input)
        scrcoords - graphics context coordinates in pixels (output)
        Since:
        Marvin 5.2.4, 07/29/2009

      • setExplicitH

        @Deprecated
public void setExplicitH​(boolean show)
        Deprecated.
        As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.
        Sets the visibility state of explicit hydrogen atoms.
        Parameters:
        show - show (true) or hide (false) explicit hydrogen atoms
        Since:
        Marvin 3.3.3

      • isExplicitHVisible

        @Deprecated
public boolean isExplicitHVisible()
        Deprecated.
        As of Marvin 5.5.1 this method always returns true. This method will be removed in a future release.
        Returns the visibility state of explicit hydrogen atoms.
        Returns:
        true if explicit hydrogens are displayed
        Since:
        Marvin 5.2.2 04/15/2009

      • setExplicitHVisible

        @Deprecated
public void setExplicitHVisible​(boolean b)
        Deprecated.
        As of Marvin 5.5.1 this method does nothing. This method will be removed in a future release.
        Sets the visibility state of explicit hydrogen atoms.
        Parameters:
        b - show (true) or hide (false) explicit hydrogen atoms
        Since:
        Marvin 5.2.2 04/15/2009

      • getDisplayQuality

        @Deprecated
public int getDisplayQuality()
        Deprecated.
        since Marvin 6.4 only high quality exists
        Gets the display quality.
        0 - low quality, faster rendering
        1 - high quality (antialiasing), slower rendering
        Returns:
        the display quality
        Since:
        Marvin 5.7, 09/08/2011ű

      • setDisplayQuality

        @Deprecated
public void setDisplayQuality​(int q)
        Deprecated.
        since Marvin 6.4 only high quality exists
        Sets the display quality.
        0 - low quality, faster rendering
        1 - high quality (antialiasing), slower rendering
        Parameters:
        q - the display quality
        Since:
        Marvin 5.7, 09/08/2011

      • isBondLengthVisible

        public boolean isBondLengthVisible()
        Return whether the bond length is visible or not.
        Returns:
        true is the bond length is visible, otherwise false
        Since:
        Marvin 5.7, 09/08/2011

      • setBondLengthVisible

        public void setBondLengthVisible​(boolean v)
        Sets the bond length visibility
        Parameters:
        v - true - visible, false - invisible
        Since:
        Marvin 5.7, 09/08/2011

      • isGraphInvariantVisible

        public boolean isGraphInvariantVisible()
        Return whether the graph invariant is visible or not.
        Returns:
        true is the graph invariant is visible, otherwise false
        Since:
        Marvin 5.7, 09/08/2011

      • setGraphInvariantVisible

        public void setGraphInvariantVisible​(boolean v)
        Sets the graph invariant visibility
        Parameters:
        v - true - visible, false - invisible
        Since:
        Marvin 5.7, 09/08/2011

      • getDownWedge

        public String getDownWedge()
        Gets the down wedge orientation.
        Returns:
        the down wedge orientation
        Since:
        Marvin 5.7, 09/08/2011

      • setDownWedge

        public void setDownWedge​(String orientation)
        Set the down wedge orientation.
        Parameters:
        orientation - the down wedge orientation
        Since:
        Marvin 5.7, 09/08/2011

      • setBondLength

        public void setBondLength​(double bondLength)
        Sets the bond length in pt.
        Parameters:
        bondLength - the required bond length in pt.

      • getBondLength

        public double getBondLength()
        Returns the actual bond length in pt.

      • setBoldBondWidth

        public void setBoldBondWidth​(double width)
        Sets the bold bond with.
        Parameters:
        width -

      • setMarginInPt

        public void setMarginInPt​(double marginPt)
        Sets the Margin of the painted molecule.
        Parameters:
        marginPt -

      • setStereoFontRatio

        public void setStereoFontRatio​(float stereoFontRatio)
        Sets the ratio of the font size of the stereo label compared to the normal atom label size. Its value must be between 1.0 and 0.1. The default value is 1/1.3
        Parameters:
        stereoFontRatio -

      • getStereoFontRatio

        public float getStereoFontRatio()
        Returns the current ratio of the font size of the stereo label compared to the normal atom label size.

      • setSgroupDataFormatted

        public void setSgroupDataFormatted​(boolean isFormatted)
        Sets if the Sgroup data to be formatted. The default value is true
        Parameters:
        isFormatted -

      • isSgroupDataFormatted

        public boolean isSgroupDataFormatted()
        Returns whether the Sgroup data is formatted.