chemaxon.marvin
Class MolPrinter

java.lang.Object
  chemaxon.marvin.MolPrinter

public class MolPrinter
extends java.lang.Object

Molecule printer. This class can be used to print a molecule to a Graphics context.

Example:

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 r = new Rectangle(20, 20, 360, 200);
        g.draw(r);
        // Paint the molecule
        MolPrinter p = new MolPrinter(mol);
        p.setScale(p.maxScale(r)); // fit image in the rectangle
        p.paint(g, r);
        return im;
    }
    public static void main(String[] args) throws Exception {
        BufferedImage im = createTestImage();
        ImageIO.write(im, "png", new File("test.png"));
    }
}

Version:

5.0, 08/22/2007

Author:

Peter Csizmadia, Tamas Vertse

Constructor Summary

MolPrinter()
Constructs a printer for an empty molecule.

MolPrinter(MDocument d)
Constructs a printer for the specified document.

MolPrinter(MoleculeGraph m)
Constructs a printer for the specified molecule.

Method Summary

double	getAtomsize() Get atom size in units of regular bond length.
double	getBondSpacing() Gets the double bond spacing.
double	getBondWidth() Deprecated. as of Marvin 4.1, replaced by getBondSpacing()
int	getChiralitySupport() Gets chirality support level.
java.lang.String	getColorScheme() Gets the color scheme.
int	getDispopts() Gets the display options.
boolean	getExplicitH() Are explicit hydrogens shown?
java.lang.String	getImplicitH() Query the display method of implicit hydrogens.
double	getMag() Deprecated. as of Marvin 2.9.11, replaced by getScale().
java.lang.String	getRendering() Gets the rendering style.
double	getScale() Gets the scaling factor.
boolean	isAtomSymbolsVisible() Gets the Atom Symbols display option.
boolean	isEzVisible() Gets the E/Z display option.
boolean	isSetColoringEnabled() Is the atom/bond set coloring enabled?
double	maxMag(java.awt.Dimension d) Deprecated. as of Marvin 2.9.11, replaced by maxScale(Dimension).
double	maxScale(java.awt.Dimension d) Calculates the maximum scaling factor for fitting the image in the specified rectangle.
double	maxScale(java.awt.Rectangle r) Calculates the maximum scaling factor for fitting the image in the specified rectangle.
void	paint(java.awt.Graphics g, java.awt.Rectangle r) Paint molecule into the center of the specified rectangle.
void	setAtomsize(double l) Set atom size in units of regular bond length.
void	setAtomSymbolsVisible(boolean v) Sets the Atom Symbols display option.
void	setBackgroundColor(java.awt.Color color) Sets the background color.
void	setBondSpacing(double w) Sets the double bond spacing.
void	setBondWidth(double w) Deprecated. as of Marvin 4.1, replaced by setBondSpacing(double)
void	setChiralitySupport(int l) Sets chirality support.
void	setColorScheme(java.lang.String s) Sets the color scheme.
void	setDispopts(int f) Sets the display options.
void	setDispopts(int f, int mask) Sets the display options.
void	setDoc(MDocument d) Sets the current document and calculates its bounds.
void	setExplicitH(boolean show) Sets the display method of explicit hydrogens.
void	setEzVisible(boolean v) Sets the E/Z display option.
void	setImplicitH(java.lang.String s) Sets the display method of implicit hydrogens.
void	setMag(double m) Deprecated. as of Marvin 2.9.11, replaced by setScale(double).
void	setMol(Molecule m) Sets the current molecule and calculate its bounds.
void	setMol(java.lang.String s) Sets the current molecule and calculate its bounds.
void	setRendering(java.lang.String s) Sets the rendering style.
void	setScale(double m) Sets the scaling factor.
void	setSetColoringEnabled(boolean v) Enable or disable atom/bond set coloring.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MolPrinter

public MolPrinter()

Constructs a printer for an empty molecule.

MolPrinter

public MolPrinter(MoleculeGraph m)

Constructs a printer for the specified molecule.

Parameters:

m - a molecule graph

Since:

Marvin 4.1.8, 04/20/2007

MolPrinter

public MolPrinter(MDocument d)

Constructs a printer for the specified document.

Parameters:

d - the document

Since:

Marvin 4.1.8, 04/20/2007

Method Detail

getDispopts

public int getDispopts()

Gets the display options.

Returns:

display options

Since:

Marvin 2.6

See Also:

DispOptConsts

setDispopts

public void setDispopts(int f)

Sets the display options.

Parameters:

f - display options

Since:

Marvin 2.6

See Also:

DispOptConsts

setDispopts

public void setDispopts(int f,
                        int mask)

Sets the display options.

Parameters:

f - display options

mask - set bits specified here

Since:

Marvin 4.1.9, 06/05/2007

See Also:

DispOptConsts

getScale

public double getScale()

Gets the scaling factor.

Since:

Marvin 2.9.11

setScale

public void setScale(double m)

Sets the scaling factor.

Since:

Marvin 2.9.11

maxScale

public double maxScale(java.awt.Rectangle r)

Calculates the maximum scaling factor for fitting the image in the specified rectangle.

Parameters:

r - the rectangle

Since:

Marvin 4.1.8, 04/20/2007

maxScale

public double maxScale(java.awt.Dimension d)

Calculates the maximum scaling factor for fitting the image in the specified rectangle.

Parameters:

d - the size of the rectangle

getAtomsize

public double getAtomsize()

Get atom size in units of regular bond length.

setAtomsize

public void setAtomsize(double l)

Set atom size in units of regular bond length.

getBondSpacing

public double getBondSpacing()

Gets the double bond spacing.

Returns:

the bond width in C-C bond length units.

Since:

Marvin 4.1, 10/19/2005

setBondSpacing

public void setBondSpacing(double w)

Sets the double bond spacing.

width = w*1.54 Å = w*scale pixels

Parameters:

w - the bond width in C-C bond length units.

Since:

Marvin 4.1, 10/19/2005

getImplicitH

public java.lang.String getImplicitH()

Query the display method of implicit hydrogens.

Returns:

IMPLICITH_OFF_S, IMPLICITH_HETERO_S, IMPLICITH_HETEROTERM_S or IMPLICITH_ALL_S.

Since:

Marvin 2.9.11

See Also:

DispOptConsts.IMPLICITH_LEVELS

setImplicitH

public void setImplicitH(java.lang.String s)

Sets the display method of implicit hydrogens.

Parameters:

s - IMPLICITH_OFF_S, IMPLICITH_HETERO_S, IMPLICITH_HETEROTERM_S or IMPLICITH_ALL_S.

Since:

Marvin 2.9.11

See Also:

DispOptConsts.IMPLICITH_LEVELS

getColorScheme

public java.lang.String getColorScheme()

Gets the color scheme.

Returns:

MONO_SCHEME_S, CPK_SCHEME_S, SHAPELY_SCHEME_S or GROUP_SCHEME_S.

Since:

Marvin 2.9.11

See Also:

DispOptConsts.COLOR_SCHEMES

setColorScheme

public void setColorScheme(java.lang.String s)

Sets the color scheme.

Parameters:

s - MONO_SCHEME_S, CPK_SCHEME_S, SHAPELY_SCHEME_S or GROUP_SCHEME_S.

Since:

Marvin 2.9.11

See Also:

DispOptConsts.COLOR_SCHEMES

isSetColoringEnabled

public boolean isSetColoringEnabled()

Is the atom/bond set coloring enabled?

Returns:

true if enabled, false if disabled

Since:

Marvin 3.3

setSetColoringEnabled

public void setSetColoringEnabled(boolean v)

Enable or disable atom/bond set coloring.

Parameters:

v - true to enable, false to disable

Since:

Marvin 3.3

getRendering

public java.lang.String getRendering()

Gets the rendering style.

Returns:

WIREFRAME_RENDERING_S, WIREKNOBS_RENDERING_S, STICKS_RENDERING_S, BALLSTICK_RENDERING_S or SPACEFILL_RENDERING_S.

Since:

Marvin 2.9.11

See Also:

DispOptConsts.RENDERING_STYLES

setRendering

public void setRendering(java.lang.String s)

Sets the rendering style.

Parameters:

s - WIREFRAME_RENDERING_S, WIREKNOBS_RENDERING_S, STICKS_RENDERING_S, BALLSTICK_RENDERING_S or SPACEFILL_RENDERING_S.

Since:

Marvin 2.9.11

See Also:

DispOptConsts.RENDERING_STYLES

setBackgroundColor

public void setBackgroundColor(java.awt.Color color)

Sets the background color.

Parameters:

color - the bakcground color

Since:

Marvin 4.1.13

isAtomSymbolsVisible

public boolean isAtomSymbolsVisible()

Gets the Atom Symbols display option.

Returns:

show (true) or hide (false)

Since:

Marvin 3.3.3

setAtomSymbolsVisible

public void setAtomSymbolsVisible(boolean v)

Sets the Atom Symbols display option.

Parameters:

v - show (true) or hide (false) Atom Symbols

Since:

Marvin 3.3.3

getExplicitH

public boolean getExplicitH()

Are explicit hydrogens shown?

Returns:

show (true) or hide (false)

Since:

Marvin 3.3.3

setExplicitH

public void setExplicitH(boolean show)

Sets the display method of explicit hydrogens.

Parameters:

show - (true) or hide (false) explicit hydrogens

Since:

Marvin 3.3.3

getChiralitySupport

public int getChiralitySupport()

Gets chirality support level.

Returns:

the chirality support level

Since:

Marvin 3.3.3

See Also:

StereoConstants.CHIRALITYSUPPORT_NONE, StereoConstants.CHIRALITYSUPPORT_SELECTED, StereoConstants.CHIRALITYSUPPORT_ALL

setChiralitySupport

public void setChiralitySupport(int l)

Sets chirality support. No molecules, selected (if ABSC flag set) or all molecules.

Parameters:

l - chirality support level

Since:

Marvin 3.3.3

See Also:

StereoConstants.CHIRALITYSUPPORT_NONE, StereoConstants.CHIRALITYSUPPORT_SELECTED, StereoConstants.CHIRALITYSUPPORT_ALL

isEzVisible

public boolean isEzVisible()

Gets the E/Z display option.

Returns:

show (true) or hide (false)

Since:

Marvin 3.3.3

setEzVisible

public void setEzVisible(boolean v)

Sets the E/Z display option.

Parameters:

v - show (true) or hide (false) E/Z

Since:

Marvin 3.3.3

setMol

public void setMol(Molecule m)

Sets the current molecule and calculate its bounds.

Parameters:

m - the molecule

setMol

public void setMol(java.lang.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(java.awt.Graphics g,
                  java.awt.Rectangle r)

Paint molecule into the center of the specified rectangle.

Parameters:

g - the graphics context

r - the rectangle

getMag

public double getMag()

Deprecated. as of Marvin 2.9.11, replaced by getScale().

setMag

public void setMag(double m)

Deprecated. as of Marvin 2.9.11, replaced by setScale(double).

maxMag

public double maxMag(java.awt.Dimension d)

Deprecated. as of Marvin 2.9.11, replaced by maxScale(Dimension).

getBondWidth

public double getBondWidth()

Deprecated. as of Marvin 4.1, replaced by getBondSpacing()

Gets bond spacing.

Returns:

the bond spacing in bond length units

setBondWidth

public void setBondWidth(double w)

Deprecated. as of Marvin 4.1, replaced by setBondSpacing(double)

Sets bond spacing.

Parameters:

w - bond spacing in bond length units