Hi,
I am working in an analytical chemistry environment and recently found a
way to render structures in various vector formats. On the outset we
wanted to deliver EPS files to the software of our NMR spectrometers for
inclusion on spectra printout. I found the FreeHEP java library
containing a vector graphics package
(http://java.freehep.org/vectorgraphics/index.html) which nicely filled
the gap.
After a recent question about SVG rendering I thought I send an example to
the list. Perhaps it is useful for others as well. It reads a MOL file and
can output EPS, PDF, SVG and PNG files.
Regards,
Ekkehard
-- vectorRender.java --
import java.io.File;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.StringReader;
import javax.imageio.ImageIO;
import java.awt.Image;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics2D;
import java.awt.image.BufferedImage;
import java.util.Properties;
import org.freehep.graphics2d.VectorGraphics;
import org.freehep.graphicsio.ps.PSGraphics2D;
import org.freehep.graphicsio.pdf.PDFGraphics2D;
import org.freehep.graphicsio.svg.SVGGraphics2D;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.renderer.Renderer2D;
import org.openscience.cdk.renderer.Renderer2DModel;
import org.openscience.cdk.tools.HydrogenAdder;
/*
* @author Ekkehard Goerlach
*/
public class vectorRender {
public static class ChemRenderer {
private int vRenderSizeX = 600;
private int vRenderSizeY = 400;
private int vFontSize = 26;
/*
* Creates a structure image based on a MOL string. The image
rendering is
* done with CDK.
*/
public final java.awt.Image getImage4MOL(String molfile) throws
Exception {
// creates CDK Molecule object and get the renderer
Molecule mol = prepareMolecule(molfile);
Renderer2D renderer = prepareRenderer(mol);
BufferedImage bimage = null;
try {
// paint molecule to java.awt.BufferedImage
bimage = new BufferedImage(vRenderSizeX, vRenderSizeY,
BufferedImage.TYPE_BYTE_INDEXED);
Graphics2D g = bimage.createGraphics();
g.setBackground(Color.WHITE);
g.setColor(Color.WHITE);
g.fillRect(0, 0, vRenderSizeX, vRenderSizeY);
renderer.paintMolecule(mol, g, false, true);
} catch (Exception e) {
e.printStackTrace();
throw new Exception("Rendering of structure(s) failed");
}
return bimage;
}
/*
* Creates a structure EPS based on a MOL string
*/
public final void writeMOL2PNGFile(String MOLString, File pngFile)
throws Exception {
BufferedImage bimage = null;
try {
bimage = (BufferedImage) getImage4MOL(MOLString);
ImageIO.write(bimage, "png", pngFile);
} catch (Exception e) {
e.printStackTrace();
throw new Exception("EPS rendering of structure(s)
failed");
}
}
/*
* Creates a structure EPS based on a MOL string
*/
public final void writeMOL2EPSFile(String MOLString, File epsFile)
throws Exception {
// creates CDK Molecule object and get the renderer
Molecule mol = prepareMolecule(MOLString);
Renderer2D renderer = prepareRenderer(mol);
try {
// paint molecule to java.awt.BufferedImage
VectorGraphics vg = new PSGraphics2D(epsFile, new
Dimension(vRenderSizeX, vRenderSizeY));
Properties p = new Properties();
p.setProperty("PageSize","A5");
vg.setProperties(p);
vg.startExport();
renderer.paintMolecule(mol, vg, false, true);
vg.endExport();
} catch (Exception e) {
e.printStackTrace();
throw new Exception("EPS rendering of structure(s)
failed");
}
}
/*
* Creates a structure PDF based on a MOL string
*/
public final void writeMOL2PDFFile(String MOLString, File epsFile)
throws Exception {
// creates CDK Molecule object and get the renderer
Molecule mol = prepareMolecule(MOLString);
Renderer2D renderer = prepareRenderer(mol);
try {
// paint molecule to java.awt.BufferedImage
VectorGraphics vg = new PDFGraphics2D(epsFile, new
Dimension(vRenderSizeX, vRenderSizeY));
Properties p = new Properties();
p.setProperty("PageSize","A5");
vg.setProperties(p);
vg.startExport();
renderer.paintMolecule(mol, vg, false, true);
vg.endExport();
} catch (Exception e) {
e.printStackTrace();
throw new Exception("PDF rendering of structure(s)
failed");
}
}
/*
* Creates a structure SVG based on a MOL string
*/
public final void writeMOL2SVGFile(String MOLString, File epsFile)
throws Exception {
// creates CDK Molecule object and get the renderer
Molecule mol = prepareMolecule(MOLString);
Renderer2D renderer = prepareRenderer(mol);
try {
// paint molecule to java.awt.BufferedImage
VectorGraphics vg = new SVGGraphics2D(epsFile, new
Dimension(vRenderSizeX, vRenderSizeY));
Properties p = new Properties();
p.setProperty("PageSize","A5");
vg.setProperties(p);
vg.startExport();
renderer.paintMolecule(mol, vg, false, true);
vg.endExport();
} catch (Exception e) {
e.printStackTrace();
throw new Exception("SVG rendering of structure(s)
failed");
}
}
private org.openscience.cdk.renderer.Renderer2D
prepareRenderer(Molecule mol)
throws Exception {
Renderer2DModel r2dm;
Renderer2D renderer;
Dimension imgSize;
try {
r2dm = new Renderer2DModel();
renderer = new Renderer2D(r2dm);
imgSize = new Dimension(vRenderSizeX, vRenderSizeY); //
1200,900
// create renderer to render MOLString into an
java.awt.Image
// renders 2D structures
r2dm.setBackgroundDimension(imgSize);
r2dm.setBackColor(Color.WHITE);
r2dm.setDrawNumbers(false);
r2dm.setUseAntiAliasing(true);
r2dm.setColorAtomsByType(false);
r2dm.setShowImplicitHydrogens(true);
r2dm.setShowReactionBoxes(false);
r2dm.setKekuleStructure(false);
r2dm.setShowAromaticityInCDKStyle(true);
r2dm.setBondWidth(3);
r2dm.setFont(new java.awt.Font("SansSerif",
java.awt.Font.PLAIN, vFontSize));
// scale and center molecule on image
GeometryTools.translateAllPositive(mol,
r2dm.getRenderingCoordinates());
GeometryTools.scaleMolecule(mol, imgSize, 1.0, r2dm
.getRenderingCoordinates());
GeometryTools.center(mol, imgSize,
r2dm.getRenderingCoordinates());
} catch (Exception e) {
e.printStackTrace();
throw new Exception("Creation of renderer failed");
}
return renderer;
}
private org.openscience.cdk.Molecule prepareMolecule(String
MOLString) throws Exception
{
// creates CDK Molecule object
Molecule mol = null;
try {
// reads MOL file
MDLReader mdlr = new MDLReader(new
StringReader(MOLString));
mol = (Molecule) mdlr.read(new Molecule());
// adds implicit H atoms to molecule
HydrogenAdder ha = new HydrogenAdder();
ha.addImplicitHydrogensToSatisfyValency(mol);
// detects aromaticity; used to display aromatic ring
systems correctly
HueckelAromaticityDetector.detectAromaticity(mol);
} catch (Exception e) {
e.printStackTrace();
throw new Exception("Rendering of structure(s) failed");
}
return mol;
}
}
public static final void main(final String[] args) {
String mf;
String molfile;
try {
BufferedReader reader = new BufferedReader(new
FileReader("renderTest.mol"));
StringBuffer sbuff = new StringBuffer();
String line;
while ( (line = reader.readLine()) != null ) {
sbuff.append(line + "\n");
}
reader.close();
molfile = sbuff.toString();
System.out.println(molfile);
ChemRenderer crender = new ChemRenderer();
crender.writeMOL2SVGFile(molfile,new File("Output.svg"));
} catch (Exception e) {
System.out.println("Error: " + e.getMessage() + ".");
e.printStackTrace();
}
}
}
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