/*
* Creates a structure image based on a MOL string. The image rendering is
* done with CDK.
*/
public final Image getImage4MOL(IAtomContainer molAC) throws Exception {
// creates CDK Molecule object and get the renderer
// Molecule mol = prepareMolecule(molfile);
IMolecule molSource = new Molecule(molAC);
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(molSource);
sdg.generateCoordinates();
IMolecule mol = sdg.getMolecule();
Java2DRenderer 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, new Rectangle(0, 0, vRenderSizeX, vRenderSizeY));
} catch (Exception e) {
e.printStackTrace();
throw new Exception("Rendering of structure(s) failed");
}
return bimage;
}
/*
* Creates a structure PDF based on a MOL string
*/
public final void writeMOL2PDFFile(IMolecule molSource, File epsFile) throws Exception {
// creates CDK Molecule object and get the renderer
// Molecule mol = prepareMolecule(MOLString);
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(molSource);
sdg.generateCoordinates();
IMolecule mol = sdg.getMolecule();
Java2DRenderer 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, new Rectangle(vRenderSizeX, vRenderSizeY));
vg.endExport();
} catch (Exception e) {
e.printStackTrace();
throw new Exception("PDF rendering of structure(s) failed");
}
}
/*
* Creates a structure gif on a MOL string
*/
public final void writeMOL2GIFFile(IAtomContainer mol, String pngFile) throws Exception {
BufferedImage bimage = null;
try {
bimage = (BufferedImage) getImage4MOL(mol);
ImageIO.write(bimage, "gif", new File(this.folder + pngFile));
} catch (Exception e) {
e.printStackTrace();
// throw new Exception("EPS rendering of structure(s) failed");
}
}
private Java2DRenderer prepareRenderer(IMolecule mol) throws Exception {
Renderer2DModel r2dm;
Java2DRenderer renderer;
Dimension imgSize;
try {
CDKHueckelAromaticityDetector.detectAromaticity(mol);
} catch (CDKException cdke) {
cdke.printStackTrace();
}
try {
imgSize = new Dimension(vRenderSizeX, vRenderSizeY);
r2dm = new Renderer2DModel();
r2dm.setDrawNumbers(false);
r2dm.showAtomTypeNames();
r2dm.setBackgroundDimension(imgSize);
r2dm.setBackColor(Color.WHITE);
r2dm.setDrawNumbers(false);
r2dm.setUseAntiAliasing(true);
r2dm.setColorAtomsByType(true);
r2dm.setShowImplicitHydrogens(true);
r2dm.setShowExplicitHydrogens(this.showHydrogen);
r2dm.setIsCompact(this.isCompact);
r2dm.setShowReactionBoxes(false);
r2dm.setKekuleStructure(false);
r2dm.setBondWidth(3);
// r2dm.setFont(new java.awt.Font("SansSerif", java.awt.Font.PLAIN, 14));
renderer = new Java2DRenderer(r2dm);
// 1200,900
// create renderer to render MOLString into an java.awt.Image
// renders 2D structures
} catch (Exception e) {
e.printStackTrace();
throw new Exception("Creation of renderer failed");
}
return renderer;
}
public static 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);
// the graph
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
PubChemWebService pw = new PubChemWebService();
String PCID = "1148";
IAtomContainer container = pw.getSingleMol(PCID);
container = AtomContainerManipulator.removeHydrogens(container);
// IAtomContainer container = sp.parseSmiles("OC1C(O)=COC(CO)C1(O)");
// Render.Draw(container, "test");
IMolecule test = new Molecule(container);
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(test);
sdg.generateCoordinates();
IMolecule mol = sdg.getMolecule();
// adds implicit H atoms to molecule
// CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(mol.getBuilder());
// for (IAtom atom : mol.atoms()) {
// IAtomType type = matcher.findMatchingAtomType(mol, atom);
// AtomTypeManipulator.configure(atom, type);
// }
//
// CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(mol.getBuilder());
// adder.addImplicitHydrogens(mol);
// AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
// detects aromaticity; used to display aromatic ring systems correctly
CDKHueckelAromaticityDetector.detectAromaticity(mol);
Render.Draw(mol, "test");
DisplayStructureVector test12 =
new DisplayStructureVector(200, 200, "/home/swolf/", true, true);
// test12.writeMOL2PNGFile(mol, "test_cdk12.png");
// test12.writeMOL2PDFFile(mol, new File("/home/swolf/test_cdk12.pdf"));
test12.writeMOL2SVGFile(mol, new File("/home/swolf/" + PCID + ".svg"));
// ChemRenderer crender = new ChemRenderer();
// crender.writeMOL2PNGFile(mol, new File("/home/swolf/test_new.png"));
// crender.writeMOL2EPSFile(mol, new File("/home/swolf/test_new.eps"));
// crender.writeMOL2PDFFile(mol, new File("/home/swolf/test_new.pdf"));
// crender.writeMOL2SVGFile(molfile,new File("Output.svg"));
} catch (Exception e) {
System.out.println("Error: " + e.getMessage() + ".");
e.printStackTrace();
}
}
