MoleculeImageCreator

MoleculeImageCreator.java

package cdk.imagecreator;

import java.awt.Color;
import java.awt.Graphics2D;
import java.awt.Image;
import java.awt.Rectangle;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.util.ArrayList;
import java.util.List;

import org.openscience.cdk.Molecule;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.renderer.AtomContainerRenderer;
import org.openscience.cdk.renderer.font.AWTFontManager;
import org.openscience.cdk.renderer.generators.BasicAtomGenerator;
import org.openscience.cdk.renderer.generators.BasicBondGenerator;
import org.openscience.cdk.renderer.generators.BasicSceneGenerator;
import org.openscience.cdk.renderer.generators.IGenerator;
import org.openscience.cdk.renderer.visitor.AWTDrawVisitor;

public class MoleculeImageCreator {


	public static Image createImage(IAtomContainer ac, List<Integer> atomsToHighlight, int width, int height){

		if (ac==null)
			return null;

		// the draw area and the image should be the same size
		Rectangle drawArea = new Rectangle(width, height);
		Image image = new BufferedImage(
				width, height, BufferedImage.TYPE_INT_RGB);

		//Generate 2D
		IMolecule mol = new Molecule(ac);
		StructureDiagramGenerator sdg = new StructureDiagramGenerator();
		sdg.setMolecule(mol, true);
		try {
			sdg.generateCoordinates();
		} catch (Exception e) { }
		mol = sdg.getMolecule();

		// generators make the image elements
		List<IGenerator<IAtomContainer>> generators = new ArrayList<IGenerator<IAtomContainer>>();

		//Add the standard generators
		generators.add(new BasicSceneGenerator());

		generators.add(new BasicBondGenerator());
		BasicAtomGenerator agen = new BasicAtomGenerator();
		generators.add(agen);

		// the renderer needs to have a toolkit-specific font manager 
		AtomContainerRenderer renderer = new AtomContainerRenderer(generators, new AWTFontManager());

		renderer.setup(mol, drawArea);

		// paint the background
		Graphics2D g2 = (Graphics2D)image.getGraphics();
		g2.setColor(Color.WHITE);
		g2.fillRect(0, 0, width, height);

		// the paint method also needs a toolkit-specific renderer
		java.awt.geom.Rectangle2D.Double bounds = new Rectangle2D.Double(0, 0, width, height);
		renderer.paint(mol, new AWTDrawVisitor(g2), bounds, true);
		//renderer.paint(mol, new AWTDrawVisitor(g2));

		return image;

	}

}