gistfile1.java

import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Rectangle;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.List;

import javax.swing.JFrame;
import javax.swing.JPanel;

import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.renderer.Renderer;
import org.openscience.cdk.renderer.RenderingParameters;
import org.openscience.cdk.renderer.font.AWTFontManager;
import org.openscience.cdk.renderer.generators.AtomContainerBoundsGenerator;
import org.openscience.cdk.renderer.generators.BasicAtomGenerator;
import org.openscience.cdk.renderer.generators.BasicBondGenerator;
import org.openscience.cdk.renderer.generators.IGenerator;
import org.openscience.cdk.renderer.visitor.AWTDrawVisitor;

/**
 * @author maclean
 *
 */
public class SDFPanel extends JPanel {

	private ArrayList<IMolecule> molecules;
	private ArrayList<Renderer> renderers;
	private ArrayList<Rectangle> bounds;
	private int rows;
	private int cols;
	private int boxWidth = 80;
	private int boxHeight = 80;
	private int boxGap = 10;

	private StructureDiagramGenerator sdg = new StructureDiagramGenerator();

	public SDFPanel() {
		this.molecules = new ArrayList<IMolecule>();
		this.renderers = new ArrayList<Renderer>();
		this.bounds = new ArrayList<Rectangle>();
		this.cols = 0;
		this.rows = 0;
		this.setBackground(Color.WHITE);
	}

	public void add(IMolecule molecule) {
		sdg.setMolecule(molecule);
		try {
			sdg.generateCoordinates();
		} catch (Exception e) {
			e.printStackTrace();
		}
		this.molecules.add(sdg.getMolecule());
		this.renderers.add(new Renderer(getGenerators(), new AWTFontManager()));
	}

	public void layoutBoxes() {
		int s = this.molecules.size();

		int width = this.getWidth();
		this.cols = (int) ((float)width / (float)(boxWidth + (boxGap * 2)));

		this.rows = s / this.cols;
		int height = boxGap + (this.rows * (boxHeight + boxGap));

		int x = boxGap;
		int y = boxGap;
		for (int row = 0; row < this.rows; row++) {
			for (int col = 0; col < this.cols; col++) {
				this.bounds.add(new Rectangle(x, y, boxWidth, boxHeight));
				x += boxWidth + boxGap;
			}
			y += boxHeight + boxGap;
			x = boxGap;
		}
		this.setPreferredSize(new Dimension(width, height));
	}

	public List<IGenerator> getGenerators() {
		List<IGenerator> generators = new ArrayList<IGenerator>();
		generators.add(new AtomContainerBoundsGenerator());
		generators.add(new BasicBondGenerator());
		generators.add(new BasicAtomGenerator());
		return generators;
	}

	public void setModelParameters() {
		for (Renderer renderer : this.renderers) {
			renderer.getRenderer2DModel().setIsCompact(true);
			renderer.getRenderer2DModel().setCompactShape(RenderingParameters.AtomShape.OVAL);
			renderer.getRenderer2DModel().setAtomRadius(5);
			renderer.getRenderer2DModel().setBondWidth(2);
			renderer.getRenderer2DModel().setBondDistance(2);
			renderer.getRenderer2DModel().setFitToScreen(true);
		}
	}

	public void paint(Graphics g) {
		super.paint(g);
		Graphics2D g2 = (Graphics2D) g;
		AWTDrawVisitor drawVisitor = new AWTDrawVisitor(g2);
		for (int i = 0; i < molecules.size(); i++) {
			if (i >= this.bounds.size()) return;
			IMolecule molecule = this.molecules.get(i);
			Renderer renderer = this.renderers.get(i);
			Rectangle bound = this.bounds.get(i);
			renderer.paintMolecule(molecule, drawVisitor, bound, true);
		}
	}

	public static void main(String[] args) {
		JFrame f = new JFrame();
		SDFPanel panel = new SDFPanel();
		try {
			IteratingMDLReader reader =
				new IteratingMDLReader(new FileInputStream(args[0]),
						NoNotificationChemObjectBuilder.getInstance());
			while (reader.hasNext()) {
				IMolecule molecule = (IMolecule) reader.next();
				panel.add(molecule);
			}

		} catch (FileNotFoundException e) {
			e.printStackTrace();
		}
		panel.setModelParameters();

		f.add(panel);
		panel.setPreferredSize(new Dimension(1100, 900));
		f.pack();
		panel.layoutBoxes();
		f.setVisible(true);
	}
}