gistfile1.java

import java.awt.Graphics2D;
import java.awt.Rectangle;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.Reader;
import java.util.ArrayList;
import java.util.List;

import javax.swing.ImageIcon;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.SwingUtilities;

import org.openscience.cdk.Molecule;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.jchempaint.renderer.AtomContainerRenderer;
import org.openscience.jchempaint.renderer.font.AWTFontManager;
import org.openscience.jchempaint.renderer.generators.BasicBondGenerator;
import org.openscience.jchempaint.renderer.generators.ExtendedAtomGenerator;
import org.openscience.jchempaint.renderer.generators.IGenerator;
import org.openscience.jchempaint.renderer.visitor.AWTDrawVisitor;


public class JCPtest {
    public static void main(String[] args) {
        Runnable runnable = new AppMainRun();
        SwingUtilities.invokeLater(runnable);
    }
}

class AppMainRun implements Runnable {
    public void run() {
        // sdfファイルから分子を読み込む
        Reader reader = null;
        try {
            reader = new FileReader(new File("./temp/test/zinc_3929508.sdf"));
        } catch (FileNotFoundException e) {
            e.printStackTrace();
        }
        MDLV2000Reader mdl = new MDLV2000Reader(reader);
        IMolecule molecule = null;
        try {
            molecule = (IMolecule)mdl.read(new Molecule());
        } catch (CDKException e) {
            e.printStackTrace();
        }
        // 3D座標系の場合は2Dに変換
        StructureDiagramGenerator sdg = new StructureDiagramGenerator();
        sdg.setMolecule(molecule);
        try {
            sdg.generateCoordinates();
        } catch (CDKException e) {
            e.printStackTrace();
        }
        molecule = sdg.getMolecule();
        // 水素原子の削除
        molecule = (IMolecule) AtomContainerManipulator.removeHydrogens((IAtomContainer) molecule);
        // 末端、ヘテロ原子上の水素のみ表示
        CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
        for (IAtom atom : molecule.atoms()) {
            try {
                IAtomType type = matcher.findMatchingAtomType(molecule, atom);
                atom.setImplicitHydrogenCount(
                        type.getFormalNeighbourCount() - molecule.getConnectedAtomsCount(atom));
            } catch (CDKException e) {
                e.printStackTrace();
            }
        }
        // 描画キャンパスの設定
        Rectangle drawArea = new Rectangle(20, 20, 360, 360);
        BufferedImage img = new BufferedImage(400, 400, BufferedImage.TYPE_INT_RGB);
        Graphics2D g2 = img.createGraphics();
        g2.fillRect(0, 0, 400, 400);
        // ジェネレーターの設定
        List<IGenerator> generators = new ArrayList<IGenerator>();
        generators.add(new BasicBondGenerator());
        generators.add(new ExtendedAtomGenerator());
        // レンダリング
        AtomContainerRenderer renderer = new AtomContainerRenderer(generators, new AWTFontManager(), true);
        renderer.paintMolecule(molecule, new AWTDrawVisitor(g2), drawArea, true);
        // パネルに構造式を表示
        JFrame frame = new JFrame();
        frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        frame.setBounds(0, 0, 400, 400);
        frame.setTitle("Oseltamivir");
        JPanel panel = new JPanel();
        JLabel label = new JLabel();
        ImageIcon icon = new ImageIcon();
        icon.setImage(img);
        label.setIcon(icon);
        panel.add(label);
        frame.add(panel);
        frame.setVisible(true);
    }
}