Source code:
@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.9')
import java.util.List;
import java.awt.*;
import java.awt.image.*;
import javax.imageio.*;
import org.openscience.cdk.*;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.layout.*;
import org.openscience.cdk.renderer.*;
import org.openscience.cdk.renderer.font.*;
import org.openscience.cdk.renderer.generators.*;
import org.openscience.cdk.renderer.visitor.*;
import org.openscience.cdk.smiles.*;
import org.openscience.cdk.silent.*;
import org.openscience.cdk.renderer.generators.BasicSceneGenerator.Margin;
import org.openscience.cdk.renderer.generators.BasicSceneGenerator.ZoomFactor;
int WIDTH = 600;
int HEIGHT = 600;
// 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
);
smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance())
pyrrole = smilesParser.parseSmiles(
"c2ccc3n([H])c1ccccc1c3(c2)"
)
fbot = new FixBondOrdersTool()
pyrrole = fbot.kekuliseAromaticRings(pyrrole)
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(pyrrole);
sdg.generateCoordinates();
pyrrole = sdg.getMolecule();
// generators make the image elements
List<IGenerator> generators = new ArrayList<IGenerator>();
generators.add(new BasicSceneGenerator());
generators.add(new BasicBondGenerator());
generators.add(new BasicAtomGenerator());
// the renderer needs to have a toolkit-specific font manager
AtomContainerRenderer renderer =
new AtomContainerRenderer(generators, new AWTFontManager());
// the call to 'setup' only needs to be done on the first paint
renderer.setup(pyrrole, drawArea);
model = renderer.getRenderer2DModel();
model.set(Margin.class, (double)0.1);
model.set(ZoomFactor.class, (double)3.0);
// 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
renderer.paint(pyrrole, new AWTDrawVisitor(g2));
ImageIO.write(
(RenderedImage)image, "PNG",
new File("FixPyrroleBondOrders.png")
);
Output: