import org.openscience.cdk.io.MDLV2000Reader; //导入依赖的package包/类
/**
 * Retrieves the IAtomContainer for a moldata string.
 * 
 * @param mol the moldata as String
 * 
 * @return the container as IAtomContainer object, null if Exception occurs
 */
public IAtomContainer getContainer(String mol) {
	if(mol.isEmpty() || mol.equals("0\n")) {
		return null;
	}
	InputStream is = new ByteArrayInputStream(mol.getBytes());
	MDLV2000Reader reader = new MDLV2000Reader(is);
	IChemFile chemFile = new ChemFile();
	IAtomContainer container = null;
	try {			
		chemFile = (IChemFile) reader.read(chemFile);
		container = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
		// hydrogen handling
		container = hydrogenHandling(container);
	} catch (CDKException e) {
		System.err.println("CDKException occured!");
		return null;
	}
	
	return container;
}
 

import org.openscience.cdk.io.MDLV2000Reader; //导入依赖的package包/类
public Structure2DComponent(String structure) throws CDKException,
    IOException {

// Create a silend CDK builder
IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();

// Create a new molecule instance
molecule = builder.newInstance(IAtomContainer.class);

// Load the structure into the molecule
MDLV2000Reader molReader = new MDLV2000Reader(new StringReader(
	structure));
molReader.read(molecule);
molReader.close();

// Suppress the hydrogens
AtomContainerManipulator.suppressHydrogens(molecule);

// If the model has no coordinates, let's generate them
if (!GeometryUtil.has2DCoordinates(molecule)) {
    StructureDiagramGenerator sdg = new StructureDiagramGenerator();
    sdg.setMolecule(molecule, false);
    sdg.generateCoordinates();
}

// Generators make the image elements
Font font = new Font("Verdana", Font.PLAIN, 14);
List<IGenerator<IAtomContainer>> generators = new ArrayList<IGenerator<IAtomContainer>>();
generators.add(new BasicSceneGenerator());
generators.add(new StandardGenerator(font));

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

// Set default atom colors for the renderer
RendererModel rendererModel = renderer.getRenderer2DModel();
rendererModel.set(StandardGenerator.AtomColor.class,
	new CDK2DAtomColors());

   }
 

import org.openscience.cdk.io.MDLV2000Reader; //导入依赖的package包/类
private IAtomContainer loadMol(String str) throws CDKException
{
  if (str.contains("V2000")) {
    try (MDLV2000Reader mdlr = new MDLV2000Reader(new StringReader(str))) {
      return mdlr.read(new AtomContainer(0, 0, 0, 0));
    } catch (CDKException | IOException e3) {
      throw new CDKException("Could not parse input");
    }
  } else {
    return smipar.parseSmiles(str);
  }
}