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Reader reader = new BufferedReader(new FileReader(new File("ChEBI_lite.sdf")),
                                   2048);
        
// instantiate the iterating reader with skip=true in the constructor
IteratingMDLReader sdf = new IteratingMDLReader(reader,
                                                SilentChemObjectBuilder.getInstance(),
                                                Boolean.TRUE);
        
while (sdf.hasNext()){
    IAtomContainer container = sdf.next();

johnmay

package demo;

import org.openscience.cdk.interfaces.IAtomContainer;
import uk.ac.ebi.mdk.domain.identifier.HMDBIdentifier;
import uk.ac.ebi.mdk.service.DefaultServiceManager;
import uk.ac.ebi.mdk.service.ServiceManager;
import uk.ac.ebi.mdk.service.query.data.MolecularFormulaService;
import uk.ac.ebi.mdk.service.query.name.IUPACNameService;
import uk.ac.ebi.mdk.service.query.name.PreferredNameService;
import uk.ac.ebi.mdk.service.query.name.SynonymService;

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IAtomContainer container = ...

Iterator<IAtom> it = container.atoms();
while(it.hasNext()){
   IAtom atom = it.next();
   if("H".equals(atom.getSymbol())){
       it.remove(); // invokes container.removeBond(IBond);
   }
}

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public List<IAtom> getAtoms() {
    return Collections.unmodifiableList(atoms);
}

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public interface AromaticityDetector {
    public void detect(IAtomContainer container);
}

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public Rectangle2D getTextBounds(String text, double x, double y,
                                 Graphics2D graphics) {

    FontMetrics fontMetrics = graphics.getFontMetrics();
    Rectangle2D bounds      = fontMetrics.getStringBounds(text, graphics);

    double widthPad  = 3;
    double heightPad = 1;

    double width  = bounds.getWidth()  + widthPad;

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TextLayout  layout = new TextLayout(text, graphics.getFont(),
                                    graphics.getFontRenderContext());
Rectangle2D bounds = layout.getBounds();

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DOMImplementation impl     = GenericDOMImplementation.getDOMImplementation();
Document          document = impl.createDocument("http://www.w3.org/2000/svg",
                                                 "svg",
                                                  null);
// SVGGraphics2D implements java.awt.Graphics2D
SVGGeneratorContext context = SVGGeneratorContext.createDefault(document)
SVGGraphics2D       g2      = new SVGGraphics2D(context,
                                                true);  // convert fonts to SVG Font glyphs

// render

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double width  = bounds.getWidth()  + bounds.getHeight() * PADDING_RATIO;
double height = bounds.getHeight() + bounds.getHeight() * PADDING_RATIO;

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HashGenerator<Integer> generator = new HashGeneratorMaker().withDepth(8)
                                                           .charged()
                                                           .chiral()      
                                                           .isotopic()
                                                           .radicals()
                                                           .withBondOrderSum()
                                                           .nullable()
                                                           .build();
// integer representation
Integer hashcode = generator.generate(container);