johnmay

if (GeometryTools.has2DCoordinates(container)) {
    renderer.paint(container, new AWTDrawVisitor(g2), bounds, true);
} else {
    // can log or invoke g2.drawString() to display "no coordinates"
}

johnmay

// creating the custom matcher
IAtomMatcher matcher = and(SymbolMatcher.class, ChargeMatcher.class);

if(UniversalIsomorphismTester.isIsomorph(container1, container2, matcher)){
    // atoms match charge and symbol
}

johnmay

new AbstractAtomMatcher(){
    @Override
    public Object getAttribute(IAtom atom) {
        return atom.getProperty("my.custom.property");
    }
};

johnmay

new AbstractAtomMatcher(){
    @Override
    public Object getAttribute(IAtom atom) {
        return atom.getProperty("stereo.descriptor");
    }
};

johnmay

public interface IMultiOrderQueryBond extends IQueryBond {
    
    /**
     *  Access the alternate bond order
     */
    public IBond.Order getAuxiliaryOrder();

    /**
     * Flips the bond primary and auxiliary orders
     */

johnmay

IAtom atom = g1.getAtom(0);
// ...
String atomSymbol = atom.getSymbol();
return g1.getAtom(0).getSymbol().equals(atomSymbol);

johnmay

new AbstractAtomMatcher(){
    @Override
    public boolean matchers(IAtom query, IAtom subject) {
        Object descriptor1 = query.getProperty("stereo.descriptor");
        Object descriptor2 = subject.getProperty("stereo.descriptor");
        return descriptor1 != null ? descriptor1.equals(descriptor2) : descriptor2 == null;
    }
};

johnmay

        } else if ("bondStereo".equals(name)) {
            for (int i = 0; i < atts.getLength(); i++) {
                if (atts.getQName(i).equals("dictRef")) {
                	if (atts.getValue(i).startsWith("cml:"))
                	bondStereo.add(atts.getValue(i).substring(4));
                    stereoGiven=true;
                }
            }
        }

johnmay

<!-- CDK expects -->
<bond atomRefs2="a2 a4" order="1">
    <bondStereo dictRef="cml:W"/>
</bond>

<!-- Normally my files have this -->
<bond atomRefs2="a2 a4" order="1">
    <bondStereo>W</bondStereo>
</bond>

johnmay

    public void generateImageWithBondsHighlighted() throws Exception {
        
        IAtomContainer molecule = MoleculeFactory.makeAdenine();
        IAtomContainer selectionMolecule = molecule.getBuilder().newInstance(IAtomContainer.class);

        for (int i = 0; i < 3; i++) {
            selectionMolecule.addBond(molecule.getBond(i));
        }
        
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);