johnmay

class ChangeAtomSymbol extends AbstractUndoableEdit {

    IAtomContainer container;
    IAtom remove, replace;

    ChangeAtomSymbol(IAtomContainer container,
                     IAtom original,
                     String newSymbol) {

        Atom copy = new Atom(original); // do not clone!

johnmay

// check for wide labels
boolean blunt = bounds.getWidth() / bounds.getHeight() > 3;
// ... 
return new RoundRectangle2D.Double(x - (width/2), y - (height/2),
                                   width, height,
                                   blunt ? height : width, height);

johnmay

public double[] transformPointDouble(double xCoord, double yCoord) {
    double[] src = new double[] {xCoord, yCoord};
    double[] dest = new double[2];
    this.transform.transform(src, 0, dest, 0, 1);
    return dest;
}

// ... used in the bounds calculation
double[] p = this.transformPointDouble(x, y);

johnmay

class CustomChemObjectBuilder implements IChemObjectBuilder {

    private final DynamicFactory factory = new DynamicFactory(200);
     
    public CustomChemObjectBuilder() {

        // basic registration
        factory.register(Element.class); // discovers Element is an instance of IElement, alternatively...
        factory.register(IElement.class, Element.class); // registers Element with IElement explicitly

johnmay

IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
SmilesParser       parser  = new SmilesParser(builder);

IAtomContainer sodiumChloride = parser.parseSmiles("[Na+].[Cl-]");
IAtomContainer adenine        = parser.parseSmiles("n1c(c2c(nc1)ncn2)N");

// if you want the separate parts
// import static org.openscience.cdk.graph.ConnectivityChecker.partitionIntoMolecules;
IAtomContainerSet  sodiumChlorideSet = partitionIntoMolecules(sodiumChloride);
IAtomContainerSet  adenineSet        = partitionIntoMolecules(adenine);

johnmay

IAtomContainer a = new AtomContainer();
a.addAtom(new Atom("C"));
a.addAtom(new Atom("C"));
a.addBond(new Bond(a.getAtom(0), a.getAtom(1), SINGLE));
        
// copy constructor
IAtomContainer b = new AtomContainer(a);
b.removeAtom(0); // atom at index 0 is removed from b, a is not affected
        
b.getBond(0).setOrder(DOUBLE);       // bond order is change in both a and b

johnmay

public class AdjacencyList implements Graph {

    private final int[][] vertexes;
    private final IAtom[] atoms;

    private final int n;

    public AdjacencyList(final IAtomContainer container) {

        this.n = container.getAtomCount();

johnmay

   private int iterate(IAtomContainer container) {
        int total = 0;
        for (int d = 0; d < 8; d++) {
            for (IAtom atom : container.atoms()) {
                for (IBond bond : container.getConnectedBondsList(atom)) {
                    IAtom other = bond.getConnectedAtom(atom);
                    total += other.getAtomicNumber();
                }
            }
        }

johnmay

public int rotate(int value, int n){
    for(int i = 0; i < n; i++)
        value = nextInt(value);
    return value;
}

public int nextInt(int seed){
    // return pseudo random number from the given seed 
}

johnmay

public int rotate(int value, int n){
    for(int i = 0; i < n; i++)
        value = nextInt(value);
    return value;
}

public int nextInt(int seed){
    // return pseudo random number from the given seed 
}