AtomContainer Shallow Copy Behaviour

gistfile1.java

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
b.getBond(0).addAtom(new Atom("H")); // as the bond is the same instance this is now

ITetrahedralChiralAtomParityEtc element = ...; // access stereo elements
element.setStereo(CLOCKWISE);        // a,b both have stereo changed