code: public static Atom[] getAtomCAArray(Structure s) {
  
  		List<Atom> atoms = new ArrayList<Atom>();
  
  		for (Chain c : s.getChains()) {
  			for (Group g : c.getAtomGroups()) {
  				if (g.hasAtom(CA_ATOM_NAME)
  						&& g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
  					atoms.add(g.getAtom(CA_ATOM_NAME));
  				}
  			}
  		}
  
  		return atoms.toArray(new Atom[atoms.size()]);
  	}
docs: Return an Atom array of the C-alpha atoms. Any atom that is a carbon and
  has CA name will be returned.
  
  @param s
  the structure object
  @return an Atom[] array
  @see #getRepresentativeAtomArray(Structure)