code: public static final Atom[] getAllAtomArray(Chain c) {
  		List<Atom> atoms = new ArrayList<Atom>();
  
  		for (Group g : c.getAtomGroups()) {
  			if (g.isWater())
  				continue;
  			for (Atom a : g.getAtoms()) {
  				atoms.add(a);
  			}
  		}
  		return atoms.toArray(new Atom[atoms.size()]);
  	}
docs: Returns and array of all atoms of the chain, including
  Hydrogens (if present) and all HETATOMs. Waters are not included.
  
  @param c
  input chain
  @return all atom array