code: public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
  		List<Atom> atoms = new ArrayList<Atom>();
  
  		for (Group g : c.getAtomGroups()) {
  			if (g.isWater())
  				continue;
  			for (Atom a : g.getAtoms()) {
  
  				if (a.getElement() == Element.H)
  					continue;
  
  				if (!hetAtoms && g.getType().equals(GroupType.HETATM))
  					continue;
  
  				atoms.add(a);
  			}
  		}
  		return atoms.toArray(new Atom[atoms.size()]);
  	}
docs: Returns and array of all non-Hydrogen atoms in the given Chain,
  optionally including HET atoms or not Waters are not included.
  
  @param c
  @param hetAtoms
  if true HET atoms are included in array, if false they are not
  @return