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()]);
	}
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 ( ) ] ) ; }
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