code: private static final Atom[] getFragment(Atom[] caall, int pos, int fragmentLength ,
  			boolean clone){
  
  		if ( pos+fragmentLength > caall.length)
  			return null;
  
  		Atom[] tmp = new Atom[fragmentLength];
  
  		for (int i=0;i< fragmentLength;i++){
  			if (clone){
  				tmp[i] = (Atom)caall[i+pos].clone();
  			} else {
  				tmp[i] = caall[i+pos];
  			}
  		}
  		return tmp;
  
  	}
docs: get a continue subset of Atoms based by the starting position and the length
  
  @param caall
  @param pos ... the start position
  @param fragmentLength .. the length of the subset to extract.
  @param clone: returns a copy of the atom (in case the coordinate get manipulated...)
  @return an Atom[] array