code: public static double getDistanceFast(Atom a, Atom b) {
  		double x = a.getX() - b.getX();
  		double y = a.getY() - b.getY();
  		double z = a.getZ() - b.getZ();
  
  		return x * x  + y * y + z * z;
  	}
docs: Will calculate the square of distances between two atoms. This will be
  faster as it will not perform the final square root to get the actual
  distance. Use this if doing large numbers of distance comparisons - it is
  marginally faster than getDistance().
  
  @param a
  an Atom object
  @param b
  an Atom object
  @return a double