code: public boolean contains(Point3d atom) {
  		double x = atom.x;
  		double y = atom.y;
  		double z = atom.z;
  		return xmin <= x && x <= xmax
  				&& ymin <= y && y <= ymax
  				&& zmin <= z && z <= zmax;
  	}
docs: Check if a given point falls within this box
  @param atom
  @return