code: private double calculateDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2) {
          double distance;
          Point3d firstPoint = atom1.getPoint3d();
          Point3d secondPoint = atom2.getPoint3d();
          distance = firstPoint.distance(secondPoint);
          return distance;
      }
docs: generic method for calculation of distance btw 2 atoms