code: private double[] calculateDistanceBetweenAtomAndBond(IAtom proton, IBond theBond) {
          Point3d middlePoint = theBond.get3DCenter();
          Point3d protonPoint = proton.getPoint3d();
          double[] values = new double[4];
          values[0] = middlePoint.distance(protonPoint);
          values[1] = middlePoint.x;
          values[2] = middlePoint.y;
          values[3] = middlePoint.z;
          return values;
      }
docs: and returns distance and coordinates of middle point