code: public static void rotate(IAtomContainer atomCon, Point2d center, double angle) {
          Point2d point;
          double costheta = Math.cos(angle);
          double sintheta = Math.sin(angle);
          IAtom atom;
          for (int i = 0; i < atomCon.getAtomCount(); i++) {
              atom = atomCon.getAtom(i);
              point = atom.getPoint2d();
              double relativex = point.x - center.x;
              double relativey = point.y - center.y;
              point.x = relativex * costheta - relativey * sintheta + center.x;
              point.y = relativex * sintheta + relativey * costheta + center.y;
          }
      }
docs: Rotates a molecule around a given center by a given angle.
  
  @param  atomCon  The molecule to be rotated
  @param  center   A point giving the rotation center
  @param  angle    The angle by which to rotate the molecule, in radians