code: public static void scaleMolecule(IAtomContainer atomCon, double scaleFactor) {
          for (int i = 0; i < atomCon.getAtomCount(); i++) {
              if (atomCon.getAtom(i).getPoint2d() != null) {
                  atomCon.getAtom(i).getPoint2d().x *= scaleFactor;
                  atomCon.getAtom(i).getPoint2d().y *= scaleFactor;
              }
          }
      }
docs: Multiplies all the coordinates of the atoms of the given molecule with the
  scalefactor.
  See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
  
  @param  atomCon      The molecule to be scaled
  @param  scaleFactor  Description of the Parameter