code: public static void scaleMolecule(IAtomContainer atomCon, Dimension areaDim, double fillFactor) {
          Dimension molDim = get2DDimension(atomCon);
          double widthFactor = (double) areaDim.width / (double) molDim.width;
          double heightFactor = (double) areaDim.height / (double) molDim.height;
          double scaleFactor = Math.min(widthFactor, heightFactor) * fillFactor;
          scaleMolecule(atomCon, scaleFactor);
      }
docs: Scales a molecule such that it fills a given percentage of a given
  dimension.
  See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
  
  @param  atomCon     The molecule to be scaled
  @param  areaDim     The dimension to be filled
  @param  fillFactor  The percentage of the dimension to be filled