code: @Override
      public void setScale(IAtomContainer atomContainer) {
          double bondLength = GeometryUtil.getBondLengthAverage(atomContainer);
          rendererModel.getParameter(Scale.class).setValue(this.calculateScaleForBondLength(bondLength));
      }
docs: Set the scale for an IAtomContainer. It calculates the average bond
  length of the model and calculates the multiplication factor to transform
  this to the bond length that is set in the RendererModel.
  
  @param atomContainer the atom container that will be drawn