code: public IRenderingElement generateCompactElement(IAtom atom, RendererModel model) {
          Point2d point = atom.getPoint2d();
          double radius = (Double) model.get(AtomRadius.class) / model.getParameter(Scale.class).getValue();
          double distance = 2 * radius;
          if (model.get(CompactShape.class) == Shape.SQUARE) {
              return new RectangleElement(point.x - radius, point.y - radius, distance, distance, true, getAtomColor(
                      atom, model));
          } else {
              return new OvalElement(point.x, point.y, radius, true, getAtomColor(atom, model));
          }
      }
docs: Generate a compact element for an atom, such as a circle or a square,
  rather than text element.
  
  @param atom the atom to generate the compact element for
  @param model the renderer model
  @return a compact rendering element