code: private static Shape createBondHighlight(IBond bond, double radius) {
  
          double x1 = bond.getBegin().getPoint2d().x;
          double x2 = bond.getEnd().getPoint2d().x;
          double y1 = bond.getBegin().getPoint2d().y;
          double y2 = bond.getEnd().getPoint2d().y;
  
          double dx = x2 - x1;
          double dy = y2 - y1;
  
          double mag = Math.sqrt((dx * dx) + (dy * dy));
  
          dx /= mag;
          dy /= mag;
  
          double r2 = radius / 2;
  
          Shape s = new RoundRectangle2D.Double(x1 - r2, y1 - r2, mag + radius, radius, radius, radius);
  
          double theta = Math.atan2(dy, dx);
  
          return AffineTransform.getRotateInstance(theta, x1, y1).createTransformedShape(s);
      }
docs: Create the shape which will highlight the provided bond.
  
  @param bond   the bond to highlight
  @param radius the specified radius
  @return the shape which will highlight the atom