JChemPaintRendererModel jcpModel = (JChemPaintRendererModel) model;
ElementGroup selectionElements = new ElementGroup();
double radius = jcpModel.getHighlightDistance() / jcpModel.getScale();
radius /= 2.0;
for(IAtom atom : model.getMerge().keySet()){
Point2d p1 = atom.getPoint2d();
Point2d p2 = model.getMerge().get( atom ).getPoint2d();
// the element size has to be scaled to model space
// so that it can be scaled back to screen space...
PathBuilder pb = new PathBuilder();
pb.color( jcpModel.getHoverOverColor() );
Vector2d vec = new Vector2d();
vec.sub( p2, p1 );
Vector2d per = GeometryTools.calculatePerpendicularUnitVector( p1, p2 );
per.scale( radius );
Vector2d per2 = new Vector2d();
per2.scale( -1 ,per);
Vector2d v1= new Vector2d(vec);
Vector2d v2= new Vector2d();
v1.normalize();
v1.scale( radius );
v2.scale( -1, v1 );
Point2d f1 = new Point2d();
Point2d f2 = new Point2d();
Point2d f3 = new Point2d();
Point2d s1 = new Point2d();
Point2d s2 = new Point2d();
Point2d s3 = new Point2d();
f1.add( p1, per );
f2.add( p1 , v2 );
f3.add( p1, per2 );
s1.add(p2, per2);
s2.add(p2, v1);
s3.add( p2, per );
pb.moveTo(f1).quadTo( f2,f3 ).lineTo( s1 ).quadTo( s2, s3 ).close();
selectionElements.add(pb.createPath());