Like on unity notifications. set_accept_focus() is not what I need, and I dont see something useful in gtk.gdk constants... Seems like my google-fu failed.
So, the answer is:
win.show_all()
#win.window.input_shape_combine_mask(img,0,0)
def set_mask(win):
#b=gtk.gdk.bitmap_create_from_data(win.window,8,win.window.get_size())
size=win.window.get_size()
print size
bitmap=gtk.gdk.Pixmap(win.window,size[0],size[1],1)
cr = bitmap.cairo_create()
cr.set_operator(cairo.OPERATOR_SOURCE)
cr.set_source_rgba(0.0,0.0,0.0,0.0)
cr.rectangle((0,0)+size)
cr.fill()
win.window.input_shape_combine_mask(bitmap,0,0)
print 'ready'
gobject.timeout_add(5000, set_mask, win)