The purple circles mark the center of the reaction, and you can move or lock the position of the reaction with the purple circle. By clicking and dragging the purple circle, you can move the center of the reaction. AutoLayout will recalculate all the reaction's curves as you move it. If you right click and select “Lock Node” you can click on the purple circle, it will change to a darker color, and it will lock the reaction's position so it won't be moved during layout.