The atom nodes are layered based on the order they are added to the play area. They retain this ordering despite being dragged. This can cause an atom to awkwardly layer in front of another and interrupt the look of a bonded molecule (see image below).
When a molecule is dragged all of its associated molecules are moved to the front of the z-order layering. This should fix the bug and the above case isn't reproducible in Master. Closing.
The atom nodes are layered based on the order they are added to the play area. They retain this ordering despite being dragged. This can cause an atom to awkwardly layer in front of another and interrupt the look of a bonded molecule (see image below).![image](https://user-images.githubusercontent.com/13894380/74162482-dbca7680-4bee-11ea-8080-6b1cd47619b7.png)