Just as in the creation process, where we have created several smaller helper methods to split up the process and make it more readable, we will have the same for the update process. Another reason besides readability is reusability. You don't want to code the same thing several times. That is why you use functions and methods.
Each atom object is also a composed object—the image object that you can see and, depending on how many connectors the atom has, several invisible circles, which we will use to detect a connection (collision) with a connector next to it.
Every object can be invisible but still act on updates and collision detection.