I have a ton of ideas for Inner Shapes. Many of them require making protein shapes that have multiple strings of shapes branching off of each other. In order to do that, I needed to add a T-shape amino, similar to a T-junction in plumbing. This was really challenging. It introduced a few problems:

1. How do you know if the goal protein is made up of multiple sub-chains, so when the finished protein is solves the puzzle the player can win? I needed to change the detection algorithm to check to see if there are multiple proteins linked together.

2. How do you change the color of all the Aminos in the final protein after the goal is completed?

My solution to this was to have each protein chain keep track of a "proteinGroup" number. Then as you connect multiple chains together with the T-Amino I just set the proteinGroup of the connected protein to the proteinGroup number of the protein that has the T-shape. To change the colors of the protein aminos or to check for the final goal, I just look at the proteinGroup numbers of the final aminos.