One of our metrics was geometric based, and the idea behind it was to create a convex hull around the protein body and find the “buriedness” or “penetration” of samples into the convex hull. How deep the ligand is buried in the pocket would tell us that the pocket is a potential binding site.

During my 7th week I worked to implement a way of getting this penetration value. I looked into the files for our collision detection method (PQP), which had functions already implemented to help calculate for this value. After some trial and errors on what some of the values I found actually meant, I successfully augmented a method that would give us the clearance information when called.

We also had our Motion planning meeting this week to discuss about on going summer projects, how far we had gone and what was left to be done. Through this, we got a bit more knowledge about each other’s projects.

At the end of the week, I checked out a the code for a new branch set up by PhD student Diane. In order to merge our code and to have the same code we work with, we made a branch for it so each of us could make changes to it and accommodate the changes other’s made.