I began my fifth week by setting up the code for the ligand binding project, with the help of a tutorial sent by Phd Student Diane. Then I worked on a new strategy for the project (LigandStrategy) that would be used in computing our different metrics for the project. I ran tests with generating samples, then I moved to working on a distance metric to compute the distance from each sample to the protein’s center of mass.

After getting the distance metric to work, I met with my group to discuss the metric we already had in mind for the project, and also to do some research on other methods and metrics we could implement and add to the project. I did some reading on different metrics and the methods used to propose new metrics to add to our project. Then I implemented an energy function and tested it with the available environment files we had.

Lastly, I worked on splitting the strategy I had (LigandStrategy) into two different strategies, so that the first would generate samples around the protein, and the second would compute the metrics given the generated samples and the protein as input.