Tenth coding week!#

Welcome to the eleventh weekly check-in. I’ll be sharing my progress for the tenth week of coding.

What did you do this week?#

  1. Implemented this paper to generate Van der Waals surface and solvent-accessible surface (PR created: PR #492). It was a good learning experience because the first time I read the paper, I didn’t understand the underlying math, it all seemed alien to me. I had to read it many times, read about the algorithms used and understand the terminologies. I had a meeting with the mentors to understand a bit of the theory which proved to be quite fruitful as I understood how to go about making the space-filling model. This blog was helpful in understanding how to use vtkMarchingCubes with numpy arrays. One of the earliest SAS rendering looked like this (this implementation was not strictly according to the paper):

    https://user-images.githubusercontent.com/65067354/129559593-baf201bf-720c-45f7-9269-3b31954efd5e.png

    Notice that it’s rather rough#

    Current implementation (this implementation was according to the paper):

    https://user-images.githubusercontent.com/65067354/129560374-14180b22-14b2-449b-88a6-b3140226418d.png

    grid dimenstions = 256 × 256 × 256, used smoothing algorithms recommended by vtk#

I also understood how to go about rendering volumes. I think that the ability to render volumes with FURY will be a cool capability and I’ll discuss my implementation and request the mentors for feedback and ideas in the weekly meeting. Example of volume rendering:

https://user-images.githubusercontent.com/65067354/129562606-50a9f0cf-e16d-4501-b0fa-a0038fda406b.png

grid dimenstions = 256 × 256 × 256#

What is coming up next week?#

I’ll try to get PR #452 merged. Documentation work to be done as GSoC coding period has come to an end.

Did you get stuck anywhere?#

No.

Au Revoir!