SunTzunami's Blog

Weekly Check-in #2

Published: 06/14/2021

First week of coding

Welcome to the second weekly check-in. I'll be sharing my progress for the first week of coding.

What did you do this week?

I implemented the space filling model for proteins and created a PR for the same.
Preview (protein: 3pgk):
The PR has:

  • Actor for space filling model
  • Two examples where I show how to visualize the proteins:
    1. In example 1, I parse a PDBx file myself and extract the atomic info essential for constructing the model which is then used by the actor to visualize it.
    2. In example 2, I parse a PDB file by using Biopython module and extract the atomic info essential for constructing the model which is then used by the actor to visualize it.
  • I created a basic test for the actor which needs to be improved. I'll discuss how to improve the test with the mentors.

What is coming up next week?

I'll try to implement ball and stick model or ribbon model depending on which model is decided in the meeting with the mentors and try to improve the tests for space filling model. Writing an algorithm to generate bonds from structure data will be the challenge

Did you get stuck anywhere?

I tried to create a class in python which inherits from a class in VTK called vtkMoleculeReaderBase but was unsuccessful in this endeavour (some classes from VTK can't be inherited apparently). I'll try to find a workaround.

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Weekly Check-in #1

Published: 06/08/2021

Welcome to my GSoC Blog!

Hi all! I'm Sajag Swami, a sophomore at Indian Institute of Technology, Roorkee. I will be working on bringing Ribbon and Molecular Surface protein representations to FURY.

As a part of my stretch goals, I’ll try to bring the following molecular representations to FURY:
  • Stick
  • Ball and stick
  • Wire
  • Pipes and Planks
  • Sphere

What did you do during the Community Bonding Period?

I had weekly meetings with my mentors and other core team members. In the first meeting I got acquainted with the team members and learnt more about FURY and its goal/vision. In the later meetings we discussed about various representations of proteins and how to go about implementing them in FURY. We talked about different libraries which can be used to parse PDB and PDBx files. I made a doc for the same to list pros and cons of using each library. I worked upon my previous PR too during the community bonding period and fixed its docstring syntax.

As my college ended early courtesy covid, I had extra time during which I experimented and learnt more about PDB and PDBx files - the details they contain and how to parse them. A small backbone visualisation of 1mb0 protein made on FURY by extracting coordinate data of its alpha carbons -

What is coming up next week?

I have two major goals for the next week -
  • Make an actor for the space filling model of the proteins and make PR for the same which will also include the unit tests and a small tutorial for the users.
  • Try understanding the documentation of vtkProteinRibbonFilter which will prove beneficial for generating Ribbon diagrams.

Did you get stuck anywhere?

Dealing with large protein structures was kinda difficult as it gets computationally taxing to render many molecules. FURY team was pretty helpful and instructed me to use shaders (luckily for me, the shader in question had been implemented by the community members). This resolved the issue of dealing with large files to a great extent.
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