Weekly Check-in #4

Published: 06/28/2021

Third week of coding

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

What did you do this week?

I made a document with code snippets and visuals to show how one can use some vtk classes in python for molecular visualization. Classes of interest :

  • vtkMolecule (store atomic information about the molecule)
  • vtkSimpleBondPerceiver (calculate bonding info for a vtkMolecule)
  • vtkMoleculeMapper (mapper to draw vtkMolecule object)
  • vtkPeriodicTable (stores chemical data sourced from the Blue Obelisk Data).
Link to the document - Molecular_viz_vtk. In addition to the document, I read some research papers recommended by my mentors to understand some other (and potentially better) methods of ribbon visualization. Tried to implement vtkProteinRibbonFilter usage without using vtkPDBReader but was unsuccessful in this endeavour. It's kinda tough to understand what exactly vtkProteinRibbonFilter requires as input. I'll have to dig deeper into its documentation.

What is coming up next week?

Three goals for next week -

  1. Implement vtkProteinRibbonFilter usage without using vtkPDBReader.
  2. Make a class that inherits from vtkMolecule. It's instances will be used to store molecular data and pass it on to different functions for rendering purposes.
  3. Start reading the theory behind molecular surface representation.

Did you get stuck anywhere?

Implementing vtkProteinRibbonFilter usage via vtkPolyData without using vtkPDBReader has confounded me for some time now. Ribbon representation's code progress is at an impasse until I implement vtkProteinRibbonFilter.