Google Summer of Code Final Work Product#

Proposed Objectives#

  • Ribbon Representation

  • Molecular Surface Representation

  • Stretch Goals:

    • Stick Representation

    • Ball and stick Representation

    • Wire Representation

    • Pipes and Planks Representation

    • Sphere Representation

Objectives Completed#

  • Ribbon Representation

    Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons. β-strands as sheets, and non-repetitive coils or loops as lines or thin strips. It was implemented by using vtkProteinRibbonFilter. Generating a vtkPolyData of appropriate format required by vtkProteinRibbonFilter was initially unclear due to lack of examples. I was able to understand what kind of output the filter required after a meeting with mentors. Tests were added and a demo was created.

    Pull Requests:

  • Ball and Stick Representation

    The ball-and-stick model is a molecular model of a chemical substance which displays both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by tubes which represent the bonds. It was created by using vtkOpenGLMoleculeMapper. Added vtkSimpleBondPerceiver for detection of bonds. Tests were added and a demo was created.

    Pull Requests:

  • Stick Representation

    Stick model is a special case of Ball and Stick model where atomic radius of all molecules is set equal to the radius of tubes used to create bonds. It was created by using vtkOpenGLMoleculeMapper. Tests were added and a demo was created.

    Pull Requests:

  • Sphere Representation

    In chemistry, a space-filling model, also known as a calotte or sphere model, is a type of three-dimensional (3D) molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms. It was created by using vtkOpenGLMoleculeMapper. Tests were added and a demo was created.

    Pull Requests:

Objectives in Progress#

  • Molecular Surfaces

    There are three types of molecular surfaces:

    • Van der Waals

    • Solvent Accessible

    • Solvent Excluded

    Currently the first two molecular surfaces i.e. Van der Waals and Solvent Accessible are implemented. The code is based on the paper “Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform” by Dong Xu and Yang Zhang.

    Pull Requests:

Other Objectives#

  • 2D Animated Surfaces

    This was a simple demonstration that animated Two-Dimensional (2D) functions using FURY. Created a grid of x-y coordinates and mapped the heights (z-values) to the corresponding x, y coordinates to generate the surfaces. Used colormaps to color the surfaces.

    Pull Requests:

  • Updated miscellaneous animations

    • Updated the demo of helical motion to stop using multiple line actors as discussed in the meeting.

    • Updated the demo of brownian motion to make it more scientifically useful (removed unnecessary rotation of camera during animation and box actor).

    • Display simulation data for brownian motion and helical motion animations (number of simulated steps for brownian motion and velocity of the particle for helical motion).

    • Created utility functions to make the code understandable and used these in emwave, helical and brownian animations.

    Pull Requests:

  • GSoC weekly Blogs

    Weekly blogs were added for FURY’s Website.

    Pull Requests:




Blog Link

Week 1(08-06-2021)

Welcome to my GSoC Blog!

Weekly Check-in #1

Week 2(14-06-2021)

First Week of coding: sphere model.

Weekly Check-in #2

Week 3(21-06-2021)

Bonding algorithms, Ball and Stick model progress.

Weekly Check-in #3

Week 4(28-06-2021)

VTK molecular visualization classes.

Weekly Check-in #4

Week 5(05-07-2021)

Genesis of molecular module.

Weekly Check-in #5

Week 6(12-07-2021)

Ribbon representation, updated molecular module (more pythonic)

Weekly Check-in #6

Week 7(19-07-2021)

More features to molecular, updated misc. animations.

Weekly Check-in #7

Week 8(26-07-2020)

Ribbon to molecular, tests for molecular, animated surfaces.

Weekly Check-in #8

Week 9(02-08-2021)

Optimized molecular with mentors, GSoC blogs to FURY docs.

Weekly Check-in #9

Week 10(09-08-2021)

Bounding box, molecular tutorial, molecular surfaces progress.

Weekly Check-in #10

Week 11(16-08-2021)

Molecular Surfaces (VDW, SAS) implementation.

Weekly Check-in #11

Detailed weekly tasks and work done can be found here.