Welcome to provis’s Wiki!

Provis is a protein visualization library based on python. As the name suggests it is used to visualize proteins from their .pdb data formats (from the 3D coordinates). One can visualize the protein as a stick and point model or as a surface, and many different options can be specified to show the desired properties.

The library and this documentation were created by Kristof Czirjak as his Bachelor’s Thesis at ETH Zurich.

You can find installation instructions under Setting up Provis, a tutorial on How to use Provis, as well as the documentation of the source code.

What provis is capable of:

The following video shows the hydrophobic trajectory of a given protein.

Getting started:

• Requirements for Provis
  • Binaries
  • Pip
• Download Provis
• Setting up Provis
  • Directory structure
  • Binaries

Documentation:

• Provis
  • Source Code
    • provis.src.plotting package
    • provis.src.processing package
    • Module contents
  • Utilities for Provis
    • provis.utils.atminfo module
    • provis.utils.charges_utils module
    • provis.utils.surface_feat module
    • provis.utils.surface_utils module
    • Module contents
  • Module contents

Use and examples:

• General information about provis
  • MSMS
  • Classes
    • Protein
    • NameChecker
    • FileConverter
    • DataHandler
    • SurfaceHandler
    • Plotter
    • DynamicPlotter
    • Residue
  • Design decisions
  • Code architecture
• How to use Provis
  • Loading a pdb
  • Initializing the Protein class
  • Plotter class
    • MSMS
    • Plotting
    • Camera
    • The output
• Example
• Dynamic Structures
  • How to use the DynamicPlotter class?

Author(s)

• Contact and motivation

Indices and tables

• Index

• Module Index

• Search Page