API Cookbook

This page provides some examples, tutorials as notebooks to help you use the API of PBxplore.

Basically, PBxplore is structured around 3 modules:

PBxplore.structure

This module handles the reading of PDB files and trajectory files. Its 2 major functions chain_from_files() and chain_from_trajectory are direclty exposed at the package level.

Look at the notebook PB assignation for further information.

PBxplore.io

This module is about the I/O of all files other than PDB. It handles the reading/writing of fasta files and the writing of text-like analysis files (Neq files).

Look at the notebook Writing PB in file for further information.

PBxplore.analysis

This module handle all analysis functions and ploting functions. You can:

  • generate map of the distribution of PBs along protein sequence with plot_map().
  • compute Neq with compute_neq() and generate the plot with plot_neq().
  • generate WebLogo-like representation of PBs frequency along protein sequence with generate_weblogo().

Look at the notebook Visualize protein deformability for further information.

Note

generate_weblogo() requires Weblogo3.