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.