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.
Note
chain_from_trajectory() requires the installation of python library MDAnalysis
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, ploting functions and clustering one available with the package. 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().
- cluster conformations of a same protein based on PB similarities.
Look at the notebook Visualize protein deformability for further information.
Note
Plotting functions require Matplotlib.
Note
generate_weblogo() requires Weblogo3.