# Utilization

There is 2 ways to use PBxplore:
  - command-line scripts
  - API

## Command-line scripts

PBxplore is bundle with a suite of command-line tools. Once installed, they should be available in your `$PATH`. Here the list:

- PBassign assign Protein Blocks (PBs) from a set of protein structures.
- PBcount computes the frequency of PBs at each position along the amino acid sequence.
- PBstat generates frequency and logo plots, and estimates the Neq.
- PBclust use clustering algorithm (k-means) to re-group similar PBs sequences.

## API

PBxplore is also a python library and provides an API to interfacing with Python applications. You will find here a list of notebooks to help you use the API.

## Demo files

PBxplore provides scripts to demonstrate its functionalities. These scripts guide the user through the different command line tools of PBxplore.

3 demonstration scripts are available:

- run_demo1_assignation.sh demonstrates the how to use `PBassign` to assign Protein Block sequences to protein structures;
- run_demo2_statistics.sh demonstrates how to analyse protein dynamics using PBxplore;
- finally, run_demo2_clusters.sh demonstrates how to use `PBclust` to cluster Protein Block sequences.

In addition to the scripts, PBxplore bundles input files to test and get accustom with the software and the python library. Call the `PBdata` program to display where these files are stored. With the –list and –list-abs arguments `PBdata` list the available name and absolute path, respectively.