How To Install plip on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 444 words

Introduction

In this tutorial we learn how to install plip on Ubuntu.

What is `plip`

plip is:

The Protein-Ligand Interaction Profiler (PLIP) is a tool to analyze and visualize protein-ligand interactions in PDB files.

Features include:

Detection of eight different types of noncovalent interactions
Automatic detection of relevant ligands in a PDB file
Direct download of PDB structures from wwPDB server if valid PDB ID is given
Processing of custom PDB files containing protein-ligand complexes (e.g. from docking)
No need for special preparation of a PDB file, works out of the box
Atom-level interaction reports in rST and XML formats for easy parsing
Generation of PyMOL session files (.pse) for each pairing, enabling easy preparation of images for publications and talks
Rendering of preview image for each ligand and its interactions with the protein

There are three methods to install plip on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install plip Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install plip using apt-get by running the following command:

sudo apt-get -y install plip

Install plip Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install plip using apt by running the following command:

sudo apt -y install plip

Install plip Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install plip using aptitude by running the following command:

sudo aptitude -y install plip

How To Uninstall plip on Ubuntu

To uninstall only the plip package we can use the following command:

sudo apt-get remove plip

Uninstall plip And Its Dependencies

To uninstall plip and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove plip

Remove plip Configurations and Data

To remove plip configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge plip

Remove plip configuration, data, and all of its dependencies

We can use the following command to remove plip configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge plip

Dependencies

plip have the following dependencies:

References

plip website

Summary

In this tutorial we learn how to install plip package on Ubuntu using different package management tools: apt, apt-get and aptitude.