How To Install pdb-tools on Debian 12
Introduction
In this tutorial we learn how to install pdb-tools on Debian 12.
What is pdb-tools
pdb-tools is:
Manipulating PDB files is often painful. Extracting a particular chain or set of residues, renumbering residues, splitting or merging models and chains, or just ensuring the file is conforming to the PDB specifications are examples of tasks that can be done using any decent parsing library or graphical interface. These, however, almost always require 1) scripting knowledge, 2) time, and 3) installing one or more programs.
pdb-tools were designed to be a swiss-knife for the PDB format. They have no external dependencies, besides the Python programming language. They are the descendant of a set of old FORTRAN77 programs that had the particular advantage of working with streams, i.e. the output of one script could be piped into another.
The philosophy of the scripts is simple: one script, one task. If you want to do two things, pipe the scripts together.
This package contains the command line tools.
There are three methods to install pdb-tools on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install pdb-tools Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install pdb-tools using apt-get by running the following command:
sudo apt-get -y install pdb-tools
Install pdb-tools Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install pdb-tools using apt by running the following command:
sudo apt -y install pdb-tools
Install pdb-tools 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install pdb-tools using aptitude by running the following command:
sudo aptitude -y install pdb-tools
How To Uninstall pdb-tools on Debian 12
To uninstall only the pdb-tools package we can use the following command:
sudo apt-get remove pdb-tools
Uninstall pdb-tools And Its Dependencies
To uninstall pdb-tools and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove pdb-tools
Remove pdb-tools Configurations and Data
To remove pdb-tools configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge pdb-tools
Remove pdb-tools configuration, data, and all of its dependencies
We can use the following command to remove pdb-tools configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge pdb-tools
Dependencies
pdb-tools have the following dependencies:
References
Summary
In this tutorial we learn how to install pdb-tools package on Debian 12 using different package management tools: apt, apt-get and aptitude.
