How To Install python3-pdbfixer on Debian 12
Introduction
In this tutorial we learn how to install python3-pdbfixer on Debian 12.
What is python3-pdbfixer
python3-pdbfixer is:
PDBFixer is an application for fixing problems in Protein Data Bank files in preparation for simulating them. It can automatically fix the following problems:
- Add missing heavy atoms.
- Add missing hydrogen atoms.
- Build missing loops.
- Convert non-standard residues to their standard equivalents.
- Select a single position for atoms with multiple alternate positions listed.
- Delete unwanted chains from the model.
- Delete unwanted heterogens.
- Build a water box for explicit solvent simulations.
This package installs the library for Python 3.
There are three methods to install python3-pdbfixer 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 python3-pdbfixer Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install python3-pdbfixer using apt-get by running the following command:
sudo apt-get -y install python3-pdbfixer
Install python3-pdbfixer Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install python3-pdbfixer using apt by running the following command:
sudo apt -y install python3-pdbfixer
Install python3-pdbfixer 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 python3-pdbfixer using aptitude by running the following command:
sudo aptitude -y install python3-pdbfixer
How To Uninstall python3-pdbfixer on Debian 12
To uninstall only the python3-pdbfixer package we can use the following command:
sudo apt-get remove python3-pdbfixer
Uninstall python3-pdbfixer And Its Dependencies
To uninstall python3-pdbfixer and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove python3-pdbfixer
Remove python3-pdbfixer Configurations and Data
To remove python3-pdbfixer configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge python3-pdbfixer
Remove python3-pdbfixer configuration, data, and all of its dependencies
We can use the following command to remove python3-pdbfixer configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge python3-pdbfixer
Dependencies
python3-pdbfixer have the following dependencies:
References
Summary
In this tutorial we learn how to install python3-pdbfixer package on Debian 12 using different package management tools: apt, apt-get and aptitude.
