How To Install python3-mdtraj on Kali Linux

In this tutorial we learn how to install python3-mdtraj on Kali Linux. python3-mdtraj is Read, write and analyze MD trajectories in Python

Introduction

In this tutorial we learn how to install python3-mdtraj on Kali Linux.

What is python3-mdtraj

python3-mdtraj is:

Read, write and analyze MD trajectories with only a few lines of Python code.

MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories. Features include:

  • Wide MD format support, including pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop, and more.
  • Extremely fast RMSD calculations (4x the speed of the original Theobald QCP).
  • Extensive analysis functions including those that compute bonds, angles, dihedrals, hydrogen bonds, secondary structure, and NMR observables.
  • Lightweight, Pythonic API.

MDTraj includes a command-line application, mdconvert-mdtraj, for converting trajectories between formats.

This package installs the library for Python 3, together with the command line utilities mdconvert-mdtraj and mdinspect.

There are three methods to install python3-mdtraj on Kali Linux. 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-mdtraj 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-mdtraj using apt-get by running the following command:

sudo apt-get -y install python3-mdtraj

Install python3-mdtraj Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install python3-mdtraj using apt by running the following command:

sudo apt -y install python3-mdtraj

Install python3-mdtraj Using aptitude

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

sudo aptitude update

After updating apt database, We can install python3-mdtraj using aptitude by running the following command:

sudo aptitude -y install python3-mdtraj

How To Uninstall python3-mdtraj on Kali Linux

To uninstall only the python3-mdtraj package we can use the following command:

sudo apt-get remove python3-mdtraj

Uninstall python3-mdtraj And Its Dependencies

To uninstall python3-mdtraj and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove python3-mdtraj

Remove python3-mdtraj Configurations and Data

To remove python3-mdtraj configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge python3-mdtraj

Remove python3-mdtraj configuration, data, and all of its dependencies

We can use the following command to remove python3-mdtraj configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge python3-mdtraj

Dependencies

python3-mdtraj have the following dependencies:

References

Summary

In this tutorial we learn how to install python3-mdtraj package on Kali Linux using different package management tools: apt, apt-get and aptitude.