How To Install openbabel on Ubuntu

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

3 minutes  • 503 words

Introduction

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

What is openbabel

openbabel is:

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

• obabel: Convert between various chemical file formats
• obenergy: Calculate the energy for a molecule
• obminimize: Optimize the geometry, minimize the energy for a molecule
• obgrep: Molecular search program using SMARTS pattern
• obgen: Generate 3D coordinates for a molecule
• obprop: Print standard molecular properties
• obfit: Superimpose two molecules based on a pattern
• obrotamer: Generate conformer/rotamer coordinates
• obconformer: Generate low-energy conformers
• obchiral: Print molecular chirality information
• obrotate: Rotate dihedral angle of molecules in batch mode
• obprobe: Create electrostatic probe grid

There are three methods to install openbabel 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 openbabel Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install openbabel

Install openbabel Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install openbabel

Install openbabel 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 openbabel using aptitude by running the following command:

sudo aptitude -y install openbabel

How To Uninstall openbabel on Ubuntu

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

sudo apt-get remove openbabel

Uninstall openbabel And Its Dependencies

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

sudo apt-get -y autoremove openbabel

Remove openbabel Configurations and Data

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

sudo apt-get -y purge openbabel

Remove openbabel configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge openbabel

Dependencies

openbabel have the following dependencies:

• libc6
• libgcc-s1
• libopenbabel7
• libstdc++6

References

• openbabel website

Summary

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