[Tutorial] How to install openbabel on Ubuntu (Linux)?

Open Babel is an open-source chemical toolbox for molecular modeling and cheminformatics tasks. It is a versatile conversion tool that supports various chemical file formats, enabling researchers to convert, analyze, and visualize molecular data across different platforms. With its comprehensive library of chemical functionalities, Open Babel allows users to perform tasks such as molecular structure conversion, property calculations, molecular fingerprint generation, and 3D structure manipulation. In this article, we are installing the openbabel on Ubuntu (Linux).

Contents

Preparing system Downloading Openbabel Installing required dependencies Installing Openbabel Installing Python bindings for Openbabel References

Preparing system

It is good to update and upgrade your Ubuntu system first. Log into your Ubuntu system and open the terminal by pressing Ctrl+Alt+T altogether, and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading Openbabel

Change to the directory where you want to download (here, it is Downloads). Open a terminal and paste the following command to download Openbabel or visit this page to download.

$ cd Downloads/

$ wget https://github.com/openbabel/openbabel/archive/refs/heads/master.zip

Installing required dependencies

Install the following libraries before proceeding.

$ sudo apt-get install cmake gcc g++ make libeigen3-dev libboost-all-dev

Installing Openbabel

Unzip the downloaded file.

$ unzip master.zip

It will create a new directory namely openbabel-master. Move inside this directory and make a new directory namely, build.

$ cd openbabel-master/

$ mkdir build

Move inside the build directory.

$ cd build/

Run the following commands to build Openbabel.

$ cmake ..

$ make

$ sudo make install

$ sudo ldconfig

Installing Python bindings for Openbabel

First, add openbabel to your environment using the following command.

$ export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

Now, install the Python bindings.

$ pip install openbabel

$ pip3 install openbabel

Check if Open Babel and the Python bindings are installed correctly:

$ obabel -V

It should display the version.

References

O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of cheminformatics, 3, 1-14.