Open Babel Installation Options on Linux

This section provides a quick introduction of Open Babel installation options for Linux computers.

There are a number of options for installing Open Babel on Linux computers:

1. Install Open Babel in an Anaconda (or Conda) environment. However, I need to install Anaconda on my CentOS 8 computer first. But it is still the best option.

2. Install Open Babel with a software package manager like DNF/YUM, which automatically find, download and install it from binary package repositories. For example, on my CentOS 8 system,

herong$ cat /etc/system-release
CentOS Linux release 8.3.2011

herong$ dnf search babel
openbabel.x86_64 : Chemistry software file format converter
openbabel-gui.x86_64 : Chemistry software file format converter - GUI version
openbabel-libs.x86_64 : Chemistry software file format converter - libraries
...

3. Search, find and download binary packages manually. For example, if you go to https://centos.pkgs.org and search for "openbabel", you see the following:

Enterprise Linux 9 (CentOS 9, RHEL 9, Rocky Linux 9, AlmaLinux 9)
openbabel-3.1.1-14.el9.x86_64.rpm - Chemistry software file format converter
openbabel-libs-3.1.1-14.el9.x86_64.rpm - The libraries ...
...
Enterprise Linux 8 (CentOS 8, RHEL 8, Rocky Linux 8, AlmaLinux 8)
openbabel-3.1.1-14.el8.x86_64.rpm - Chemistry software file format converter
openbabel-libs-3.1.1-14.el8.x86_64.rpm - The libraries ...
...
Debian 11 (Bullseye)
libopenbabel7_3.1.1+dfsg-6_amd64.deb - Chemical toolbox library
openbabel_3.1.1+dfsg-6_amd64.deb - Chemical toolbox utilities (cli)
...
Ubuntu 22.04 LTS (Jammy Jellyfish)
libopenbabel7_3.1.1+dfsg-6ubuntu5_amd64.deb - Chemical toolbox library
openbabel_3.1.1+dfsg-6ubuntu5_amd64.deb - Chemical toolbox utilities (cli)
...

4. Install Open Babel with source code using "make" and "gcc" build tools. This is not a very bad option, if you are developer on CentOS systems. You can get Open Babel source code from Repository Websites listed below:

Table of Contents

 About This Book

 SMILES (Simplified Molecular-Input Line-Entry System)

Open Babel: The Open Source Chemistry Toolbox

 What Is Open Babel

 Install Open Babel with Anaconda

 Install Open Babel on Windows Computers

 Run Open Babel GUI on Windows Computers

 Change Display Command on Open Babel GUI

Open Babel Installation Options on Linux

 Install Open Babel Binary Package on CentOS

 "Open Babel Error in LoadAllPlugins" Error

 Install Open Babel from Source Code

 Install Open Babel 2.4.1 from Source Code

 Open Babel Installation Options on macOS

 Install Open Babel Binary Package on macOS

 Using Open Babel Command: "obabel"

 Generating SVG Pictures with Open Babel

 Substructure Search with Open Babel

 Similarity Search with Open Babel

 Fingerprint Index for Fastsearch with Open Babel

 Stereochemistry with Open Babel

 Command Line Tools Provided by Open Babel

 RDKit: Open-Source Cheminformatics Software

 rdkit.Chem.rdchem - The Core Module

 rdkit.Chem.rdmolfiles - Molecular File Module

 rdkit.Chem.rdDepictor - Compute 2D Coordinates

 rdkit.Chem.Draw - Handle Molecule Images

 Molecule Substructure Search with RDKit

 rdkit.Chem.rdmolops - Molecule Operations

 RDKit Performance on Substructure Search

 OCSR (Optical Chemical Structure Recognition)

 AlphaFold - Protein Structure Prediction

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB