Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Install Open Babel Binary Package on CentOS
This section provides a tutorial example on how to install Open Babel from a binary package on CentOS Systems.
If for some reason, you don't want to use Open Babel in an Anaconda (or Conda) environment, you can try to install the binary package for your computer platform. Here is what I did on my CentOS 8 system.
1. Search for Open Babel packages in DNF repositories. openbabel 3.1.1 for CentOS 8 is available in "epel" repository at http://mirrors.mit.edu/epel/8/Everything/x86_64/.
herong$ cat /etc/centos-release CentOS Linux release 8.2.2004 (Core) herong$ dnf search openbabel openbabel.x86_64 : Chemistry software file format converter openbabel-devel.x86_64 : Development tools for programs which will use ... openbabel-doc.noarch : Additional documentation for the Open Babel library openbabel-gui.x86_64 : Chemistry software file format converter - GUI version openbabel-libs.x86_64 : Chemistry software file format converter - libraries perl-openbabel.x86_64 : Perl wrapper for the Open Babel library python3-openbabel.x86_64 : Python wrapper for the Open Babel library ruby-openbabel.x86_64 : Ruby wrapper for the Open Babel library herong$ dnf info openbabel Available Packages Name : openbabel Version : 3.1.1 Release : 14.el8 Architecture : x86_64 Size : 185 k Source : openbabel-3.1.1-14.el8.src.rpm Repository : epel herong$ dnf repoinfo epel Repo-id : epel Repo-name : Extra Packages for Enterprise Linux 8 - x86_64 Repo-status : enabled Repo-baseurl : http://mirrors.mit.edu/epel/8/Everything/x86_64/
2. Install "openbabel" as the core package of Open Babel. The "openbabel-libs" is also installed as a dependence. The
herong$ sudo dnf install openbabel installed: openbabel-3.1.1-14.el8.x86_64 openbabel-libs-3.1.1-14.el8.x86_64
3. Try the "obabel" command.
herong$ obabel -V Open Babel 3.1.1 -- Sep 27 2022 -- 18:26:52 herong$ which obabel /usr/bin/obabel herong$ ls -l /usr/bin/obabel -rwxr-xr-x. 1 root root 33760 Sep 28 02:29 /usr/bin/obabel
Okay. The "obabel" command is installed at /usr/bin/obabel and ready to run.
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
►Open Babel: The Open Source Chemistry Toolbox
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
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction