Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
Install Open Babel Binary Package on macOS
This section provides a tutorial example on how to install Open Babel from a binary package on macOS computers.
The easiest option to install Open Babel on macOS computers is to install the Open Babel pre-compiled binary package as shown in this tutorial.
1. Go to Open Babel SourceForge.net Website at https://sourceforge.net/projects/openbabel.
2. Click to open "Files > openbabel > 2.3.1" folder. You see a list of Open Babel 2.3.1 download files.
3. Click "OpenBabel-2.3.1.mac.zip" to download the Open Babel binary package for macOS computers.
4. Unzip the donwlodad file "OpenBabel-2.3.1.mac.zip". You see the 3 files in a sub-folder:
-rw-r--r--@ 1 herong staff 1804 Oct 17 2011 ReadMe.rtf -rw-r--r--@ 1 herong admin 18504 May 10 2006 License.rtf -rw-r--r--@ 1 herong admin 11429471 Oct 17 2011 OpenBabel.pkg
5. Click to open "OpenBabel.pkg" to start the installation. And finish the installation with default options.
6. Open a terminal window and verify the installation.
herong$ babel -V Open Babel 2.3.1 -- Oct 13 2011 -- 15:14:47
7. Verify all commands provided by Open Babel.
herong$ ls -l /usr/local/bin -rwxr-xr-x 1 root wheel 123424 Oct 17 2011 babel -rwxr-xr-x 1 root wheel 123104 Oct 17 2011 obabel -rwxr-xr-x 1 root wheel 89520 Oct 17 2011 obchiral -rwxr-xr-x 1 root wheel 86968 Oct 17 2011 obconformer -rwxr-xr-x 1 root wheel 96184 Oct 17 2011 obenergy -rwxr-xr-x 1 root wheel 121888 Oct 17 2011 obfit -rwxr-xr-x 1 root wheel 96448 Oct 17 2011 obgen -rwxr-xr-x 1 root wheel 99856 Oct 17 2011 obgrep -rwxr-xr-x 1 root wheel 105248 Oct 17 2011 obminimize -rwxr-xr-x 1 root wheel 97008 Oct 17 2011 obprobe -rwxr-xr-x 1 root wheel 105808 Oct 17 2011 obprop -rwxr-xr-x 1 root wheel 96640 Oct 17 2011 obrotamer -rwxr-xr-x 1 root wheel 94712 Oct 17 2011 obrotate -rwxr-xr-x 1 root wheel 180768 Oct 17 2011 obspectrophore ...
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