Cheminformatics Tutorials - Herong's Tutorial Examples

∟Open Babel: The Open Source Chemistry Toolbox

∟Install Open Babel on Windows Computers

This section provides a tutorial example on how to install Open Babel on a Windows computer.

The best option to install Open Babel on Windows computers is to install it in an Anaconda (or Conda) environment as shown in the previous tutorial.

But if you have Conda on your Windows computer, you can install the Open Babel pre-compiled binary package as shown below:

1. Go to GitHub Website for Open Babel at https://github.com/openbabel/openbabel/releases.

2. Click to download "OpenBabel-3.1.1-x64.exe" file. Save the downloaded file to your Windows computer.

3. Double-click the downloaded file "OpenBabel-3.1.1-x64.exe" to install it.

4. Follow the installation wizard to finish it.

5. View installed program files in a command window: 

herong> dir "C:\Program Files\OpenBabel-3.1.1\*.exe"

2020/05/16  18:57            34,816 obabel.exe
2020/05/16  18:57            31,744 obconformer.exe
2020/05/16  18:57            30,720 obdistgen.exe
2020/05/16  18:58            31,744 obenergy.exe
2020/05/16  18:58            40,448 obfit.exe
2020/05/16  18:58            38,912 obfitall.exe
2020/05/16  18:58            34,304 obgen.exe
2020/05/16  18:58            38,912 obgrep.exe
2020/05/16  18:58         3,880,960 obgui.exe
2020/05/16  18:58            36,864 obminimize.exe
2020/05/16  18:58            41,472 obmm.exe
2020/05/16  18:58            33,280 obprobe.exe
2020/05/16  18:58            36,352 obprop.exe
2020/05/16  18:58            47,616 obrms.exe
2020/05/16  18:58            34,816 obrotamer.exe
2020/05/16  18:58            32,256 obrotate.exe
2020/05/16  18:58            70,144 obspectrophore.exe
2020/05/16  18:58            27,648 obsym.exe
2020/05/16  18:58            30,720 obtautomer.exe
2020/05/16  18:58            33,792 obthermo.exe
2021/09/15  16:20            61,475 Uninstall.exe
2020/05/02  19:01        14,974,024 vc_redist.x64.exe

6. Check Open Babel version: 

herong> obabel -V
Open Babel 3.1.1 -- May 16 2020 -- 11:57:55

Open Babel 3.1.1 is ready to use!

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

 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

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB