Cheminformatics Tutorials - Herong's Tutorial Examples

∟Open Babel: The Open Source Chemistry Toolbox

∟Change Display Command on Open Babel GUI

This section provides a tutorial example on how to change structure display command on Open Babel GUI to use Google Chrome browser.

By default, Open Babel GUI uses Firefox to display molecule structure. If you don't have Firefox installed, you will get an error:

Obgui Error:
Execution of command "firefox ..." failed.
System cannot find the file.

To fix the problem, you can change the display command as shown in this tutorial.

1. Start Open Babel GUI and go to "View > Configure Structure Display" menu. You see a small window showing the current display command.

2. Enter a new command to use a different browser. For example, enter the following to use the Google Chrome browser:

\Progra~1\Google\Chrome\Application\Chrome file:///
C:\Users\herong\AppData\Local\Temp/gui.svg

3. Enter a new molecule in the input section on the left.

4. Click to select the "Display in ..." checkbox in the output section on the right.

5. Click the "CONVERT" button. You see the molecule structure displayed in the Google Chrome browser.

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

Change Display Command on Open Babel GUI - Updated in 2023, by Herong Yang