Cheminformatics Tutorials - Herong's Tutorial Examples

∟Open Babel: The Open Source Chemistry Toolbox

∟Run Open Babel GUI on Windows Computers

This section provides a tutorial example on how to run Open Babel GUI tool on a Windows computer.

Open Babel GUI is the graphical user interface for Open Babel. You can use Open Babel GUI to open a molecule file in any supported format and convert it to any other format.

Here is how to Open Babel GUI on a Windows computer.

1. Search for "Open Babel GUI" in "Start > Search" box.

2. Click "Open Babel GUI" in the search result list. You see Open Babel GUI window displayed.

3. Keep "smi -- SMILES format" as the INPUT FORMAT.

4. Check to select the "Input below (ignore input file)" checkbox. And enter the following SMILES string: 

F[C@@](Cl)(Br)I

5. Change the OUTPUT FORMAT to "sdf -- MDL MOL format" on the right side.

6. Click the "CONVERT" button in the middle. You see the converted molecule displayed in SDF/Mol format.

Open Babel GUI Screenshot
Open Babel GUI Screenshot

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