Cheminformatics Tutorials - Herong's Tutorial Examples

∟Open Babel: The Open Source Chemistry Toolbox

∟Open Babel Installation Options on macOS

This section provides a quick introduction of Open Babel installation options for macOS computers.

There are a number of options for installing Open Babel on macOS computers:

1. Install Open Babel in a Anaconda (or Conda) environment using "conda install -c conda-forge openbabel" command.

2. Install Open Babel with a pre-compiled binary package. Open Babel 2.3.1 macOS binary package is available. This is the easiest option to install Open Babel on macOS computers.

3. Install Open Babel with homeBrew installer using "brew install open-babel".

4. Install Open Babel with source code using "clang" or "gcc" compiler.

There is also a GUI (Graphical User Interface) for Open Babel called iBabel available for macOS system. See iBabel Website http://www.macinchem.org/ibabel/ for more information.

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