Open Babel: The Open Source Chemistry Toolbox

This chapter provides introductions and tutorial examples on Open Babel, The Open Source Chemistry Toolbox. Topics include installing options; install Open Babel with Anaconda; installation from binary packages on Windows and macOS; installation from source code on CentOS.

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

Takeaways:

Table of Contents

 About This Book

 SMILES (Simplified Molecular-Input Line-Entry System)

Open Babel: The Open Source Chemistry Toolbox

 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

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