List of Open Babel Command Line Tools

This section provides a list of command line tools provided by Open Babel.

As of release 3.1.0, Open Babel package provides the following command line tools:

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

List of Open Babel Command Line Tools

 "obchiral" - Print Chirality Information

 "obconformer" - Generate Best Conformer

 "obenergy" - Calculate Molecule Energy

 "obfit" - Superimpose Two Molecules

 "obgen" - Generate Molecule 3D Structures

 "obgrep" - Search Molecules using SMARTS

 "obminimize" - Optimize Geometry/Energy of Molecule

 "obprobe" - Create Electrostatic Probe Grid

 "obrotamer" - Generate Random Rotational Isomers

 "obrotate" - Rotate Dihedral Angles with SMARTS

 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