List of Open Babel Command Line Tools

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Command Line Tools Provided by Open Babel

∟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:

obabel - Convert chemistry and molecular modeling data files.
obchiral - Print molecular chirality information. Removed since Open Babel 3.1.0.
obconformer - Generate conformer coordinates.
obdistgen - Generate rough 3D coordinates for SMILES (or other 0D files)
obenergy - Calculate the energy for a molecule.
obfit - Superimpose two molecules based on a pattern.
obfitall - Superimpose multiple molecules based on a pattern.
obgen - Generate 3D coordinates for a molecule.
obgrep - Advanced-search molecules using SMARTS.
obminimize - Optimize the geometry, minimize the energy for a molecule.
obmm - Molecule mechanics tools.
obprobe - Create electrostatic probe grid.
obprop - Print standard molecular properties.
obrms - Calculate the heavy-atom RMSD between two chemically identical structures.
obrotamer - Generate conformer/rotamer coordinates.
obrotate - Batch-rotate dihedral angles matching SMARTS patterns.
obspectrophore - Generate Spectrophores, which are one-dimensional descriptors generated from the property fields surrounding the molecules.
obsym - Detect 3D point group symmetry.
obtautomer - Enumerate tautomer SMILES and canonical tautomer SMILES.
obthermo - Extract the thermochemistry for a molecule.

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

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