Install Open Babel with Anaconda

This section provides a tutorial example on how to install Open Babel in an Anaconda (or Conda) environment on any computer system platform: Windows, macOS or Linux.

The best way to install Open Babel on any computer system platforms, Windows, macOS or Linux, is to use Anaconda, which is software environment manager for multiple systems platforms. Here is what I did to install Open Babel as a Conda environment on my CentOS computer.

1. Verify Open Babel Conda package for my system platform by look at the Open Babel page on the Conda Forge Website at https://anaconda.org/conda-forge/openbabel. I see 4 packages:

conda-forge  / packages / openbabel 3.1.1

  osx-arm64  v3.1.1
  linux-64  v3.1.1
  win-64  v3.1.1
  osx-64  v3.1.1

2. Verify my Conda version.

herong$ conda -V
conda 4.10.3

3. Create a new Conda environment as a root user.

herong$ su

herong# conda create -n hy-obabel
  environment location: /usr/local/anaconda3/envs/hy-obabel

4. Activate the environment and install Open Babel.

herong$ conda activate hy-obabel

(hy-obabel) herong# conda install -c conda-forge openbabel

5. Verify "obabel" command inside the Conda environment.

(hy-obabel) herong# obabel -V
Open Babel 3.1.0 -- Aug 18 2021 -- 08:52:33

6. Verify "obabel" command outside the Conda environment.

(hy-obabel) herong# conda deactivate

herong# /usr/local/anaconda3/envs/hy-obabel/bin/obabel -V
Open Babel 3.1.0 -- Aug 18 2021 -- 08:52:33

7. Verify "obabel" command as non-root user.

herong# exit

herong$ ls -l /usr/local/anaconda3/envs
drwxr-sr-x. 13 root   root  195 hy-obabel

herong$ /usr/local/anaconda3/envs/hy-obabel/bin/obabel -V
Open Babel 3.1.0 -- Aug 18 2021 -- 08:52:33

herong$ conda activate hy-obabel
(hy-obabel) herong$ obabel -V
Open Babel 3.1.0 -- Aug 18 2021 -- 08:52:33

8. Verify all commands provided by Open Babel.

herong$ cd /usr/local/anaconda3/envs/hy-obabel/bin/
herong$ ls -l o*

drwxr-sr-x. 13 root root  41456 obabel
drwxr-sr-x. 13 root root  23712 obconformer
drwxr-sr-x. 13 root root  24064 obdistgen
drwxr-sr-x. 13 root root  24128 obenergy
drwxr-sr-x. 13 root root  37048 obfit
drwxr-sr-x. 13 root root  32848 obfitall
drwxr-sr-x. 13 root root  28872 obgen
drwxr-sr-x. 13 root root  23792 obgrep
drwxr-sr-x. 13 root root  33240 obminimize
drwxr-sr-x. 13 root root  41272 obmm
drwxr-sr-x. 13 root root  34280 obprobe
drwxr-sr-x. 13 root root  33208 obprop
drwxr-sr-x. 13 root root  48696 obrms
drwxr-sr-x. 13 root root  37184 obrotamer
drwxr-sr-x. 13 root root  27512 obrotate
drwxr-sr-x. 13 root root  74488 obspectrophore
drwxr-sr-x. 13 root root  22792 obsym
drwxr-sr-x. 13 root root  23584 obtautomer
drwxr-sr-x. 13 root root  23008 obthermo

Note that:

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