Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
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
SMILES (Simplified Molecular-Input Line-Entry System)
►Open Babel: The Open Source Chemistry Toolbox
►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