Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
What Is Stereochemistry
This section provides a quick introduction on stereochemistry, which is the study of stereoisomers, which are molecules having same atoms and same connectivities, but with different spatial arrangements.
What Is Stereochemistry? - Stereochemistry is the study of stereoisomers, which are molecules having same atoms and same connectivities, but with different spatial arrangements.
Here are some stereoisomers listed in the picture below:
You can do stereochemistry with Open Babel. But you need to understand how stereoinformation (information for stereochemistry) is managed in Open Babel.
The next tutorials will show you some features, limitations and issues with stereoinformation in Open Babel. More more information, see the official documentation of "Open Babel 3.0.1 documentation - Stereochemistry" at https://open-babel.readthedocs.io/en/latest/Stereochemistry/stereo.html.
Table of Contents
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
Read Stereoinformation from Input with Open Babel
Stereo Perception Performed by Open Babel
Write Stereoinformation to Output by Open Babel
Wedge-Hash Bond Changed by Open Babel
Hash Bond with Solid Line by Open Babel
Hash over Double Bond by 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