Hash over Double Bond by Open Babel

This section provides a tutorial example demonstrating how Open Babel 'correcting' wedge-hash bond representations of stereo centers from molecule input data.

If a stereo center has a double bond, and Open Babel decides to bend it for representing the chirality, the double bond will be displayed as a wedge or hash bond.

Here is an example, where Open Babel replaces the double bond sign with the hash sign to represent the chirality for the first molecule structure:

herong$ obabel '-:OC([P@](=O)(NC)O)' -O chirality-1.smi

herong$ obabel '-:OC([P@](=OCC)(NC)O)' -O chirality-2.smi

herong$ obabel chirality-1.smi chirality-2.smi -O output.svg 

herong$ chrome output.svg
Hash over Double Bond by Open Babel
Hash over Double Bond by Open Babel

If you look at the first molecule structure, you can see that the P=O branch is the most simple branch of the stereo center. So Open Babel decided to bend P=O with a hash sign.

If you look at the second molecule structure, you can see that the PO branch is the most simple branch of the stereo center. Open Babel decided to bend PO with a hash sign.

In other words, Open Babel selects the most simple branch and bends it with a wedge or hash sign to represent the chirality. It doesn't care if selected branch is a single bond or double bond.

By the way, phosphorus (P) is a multivalent atom and can form +3 and +5 cations. So it can have 3 or 5 pairs of bonds in stable state.

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

 What Is Stereochemistry

 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

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB