Hash over Double Bond by Open Babel

Cheminformatics Tutorials - Herong's Tutorial Examples

∟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

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.