Stereochemistry with Open Babel

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Stereochemistry with Open Babel

This chapter provides introductions and tutorial examples on stereochemistry with Open Babel. Topics include introduction of stereochemistry; reading stereochemistry information from input molecule defined in 0D, 2D and 3D format; Stereo Perception performed by 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

Takeaways:

Stereochemistry is the study of stereoisomers, which are molecules having same atoms and same connectivities, but with different spatial arrangements.
0D stereoinformation in SMILES can be specified with [C@...] expressions.
0D Stereoinformation in SDF/MOL can be specified as atom parity codes.
2D Stereoinformation in SDF/MOL can be specified as bond stereo codes.
3D Stereoinformation in SDF/MOL can be specified as atom z-axis coordinates.
Stereo perception performed by Open Babel is the process of constructing stereo centers with stereoinformation received from input data.