Stereo Perception Performed by Open Babel

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Stereo Perception Performed by Open Babel

This section provides a quick introduction on the stereo perception performed by Open Babel, which is the process of constructing stereo centers with stereoinformation received from input data.

What Is the Stereo Perception performed by Open Babel? - Stereo perception performed by Open Babel is the process of constructing stereo centers with stereoinformation received from input data.

Stereo perception is performed in the following order of precedence:

1. Constructing stereo centers with 3D stereoinformation from input data. A symmetry analysis identifies stereogenic centers whose stereo-configurations are perceived from the coordinates.

2. Adding stereo centers with 2D stereoinformation from input data. This is done based on a symmetry analysis, and their configuration inferred either from the geometry (for cis/trans bonds) or from bonds marked as wedge/hash (tetrahedral centers). Only new stereo centers are added. Existing stereo centers perceived from 3D stereoinformation are not changed.

3. Adding stereo centers with 0D stereoinformation from input data depends on the format of input data. Here are two examples:

SDF/MOL Format - By default, 0D stereoinformation from input data is ignored, unless "-as" option is provided. If processed, only new stereo centers are added. Existing stereo centers perceived from 3D and 2D stereoinformation are not changed.
SMILES Format - By default, 0D stereoinformation from input data is processed, unless "-aS" option is provided.