Write Stereoinformation to Output by Open Babel

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Write Stereoinformation to Output by Open Babel

This section provides a quick introduction on how stereoinformation is written to output by Open Babel.

Stereoinformation is being written to output data based on stereo centers maintained by Open Babel according the following rules:

1. 3D Stereoinformation - By default, 3D coordinates are copied over from input data to output data without any changes.

If needed, you can specify "--gen3d" option to re-generate 3D coordinates.

2. 2D Stereoinformation - By default, 2D Stereoinformation is always re-generated from perceived stereo centers. And there is no option to change this behavior.

In other words, the file writers re-generate the wedges or hashes from the stereo data at the point of writing; in other words, the particular location of the wedge/hash (or even whether it is present) may change on writing. This was done to ensure that the written structure accurately represents Open Babel’s internal view of the molecule; passing wedges/hashes through unchanged may not represent this (consider the case where a wedge bond is attached to a tetrahedral center which cannot be a stereocenter).

3. 0D Stereoinformation - 0D Stereoinformation is always written to output data according stereo centers perceived by Open Babel from input data. 0D Stereoinformation from input data fully replaced.

As you can see, Open Babel is not simply copy Stereoinformation from input to output. It reads stereoinformation from input, constructs stereo centers, and writes normalized stereoinformation to output.