Extract molecule scaffolds

This example is a program that removes all atoms that are neither ring atoms nor atoms in linkers between rings. By default, double bonded atoms exo to a ring are included as ring atoms. This can be changed by using the flag -exo.

Example

prompt> extractscaffold.py dbase.oeb.gz
prompt> extractscaffold.py -exo false -i dbase.oeb.gz -o output.oeb.gz

Code

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extractscaffold.py