Extract molecule scaffolds

A program that removes all atoms that are not 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 dbase.oeb.gz
prompt> ExtractScaffold -exo false -i dbase.oeb.gz -o output.oeb.gz

Code

Download code

ExtractScaffold.java