Ok, I figured out one way, but am curious if there are any more streamlined approaches. For the sake of anyone else with this issue: After the metabolites are calculated, in the tree click on the heading for the metabolites (which shows up between the SMILES for the parent and the list of SMILES for the metabolites), and the structure image in the big panel will have the number of metabolites in that category written in bold in one corner. Double-click on the structure image, and a window of all of the metabolites will pop up, and it is possible to save a tab-delimited text file of SMILES strings from there.
The drawback here is that for multiple generations of metabolites, I have to save a SMILES file for every metabolite in every generation, and that becomes tedious very quickly. At least this is still much faster than copying and pasting each SMILES string individually, but is it possible to accomplish this in a more elegant way? Thanks!
To solve this issue, I use to perform metabolization on the "Profiling" tab instead of the "Input" tab. This will produce an output on the main screen, under the profiling node instead of the left pane.
After applying the desired simulator or observed metabolism, just expand the Profile>>Metabolism/Transformations>>"Applied simulator" on the main screen and you can simply double click in order to search or export to a .smi file all the created metabolites.
Hop this helps.
Many thanks, Alexandre!