5-amino-5-deoxy-D-glucopyranose

[JonasSchaub]

Hi,
I have been testing OPSIN on sugar names lately, and first of all, I was very happy with how well it worked! The only name I encountered that it had problems with was "5-amino-5-deoxy-D-glucopyranose". I got "Unable to find terminal atom of type: O at locant 5 for subtractive nomenclature using OPSIN" and I can't see the reason why. Is it a problem with the name or an OPSIN bug, what do you think?

The structure is Nojirimycin (https://www.ebi.ac.uk/chebi/CHEBI:28945).

[dan2097]

The name is correct cf. https://iupac.qmul.ac.uk/2carb/noGreek/34.html#341
It looks like an oversight, but it also looks like quite ugly to support properly. The issue is that operations are normally applied in a step-wise manner, and in this nomenclature 5-deoxy-D-glucopyranose doesn't correspond to a meaningful compound

[JonasSchaub]

"5-deoxy-D-glucopyranose" would basically be equal to "5-O-Carba-D-glucopyranose", which OPSIN seems to be able to parse.

[dan2097]

"5-deoxy-D-glucopyranose" would basically be equal to "5-O-Carba-D-glucopyranose", which OPSIN seems to be able to parse.

Maybe, deoxy normally corresponds to replacement of oxygen with hydrogen

[JonasSchaub]

deoxy normally corresponds to replacement of oxygen with hydrogen

true, you're absolutely right! I was already thinking of how to represent such a case internally when the structure is built step-by-step, sorry.