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Issue parsing this molecule about opsin HOT 2 CLOSED

dan2097 avatar dan2097 commented on August 29, 2024
Issue parsing this molecule

from opsin.

Comments (2)

dan2097 avatar dan2097 commented on August 29, 2024

Original comment by guillaume godin (Bitbucket: guillaumegodin, ).


I try removing all the ' & '' and it works:
acetic acid 2-methyl-2-(1,2,4-trimethylpent-2-enyloxy)propyl ester
CC(COC(C)=O)(C)OC(C(=CC(C)C)C)C

Is it possible to accept those ' & '' values in the input name ?

Guillaume GODIN

from opsin.

dan2097 avatar dan2097 commented on August 29, 2024

Original comment by Daniel Lowe (Bitbucket: dan2097, GitHub: dan2097).


Hi Guillaume,
As you correctly spotted OPSIN does not like the additional primes which as you can see from your simplified name are redundant.

The logic behind the primes is somewhat like http://www.acdlabs.com/iupac/nomenclature/79/r79_36.htm Rule 2.5b (which OPSIN does not currently implement, mainly as names constructed in this manner are very rare, and this rule does not appear in more recent IUPAC recommendations)... but the combination of primes to indicate level of branching and brackets is idiosyncratic.

Do you where the name came from? Some name to structure algorithms, like ChemDraw's are quite sloppy about primes (as long as all locants referring to the same group have the same number of primes) and will accept the name, but unless the issue is common I prefer to be strict.

from opsin.

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