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Formula is incorrect for charged compounds #349

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tsufz opened this issue Aug 14, 2023 · 3 comments
Open

Formula is incorrect for charged compounds #349

tsufz opened this issue Aug 14, 2023 · 3 comments

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@tsufz
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tsufz commented Aug 14, 2023

The validator catch for example:

Formula from CH$IUPAC: [C27H42NO2]+ (estimated by validator)
Formula from CH$FORMULA: C27H42NO2 (used in record)

for Benzethonium.

Should be correct as the smiles is correctly annotated.

@tsufz tsufz added the bug label Aug 14, 2023
@tsufz tsufz added this to the Adduct and formula annotation milestone Aug 14, 2023
@tsufz
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tsufz commented Aug 14, 2023

See comment by @meier-rene in MassBank/MassBank-data#237 (comment) how the validator handles smiles, iupac, formulas.

@tsufz
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tsufz commented Aug 16, 2023

@sneumann, @meowcat and @schymane, any opinion on @meier-rene 's suggestions?

@schymane
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@schymane is in poor connectivity and unable to comment with traces/comments now spread across multiple issues. Seems there are inconsistencies with how major resources/ toolkits handle this and we should decide how to deal with this carefully.

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