Formula is incorrect for charged compounds

MassBank / RMassBank

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html

Other

12 stars 15 forks source link

Formula is incorrect for charged compounds #349

Open tsufz opened 1 year ago

tsufz commented 1 year ago

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 commented 1 year ago

See comment by @meier-rene in https://github.com/MassBank/MassBank-data/pull/237#issuecomment-1677244551 how the validator handles smiles, iupac, formulas.

tsufz commented 1 year ago

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

schymane commented 1 year ago

@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.