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rformassspectrometry / CompoundDb

Creating and using (chemical) compound databases
https://rformassspectrometry.github.io/CompoundDb/index.html
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loading invalid sdf #69

Closed jmbadia closed 3 years ago

jmbadia commented 3 years ago

Hi, I parsed negative LC-MS/MS spectra from MoNA by using the compound_tbl_sdf(sdf file)function. It returns the following warning;

In read.SDFset(file) :
    54 invalid SDFs detected. To fix, run: valid <- validSDF(sdfset); sdfset <- sdfset[valid]

resulting in a result with invalid SDF we know nothing about Maybe we could offer an argument ( compound_tbl_sdf(..., onlyValid)) in order not to load such invalid SDFs by applying the code suggested by the warning.

jmbadia commented 3 years ago

Thanks @jorainer . Looks great to me.

jorainer commented 3 years ago

I'm closing the issue now - feel free to re-open if it's not working.