loading invalid sdf

[jmbadia]

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]

Thanks @jorainer . Looks great to me.

[jorainer]

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