output formats

[cbroeckl]

thanks for the work on this - i am excited to give it a go! noticed a few issues with the output format:

1. msp format does not add ion annotations, even when the --annotation flag is used.
2. i would request that there are two additional bits of information exported in msp and mgf format
   a. molecular formula of the parent molecule (not ion)
   b. precursor accurate mass, or monoisotopic molecular weight of parent ion.

[cbroeckl]

it could also be useful to implement a relative ion intensity filter - i.e. only ions with intensity >= 1% of the most intense signal are exported.

Less important - It appears that the ion intensities are proportions - it is more common to have these reported in relative units such that the base peak intensity ion is reported as 1, or 100, or 1000.

could be useful to export the smiles string with the spectrum as well, so that the structure is always associated.

[ch4perone]

Hi Corey,
thanks for noting down these issues. I have added the ion annotations to the MSP format now, as well as the additional output information you suggested. Furthermore, you can select a min probability threshold to drop small peaks via the CML option --min_prob. For now, I kept the scale of relative intensities as the are, since they reflect the probabilistic model of FIORA.

Let me know if you notice anything still wrong or missing