Molecular formula for v2

[RalfG]

Should we switch notation for molecular formula's? For instance, in ProForma, the ChemForma notation is used.

[douweschulte]

I would propose to use the exact same format as ProForma (based on ChemForma indeed but better specified and missing some of the hinted at features), and I would propose to include the charge in there as well in the same ProForma notation. If we want to switch I would propose to switch XLMOD as well that should reduce the number of different molecular formula notations you need to read in to be fully ProForma compliant from 5 to 3 (Left are: ProForma, Unimod, & Resid). If we adopt the OBO linting and fixing workflow I have been working on it would be quite easy to switch over, just ask the code to write it out as a different format.