Parsing of parameters for fraggraph instead of fragmentation dropdown

Structure of parameters for fraggraph:

"ETD": {
        "start_ioncaps_types": ["zdot","z+1","z+2"], 
        "end_ioncaps_types": ["cdot","c"],
        "msms_tol": 10,
        "msms_tol_unit": "ppm",
        "charge_loss": false, 
        "max_prec_charge": 10,
        "monoisotopic": false,
        "max_isotope": "auto"
}

Nomenclature of ions basically overlaps with https://github.com/michabirklbauer/internal_ions/blob/69cbf2e852bba7d18899b47fbfd895f9eb3e2cb7/util/constants.py#L4 However, we don't have the decoy ions here. Do we need them? Also we need to split into start and end, but this is straight forward. Also tolerance is in ppm, for fragannot we have Da. Max_charge and Max_isotope would be fraggraph specific parameters. The charges from fragannot are not directly translatable to max_charge I guess

michabirklbauer / internal_ions

Parsing of parameters for fraggraph instead of fragmentation dropdown #26