CandyCrunch

--mode, type=string: mass spectrometry mode; options are 'negative' or 'positive'; default: 'negative' 

--modification, type=string: chemical derivatization of glycans; options are “reduced”, “permethylated”, “2AA”, “2AB” or “custom”; default:”reduced”
| 
|--mass_tag, type=float: only if modification = "custom", mass of custom reducing end tag ; default:None 

--lc, type=string: type of liquid chromatography; options are 'PGC', 'C18', and 'other'; default:'PGC' 

--trap, type=string: type of mass detector used; options are 'linear', 'orbitrap', 'amazon', and 'other'; default:'linear' 

--rt_min, type=float: whether only spectra from a minimum retention time (in minutes) onward should be considered; default:0 

--rt_max, type=float: whether only spectra up to a maximum retention time (in minutes) should be considered; default:0 

--rt_diff, type=float: maximum retention time difference (in minutes) to peak apex that can be grouped with that peak; default:1.0 

--spectra, type=float: whether to also output the actual spectra used for prediction; default:False 

--get_missing, type=bool: whether to also organize spectra without a matching prediction but a valid composition; default:False
|
|--filter_out, type=set: only if get_missing = "True", set of monosaccharide or modification types that is used to filter out compositions (e.g., if you know there is no Pen); default:{'Kdn', 'P', 'HexA', 'Pen', 'HexN', 'Me', 'PCho', 'PEtN'} 
  
--mass_tolerance, type=float: permitted variation in Da, to still consider two masses to stem from the same molecule.; default:0.5 

--supplement, type=bool: whether to impute observed biosynthetic intermediaries from biosynthetic networks; default:True 

--experimental, type=bool: whether to impute missing predictions via database searches etc.; default:True
|
|--taxonomy_class, type=string: only if experimental = "True", which taxonomy class to pull glycans for populating the mass_dic for experimental=True; default:'Mammalia' 

--plot_glycans, type=bool: whether you want to save an output.xlsx file that contains SNFG images of all top1 predictions, will be saved in the same folder as spectra_filepath; default:False

model, type=Pytorch object: loaded from a checkpoint of a trained CandyCrunch model  

glycans, type=list: ordered list of glycans used to train CandyCrunch which can be predicted by the model 

libr, type=list: library of monosaccharides, used as a mapping index to ensure unique graph construction 

bin_num, type=list: number of bins to separate the ms2 spectrum into 

frag_num, type=list: number of top fragments to show in df_out per spectrum; default:100 

mode, type=string: mass spectrometry mode; options are 'negative' or 'positive'; default: 'negative' 

modification, type=string: chemical derivatization of glycans; options are “reduced”, “permethylated”, “2AA”, “2AB” or “custom”; default:”reduced”
| 
|--mass_tag, type=float: only if modification = "custom", mass of custom reducing end tag ; default:None 

lc, type=string: type of liquid chromatography; options are 'PGC', 'C18', and 'other'; default:'PGC' 

trap, type=string: type of mass detector used; options are 'linear', 'orbitrap', 'amazon', and 'other'; default:'linear' 

rt_min, type=float: whether only spectra from a minimum retention time (in minutes) onward should be considered; default:0 

rt_max, type=float: whether only spectra up to a maximum retention time (in minutes) should be considered; default:0 

rt_diff, type=float: maximum retention time difference (in minutes) to peak apex that can be grouped with that peak; default:1.0 

pred_thresh, type=float: prediction confidence threshold used for filtering; default:0.01 

temperature, type=float: the temperature factor used to calibrate logits; default:1.15 

spectra, type=float: whether to also output the actual spectra used for prediction; default:False 

get_missing, type=bool: whether to also organize spectra without a matching prediction but a valid composition; default:False
|
|--filter_out, type=set: only if get_missing = "True", set of monosaccharide or modification types that is used to filter out compositions (e.g., if you know there is no Pen); default:{'Kdn', 'P', 'HexA', 'Pen', 'HexN', 'Me', 'PCho', 'PEtN'} 

mass_tolerance, type=float: permitted variation in Da, to still consider two masses to stem from the same molecule.; default:0.5 

extra_thresh, type=float: prediction confidence threshold at which to allow cross-class predictions (e.g., predicting N-glycans in O-glycan samples); default:0.2 

supplement, type=bool: whether to impute observed biosynthetic intermediaries from biosynthetic networks; default:True 

experimental, type=bool: whether to impute missing predictions via database searches etc.; default:True
|
|--mass_dic, type=dict: only if experimental = "True", dictionary of form mass : list of glycans; will be generated internally 
|
|--taxonomy_class, type=string: only if experimental = "True", which taxonomy class to pull glycans for populating the mass_dic for experimental=True; default:'Mammalia' 
|
|--df_use, type=DataFrame: only if experimental = "True", sugarbase-like database of glycans with species associations etc.; default: use glycowork-stored df_glycan 

plot_glycans, type=bool: whether you want to save an output.xlsx file that contains SNFG images of all top1 predictions, will be saved in the same folder as spectra_filepath; default:False 

{'my_spectra_exp1: pd.DataFrame(...),
 'my_spectra_exp2: pd.DataFrame(...),
 'my_spectra_exp3: pd.DataFrame(...),
 'my_spectra_exp4: pd.DataFrame(...)}

max_cleavages, type=int: maximum number of allowed concurrent cleavages per possible fragment; default:3 

simplify, type=bool: whether to select a single fragment for each mass based on mass difference, number of cleavages, and other fragments; default:True 

charge, type=int: the charge state of the precursor ion (singly-charged, doubly-charged, etc.); default:-1 

label_mass, type=float: mass of the glycan label or reducing end modification; default:2.0156 

iupac, type=bool: whether to also return the fragment sequence in IUPAC-condensed nomenclature; default:False 

libr, type=list: library of monosaccharides, used as a mapping index to ensure unique graph construction 

{425.07: {'Theoretical fragment masses': [425.12955],
  'Domon-Costello nomenclatures': [['02A_3_Alpha', 'M_H2O']],
  'Fragment charges': [-1]},
 443.07: {'Theoretical fragment masses': [443.1401],
  'Domon-Costello nomenclatures': [['02A_3_Alpha']],
  'Fragment charges': [-1]},
 546.19: {'Theoretical fragment masses': [546.18775],
  'Domon-Costello nomenclatures': [['Y_3_Beta', 'Y_2_Alpha']],
  'Fragment charges': [-1]},
 1216.32: {'Theoretical fragment masses': [1216.43105],
  'Domon-Costello nomenclatures': [['M_C2H4O2']],
  'Fragment charges': [-1]}}