BiGG models can raise invalid decimal literal errors

[Kivean]

BiGG naming conventions allow metabolite names to start with a number, which apparently causes issues when parsing the SBML file. Running DNNGIOR on this model. Also running it with the Phylum_Proteobacteria NN.

Here's the error DNNGIOR is throwing:

Traceback (most recent call last):

  File ~/miniforge3/envs/dnngior/lib/python3.11/site-packages/IPython/core/interactiveshell.py:3748 in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)

  Cell In[17], line 2
    gapfilled_model_complete = dnngior.Gapfill(draftModel = path_to_model, trainedNNPath=path_to_NN, dbType='BiGG',

  File ~/miniforge3/envs/dnngior/lib/python3.11/site-packages/dnngior/gapfill_class.py:70 in __init__
    self.db_reactions   =   Reaction(biochem_input = self.path_to_biochem, dbType=self.dbType)

  File ~/miniforge3/envs/dnngior/lib/python3.11/site-packages/dnngior/reaction_class.py:63 in __init__
    self.biochem_input = self.__get_reactions_from_biochem_input(biochem_input)

  File ~/miniforge3/envs/dnngior/lib/python3.11/site-packages/dnngior/reaction_class.py:163 in __get_reactions_from_biochem_input
    reactions[reaction]['metabolites'] = eval(react_d[reaction][0]) #Evaluate the string as a dictionary.

  File <string>:1
    4crsol_c <->
    ^
SyntaxError: invalid decimal literal

If I'm reading get_reactions_from_biochem_input correctly, its reading reaction titles. The model itself includes 4crsol in only one reaction title, "R_sink_4crsol_c". There are other compounds (and therefore reaction titles) which start with numbers, I don't know why its throwing the error with this one in particular.

[Biomerene]

As you mentioned the BiGG database can behave a little erratic due to the naming convention, this might be fixable using the cleaner version from the development branch: here. You could fix this by placing it in you local install installation of your package: ~/miniforge3/envs/dnngior/lib/python3.11/site-packages/dnngior/files/biochemistry/.