Getting an Error when i used a metabolite Identifier that contains a number

[Rahmaabubakr]

Hello,

when i used this
model.metabolites.5mthf_LSQBKTc_RSQBKT.summary()

and the metabolite identifier contains a number, i get this error:
Cell In[72], line 1
model.metabolites.5mthf_LSQBKTc_RSQBKT.summary()
^
SyntaxError: invalid decimal literal

it works fine with other metabolites that their identifier don't contain a number, however, it occurs with all id with numbers, what should i do?

Thank you very much in advance

[matthiaskoenig]

Hi @Rahmaabubakr,
will not work with numbers. It is just a very bad idea to have identifiers starting with numbers.
These are not valid SBML identifiers nor valid python variable names. So they will create a ton of issues everywhere in your workflows.
There is a lot of discussion about this in the issues, see for instance: #883

My personal recommendation: replace the identifiers of these metabolites.
Best Matthias

[Rahmaabubakr]

Thank you very much.
So, should i Edit the model and work from the Edited version?
So, how can i open a file from the computer not from biomodels?

[matthiaskoenig]

You can download the SBML from biomodels. You can select the SBML file from Biomodels.
First I would check that the model is valid SBML, i.e. run it once through a validator: https://sbml.org/validator_servlet/
I.e. the identifier problem could be a hint for more things to be wrong in the model.

If you are sure the model is valid you could replace the ids either manually (which I would not recommend) or based on a python script.