Loading and Editing a model

[Rahmaabubakr]

Hello Cobrapy Community,

Hope everyone is doing well. I would really appreciate your capacity to answer my basic questions since I am new to Cobrapy. First, how can I load a model from the computer? how can i edit the id names of some metabolites since they contain numbers, should i open the file and just change it?

Thank you very much,
Rahma A. Abubakr

[Rahmaabubakr]

I would really appreciate getting answers here, please :)

[cdiener]

Hi,

It's a pretty general question. There are many ways to load models with COBRAPY. They are documented at https://cobrapy.readthedocs.io/en/latest/io.html . You can change metabolite names by setting their id (like model.metabolites[0].id = ...). But it's not necessarily required, you can access metabolites whose IDs start with numbers perfectly fine as well. For instance, if your metabolite is named "1,3-abc" model.metabolites.1,3-abc will not work but model.metabolites.get_by_id("1,3-abc") will work just fine.

[Rahmaabubakr]

Hello,

Thank you very much for your answer.

It is working fine with model.metabolites.get_by_id ("...")

but with this model.metabolites.("2ahhmp_LSQBKTc_RSQBKT").summary() command it is not working

it gives this error

Cell In[30], line 1
model.metabolites.("2ahhmp_LSQBKTc_RSQBKT").summary()
^
SyntaxError: invalid syntax

[matthiaskoenig]

you forgot the get_by_id