Adding new metabolites

[amarsh26]

Is there an existing issue for this?

• I have searched the existing issues

Problem description

Hello,

I am trying to add new reactions with new metabolites to my models, but I am receiving errors such as the following (using the steps outlined in the documentation for building a model).

ValueError: Reaction 'ALPHNH' does not belong to a model. Either add the reaction to a model or use Metabolite objects instead of strings as keys.

Is there better way to add reactions to existing models?

Thanks for your help.

Code sample

Code run:

Traceback:

Environment

Anything else?

No response

[Midnighter]

Can you please share the code that you used (or something very similar)?

[amarsh26]

I think the root of my issue is actually with using Model.get_by_id (see example below) as if I add all of the metabolites in the reactions like they are new, adding the reaction works.

iML1515_model.get_by_id("nh4_c")

`---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Input In [30], in <cell line: 1>()
----> 1 iML1515_model.get_by_id("nh4_c")

AttributeError: 'Model' object has no attribute 'get_by_i`

I believe how I was referencing existing metabolites was causing the issue in the previous post. My updated question is regarding referencing existing metabolites. Below is an example of working code.

`
co2_c = Metabolite('co2_c', formula='CO2', name='CO2', compartment='c')

h_c = Metabolite('h_c', formula='H', name='H', compartment='c')

h2o_c = Metabolite('h2o_c', formula='H2O', name='H2O', compartment='c')

nh4_c = Metabolite('nh4_c', formula='H4N', name='Ammonium', compartment='c')

allphn_c = Metabolite(
'allphn_c',
formula='C2H3N2O3',
name='Allophanate C2H3N2O3',
compartment='c')

reaction.add_metabolites({

co2_c: 2.0,

h_c: -3.0,
h2o_c: -1.0,
nh4_c: 2.0,
allphn_c: -1.0

})

reaction.reaction`

Is there a method I can use that does not require creating a metabolite object for metabolites already in the model?

Thank you so much for your help!

[Midnighter]

As described in the method help, the dictionary with stoichiometric coefficients can also contain string keys that reference metabolite identifiers. For that to work, the reaction has to be added to a model beforehand. This is not well explained in the documentation.

Alternatively, you use the get_by_id method to fetch the metabolite objects from your model. You seem to have a typo with the method, hence the AttributeError.

[amarsh26]

Thanks. I had not realized you need to add 'metabolite'. Solution: iML1515_model.metabolites.get_by_id("nh4_c")