Adding metabolites to a reaction using a dictionary

[Kristy Chang]

Hi, 

I am stuck at this problem:

I have my reaction equation as a dictionary:

reaction= {'glu__L_c': -1.0, 'h2o_c': -1.0, 'nadp_c': -1.0, 'akg_c': 1.0, 'h_c': 1.0, 'nadph_c': 1.0, 'nh4_c': 1.0}

but when I do:

reaction.add_metabolite(reaction)

it gives a blank result and the following error:

TypeError: 'dict' object is not callable

or TypeError: Either add the reaction to a model or use Metabolite objects instead of strings as keys

How do I use metabolite objects as keys? (or rather, how do I convert my keys into objects?)

[Dennis van den Berg]

Hi Kristy,

To convert your keys to objects you can simple use {model.metabolites.glu__L_c:-1.0, model.metabolites.h2o_c:-1.0, etc, ect.}

Then you refer to the objects in your model, if you called it model at least. If you called it ecoli then use ecoli.metabolites.glu__L_c .

One warning: If your metabolite has a name which is illegal according to python use .get_by_id("string with name"), f.i. objects can not start with a number, so 4abz_c is not a valid name.

Then you do: model.metabolites.get_by_id('4abz_c'):-1.0 and it will work fine.

Good luck with your modeling,

Dennis

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