Possible to add reactions with reagents whose corresponding species are not part of the model

[willigott]

When one builds a reaction object and adds reagents to it, one can add this reaction to the model no matter whether the corresponding species exists or not. For example,

import cbmpy as cbm
from cbmpy.CBModel import Reaction, Reagent

mod_name = 'e_coli_core.xml'
model = cbm.CBRead.readSBML3FBC(mod_name)

reagent1 = Reagent("dummy_1", "i_dont_exist", -1.0)
reagent2 = Reagent("dummy_2", "i_dont_exist_either", 1.0)

rea = Reaction("dummy")

rea.addReagent(reagent1)
rea.addReagent(reagent2)

model.addReaction(rea)

print(model.getReaction("dummy").getStoichiometry())
# prints [(-1.0, 'i_dont_exist'), (1.0, 'i_dont_exist_either')]

if model.getSpecies('i_dont_exist') is None:
    print("species does not exist") # this will be printed

This might be confusing as it looks like these species exist but they actually don't.

I guess the easiest would be to add an additional check in addReagent whether reag.getSpecies() already exists in the model and if not either create the species or throw an error (I would prefer the error).