biosustain / multitfa Goto Github PK

Is there a better way to check if the new variables are added or not ?

Originally posted by @vishnumahamkali in #6 (comment)

Is your feature related to a problem? Please describe it.

I would like to change the temperature for the calculation of $\Delta G_f$. As far as I understand, right now it uses the default temperature 298.15K.

Describe the solution you would like.

It can be added to one of the input dictionaries that are supplied for the tmodel construction, or to a new one.

comp_info = {
    "pH": {"c": 7, "e": 6.4},
    "I": {"c": 0.25, "e": 0},
    "T": "310K",
}
thermo_model = tmodel(
    model,
    compartment_info=pd.DataFrame(data=comp_info),
)

I can make a PR, maybe after #28.

Describe alternatives you considered

Perhaps, the comparment_info argument should be changed after this since T is not particularly tied to a compartment (someone might have a use case for different temperatures per compartment, I don't know). As aforementioned, it could be a different argument to the __init__ function.

https://github.com/biosustain/multivariate-tmfa/blob/fa65fa4324889d3261bca8cb7197c9f2c0f7e32d/src/tmfa/core/tmodel.py#L250-L250

Importing tmodel fails at from .thermo_constants import * at line 20: params = CCModelParameters.from_quilt() with the error message that CCModelParameters has no attribute 'from_quilt'. It appears that an update on the Equilibrator side may have changed/removed some features.

When defining a mixture of identifiers for a model, e.g; seed, kegg and some no identifiers at all, multitfa is throwing error that it can't cache from equilibrator-api.

When using pip to install, 'pip3 install git+https://github.com/biosustain/multivariate-tmfa.git', it doesn't include 'data' directory. We need 'data/component_data.npz' for 'thermo_constants.py'.

I think this function broke when the cache file was removed. As a temp fix I made this change. Could you check the function to properly do the cache file location

Originally posted by @vishnumahamkali in #6 (comment)