Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

load_yaml_model does not seem to load inhibitory mechanisms #15

Open
PHvanLent opened this issue Dec 22, 2022 · 1 comment
Open

load_yaml_model does not seem to load inhibitory mechanisms #15

PHvanLent opened this issue Dec 22, 2022 · 1 comment
Labels
bug Something isn't working

Comments

@PHvanLent
Copy link

PHvanLent commented Dec 22, 2022

Dear Skimpy developers,

I noticed that when adding inhibitory mechanisms to the model, these can be in principle exported with the export_to_yaml function, but not imported with the load_yaml_model(). Is this correct, or is there already something missing in how I add the mechanisms in the mode?

name="Enz_B"
SpecificConvenience = make_generalized_reversible_hill_n_n_h1_with_inhibition([-1, 1,1], [1])
metabolites=SpecificConvenience.Reactants(substrate1='A_c',product1='B_c',product2='pi_c')
inhibitors=SpecificConvenience.Inhibitors(inhibitor1='L_c')
parameters=SpecificConvenience.Parameters(
    vmax_forward=None,
    km_substrate1=None,
    km_product1=None,
    ki_inhibitor1=None)
Enz_B=Reaction(name=name,
                   mechanism=SpecificConvenience,
                   reactants=metabolites,
                   inhibitors=inhibitors,)
Enz_B.modifiers['DSM__h_c']=DisplacementSmallMoleculeModifier("h_c",1)           
kmodel.add_reaction(Enz_B)
kmodel.parametrize_by_reaction({Enz_B.name:parameters})
kmodel.reactants.B_c.compartment=kmodel.compartments.c

I have been using your kinetic modelling package quite a lot, so thank you for this nice package.

Kind regards,

Paul

@weilandtd weilandtd added the bug Something isn't working label Dec 30, 2022
@weilandtd
Copy link
Contributor

Hi Paul,

Thank you for bringing this to our attention. It looks like you add everything correctly.
We will try to come back with a fix solution for this!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

2 participants