Location: BG_ABC @ 48649265a58b / parameter_finder / kinetic_parameters_ABC.py

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2025-03-18 11:11:13+13:00
Desc:
Adding RDF
Permanent Source URI:
https://staging.physiomeproject.org/workspace/c2a/rawfile/48649265a58bd9aa3a27fbf577aba12084e1cbb3/parameter_finder/kinetic_parameters_ABC.py
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# ABC module

# Solute S can be a myriad of things, so leaving unspecified for now

# Return kinetic parameters, constraints, and vector of volumes in each
# compartment (pL) (1 if gating variable, or in element corresponding to
# kappa)

# Translated from Pan 2018 cardiac AP

import numpy as np

def kinetic_parameters(M, include_type2_reactions, dims, V):
    # Set the kinetic rate constants

    num_cols = dims['num_cols'] # numRxn
    num_rows = dims['num_rows'] # numSpecies

    # constants are stored in V

    fkc = 1e6 # fastkineticconstant, 1/s
    skc = 1e-6 # smallkineticconstant

    # ReABind
    # ReSBind
    # ReHyd
    # ReRel

    kf = [fkc]*num_cols
    kr = [skc]*num_cols

    k_kinetic = kf + kr #[kf,    kr]

    # CONSTRAINTS
    N_cT = []
    K_C = []

    # volume vector
    W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))


    return (k_kinetic, N_cT, K_C, W)