# Ks module, translated from Kernik 19

# 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']
    num_rows = dims['num_rows']
    # constants are stored in V
    F = V['F']
    R = V['R']
    T = V['T']
    N_A = V['N_A']

    G_GHK = 4.148559068672240e-10    # G_GHK [=] mA/mM
    P_ks = G_GHK/F * 1e12 # Unit pL/s .

    x_Ks_channel = 3000/N_A*1e15
    x_Ks_channel = V['numChannels']/N_A*1e15 # unit fmol

    # load gate transition parameters
    params_xs = [0.00116560000000183,	0.000400323747581994,	0.000326899999998023,	-1.41544821457997]

    alpha_xs = params_xs[0]*1e3 # unit    s ^ -1
    beta_xs = params_xs[2]*1e3 # unit    s ^ -1

    # Calculate bond graph constants from kinetic parameters
    # Note: units of kappa are fmol/s, units of K are fmol^-1
    # gate particle is squared, so there are 4 reactions
    kf_Ks = [P_ks / x_Ks_channel,     # R_GHK
    2*alpha_xs,     # Rx0
    alpha_xs]       # Rx1

    kr_Ks = [P_ks / x_Ks_channel,     # R_GHK
    beta_xs,     # Rx0
    2*beta_xs]     # Rx1

    k_kinetic = kf_Ks + kr_Ks

    # CONSTRAINTS
    N_cT = []
    K_C = []

    # volume vector
    # W = list(np.append([1] * num_cols, [V['V_myo']] * num_rows))
    W = [1] * num_cols + [V['V_myo'], V['V_o']] + [1] * (num_rows-2)

    return (k_kinetic, N_cT, K_C, W)