# Kr module, translated from Kernik19

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

# Based on 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']
    cKo = V['cKo']

    G_GHK = 2.134709059004477e-08   # G_GHK [=] mA/mM
    P_Kr = G_GHK/F * 1e12 # Unit pL/s .
    x_Kr_channel = 143*414/N_A*1e15
    x_Kr_channel = 3000/N_A*1e15
    x_Kr_channel = V['numChannels']/N_A*1e15 # unit fmol

    # load gate transition parameters
    params_xr1 = [0.003702708442915483,	1.6149028778859738,	4.5365827167917646E-4,	-1.3218634652232777]
    params_xr2 = [0.01245000000189733,	-1.0273976425216251,	0.4649999999963666,	-0.18153135376657775]
    alpha_xr1 = params_xr1[0]*1e3 # unit    s ^ -1
    beta_xr1 = params_xr1[2]*1e3 # unit    s ^ -1

    alpha_xr2 = params_xr2[0]*1e3 # unit    s ^ -1
    beta_xr2 = params_xr2[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

    kf_Kr = [P_Kr / x_Kr_channel/np.sqrt(cKo),     # R_GHK
    alpha_xr1,     # Rx1_0
    alpha_xr1,     # Rx1_1
    alpha_xr2,     # Rx2_0
    alpha_xr2] # Rx2_1

    kr_Kr = [P_Kr / x_Kr_channel/np.sqrt(cKo),     # R_GHK
    beta_xr1,     # Rx1_0
    beta_xr1,     # Rx1_1
    beta_xr2,     # Rx2_0
    beta_xr2] # Rx2_1


    k_kinetic = kf_Kr + kr_Kr

    # 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)