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plot_rate_constants.py
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#Author - Anal Kumar
#disclaimer - The code uses eval() function. Use at your own discretion.
import moose
import rdesigneur as rd
import numpy as np
import matplotlib.pyplot as plt
import Channelprotos as Cp #Channelprotos and rdesigneurProtos should be in the same directory as the pwd
import rdesigneurProtos as rp
Cp_list = dir(Cp) #getting a list of all variables and functions in the Channelprotos and rdesigneurProtos
rp_list = dir(rp)
for func in Cp_list: #Channelprotos
if callable( eval('Cp.%s' %(func)) ): #checking if its a function or another variable
moose.Neutral('/library') #setting up library
try:
eval('Cp.%s(\'%s\')' %(func, func)) # setting up the channel
Chan = moose.element('/library/' + func)
except:
continue
if Chan.className == 'HHChannel': #use this if the channel setup is HHChanel
#Xgate
if Chan.Xpower >=1 and Chan.instant != 1:
Chanxgate = moose.element(Chan.path + '/gateX')
min = Chanxgate.min
max = Chanxgate.max
alpha = Chanxgate.tableA
beta = Chanxgate.tableB - alpha
plt.figure()
plt.plot(np.linspace(min, max, len(alpha)), alpha, color = 'red', label = 'alpha')
plt.plot(np.linspace(min, max, len(beta)), beta, color = 'blue', label = 'beta')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Rate constant (1/s)')
plt.title(func + ' rate constants for its x gate')
plt.legend()
plt.savefig('./gateparams/Cp_' + func + '_xgate.png')
elif Chan.Xpower >=1 and Chan.instant == 1:
Chanxgate = moose.element(Chan.path + '/gateX')
min = Chanxgate.min
max = Chanxgate.max
value = Chanxgate.tableA
plt.figure()
plt.plot(np.linspace(min, max, len(value)), value, color = 'red')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Gate value')
plt.title(func + ' value of its x gate')
plt.legend()
plt.savefig('./gateparams/Cp_' + func + '_xgate.png')
# Ygate
if Chan.Ypower >=1 and Chan.instant != 2:
Chanygate = moose.element(Chan.path + '/gateY')
min = Chanygate.min
max = Chanygate.max
alpha = Chanygate.tableA
beta = Chanygate.tableB - alpha
plt.figure()
plt.plot(np.linspace(min, max, len(alpha)), alpha, color = 'red', label = 'alpha')
plt.plot(np.linspace(min, max, len(beta)), beta, color = 'blue', label = 'beta')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Rate constant (1/s)')
plt.title(func + ' rate constants for its y gate')
plt.legend()
plt.savefig('./gateparams/Cp_' + func + '_ygate.png')
elif Chan.Ypower >=1 and Chan.instant == 2:
Chanygate = moose.element(Chan.path + '/gateY')
min = Chanygate.min
max = Chanygate.max
value = Chanygate.tableA
plt.figure()
plt.plot(np.linspace(min, max, len(value)), value, color = 'red')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Gate value')
plt.title(func + ' value of its y gate')
plt.legend()
plt.savefig('./gateparams/Cp_' + func + '_ygate.png')
# Zgate
if Chan.Zpower >=1 and Chan.instant != 4 and Chan.useConcentration == 0:
Chanzgate = moose.element(Chan.path + '/gateZ')
min = Chanzgate.min
max = Chanzgate.max
alpha = Chanzgate.tableA
beta = Chanzgate.tableB - alpha
plt.figure()
plt.plot(np.linspace(min, max, len(alpha)), alpha, color = 'red', label = 'alpha')
plt.plot(np.linspace(min, max, len(beta)), beta, color = 'blue', label = 'beta')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Rate constant (1/s)')
plt.title(func + ' rate constants for its z gate')
plt.legend()
plt.savefig('./gateparams/Cp_' + func + '_zgate.png')
elif Chan.Zpower >=1 and Chan.instant != 4 and Chan.useConcentration == 1:
Chanzgate = moose.element(Chan.path + '/gateZ')
min = Chanzgate.min
max = Chanzgate.max
alpha = Chanzgate.tableA
beta = Chanzgate.tableB - alpha
plt.figure()
plt.plot(np.linspace(min, max, len(alpha)), alpha, color = 'red', label = 'alpha')
plt.plot(np.linspace(min, max, len(beta)), beta, color = 'blue', label = 'beta')
plt.xlabel('Calcium concentration (mol/m^3)')
plt.ylabel('Rate constant (1/s)')
plt.title(func + ' rate constants for its z gate')
plt.legend()
plt.savefig('./gateparams/Cp_' + func + '_zgate.png')
elif Chan.Zpower >=1 and Chan.instant == 4 and Chan.useConcentration == 0:
Chanzgate = moose.element(Chan.path + '/gateZ')
min = Chanzgate.min
max = Chanzgate.max
value = Chanzgate.tableA
plt.figure()
plt.plot(np.linspace(min, max, len(value)), value, color = 'red')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Gate value')
plt.title(func + ' value of its z gate')
plt.legend()
plt.savefig('./gateparams/Cp_' + func + '_zgate.png')
elif Chan.Zpower >=1 and Chan.instant == 4 and Chan.useConcentration == 1:
Chanzgate = moose.element(Chan.path + '/gateZ')
min = Chanzgate.min
max = Chanzgate.max
value = Chanzgate.tableA
plt.figure()
plt.plot(np.linspace(min, max, len(value)), value, color = 'red')
plt.xlabel('Calcium concentration (mol/m^3)')
plt.ylabel('Gate value')
plt.title(func + ' value of its z gate')
plt.legend()
plt.savefig('./gateparams/Cp_' + func + '_zgate.png')
if Chan.className == 'CaConc':
pass
print 'Cp_' + str(func)
moose.delete('/library')
for func in rp_list: #rdesigneurProtos
if callable(eval('rp.%s' %(func))):
moose.Neutral('/library') #setting up library
try:
eval('rp.%s(\'%s\')' %(func, func)) # setting up the channel
Chan = moose.element('/library/' + func)
except:
continue
if Chan.className == 'HHChannel': #use this if the channel setup is HHChanel
#Xgate
if Chan.Xpower >=1 and Chan.instant != 1:
Chanxgate = moose.element(Chan.path + '/gateX')
min = Chanxgate.min
max = Chanxgate.max
alpha = Chanxgate.tableA
beta = Chanxgate.tableB - alpha
plt.figure()
plt.plot(np.linspace(min, max, len(alpha)), alpha, color = 'red', label = 'alpha')
plt.plot(np.linspace(min, max, len(beta)), beta, color = 'blue', label = 'beta')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Rate constant (1/s)')
plt.title(func + ' rate constants for its x gate')
plt.legend()
plt.savefig('./gateparams/rp_' + func + '_xgate.png')
elif Chan.Xpower >=1 and Chan.instant == 1:
Chanxgate = moose.element(Chan.path + '/gateX')
min = Chanxgate.min
max = Chanxgate.max
value = Chanxgate.tableA
plt.figure()
plt.plot(np.linspace(min, max, len(value)), value, color = 'red')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Gate value')
plt.title(func + ' value of its x gate')
plt.legend()
plt.savefig('./gateparams/rp_' + func + '_xgate.png')
# Ygate
if Chan.Ypower >=1 and Chan.instant != 2:
Chanygate = moose.element(Chan.path + '/gateY')
min = Chanygate.min
max = Chanygate.max
alpha = Chanygate.tableA
beta = Chanygate.tableB - alpha
plt.figure()
plt.plot(np.linspace(min, max, len(alpha)), alpha, color = 'red', label = 'alpha')
plt.plot(np.linspace(min, max, len(beta)), beta, color = 'blue', label = 'beta')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Rate constant (1/s)')
plt.title(func + ' rate constants for its y gate')
plt.legend()
plt.savefig('./gateparams/rp_' + func + '_ygate.png')
elif Chan.Ypower >=1 and Chan.instant == 2:
Chanygate = moose.element(Chan.path + '/gateY')
min = Chanygate.min
max = Chanygate.max
value = Chanygate.tableA
plt.figure()
plt.plot(np.linspace(min, max, len(value)), value, color = 'red')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Gate value')
plt.title(func + ' value of its y gate')
plt.legend()
plt.savefig('./gateparams/rp_' + func + '_ygate.png')
# Zgate
if Chan.Zpower >=1 and Chan.instant != 4 and Chan.useConcentration == 0:
Chanzgate = moose.element(Chan.path + '/gateZ')
min = Chanzgate.min
max = Chanzgate.max
alpha = Chanzgate.tableA
beta = Chanzgate.tableB - alpha
plt.figure()
plt.plot(np.linspace(min, max, len(alpha)), alpha, color = 'red', label = 'alpha')
plt.plot(np.linspace(min, max, len(beta)), beta, color = 'blue', label = 'beta')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Rate constant (1/s)')
plt.title(func + ' rate constants for its z gate')
plt.legend()
plt.savefig('./gateparams/rp_' + func + '_zgate.png')
elif Chan.Zpower >=1 and Chan.instant != 4 and Chan.useConcentration == 1:
Chanzgate = moose.element(Chan.path + '/gateZ')
min = Chanzgate.min
max = Chanzgate.max
alpha = Chanzgate.tableA
beta = Chanzgate.tableB - alpha
plt.figure()
plt.plot(np.linspace(min, max, len(alpha)), alpha, color = 'red', label = 'alpha')
plt.plot(np.linspace(min, max, len(beta)), beta, color = 'blue', label = 'beta')
plt.xlabel('Calcium concentration (mol/m^3)')
plt.ylabel('Rate constant (1/s)')
plt.title(func + ' rate constants for its z gate')
plt.legend()
plt.savefig('./gateparams/rp_' + func + '_zgate.png')
elif Chan.Zpower >=1 and Chan.instant == 4 and Chan.useConcentration == 0:
Chanzgate = moose.element(Chan.path + '/gateZ')
min = Chanzgate.min
max = Chanzgate.max
value = Chanzgate.tableA
plt.figure()
plt.plot(np.linspace(min, max, len(value)), value, color = 'red')
plt.xlabel('Membrane potential (V)')
plt.ylabel('Gate value')
plt.title(func + ' value of its z gate')
plt.legend()
plt.savefig('./gateparams/rp_' + func + '_zgate.png')
elif Chan.Zpower >=1 and Chan.instant == 4 and Chan.useConcentration == 1:
Chanzgate = moose.element(Chan.path + '/gateZ')
min = Chanzgate.min
max = Chanzgate.max
value = Chanzgate.tableA
plt.figure()
plt.plot(np.linspace(min, max, len(value)), value, color = 'red')
plt.xlabel('Calcium concentration (mol/m^3)')
plt.ylabel('Gate value')
plt.title(func + ' value of its z gate')
plt.legend()
plt.savefig('./gateparams/rp_' + func + '_zgate.png')
if Chan.className == 'CaConc':
pass
print 'rp_' + str(func)
moose.delete('/library')