#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import math
# The PYTHONPATH should contain the location of moose.py and _moose.so
# files. Putting ".." with the assumption that moose.py and _moose.so
# has been generated in ${MOOSE_SOURCE_DIRECTORY}/pymoose/ (as default
# pymoose build does) and this file is located in
# ${MOOSE_SOURCE_DIRECTORY}/pymoose/examples
# sys.path.append('..\..')
try:
import moose
except ImportError:
print "ERROR: Could not import moose. Please add the directory containing moose.py in your PYTHONPATH"
import sys
sys.exit(1)
from channelConstants import *
# This Na channel is the same for mitral and granule 'naxn.mod' in Migliore and Shepherd 2008,
# except for VNa and sh.
# sh and VNa are passed to the constructor
#VNa = 50e-3 # Volts # Migliore and Shepherd 2008 mitral - different from granule 60mV
GNa = 200*sarea # Siemens, from mit4.hoc and then multiplying by area of mitral soma
## Lifted directly from Migliore and Shepherd 2008 Na gran channel
#sh = 10e-3 # V # (5mV in nmdol but 10mV in hoc file - mitral.hoc) - 15mV for granule
mmin=0.02e-3 # s
hmin=0.5e-3 # s
qt = 2.0**((CELSIUS-24.0)/10.0) # CELSIUS is defined in globalConstants.py
#Na_alpha_m:
tha = -30e-3 #V
Ra=0.4e6 # /s/V,
qa=7.2e-3 #V
#Na_beta_m:
tha = -30e-3 #V
Rb=0.124e6 # /s/V
qa=7.2e-3 # V
#Na_alpha_h:
thi1 = -45e-3 #V
Rd=0.03e6 # /s/V
qd=1.5e-3 #V
#Na_beta_h:
thi2 = -45e-3 #V
Rg=0.01e6 # /s/V
qg=1.5e-3 #V
### They use the above to calculate minf, mtau, htau, BUT finally have a different formula for hinf!!!
thinf = -50e-3 #V
qinf = 4e-3 #V
def trap0(vminusth,a,q):
if (abs(vminusth) > 1e-9):
return a * (vminusth) / (1 - math.exp(-(vminusth)/q))
else:
return a * q
#### V IMP: 10^6 factor in alpha_m and beta_m, as there is V in Nr, so the constant in front had units ms-1 mV^-1, so the 10^6 factor.
#def calc_Na_alpha_m(v):
# #return 0.32e6*(v+42e-3)/(1-math.exp(-(42e-3+v)/4e-3)) # From Bhalla and Bower 1993 paper
# return 400.0*(v+15e-3)/(1-math.exp(-(15e-3+v)/7.2e-3)) # tha+sh=-15mV. Use 15mV instead of 42mV
#
#def calc_Na_beta_m(v):
# #return 0.28e6*(v+15e-3)/(-1+math.exp((15e-3+v)/5e-3)) # From Bhalla and Bower 1993 paper
# return 124.0*(v-15e-3)/(-1+math.exp((-15e-3+v)/7.2e-3)) # -tha-sh=15mV. Use -15mV instead of 15mV
#
#def calc_Na_alpha_h(v):
# #return 0.128e3/math.exp((v+38e-3)/18e-3) # From Bhalla and Bower 1993 paper
# return 30.0*(v+30e-3)/math.exp((v+30e-3)/1.5e-3) # thi1+sh = -30mV, Use 30mV instead of 38mV.
#
#def calc_Na_beta_h(v):
# #return 4.0e3/(1+math.exp(-(v+15e-3)/5.0e-3)) # From Bhalla and Bower 1993 paper
# return 10.0*(v-30e-3)/(1+math.exp(-(v-30e-3)/1.5e-3)) # -thi2-sh = 30mV, Use -30mV instead of 15mV.
#####
class NaMitChannelMS(moose.HHChannel):
"""Na channel inherits from HHChannel."""
def __init__(self, sh, VNa, *args):
"""Setup the Na channel with defaults"""
moose.HHChannel.__init__(self,*args)
self.Ek = VNa
self.Gbar = GNa
self.addField('ion')
self.setField('ion','Na')
self.Xpower = 3 # This will create HHGate instance xGate inside the Na channel
self.Ypower = 1 # This will create HHGate instance yGate inside the Na channel
## Below gates get created after Xpower or Ypower are set to nonzero values
## I don't anymore have to explicitly create these attributes in the class
#self.xGate = moose.HHGate(self.path + "/xGate")
#self.yGate = moose.HHGate(self.path + "/yGate")
self.xGate.A.xmin = VMIN
self.xGate.A.xmax = VMAX
self.xGate.A.xdivs = NDIVS
self.xGate.B.xmin = VMIN
self.xGate.B.xmax = VMAX
self.xGate.B.xdivs = NDIVS
self.yGate.A.xmin = VMIN
self.yGate.A.xmax = VMAX
self.yGate.A.xdivs = NDIVS
self.yGate.B.xmin = VMIN
self.yGate.B.xmax = VMAX
self.yGate.B.xdivs = NDIVS
v = VMIN
for i in range(NDIVS+1):
a = trap0(v-(tha+sh),Ra,qa)
b = trap0(-v+(tha+sh),Rb,qa)
mtau = 1/(a+b)/qt
if mtau<mmin: mtau=mmin
minf = a/(a+b)
self.xGate.A[i] = minf/mtau
self.xGate.B[i] = 1/mtau
#self.xGate.tweakTau() # convert mtau and minf to A and B tables
a = trap0(v-(thi1+sh),Rd,qd)
b = trap0(-v+(thi2+sh),Rg,qg)
htau = 1/(a+b)/qt
if htau<hmin: htau=hmin
hinf = 1/(1+math.exp((v-thinf-sh)/qinf))
self.yGate.A[i] = hinf/htau
self.yGate.B[i] = 1/htau
#self.yGate.tweakTau() # convert htau and hinf tables to A and B tables.
v = v + dv
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