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channel.py
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channel.py
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#!/usr/bin/env python
"""
author: Joshua C Chang
email: joshchang@ucla.edu
"""
from numpy import power, exp, log, sqrt, sum
from params import *
from species import *
import numpy as np
import math
def scalar_mult_dict(dictionary, scalar):
return { key: scalar*value for key,value in dictionary.items()}
class Channel(object):
system_state_offset = 0
N = 1
"""Generic ion channel class (also emcompasses pumps)
Args:
name (String): name of channel
species ([Species]): species that are possibly permeable
gmax ([float]): maximum conductance for each species (for single channel)
"""
def current(self, system_state=None):
"""
Return the current as a dict with ion: current pairs
If V_m is defined, use it as the potential. Otherwise, use
V_m()
"""
return
def water_permeability(self, system_state=None):
"""
Water permeability of channel as a function of V_m
Units of permeability are L/Molarity/s for each single channel
"""
if self.N>1:
return np.zeros(self.N)
return 0.0
def current_infty(self,system_state = None):
""" This is the current if the opening/closing is able to immediately adjust to the environment
Override this method for GHK channels
"""
return self.current(system_state = system_state)
def equilibriate(self):
"""
Equilibriate the internal state
"""
return
def getInternalVars(self): return None
def setInternalVars(self,system_state): return None
def vectorizevalues(self):
pass
class GHKChannel(Channel):
m = 0.0
h = 1.0
def current(self, system_state = None):
V_m = self.membrane.phi(system_state)
h = self.get_h(system_state)
m = self.get_m(system_state)
invalues = self.membrane.inside.get_val_dict(system_state)
outvalues = self.membrane.outside.get_val_dict(system_state)
print "calling GHKcurrent, want GHK conductance call instead!!"
gating = power(m,self.p)*power(h,self.q)*F*species.z*V_m/phi
#For safety, but SLOW!!!
if not hasattr(V_m, '__iter__'):
# V_m is not iterable, use ternary operator
I = [ gmax* gating\
*( (invalues[species] - exp(-V_m*species.z/phi)*outvalues[species])/(1.0-exp(-V_m*species.z/phi)) \
if V_m*species.z >0 else \
(invalues[species]*exp(V_m*species.z/phi) -outvalues[species])/(exp(V_m*species.z/phi)-1.0 ) )\
for gmax,species in zip(self.gmax,self.species)]
else:
"""
I = [ gmax*gating \
*np.fromiter( [ (invalues[species]-exp(-vm*species.z/phi)*outvalues[species])/(1.0-exp(-vm*species.z/phi)) \
if vm*species.z>0 else \
(invalues[species]*exp(vm*species.z/phi)-outvalues[species])/(exp(vm*species.z/phi)-1.0)
for vm in V_m], np.float64)
for gmax,species in zip(self.gmax,self.species)]
"""
insidestuff = vm*species.z/phi
condition = (insidestuff>0)
I = [
gmax*gating*(condition*(invalues[species]-exp(-insidestuff)*outvalues[species])/(1.0-exp(-insidestuff)) +\
(condition-1)*(invalues[species]*exp(insidestuff)-outvalues[species])/(exp(insidestuff)-1.0)) \
for gmax, species in zip(self.gmax, self.species)
]
return {ion:current for ion,current in zip(self.species,I)}
def get_h(self, system_state=None):
"""
m^p h^q
:param system_state: Vector of the system state
:return: numpy array of h value or ones
"""
if self.q == 0:
return np.ones(self.N)
if system_state is None:
V_m = self.membrane.phi(system_state)
return self.hinfty(V_m)
if self.p == 0:
return system_state[self.system_state_offset:self.system_state_offset+self.N]
else:
return system_state[self.system_state_offset+self.N:self.system_state_offset+2*self.N]
def get_m(self, system_state = None):
"""
:param system_state: numpy array of the system state
:return:
"""
if self.p == 0:
return np.ones(self.N)
if system_state is None:
V_m = self.membrane.phi(system_state)
return self.minfty(V_m)
return system_state[self.system_state_offset:self.system_state_offset+self.N]
def conductance(self, system_state = None):
V_m = self.membrane.phi(system_state)
h = self.get_h(system_state)
m = self.get_m(system_state)
invalues = self.membrane.inside.get_val_dict(system_state)
outvalues = self.membrane.outside.get_val_dict(system_state)
gate = power(m,self.p)*power(h,self.q)
return {ion: gmax*gate for gmax,ion in zip(self.gmax,self.species)}
def dIdV(self, system_state=None):
"""
For constructing a Jacobian. This is the change in the total current
through the membrane
"""
V_m = self.membrane.phi(system_state)
h = self.h(system_state)
m = self.m(system_state)
invalues = self.membrane.inside.get_val_dict(system_state)
outvalues = self.membrane.outside.get_val_dict(system_state)
dIdV = [ gmax*species.z*(V_m*outvalues[species]*species.z*(exp(V_m*species.z/phi) - 1.0) + \
V_m*species.z*(outvalues[species] - invalues[species]*exp(V_m*species.z/phi)) - \
phi*(outvalues[species] - invalues[species]*exp(V_m*species.z/phi))*(exp(V_m*species.z/phi) - 1.0)) \
/(phi**2*power(exp(V_m*species.z/phi) - 1.0,2))
for gmax, species in zip(self.gmax,self.species)]
return power(m,p)*power(h,q)*F*sum(dIdV)
def dIdm(self, system_state = None):
if self.p == 0: return 0.0
def dIdh(self, system_state = None):
if self.q == 0: return 0.0
def dmdV(self, system_state = None):
return self.dalphadV(m,system_state)
def dhdV(self, system_state = None):
pass
def conductance_infty(self, system_state = None):
V_m = self.membrane.phi(system_state)
alpham = self.alpham(V_m)
betam = self.betam(V_m)
alphah = self.alphah(V_m)
betah = self.betah(V_m)
m_infty = alpham/(alpham+betam)
h_infty = alphah/(alphah+betah)
gate = power(m_infty,self.p)*power(h_infty,self.q)
return {ion: gmax*gate for gmax,ion in zip(self.gmax,self.species) }
def current_infty(self, system_state = None):
"""
This is the current when the gates have equilibriated to V_m, and the
given intra- and extra- cellular concentrations
invalues and outvalues are dicts taken species are arguments
"""
V_m = self.membrane.phi(system_state)
invalues = self.membrane.inside.get_val_dict(system_state)
outvalues = self.membrane.outside.get_val_dict(system_state)
alpham = self.alpham(V_m)
betam = self.betam(V_m)
alphah = self.alphah(V_m)
betah = self.betah(V_m)
m_infty = alpham/(alpham+betam)
h_infty = alphah/(alphah+betah)
# Maybe let's not compute this multiple times, once for each channel!
if not hasattr(V_m, '__iter__'):
# V_m is not iterable, use ternary operator
I = [ gmax*power(m_infty,self.p)*power(h_infty,self.q)*F*species.z*V_m/phi \
*( (self.membrane.inside.value(species) - exp(-V_m*species.z/phi)*self.membrane.outside.value(species))/(1.0-exp(-V_m*species.z/phi)) \
if V_m*species.z >0 else \
(self.membrane.inside.value(species)*exp(V_m*species.z/phi) -self.membrane.outside.value(species))/(exp(V_m*species.z/phi)-1.0 ) )\
for gmax,species in zip(self.gmax,self.species)]
else:
c_in = self.membrane.inside.value(species)
c_out = self.membrane.outside.value(species)
I = [ gmax*power(m_infty,self.p)*power(h_infty,self.q)*F*species.z*V_m/phi \
*np.fromiter( [ (cin-exp(-vm*species.z/phi)*cout)/(1.0-exp(-vm*species.z/phi)) \
if vm*species.z>0 else \
(cin*exp(vm*species.z/phi)-cout)/(exp(vm*species.z/phi)-1.0)
for (vm,cin,cout) in zip(V_m,c_in,c_out) ], np.float64)
for gmax,species in zip(self.gmax,self.species)]
return {ion:current for ion,current in zip(self.species,I)}
def mdot(self, V_m=None, m=None ):
""" Compute dm/dt
"""
if V_m is None: V_m = self.membrane.phi()
if m is None: m = self.m
return self.alpham(V_m)*(1.0-m)-self.betam(V_m)*m
def hdot(self, V_m=None, h=None):
""" Compute dh/dt
"""
if V_m is None: V_m = self.membrane.phi()
if h is None: h = self.h
return self.alphah(V_m)*(1.0-h)-self.betah(V_m)*h
def minfty(self, V_m=None):
if V_m is None: V_m = self.membrane.phi()
am = self.alpham(V_m)
bm = self.betam(V_m)
return am/(am+bm)
def hinfty(self, V_m=None):
if V_m is None: V_m = self.membrane.phi()
ah = self.alphah(V_m)
bh = self.betah(V_m)
return ah/(ah+bh)
def equilibriate(self,V_m=None):
if V_m is None: V_m = self.membrane.phi()
if not self.p == 0:
self.m = self.minfty(V_m)
else:
self.m = 1.0
if not self.q ==0:
self.h = self.hinfty(V_m)
else:
self.h = 1.0
def alpham(self, system_state = None):
"""
Over-ride this method
"""
return 1.0
def betam(self, system_state = None):
"""
Over-ride this method
"""
return 1.0
def alphah(self, system_state = None):
return 1.0
def betah(self, system_state = None):
return 1.0
def equilibriate_gates(self, system_state = None):
V_m = self.membrane.phi(system_state)
self.m = self.minfy(V_m)
self.h = self.hinfty(V_m)
def vectorizevalues(self):
if not hasattr(self.m,'__iter__') and self.m is not None:
self.m = np.ones(self.N)*self.m
if not hasattr(self.h,'__iter__') and self.h is not None:
self.h = np.ones(self.N)*self.h
# Internal vars for the standard GHK equation are the gating variables
# [p, q]
# expect that system_state offset is set??
def getInternalVars(self,system_state = None):
if self.p == 0 and self.q==0: return None
elif self.q ==0: return self.get_m(system_state)
elif self.q == 0: return self.get_h(system_state)
return np.array([self.get_m(system_state),self.get_h(system_state)]).flatten()
def setInternalVars(self,system_state):
if self.p == 0: self.h = self.get_h(system_state)
elif self.q ==0: self.m = self.get_m(system_state)
else:
self.m = self.get_m(system_state)
self.h = self.get_h(system_state)
pass
def get_dot_InternalVars(self,system_state,t):
if self.p ==0 and self.q==0: return None
elif self.p == 0:
temp = self.hdot(self.membrane.phi(system_state),self.get_h(system_state))
elif self.q == 0:
temp = self.mdot(self.membrane.phi(system_state),self.get_m(system_state))
else:
temp = np.zeros(2*self.N)
temp[:self.membrane.N] = self.mdot(self.membrane.phi(system_state),self.get_m(system_state))
temp[self.membrane.N:] = self.hdot(self.membrane.phi(system_state),self.get_h(system_state))
return temp
class HHChannel(Channel):
gmax = []
def current(self,system_state = None):
V_m = self.membrane.phi(system_state)
h = self.h(system_state)
m = self.m(system_state)
invalues = self.membrane.inside.get_val_dict(system_state)
outvalues = self.membrane.outside.get_val_dict(system_state)
Eion = [ phi/species.z*(np.log(outvalues[species])-np.log(invalues[species])) for species in self.species]
return self.gmax*(V_m-Eion)
def species_current(self,species,system_state = None):
E = [ phi/species.z*(np.log(outvalues[species])-np.log(invalues[species])) for species in self.species]
return self.gmax[self.species.index(species)]*(V_m-E)
class LeakChannel(HHChannel):
def __init__(self,species):
self.gmax = 0 # reset this to balance the specific ion current
self.species = species # only a single species
def current(self,system_state = None):
V_m = self.membrane.phi(system_state)
invalues = self.membrane.inside.get_val_dict(system_state)
outvalues = self.membrane.outside.get_val_dict(system_state)
species = self.species
return {species: self.gmax*(V_m-phi/species.z*(np.log(outvalues[species])-np.log(invalues[species])))}
def set_gmax(self,gmax):
self.gmax = gmax