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set_params.py
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import re
from defs import *
from values import *
import time
# pick out compartment IDs. E.g. given label=Area_Lumen_Cell, it would return
# (0,1) for (lumen, cell)
def get_interface_id(label):
tmp = (label).split('_')
if len(tmp)==3: # only have two compartment IDs
ind1,ind2 = compart_id[tmp[1]],compart_id[tmp[2]]
return ind1, ind2
elif len(tmp)==4: # solute ID, followed by two compartment IDs
sid,ind1,ind2 = solute_id[tmp[1]],compart_id[tmp[2]],compart_id[tmp[3]]
return sid,ind1,ind2
# for coupled transpoters
# pick out solute IDs, compartment IDs, and coefficients
def get_coupled_id(label):
tmp = (label).split('_')
# print(tmp)
sid1,sid2 = solute_id[tmp[3]],solute_id[tmp[4]]
ind1,ind2 = compart_id[tmp[1]],compart_id[tmp[2]]
if len(tmp)==5: # only involves 2 solutes
return ind1,ind2,sid1,sid2
elif len(tmp)==6: # involves 3 solutes
sid3 = solute_id[tmp[5]]
return ind1,ind2,sid1,sid2,sid3
else:
print("Wrong label",tmp)
# is str_short at the beginning of str_long?
# case insensitive
def compare_string_prefix(str_long,str_short):
return (str_long.lower())[:len(str_short)] == str_short.lower()
def compare_sex(sex, cell):
if sex.lower() == 'male' or sex.lower() == 'female':
return cell.sex.lower() == sex.lower()
else:
return True
def set_torq_params(species,sex,preg):
if species == 'hum':
Radref = 0.0037/2.0e0 # Fortran:Change this to be half of the male diameter given in PTparams_M.dat.diam=0.0036 but this is changed to match Fortran code.
torqR = 0.0014 #Reference radius
torqL = 2.50e-4 #Microvillous length
torqd = 1.5e-05 #Height above the microvillous tip
torqvm = 0.02 #Compliance Fortran Code
PbloodPT = 20.0e0 #Reference pressure
elif species == 'rat':
if sex == 'male':
# Radref = 0.0025/2.0
Radref = 0.00265/2.0
torqR = 0.00112
# torqvm = 0.030
torqvm = 0.02
PbloodPT = 9.0e0
elif sex == 'female':
if preg == 'non':
torqR = 0.00095
torqvm = 0.030
Radref = 0.002125/2.0 #female radius
PbloodPT = 8.0e0
elif preg == 'mid':
torqR = 0.00101
torqvm = 0.050
Radref = 0.00227375/2.0
PbloodPT = 8.0e0
elif preg == 'late':
torqR = 0.00101
torqvm = 0.050
Radref = 0.00227375/2.0
PbloodPT = 8.0e0
torqL = 2.50e-4
torqd = 1.50e-5
elif species == 'mou':
if sex == 'male':
Radref = 0.002/2.0
torqR = 0.001
torqvm = 0.0275
PbloodPT = 9.0e0
elif sex == 'female':
Radref = 0.0018/2.0 #female radius
torqR = 0.00095
torqvm = 0.030
PbloodPT = 8.0e0
torqL = 2.50e-4
torqd = 1.50e-5
else:
print('cell.species: ' + str(species))
raise Exception('what is species?')
return Radref,torqR,torqvm,PbloodPT,torqL,torqd
def read_params(cell,filename,j):
file = open(filename,'r')
cell.segment=filename[12:-16]
# error messages
if cell.preg != 'non':
print('cell.preg: ' + cell.preg)
raise Exception('cell.preg != non needs to use read_params_preg in set_params_preg')
line = file.readline()
while (line):
line = line.replace('\t',' ')
terms = line.split(' ')
if line[0][0]!='#':
id = terms[0] #re.findall(r'[A-Za-z_]+', line)
sex = id.split('_')[-1].lower()
if compare_sex(sex, cell):
id = id.replace('_male', '')
id = id.replace('_female', '')
else:
line = file.readline()
continue;
# Skip over the label, which may contain numbers like in HCO3
first_space_pos = line.index(' ')
num = re.findall(r'-?\d+\.?\d*[Ee]?[+-]?\d*', line[first_space_pos:len(line)])
if num: # if this line is numerical parameter
value = float(num[0])
if id.lower() == "Sex".lower():
find = re.findall("Female".lower(), terms[-1].lower())
if find:
cell.sex = "Female".lower()
# Diameter:
elif compare_string_prefix(id,"Diameter"):
# diabetic diameter
if cell.diabete == 'Non':
cell.diam = value
if cell.type != 'sup':
cell.diam = value*1.02 #slight increase in juxt diam size
elif cell.diabete == 'Moderate':
if cell.segment == 'PT' or cell.segment == 'S3':
cell.diam = value*1.1
elif cell.segment == 'SDL' or cell.segment == 'mTAL' or cell.segment == 'cTAL' or cell.segment == 'DCT' or cell.segment == 'CNT' or cell.segment == 'CCD' or cell.segment == 'OMCD':
cell.diam = value*1.18
else:
cell.diam = value
elif cell.diabete == 'Severe':
if cell.segment == 'PT' or cell.segment == 'S3':
cell.diam = value*1.28
elif cell.segment == 'SDL' or cell.segment == 'mTAL' or cell.segment == 'cTAL' or cell.segment == 'DCT' or cell.segment == 'CNT' or cell.segment == 'CCD' or cell.segment == 'OMCD':
cell.diam = value*1.42
else:
cell.diam = value
else:
print('What is the diabete status?')
if cell.inhib == 'NHE3-50':
if cell.sex == 'male':
if cell.segment == 'CCD' or cell.segment == 'OMCD' or cell.segment == 'IMCD':
cell.diam = value*1.05
if cell.sex == 'female':
if cell.segment == 'CCD' or cell.segment == 'OMCD' or cell.segment == 'IMCD':
cell.diam = value*0.95
if cell.inhib == 'NKCC2-100':
if cell.sex == 'male':
if cell.segment == 'CCD' or cell.segment == 'OMCD' or cell.segment == 'IMCD':
cell.diam = value*0.95
if cell.sex == 'female':
if cell.segment == 'CCD' or cell.segment == 'OMCD' or cell.segment == 'IMCD':
cell.diam = value*0.95
if cell.unx == 'Y':
if cell.sex == 'male':
if cell.segment == 'PT' or cell.segment == 'S3':
cell.diam = value*1.1
else:
cell.diam = value*1.1
elif cell.sex == 'female':
if cell.segment == 'PT' or cell.segment == 'S3':
cell.diam = value*1.085
else:
cell.diam = value*1.085
# Length:
elif compare_string_prefix(id,"Length"):
if cell.segment == 'LDL' or cell.segment == 'LAL':
if cell.type == 'jux1':
looplen = 0.2
elif cell.type == 'jux2':
looplen = 0.4
elif cell.type == 'jux3':
looplen = 0.6
elif cell.type == 'jux4':
looplen = 0.8
elif cell.type == 'jux5':
looplen = 1.0
cell.len = value*looplen
else:
cell.len = value
# parameter files specify superficial segmental lengths; for some segments, lengths are different for juxtamedullary nephrons, so we overwrite them here...
if cell.type != 'sup' and cell.species == 'rat':
if cell.segment == 'cTAL':
# cTAL is short in jux nephrons
if cell.sex == 'male':
cell.len = 0.05
elif cell.sex == 'female':
cell.len = 0.05*0.9
elif cell.segment == 'CNT':
# CNT is longer in jux nephrons
if cell.sex == 'male':
cell.len = 0.3
elif cell.sex == 'female':
cell.len = 0.3*0.9
#if cell.type != 'sup' and cell.species == 'mou':
#if cell.segment == 'PT':
# if cell.sex == 'male':
# cell.len = 0.6
# elif cell.sex == 'female':
# cell.len = 0.6*0.9 #0.05*0.85, updated female
#elif cell.segment == 'CNT':
# if cell.sex == 'male':
# cell.len = 0.12
# elif cell.sex == 'female':
# cell.len = 0.3*0.9 #0.3*0.85, updated female
if cell.type != 'sup' and cell.species == 'hum':
if cell.segment == 'cTAL':
if cell.sex == 'male':
cell.len = 0.125
elif cell.sex == 'female':
cell.len = 0.125
elif cell.segment == 'CNT':
if cell.sex == 'male':
cell.len = 0.6
elif cell.sex == 'female':
cell.len = 0.6
if cell.diabete == 'Non':
cell.len = cell.len
elif cell.diabete == 'Moderate':
if cell.segment == 'PT':
cell.len = value*1.1
elif cell.segment == 'SDL' or cell.segment == 'mTAL' or cell.segment == 'cTAL' or cell.segment == 'DCT' or cell.segment == 'CNT' or cell.segment == 'CCD' or cell.segment == 'OMCD':
cell.len = value*1.07
else:
cell.len = value
elif cell.diabete == 'Severe':
if cell.segment == 'PT':
cell.len = value*1.28
elif cell.segment == 'SDL' or cell.segment == 'mTAL' or cell.segment == 'cTAL' or cell.segment == 'DCT' or cell.segment == 'CNT' or cell.segment == 'CCD' or cell.segment == 'OMCD':
cell.len = value*1.07
else:
cell.len = value
else:
print('What is the diabete status?')
if cell.unx == 'Y':
if cell.sex == 'male':
if cell.segment == 'PT' or cell.segment == 'S3':
cell.len = value*1.1
else:
cell.len = value*1.1
elif cell.sex == 'female':
if cell.segment == 'PT' or cell.segment == 'S3':
cell.len = value*1.085
else:
cell.len = value*1.085
# Total number of cells:
elif compare_string_prefix(id,"Total"):
cell.total = value
# Luminal pressure:
elif compare_string_prefix(id,"Pressure"):
cell.pres[0] = value
# parameter files specify pressure (value) for superficial nephrons
if cell.type !='sup' and cell.segment == 'PT' and cell.species == 'rat':
if cell.sex == 'male':
cell.pres[0] = 14.0
elif cell.sex == 'female':
cell.pres[0] = 14.0 #12.75
if cell.type !='sup' and cell.segment == 'PT' and cell.species == 'mou':
if cell.sex == 'male':
cell.pres[0] = 8.5
elif cell.sex == 'female':
cell.pres[0] = 8.5
if cell.diabete != 'Non' and cell.species == 'hum':
if cell.type == 'sup' and cell.segment == 'PT':
if cell.sex == 'male':
cell.pres[0] = 25.0
elif cell.sex == 'female':
cell.pres[0] = 25.0
elif cell.type !='sup' and cell.segment == 'PT':
if cell.sex == 'male':
cell.pres[0] = 30.0
elif cell.sex == 'female':
cell.pres[0] = 30.0
if cell.unx == 'Y' and cell.species == 'hum':
if cell.type == 'sup' and cell.segment == 'PT':
if cell.sex == 'male':
cell.pres[0] = 25.0
elif cell.sex == 'female':
cell.pres[0] = 25.0
elif cell.type !='sup' and cell.segment == 'PT':
if cell.sex == 'male':
cell.pres[0] = 25.0
elif cell.sex == 'female':
cell.pres[0] = 25.0
# pH:
elif compare_string_prefix(id,"pH"):
for i in range(6):
cell.pH[i] = num[i]
# Surface area multiplication factor:
elif compare_string_prefix(id,"Area"):
ind1,ind2 = get_interface_id(id)
cell.area[ind1][ind2] = value
cell.area[ind2][ind1] = value # symmetry
cell.area_init[ind1][ind2] = value
cell.area_init[ind2][ind1] = value
if cell.type != 'sup' and (cell.species == 'rat'):
if cell.segment == 'PT' or cell.segment == 'S3':
cell.area[ind1][ind2] = 1.75*cell.area[ind1][ind2]
cell.area[ind2][ind1] = cell.area[ind1][ind2]
# Water permeabilities:
elif compare_string_prefix(id,"Pf"):
ind1,ind2 = get_interface_id(id)
# Units of dimensional water flux (in 'value'): cm3/s/cm2 epith
# Non-dimensional factor for water flux: (Pfref)*Vwbar*Cref
# Calculate non-dimensional dLPV = Pf*Vwbar*Cref / (Pfref*Vwbar*Cref)
# dLPV = Pf/Pfref
cell.dLPV[ind1][ind2] = value/Pfref
# symmetry
cell.dLPV[ind2][ind1] = value/Pfref
if cell.segment == 'SDL' and cell.type == 'sup':
if j>=0.46*cell.total:
cell.dLPV[0,1]=0.00*cell.dLPV[0,1]
cell.dLPV[0,4]=0.00*cell.dLPV[0,4]
elif cell.segment == 'LDL':
if cell.sex == 'male':
if j>=0.4*cell.total:
cell.dLPV[0,1]=0.00*cell.dLPV[0,1]
cell.dLPV[0,4]=0.00*cell.dLPV[0,4]
elif cell.sex == 'female':
if j>=0.5*cell.total:
cell.dLPV[0,1]=0.00*cell.dLPV[0,1]
cell.dLPV[0,4]=0.00*cell.dLPV[0,4]
if cell.segment == 'CNT' and cell.type !='sup':
if cell.sex == 'female':
cell.dLPV = cell.dLPV*4/3
if cell.diabete != 'Non':
if cell.segment == 'CCD':
cell.dLPV[0,1] = cell.dLPV[0,1]*1.55
cell.dLPV[1,5] = cell.dLPV[1,5]*1.55
elif cell.segment == 'IMCD':
cell.dLPV[0,1] = cell.dLPV[0,1]*1.4
cell.dLPV[1,5] = cell.dLPV[1,5]*1.4
if cell.HT != 'N':
# AQP2 changed
HT_rat = 1.0
# AQP2 on the apical interface
if ind1 == 0 and ind2 == 1:
if cell.segment == 'CCD':
HT_rat = 1.3
elif cell.segment == 'OMCD':
HT_rat = 1.3
elif cell.segment == 'IMCD':
HT_rat = 1.3
# basolateral interface
elif ind1 == 1:
if ind2 == 4 or ind2 == 5:
if cell.segment == 'CCD':
HT_rat = 1.3
elif cell.segment == 'OMCD':
HT_rat = 1.3
elif cell.segment == 'IMCD':
HT_rat = 1.3
cell.dLPV[ind1][ind2] = value/Pfref*HT_rat
if cell.inhib == 'empa':
# AQP2 changed
empa_rat = 1.0
# apical interface
if ind1 == 0 and ind2 == 1:
# AQP1
if cell.segment == 'PT' or cell.segment == 'S3' or cell.segment == 'SDL':
empa_rat = 1.05
# AQP2
elif cell.segment == 'CCD' or cell.segment == 'OMCD' or cell.segment == 'IMCD':
empa_rat = 1.12
# basolateral interface
elif ind1 == 1:
if ind2 == 4 or ind2 == 5:
# AQP1
if cell.segment == 'PT' or cell.segment == 'S3' or cell.segment == 'SDL':
empa_rat = 1.05
# AQP2
elif cell.segment == 'CCD' or cell.segment == 'OMCD' or cell.segment == 'IMCD':
empa_rat = 1.12
cell.dLPV[ind1][ind2] = value/Pfref*empa_rat
# Reflection coefficients:
elif compare_string_prefix(id,"sig"):
sid,ind1,ind2 = get_interface_id(id)
cell.sig[sid][ind1][ind2] = value
# symmetry
cell.sig[sid][ind2][ind1] = value
cell.sig[sid][4][5] = 0.0
cell.sig[sid][5][4] = 0.0
# Membrane solute permeabilities:
elif compare_string_prefix(id,"perm"):
sid,ind1,ind2 = get_interface_id(id)
cell.h[sid][ind1][ind2] = value*1.0e-5/href
# Symmetry:
cell.h[sid][ind2][ind1] = value*1.0e-5/href
# Same permeability on basolateral membrane (around bath or LIS):
if ind1==1 and ind2==5:
cell.h[sid][ind1][4] = value*1.0e-5/href
cell.h[sid][4][ind1] = value*1.0e-5/href
elif ind1==1 and ind2==4:
cell.h[sid][ind1][5] = value*1.0e-5/href
cell.h[sid][5][ind1] = value*1.0e-5/href
elif ind1==2 and ind2==4:
cell.h[sid][ind1][5] = value*1.0e-5/href
elif ind1==3 and ind2==4:
cell.h[sid][ind1][5] = value*1.0e-5/href
if cell.segment == 'OMCD':
cell.h[sid][0][3] = 0.0
cell.h[sid][3][4] = 0.0
cell.h[sid][3][5] = 0.0
if cell.segment == 'IMCD':
if cell.sex == 'male':
if j>3*cell.total/4-1:
cell.h[8,0,1] = 300.0*1.0e-5/href
elif cell.sex == 'female':
if j>2*cell.total/3-1:
cell.h[8,0,1] = 300.0*1.0e-5/href
if cell.segment == 'LDL':
if cell.sex == 'male':
if j>=0.4*cell.total:
cell.h[0,0,1]=80.0
cell.h[0,0,4]=80.0
cell.h[1,0,1]=100.0
cell.h[1,0,4]=100.0
cell.h[2,0,1]=80.0
cell.h[2,0,4]=80.0
cell.h[3,0,1]=20.0
cell.h[3,0,4]=20.0
cell.h[10,0,1]=20.0
cell.h[10,0,4]=20.0
cell.h[8,0,1]=80.0 #80
cell.h[8,0,4]=80.0 #80
elif cell.sex == 'female':
if j>=0.5*cell.total:
cell.h[0,0,1]=40.0
cell.h[0,0,4]=80.0
cell.h[1,0,1]=100.0
cell.h[1,0,4]=100.0
cell.h[2,0,1]=40.0
cell.h[2,0,4]=80.0
cell.h[3,0,1]=20.0
cell.h[3,0,4]=20.0
cell.h[10,0,1]=20.0
cell.h[10,0,4]=20.0
cell.h[8,0,1]=80.0
cell.h[8,0,4]=80.0
if cell.inhib == 'ACE' and cell.segment == 'DCT':
cell.h[1,0,1] = 0.5*value*1.0e-5/href
# ROMK2 (K secretion) change in HT rat
if cell.HT != 'N':
temp = cell.h[1,0,1]
if cell.segment == 'DCT':
if j>0.66*cell.total:
# DCT2
HT_rat = 0.3 #0.175
cell.h[1,0,1] = HT_rat*0.6
elif cell.segment == 'CNT':
HT_rat = 0.3 #0.2
cell.h[1,0,1] = HT_rat*8.0
if cell.inhib == 'empa':
if cell.segment == 'DCT':
# ROMK
if j>0.66*cell.total:
#DCT2
empa_rat_ROMK = 1.14 #1.02
cell.h[1,0,1] = empa_rat_ROMK*0.6
elif cell.segment == 'CNT':
empa_rat_ROMK = 1.14 #1.02
cell.h[1,0,1] = empa_rat_ROMK*8.0
elif cell.segment == 'CCD':
# PNaCl
empa_rat = 1.14 #1.21
# lumen LIS
cell.h[2,0,4] = empa_rat*1.2e3 # male PCL
cell.h[0,0,4] = empa_rat*1.0e3 # male PNa
# LIS bath
cell.h[2,4,5] = empa_rat*16.0e3 # male PCL
cell.h[0,4,5] = empa_rat*12.0e3 # male PNa
# Coupled transporters:
elif compare_string_prefix(id,"coupled"):
# retrieve interface and solute id
vals = get_coupled_id(id)
newdLA = coupled_transport()
newdLA.perm = value / (href*Cref)
newdLA.membrane_id = [vals[0],vals[1]]
coef = [] # retrieve coupling coefficients
for i in range(1,len(num)):
coef.append(int(num[i]))
newdLA.coef = coef
newdLA.solute_id = vals[2:len(vals)]
# HTN
if cell.HT != 'N':
# NaPi2
if newdLA.solute_id == (0,7):
if cell.segment == 'PT' or cell.segment == 'S3':
HT_rat = 0.85
newdLA.perm = HT_rat*newdLA.perm
# empa
if cell.inhib == 'empa':
# NaPi2
if newdLA.solute_id == (0,7):
if cell.segment == 'PT' or cell.segment == 'S3':
empa_rat = 0.88
newdLA.perm = empa_rat*newdLA.perm
cell.dLA.append(newdLA)
# Specific transporters:
elif compare_string_prefix(id,"transport"):
tmp = (id).split('_')
ind1,ind2 = compart_id[tmp[1]],compart_id[tmp[2]]
newTransp = transporter()
newTransp.membrane_id = [ind1,ind2]
newTransp.type = tmp[3]
newTransp.act = value/(href*Cref)
#print('transporter')
#print(newTransp.membrane_id,newTransp.type,newTransp.act)
if cell.type != 'sup' and cell.sex == 'female' and (cell.species == 'rat' or cell.species == 'mou'):
if cell.segment == 'mTAL' or cell.segment == 'cTAL':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F' or newTransp.type == 'NaKATPase':
newTransp.act = 1.5*value/(href*Cref)
elif newTransp.type == 'KCC4':
newTransp.act = 2.0*value/(href*Cref)
if cell.diabete == 'Moderate':
if cell.segment == 'PT' or cell.segment == 'S3':
if newTransp.type == 'SGLT2':
if cell.sex == 'male':
newTransp.act = (1+0.38)*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = (1+0.38)*value/(href*Cref)
# elif newTransp.type == 'GLUT2': # optional
# if cell.sex == 'male':
# newTransp.act = (1+0.5)*value/(href*Cref)
# if cell.sex == 'female':
# newTransp.act = (1+0.3)*value/(href*Cref)
elif newTransp.type == 'SGLT1':
newTransp.act = (1-0.33)*value/(href*Cref)*3.5
# elif newTransp.type == 'GLUT1': # optional
# if cell.sex == 'male':
# newTransp.act = 0.5*value/(href*Cref)
elif newTransp.type == 'NaKATPase':
newTransp.act = 1.1*value/(href*Cref)
elif cell.segment == 'mTAL':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2F':
if cell.sex =='male':
newTransp.act = 1.1*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.1*value/(href*Cref)
elif newTransp.type == 'NaKATPase':
if cell.sex == 'male':
newTransp.act = 1.2*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.2*value/(href*Cref)
elif cell.segment == 'cTAL' or cell.segment == 'DCT' or cell.segment == 'CNT' or cell.segment == 'CCD':
if newTransp.type == 'NaKATPase':
if cell.sex == 'male':
newTransp.act = 1.1*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.1*value/(href*Cref)
elif cell.segment == 'OMCD':
if newTransp.type == 'NaKATPase':
if cell.sex == 'male':
newTransp.act = 1.1*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.1*value/(href*Cref)
elif cell.segment == 'IMCD':
if newTransp.type == 'NaKATPase':
if cell.sex == 'male':
if j<2/3*cell.total:
newTransp.act = 1.5*value/(href*Cref)
else:
newTransp.act = 2.5*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 2.5*value/(href*Cref)
elif newTransp.type == 'HKATPase' and cell.inhib == 'SGLT2':
if cell.sex == 'male':
newTransp.act = 5*value/(href*Cref)
elif cell.diabete == 'Severe':
if cell.segment == 'PT' or cell.segment == 'S3':
if newTransp.type == 'SGLT2':
if cell.sex == 'male':
newTransp.act = (1+0.38)*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = (1+0.28)*value/(href*Cref)
elif newTransp.type == 'GLUT2':
if cell.sex == 'male':
newTransp.act = (1+0.5)*value/(href*Cref)
if cell.sex == 'female':
newTransp.act = (1+0.3)*value/(href*Cref)
elif newTransp.type == 'SGLT1':
newTransp.act = (1-0.33)*value/(href*Cref)*3.5
elif newTransp.type == 'NaKATPase':
newTransp.act = 1.1*value/(href*Cref)
elif cell.segment == 'mTAL':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2F':
if cell.sex =='male':
newTransp.act = 1.1*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.05*value/(href*Cref)
elif newTransp.type == 'NaKATPase':
if cell.sex == 'male':
newTransp.act = 1.2*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.1*value/(href*Cref)
elif cell.segment == 'cTAL' or cell.segment == 'DCT' or cell.segment == 'CNT' or cell.segment == 'CCD':
if newTransp.type == 'NaKATPase':
if cell.sex == 'male':
newTransp.act = 1.1*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.05*value/(href*Cref)
elif cell.segment == 'OMCD':
if newTransp.type == 'NaKATPase':
if cell.sex == 'male':
newTransp.act = 1.1*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.05*value/(href*Cref)
elif cell.segment == 'IMCD':
if newTransp.type == 'NaKATPase':
if cell.sex == 'male':
newTransp.act = 2.5*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.5*value/(href*Cref)
if cell.inhib == 'NHE3-50':
if cell.segment == 'PT':
if newTransp.type == 'NHE3':
newTransp.act = (1-0.5)*value/(href*Cref)
elif cell.segment == 'mTAL' or cell.segment == 'cTAL':
if newTransp.type == 'NHE3':
newTransp.act = (1-0.5*0.5)*value/(href*Cref)
if cell.segment == 'mTAL':
if newTransp.type == 'NaKATPase':
newTransp.act = (1+0.5*0.5)*value/(href*Cref)
if cell.segment == 'cTAL':
if newTransp.type == 'NaKATPase':
newTransp.act = (1-0.5*0.5)*value/(href*Cref)
elif cell.segment == 'DCT':
if newTransp.type == 'NHE3':
newTransp.act = (1-0.5)*value/(href*Cref)
elif cell.inhib == 'NHE3-80':
if cell.segment == 'PT':
if newTransp.type == 'NHE3':
newTransp.act = (1-0.8)*value/(href*Cref)
elif cell.segment == 'mTAL' or cell.segment == 'cTAL':
if newTransp.type == 'NHE3':
newTransp.act = (1-0.8*0.5)*value/(href*Cref)
if cell.segment == 'mTAL':
if newTransp.type == 'NaKATPase':
newTransp.act = (1+0.8*0.5)*value/(href*Cref)
if cell.segment == 'cTAL':
if newTransp.type == 'NaKATPase':
newTransp.act = (1-0.8*0.5)*value/(href*Cref)
elif cell.segment == 'DCT':
if newTransp.type == 'NHE3':
newTransp.act = (1-0.8)*value/(href*Cref)
elif cell.inhib == 'NKCC2-70':
if cell.segment == 'mTAL' or cell.segment == 'cTAL':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F':
newTransp.act = (1-0.7)*value/(href*Cref)
elif cell.inhib == 'NKCC2-100':
if cell.segment == 'mTAL' or cell.segment == 'cTAL':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F':
newTransp.act = (1-1)*value/(href*Cref)
elif cell.inhib == 'NCC-70':
if cell.segment == 'DCT':
if newTransp.type == 'NCC':
newTransp.act = (1-0.7)*value/(href*Cref)
elif cell.inhib == 'NCC-100':
if cell.segment == 'DCT':
if newTransp.type == 'NCC':
newTransp.act = (1-1)*value/(href*Cref)
elif cell.inhib == 'ENaC-70':
if newTransp.type == 'ENaC':
newTransp.act = (1-0.7)*value/(href*Cref)
elif cell.inhib == 'ENaC-100':
if newTransp.type == 'ENaC':
newTransp.act = (1-1)*value/(href*Cref)
elif cell.inhib == 'SNB-70':
if cell.segment == 'mTAL' or cell.segment == 'cTAL':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F':
newTransp.act = (1-0.7)*value/(href*Cref)
if cell.segment == 'DCT':
if newTransp.type == 'NCC':
newTransp.act = (1-0.7)*value/(href*Cref)
if newTransp.type == 'ENaC':
newTransp.act = (1-0.7)*value/(href*Cref)
elif cell.inhib == 'SNB-100':
if cell.segment == 'mTAL' or cell.segment == 'cTAL':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F':
newTransp.act = (1-1)*value/(href*Cref)
if cell.segment == 'DCT':
if newTransp.type == 'NCC':
newTransp.act = (1-1)*value/(href*Cref)
if newTransp.type == 'ENaC':
newTransp.act = (1-1)*value/(href*Cref)
if cell.inhib == 'ACE':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F':
newTransp.act = 0.5*value/(href*Cref)
if cell.segment == 'DCT':
if newTransp.type == 'NCC' or newTransp.type == 'NaKATPase' or newTransp.type == 'ENaC':
newTransp.act == 0.5*value/(href*Cref)
if cell.inhib == 'SGLT2':
if newTransp.type == 'SGLT2':
newTransp.act = value/(href*Cref)*0.2
if newTransp.type == 'SGLT1':
newTransp.act = value/(href*Cref)*3.5
if cell.inhib == 'empa':
empa_rat = 1.0
if newTransp.type == 'NHE3':
if cell.segment == 'PT' or cell.segment == 'cTAL':
empa_rat = 1.36
elif cell.segment == 'S3' or cell.segment == 'mTAL':
empa_rat = 1.45
elif newTransp.type == 'SGLT2':
empa_rat = 0.46*(1-0.9)
elif newTransp.type == 'SGLT1':
empa_rat = 0.93
elif newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F':
if cell.segment == 'mTAL':
empa_rat = 1.27
elif cell.segment == 'cTAL':
empa_rat = 1.15
elif newTransp.type == 'NaKATPase':
if cell.segment == 'PT':
empa_rat = 1.20
if cell.segment == 'mTAL':
empa_rat = 1.22
elif cell.segment == 'cTAL':
empa_rat = 1.20
elif newTransp.type == 'NCC':
empa_rat = 1.0
elif newTransp.type == 'Pendrin':
empa_rat = 1.52
elif newTransp.type == 'ENaC':
empa_rat = 0.93
# update activity based on empa change
newTransp.act = empa_rat*value/(href*Cref)
if cell.unx == 'Y':
if newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F':
newTransp.act = 1.05*value/(href*Cref)
elif newTransp.type == 'NCC':
newTransp.act = 1.1*value/(href*Cref)
elif newTransp.type == 'ENaC':
if cell.sex == 'male':
newTransp.act = 1.3*value/(href*Cref)
elif cell.sex == 'female':
newTransp.act = 1.2*value/(href*Cref)
if cell.HT != 'N':
if newTransp.type == 'NCC':
HT_rat = 1.95
newTransp.act = HT_rat*value/(href*Cref)
elif newTransp.type == 'NHE3':
if cell.segment == 'PT' or cell.segment == 'S3' or cell.segment == 'mTAL':
HT_rat = 0.82
elif cell.segment == 'cTAL' or cell.segment == 'DCT':
HT_rat = 1.0
else:
print('segment: ' + cell.segment)
raise Exception('NHE3 activity not done for this segment in HT rat model')
newTransp.act = HT_rat*value/(href*Cref)
elif newTransp.type == 'NKCC2A' or newTransp.type == 'NKCC2B' or newTransp.type == 'NKCC2F':
if cell.segment == 'mTAL':
HT_rat = 0.7
elif cell.segment == 'cTAL':
HT_rat = 1.74
else:
print('segment: ' + cell.segment)
raise Exception('NKCC2 activity not done for this segment in HT rat model')
newTransp.act = HT_rat*value/(href*Cref)
elif newTransp.type == 'NaKATPase':
if cell.segment == 'mTAL':
HT_rat = 0.70
else:
HT_rat = 1.0
newTransp.act = HT_rat*value/(href*Cref)
elif newTransp.type == 'ENaC':
HT_rat = 1.45
newTransp.act = HT_rat*value/(href*Cref)
cell.trans.append(newTransp)
# Solute concentrations:
elif compare_string_prefix(id,"conc"):
tmp = (id).split('_')
cell.conc[solute_id[tmp[1]]][0] = float(num[0])
cell.conc[solute_id[tmp[1]]][1] = float(num[1])
cell.conc[solute_id[tmp[1]]][4] = float(num[2])
cell.conc[solute_id[tmp[1]]][5] = float(num[3])
if len(num) > 4:
cell.conc[solute_id[tmp[1]]][2] = float(num[4])
if len(num) > 5:
cell.conc[solute_id[tmp[1]]][3] = float(num[5])
if cell.diabete == 'Moderate':
if cell.segment == 'PT':
cell.conc[14,0] = 8.6
elif cell.diabete == 'Severe':
if cell.segment == 'PT' and cell.species == 'hum':
cell.conc[14,0] = 20.0
elif cell.segment == 'PT' and cell.species == 'rat':
cell.conc[14,0] = 25.0
elif cell.segment == 'PT' and cell.species == 'mou':
cell.conc[14,0] = 25.0
# Reference impermeat concentration (for cell)
# or oncotic pressure for lumen/LIS/bath
elif compare_string_prefix(id,"cimpref"):
tmp = (id).split('_')
cell.cimpref[compart_id[tmp[1]]] = float(num[0])
# Impermeant properties
elif compare_string_prefix(id,"zimp"):
tmp = (id).split('_')
cell.zimp[compart_id[tmp[1]]] = float(num[0])
# Reference buffer concentrations (for cell):
elif compare_string_prefix(id,"cbuftot"):
tmp = (id).split('_')
cell.cbuftot[compart_id[tmp[1]]] = float(num[0])
# Rates used in HCO3/H2CO3 reaction:
elif compare_string_prefix(id,"dkd"):
tmp = (id).split('_')
cell.dkd[compart_id[tmp[1]]] = float(num[0])
elif compare_string_prefix(id,"dkh"):
tmp = (id).split('_')
cell.dkh[compart_id[tmp[1]]] = float(num[0])
# Reference volume flows:
elif compare_string_prefix(id,"volref"):
tmp = (id).split('_')
cell.volref[compart_id[tmp[1]]] = float(num[0])
# Actual volume flows:
elif compare_string_prefix(id,"vol"):
tmp = (id).split('_')
# data files specify values for superficial nephrons, juxmedullary nephron values are hardcoded here
if cell.segment == 'PT' and cell.type != 'sup' and cell.species == 'rat':
if compart_id[tmp[1]] == 0:
if cell.type == 'jux1':
if cell.sex == 'male':
cell.vol[0] = 0.0075
elif cell.sex == 'female':
cell.vol[0] = 0.0056
cell.vol_init[0] = cell.vol[0]
elif cell.type == 'jux2':
if cell.sex == 'male':
cell.vol[0] = 0.0075
elif cell.sex == 'female':
cell.vol[0] = 0.0056
cell.vol_init[0] = cell.vol[0]
elif cell.type == 'jux3':
if cell.sex == 'male':
cell.vol[0] = 0.0075
elif cell.sex == 'female':
cell.vol[0] = 0.0056
cell.vol_init[0] = cell.vol[0]
elif cell.type == 'jux4':
if cell.sex == 'male':
cell.vol[0] = 0.0075
elif cell.sex == 'female':
cell.vol[0] = 0.0056
cell.vol_init[0] = cell.vol[0]
elif cell.type == 'jux5':
if cell.sex == 'male':
cell.vol[0] = 0.0075
elif cell.sex == 'female':
cell.vol[0] = 0.0056
cell.vol_init[0] = cell.vol[0]
else:
cell.vol[compart_id[tmp[1]]] = float(num[0])
cell.vol_init[compart_id[tmp[1]]] = float(num[0])
elif cell.segment == 'PT' and cell.type != 'sup' and cell.species == 'mou':
if compart_id[tmp[1]] == 0:
if cell.sex == 'male':
cell.vol[0] = 0.00204
elif cell.sex == 'female':
cell.vol[0] = 0.001632
cell.vol_init[0] = cell.vol[0]
else:
cell.vol[compart_id[tmp[1]]] = float(num[0])
cell.vol_init[compart_id[tmp[1]]] = float(num[0])
elif cell.segment == 'PT' and cell.type != 'sup' and cell.species == 'hum':
if compart_id[tmp[1]] == 0:
cell.vol[0] = 0.02222
cell.vol_init[0] = cell.vol[0]
else:
cell.vol[compart_id[tmp[1]]] = float(num[0])
cell.vol_init[compart_id[tmp[1]]] = float(num[0])
else:
cell.vol[compart_id[tmp[1]]] = float(num[0])
cell.vol_init[compart_id[tmp[1]]] = float(num[0])
if cell.diabete != 'Non' and cell.species == 'rat':
if cell.sex == 'male':
if cell.segment == 'PT' and cell.type == 'sup':
cell.vol[0] = 0.0075
cell.vol_init[0] = cell.vol[0]
if cell.segment == 'PT' and cell.type != 'sup':
cell.vol[0] = 0.008775
cell.vol_init[0] = cell.vol[0]
elif cell.sex == 'female':
if cell.segment == 'PT' and cell.type == 'sup':
cell.vol[0] = 0.004*1.75#1.5
cell.vol_init[0] = cell.vol[0]
if cell.segment == 'PT' and cell.type != 'sup':
cell.vol[0] = 0.006*1.17
cell.vol_init[0] = cell.vol[0]
if cell.diabete != 'Non' and cell.species == 'mou':
if cell.sex == 'male':
if cell.segment == 'PT' and cell.type == 'sup':
cell.vol[0] = 0.0075
cell.vol_init[0] = cell.vol[0]
if cell.segment == 'PT' and cell.type != 'sup':
cell.vol[0] = 0.008775
cell.vol_init[0] = cell.vol[0]
elif cell.sex == 'female':
if cell.segment == 'PT' and cell.type == 'sup':
cell.vol[0] = 0.0075
cell.vol_init[0] = cell.vol[0]
if cell.segment == 'PT' and cell.type != 'sup':
cell.vol[0] = 0.008775
cell.vol_init[0] = cell.vol[0]
if cell.diabete == 'Moderate' and cell.species == 'hum':
if compart_id[tmp[1]] == 0:
if cell.sex == 'male':
if cell.segment == 'PT' and cell.type == 'sup':
cell.vol[0] = 0.0195
cell.vol_init[0] = cell.vol[0]
if cell.segment == 'PT' and cell.type != 'sup':
cell.vol[0] = 0.026
cell.vol_init[0] = cell.vol[0]
elif cell.sex == 'female':
if cell.segment == 'PT' and cell.type == 'sup':
cell.vol[0] = 0.0195
cell.vol_init[0] = cell.vol[0]
if cell.segment == 'PT' and cell.type != 'sup':
cell.vol[0] = 0.026
cell.vol_init[0] = cell.vol[0]
elif cell.diabete == 'Severe' and cell.species == 'hum':
if compart_id[tmp[1]] == 0:
if cell.sex == 'male':
if cell.segment == 'PT' and cell.type == 'sup':
cell.vol[0] = 0.0212