proc celldef() {
  topol()
  subsets()
  geom()
  biophys()
  geom_nseg()
diam_seg()
}

create soma, dend1[3], dend1_1[3], dend2[5], SDI, SIprox, SIdistal
create axon

proc topol() { local i
  connect dend1(0), soma(0)
  for i = 1, 2 connect dend1[i](0), dend1[i-1](1)
  for i = 0, 2 connect dend1_1[i](0), soma(1)
  for i = 0, 1 connect dend2[i](0), dend1(1)
  for i = 2, 3 connect dend2[i](0), dend1[1](1)
  connect dend2[4](0), dend1[2](1)
  connect SDI(0), dend1[2](1)
  connect SIprox(0), SDI(1)
  connect SIdistal(0), SIprox(1)
  connect axon(0), SIdistal(1)
  basic_shape()
}
proc basic_shape() {
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
  dend1 {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-29, 0, 0, 1)}
  dend1[1] {pt3dclear() pt3dadd(-29, 0, 0, 1) pt3dadd(-59, 0, 0, 1)}
  dend1[2] {pt3dclear() pt3dadd(-59, 0, 0, 1) pt3dadd(-104, 0, 0, 1)}
  dend1_1 {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(90, -59, 0, 1)}
  dend1_1[1] {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(120, 0, 0, 1)}
  dend1_1[2] {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(105, 60, 0, 1)}
  dend2 {pt3dclear() pt3dadd(-29, 0, 0, 1) pt3dadd(-29, 60, 0, 1)}
  dend2[1] {pt3dclear() pt3dadd(-29, 0, 0, 1) pt3dadd(-29, -59, 0, 1)}
  dend2[2] {pt3dclear() pt3dadd(-59, 0, 0, 1) pt3dadd(-59, 60, 0, 1)}
  dend2[3] {pt3dclear() pt3dadd(-59, 0, 0, 1) pt3dadd(-59, -59, 0, 1)}
  SDI {pt3dclear() pt3dadd(-104, 0, 0, 1) pt3dadd(-119, 15, 0, 1)}
  SIprox {pt3dclear() pt3dadd(-119, 15, 0, 1) pt3dadd(-134, 30, 0, 1)}
  SIdistal {pt3dclear() pt3dadd(-134, 30, 0, 1) pt3dadd(-164, 60, 0, 1)}
  axon {pt3dclear() pt3dadd(-164, 60, 0, 1) pt3dadd(-194, 165, 0, 1)}
  dend2[4] {pt3dclear() pt3dadd(-104, 0, 0, 1) pt3dadd(-164, -44, 0, 1)}
}

objref all, Secdend
proc subsets() { local i
  objref all, Secdend
  all = new SectionList()
  Secdend = new SectionList()
  
    soma all.append()
    for i=0, 2 dend1[i] all.append()
    for i=0, 2 dend1_1[i] all.append()
    for i=0, 4 dend2[i] all.append()
    SDI all.append()
    SIprox all.append()
    SIdistal all.append()
    axon all.append()
	for i=0, 4 dend2[i] Secdend.append()

}
proc geom() {
  forsec all {  }
   soma.L = 20
   dend1.L = 13
   dend1[1].L = 14
   dend1[2].L = 13
   dend1_1.L = 500
   dend1_1[1].L = 500
   dend1_1[2].L = 500
    dend2.L = 500
   dend2[1].L =500
   dend2[2].L = 0.00001
   dend2[3].L = 0.00001
   dend2[4].L = 500 //axonal
   SDI.L = 21
   SIprox.L = 15
   SIdistal.L = 15
   axon.L = 800
   
  
  
}
proc geom_nseg() {
  forsec all { nseg = int((L/(0.1*lambda_f(1000))+.999)/2)*2 + 1 }
}

proc diam_seg() {
 soma.diam = 20
   dend1.diam = 3.3
   dend1[1].diam = 2.75
   dend1[2].diam = 2.4
   dend1_1.diam(0:1) = 3:0.5
   dend1_1[1].diam(0:1) = 3:0.5
   dend1_1[2].diam(0:1) = 3:0.5
   dend2.diam(0:1) = 2 : 0.5
   dend2[1].diam(0:1) = 2 : 0.5
   dend2[2].diam(0:1) = 2 : 0.5
   dend2[3].diam(0:1) = 2 : 0.5
    dend2[4].diam(0:1) = 2:0.5
   SDI.diam = 1.5
   SIprox.diam = 1.15
   SIdistal.diam = 1
   axon.diam = 0.7
   
}


proc biophys() {
  forsec all {
    Ra = 150
    cm = 0.75

  }
  hhN=75 // for Ina and *2 for kdrDA (homo)
CaN = 1// for Ica and *x for kca (homo)
KCA= 0.1
hhsec = 75 // for Ina and *2 for kdrDA (secondary dendrites : hetero)
Casec =1// for Ica and *x (secondary dendrites : hetero)
KCAsec= 0.1

hhABD =75 // for Ina and *2 for kdrDA (ABD : hetero)
CaABD = 1// for Ica and *x (ABD: hetero)
KCAABD =0.1

  
  soma {
    insert Na12
      gbar_Na12 = hhN
   insert kdrDA
      gbar_kdrDA = hhN*2 
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
insert kaDasoma
gbar_kaDasoma = 150
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaN
insert cad
insert kca
gbar_kca = KCA


ena=60
ek=-90
  }
  dend1 {
    insert Na12
      gbar_Na12 = hhN
insert kdrDA
      gbar_kdrDA = hhN*2
   insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend1[1] {
    insert Na12
      gbar_Na12 = hhN
   insert kdrDA
      gbar_kdrDA = hhN*2
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
 insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend1[2] {
    insert Na12
      gbar_Na12 = hhN
    insert kdrDA
      gbar_kdrDA = hhN*2
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend1_1 {
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
    insert Na12
      gbar_Na12 = hhN
    insert kdrDA
      gbar_kdrDA = hhN*2
insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend1_1[1] {
    insert Na12
      gbar_Na12 = hhN
    insert kdrDA
      gbar_kdrDA = hhN*2
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend1_1[2] {
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
    insert kdrDA
      gbar_kdrDA = hhN*2
    insert Na12
      gbar_Na12 = hhN
insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend2 {
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
    insert Na12
      gbar_Na12 = hhN
    insert kdrDA
      gbar_kdrDA = hhN*2
 insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend2[1] {
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
    insert kdrDA
      gbar_kdrDA = hhN*2
    insert Na12
      gbar_Na12 = hhN
 insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend2[2] {
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
    insert Na12
      gbar_Na12 = hhN
    insert kdrDA
      gbar_kdrDA = hhN*2
insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  dend2[3] {
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
    insert kdrDA
      gbar_kdrDA = hhN*2
    insert Na12
      gbar_Na12 = hhN
insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
   dend2[4] {
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
    insert Na12
      gbar_Na12 = hhN
    insert kdrDA
      gbar_kdrDA = hhN*2
insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  SDI {
insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
        insert Na12
      gbar_Na12 = hhN
  insert kdrDA
      gbar_kdrDA = hhN*2
	  insert kaDa
gbar_kaDa = 100
insert Ih
gbar_Ih = 3
insert CAV13
gbar_CAV13 = CaABD
insert cad
insert kca
gbar_kca = KCAABD

ena=60
ek=-90
  }
  SIprox {
insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
      insert Na12
      gbar_Na12 = 2000
	   
    insert kdrDA
      gbar_kdrDA = 1000

ena=60
ek=-90
  }
  SIdistal {
insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
       insert Na12
      gbar_Na12 = 2000
	   
        insert kdrDA
      gbar_kdrDA =1000
ena=60
ek=-90
  }
  axon {
    insert Na12
      gbar_Na12 = 400
	   
    insert kdrDA
      gbar_kdrDA = 400
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
ena=60
ek=-90
  }
}