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

create soma, ABD[4], axonstart, AIS, axon, axoD, axoD_sec[4]
create interD[3], interD_sec[14], nABD[3], nABD_sec[18]

proc topol() { local i
  connect ABD(0), soma(1)
  for i = 1, 3 connect ABD[i](0), ABD[i-1](1)
  connect axonstart(0), ABD[3](1)
  connect AIS(0), axonstart(1)
  connect axon(0), AIS(1)
  connect axoD(0), ABD[3](1)
  for i = 0, 1 connect axoD_sec[i](0), axoD(1)
  for i = 2, 3 connect axoD_sec[i](0), axoD_sec[1](1)
  for i = 0, 2 connect interD[i](0), ABD[i](1)
  for i = 0, 1 connect interD_sec[i](0), interD(1)
  for i = 2, 3 connect interD_sec[i](0), interD_sec[1](1)
  for i = 4, 5 connect interD_sec[i](0), interD_sec[3](1)
  for i = 6, 7 connect interD_sec[i](0), interD[1](1)
  for i = 8, 9 connect interD_sec[i](0), interD[2](1)
  for i = 10, 11 connect interD_sec[i](0), interD_sec[9](1)
  for i = 12, 13 connect interD_sec[i](0), interD_sec[8](1)
  for i = 0, 2 connect nABD[i](0), soma(0)
  connect nABD_sec(0), nABD(1)
  for i = 1, 2 connect nABD_sec[i](0), nABD_sec(1)
  connect nABD_sec[3](0), nABD(1)
  for i = 4, 5 connect nABD_sec[i](0), nABD_sec[3](1)
  for i = 6, 7 connect nABD_sec[i](0), nABD[1](1)
  for i = 8, 9 connect nABD_sec[i](0), nABD_sec[7](1)
  for i = 10, 11 connect nABD_sec[i](0), nABD_sec[9](1)
  for i = 12, 13 connect nABD_sec[i](0), nABD_sec[6](1)
  for i = 14, 15 connect nABD_sec[i](0), nABD_sec[13](1)
  for i = 16, 17 connect nABD_sec[i](0), nABD[2](1)
  basic_shape()
}
proc basic_shape() {
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
  ABD {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(15, 30, 0, 1)}
  ABD[1] {pt3dclear() pt3dadd(15, 30, 0, 1) pt3dadd(30, 45, 0, 1)}
  ABD[2] {pt3dclear() pt3dadd(30, 45, 0, 1) pt3dadd(60, 60, 0, 1)}
  ABD[3] {pt3dclear() pt3dadd(60, 60, 0, 1) pt3dadd(90, 60, 0, 1)}
  axonstart {pt3dclear() pt3dadd(90, 60, 0, 1) pt3dadd(105, 75, 0, 1)}
  AIS {pt3dclear() pt3dadd(105, 75, 0, 1) pt3dadd(120, 90, 0, 1)}
  axon {pt3dclear() pt3dadd(120, 90, 0, 1) pt3dadd(150, 120, 0, 1)}
  axoD {pt3dclear() pt3dadd(90, 60, 0, 1) pt3dadd(120, 45, 0, 1)}
  axoD_sec {pt3dclear() pt3dadd(120, 45, 0, 1) pt3dadd(150, 60, 0, 1)}
  axoD_sec[1] {pt3dclear() pt3dadd(120, 45, 0, 1) pt3dadd(135, 30, 0, 1)}
  axoD_sec[2] {pt3dclear() pt3dadd(135, 30, 0, 1) pt3dadd(165, 30, 0, 1)}
  axoD_sec[3] {pt3dclear() pt3dadd(135, 30, 0, 1) pt3dadd(150, 0, 0, 1)}
  interD {pt3dclear() pt3dadd(15, 30, 0, 1) pt3dadd(-14, 45, 0, 1)}
  interD[1] {pt3dclear() pt3dadd(30, 45, 0, 1) pt3dadd(15, 75, 0, 1)}
  interD[2] {pt3dclear() pt3dadd(60, 60, 0, 1) pt3dadd(60, 90, 0, 1)}
  interD_sec {pt3dclear() pt3dadd(-14, 45, 0, 1) pt3dadd(-44, 30, 0, 1)}
  interD_sec[1] {pt3dclear() pt3dadd(-14, 45, 0, 1) pt3dadd(-29, 75, 0, 1)}
  interD_sec[2] {pt3dclear() pt3dadd(-29, 75, 0, 1) pt3dadd(-29, 105, 0, 1)}
  interD_sec[3] {pt3dclear() pt3dadd(-29, 75, 0, 1) pt3dadd(-59, 90, 0, 1)}
  interD_sec[4] {pt3dclear() pt3dadd(-59, 90, 0, 1) pt3dadd(-74, 120, 0, 1)}
  interD_sec[5] {pt3dclear() pt3dadd(-59, 90, 0, 1) pt3dadd(-89, 90, 0, 1)}
  interD_sec[6] {pt3dclear() pt3dadd(15, 75, 0, 1) pt3dadd(30, 105, 0, 1)}
  interD_sec[7] {pt3dclear() pt3dadd(15, 75, 0, 1) pt3dadd(0, 105, 0, 1)}
  interD_sec[8] {pt3dclear() pt3dadd(60, 90, 0, 1) pt3dadd(45, 105, 0, 1)}
  interD_sec[9] {pt3dclear() pt3dadd(60, 90, 0, 1) pt3dadd(75, 105, 0, 1)}
  interD_sec[10] {pt3dclear() pt3dadd(75, 105, 0, 1) pt3dadd(75, 135, 0, 1)}
  interD_sec[11] {pt3dclear() pt3dadd(75, 105, 0, 1) pt3dadd(105, 120, 0, 1)}
  interD_sec[12] {pt3dclear() pt3dadd(45, 105, 0, 1) pt3dadd(60, 135, 0, 1)}
  interD_sec[13] {pt3dclear() pt3dadd(45, 105, 0, 1) pt3dadd(30, 135, 0, 1)}
  nABD {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(60, -14, 0, 1)}
  nABD[1] {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, -44, 0, 1)}
  nABD[2] {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-44, 0, 0, 1)}
  nABD_sec {pt3dclear() pt3dadd(60, -14, 0, 1) pt3dadd(75, 0, 0, 1)}
  nABD_sec[1] {pt3dclear() pt3dadd(75, 0, 0, 1) pt3dadd(75, 30, 0, 1)}
  nABD_sec[2] {pt3dclear() pt3dadd(75, 0, 0, 1) pt3dadd(105, 15, 0, 1)}
  nABD_sec[3] {pt3dclear() pt3dadd(60, -14, 0, 1) pt3dadd(75, -29, 0, 1)}
  nABD_sec[4] {pt3dclear() pt3dadd(75, -29, 0, 1) pt3dadd(75, -59, 0, 1)}
  nABD_sec[5] {pt3dclear() pt3dadd(75, -29, 0, 1) pt3dadd(105, -44, 0, 1)}
  nABD_sec[6] {pt3dclear() pt3dadd(0, -44, 0, 1) pt3dadd(-14, -59, 0, 1)}
  nABD_sec[7] {pt3dclear() pt3dadd(0, -44, 0, 1) pt3dadd(15, -59, 0, 1)}
  nABD_sec[8] {pt3dclear() pt3dadd(15, -59, 0, 1) pt3dadd(15, -89, 0, 1)}
  nABD_sec[9] {pt3dclear() pt3dadd(15, -59, 0, 1) pt3dadd(45, -74, 0, 1)}
  nABD_sec[10] {pt3dclear() pt3dadd(45, -74, 0, 1) pt3dadd(45, -104, 0, 1)}
  nABD_sec[11] {pt3dclear() pt3dadd(45, -74, 0, 1) pt3dadd(75, -89, 0, 1)}
  nABD_sec[12] {pt3dclear() pt3dadd(-14, -59, 0, 1) pt3dadd(-44, -59, 0, 1)}
  nABD_sec[13] {pt3dclear() pt3dadd(-14, -59, 0, 1) pt3dadd(-14, -89, 0, 1)}
  nABD_sec[14] {pt3dclear() pt3dadd(-14, -89, 0, 1) pt3dadd(-29, -119, 0, 1)}
  nABD_sec[15] {pt3dclear() pt3dadd(-14, -89, 0, 1) pt3dadd(0, -119, 0, 1)}
  nABD_sec[16] {pt3dclear() pt3dadd(-44, 0, 0, 1) pt3dadd(-59, 15, 0, 1)}
  nABD_sec[17] {pt3dclear() pt3dadd(-44, 0, 0, 1) pt3dadd(-59, -14, 0, 1)}
}

objref all, all_biophys, all_ABD
proc subsets() { local i
  objref all, all_biophys, all_ABD
  all = new SectionList()
    soma all.append()
    for i=0, 3 ABD[i] all.append()
    axonstart all.append()
    AIS all.append()
    axon all.append()
    axoD all.append()
    for i=0, 3 axoD_sec[i] all.append()
    for i=0, 2 interD[i] all.append()
    for i=0, 13 interD_sec[i] all.append()
    for i=0, 2 nABD[i] all.append()
    for i=0, 17 nABD_sec[i] all.append()

  all_biophys = new SectionList()
    for i=0, 3 ABD[i] all_biophys.append()
    axonstart all_biophys.append()
    axoD all_biophys.append()
    for i=0, 3 axoD_sec[i] all_biophys.append()
    for i=0, 2 interD[i] all_biophys.append()
    for i=0, 13 interD_sec[i] all_biophys.append()
    for i=0, 2 nABD[i] all_biophys.append()
    for i=0, 17 nABD_sec[i] all_biophys.append()

      all_ABD= new SectionList()
     for i=0, 3 ABD[i] all_ABD.append()
    axonstart all_ABD.append()
        axoD all_ABD.append()
    for i=0, 3 axoD_sec[i] all_ABD.append()
    for i=0, 2 interD[i] all_ABD.append()
    for i=0, 13 interD_sec[i] all_ABD.append()


}
proc geom() {

  soma {  L = 27   }
  ABD {  L = 18    }
  ABD[1] {  L = 18    }
  ABD[2] {  L = 5    }
  ABD[3] {  L = 11    }
  axonstart {  L = 20.3    }
  AIS {  L = 36    }
  axon {  L = 800    }
  axoD {  L = 34    }
  axoD_sec {  L = 38    }
  axoD_sec[1] {  L = 71    }
  axoD_sec[2] {  L = 502    }
  axoD_sec[3] {  L = 177    }
  interD {  L = 55    }
  interD[1] {  L = 50    }
  interD[2] {  L = 11    }
  interD_sec {  L = 137    }
  interD_sec[1] {  L = 145    }
  interD_sec[2] {  L = 86    }
  interD_sec[3] {  L = 302    }
  interD_sec[4] {  L = 6    }
  interD_sec[5] {  L = 34    }
  interD_sec[6] {  L = 5    }
  interD_sec[7] {  L = 36    }
  interD_sec[8] {  L = 88    }
  interD_sec[9] {  L = 20    }
  interD_sec[10] {  L = 16    }
  interD_sec[11] {  L = 19    }
  interD_sec[12] {  L = 25    }
  interD_sec[13] {  L = 22    }
  nABD {  L = 23    }
  nABD[1] {  L = 38    }
  nABD[2] {  L = 49    }
  nABD_sec {  L = 88    }
  nABD_sec[1] {  L = 92    }
  nABD_sec[2] {  L = 55    }
  nABD_sec[3] {  L = 522    }
  nABD_sec[4] {  L = 85    }
  nABD_sec[5] {  L = 86    }
  nABD_sec[6] {  L = 24    }
  nABD_sec[7] {  L = 137    }
  nABD_sec[8] {  L = 443    }
  nABD_sec[9] {  L = 108    }
  nABD_sec[10] {  L = 207    }
  nABD_sec[11] {  L = 288    }
  nABD_sec[12] {  L = 113    }
  nABD_sec[13] {  L = 43    }
  nABD_sec[14] {  L = 132    }
  nABD_sec[15] {  L = 148    }
  nABD_sec[16] {  L = 7    }
  nABD_sec[17] {  L = 47    }
  
 // nseg definition has to be launched before diam definition for tapering to be taken into account

  forsec all { nseg = int((L/(0.1*lambda_f(1000))+.999)/2)*2 + 1  }

   soma {    diam = 10  }
  ABD {   diam(0:1) = 3.8:3.5  }
  ABD[1] {   diam(0:1) = 3.5:2.5  }
  ABD[2] {   diam(0:1) = 2.5:2.2  }
  ABD[3] {    diam(0:1) = 2.2:1.8 }
  axonstart {   diam(0:1) = 1.18:1.2  }
  AIS {   diam(0:1) = 1.2:0.8  }
  axon {    diam = 0.8  }
  axoD {   diam(0:1) = 1.5:1  }
  axoD_sec {   diam = 1  }
  axoD_sec[1] {   diam = 1  }
  axoD_sec[2] {    diam = 0.8 }
  axoD_sec[3] {    diam = 0.8 }
  interD {  diam(0:1) = 1.5:1.3  }
  interD[1] {   diam(0:1) = 1.7:1.5  }
  interD[2] {   diam(0:1) = 1.4:1.2  }
  interD_sec {  diam = 1  }
  interD_sec[1] {    diam = 1  }
  interD_sec[2] {   diam = 0.8 }
  interD_sec[3] {    diam = 1  }
  interD_sec[4] {   diam = 0.8  }
  interD_sec[5] {   diam = 0.8  }
  interD_sec[6] {   diam = 0.8  }
  interD_sec[7] {   diam = 0.8  }
  interD_sec[8] {   diam = 1  }
  interD_sec[9] {   diam = 1  }
  interD_sec[10] {   diam = 0.8  }
  interD_sec[11] {   diam = 0.8  }
  interD_sec[12] {   diam = 0.8  }
  interD_sec[13] {   diam = 0.8 }
  nABD {  diam(0:1) = 2.5:2  }
  nABD[1] {   diam(0:1) = 3:2.5  }
  nABD[2] {   diam(0:1) = 2.2:2  }
  nABD_sec {  diam = 1.5 }
  nABD_sec[1] {  diam = 0.8  }
  nABD_sec[2] {  diam = 0.8 }
  nABD_sec[3] {   diam = 1  }
  nABD_sec[4] {  diam = 0.8  }
  nABD_sec[5] {  diam = 0.8  }
  nABD_sec[6] {  diam = 1.5  }
  nABD_sec[7] {   diam = 1.5  }
  nABD_sec[8] {   diam = 1  }
  nABD_sec[9] {   diam = 1  }
  nABD_sec[10] {   diam = 0.8  }
  nABD_sec[11] {   diam = 0.8  }
  nABD_sec[12] {   diam = 1  }
  nABD_sec[13] {  diam = 1  }
  nABD_sec[14] {   diam = 0.8  }
  nABD_sec[15] {   diam = 0.8  }
  nABD_sec[16] {  diam = 1  }
  nABD_sec[17] {   diam = 1  }
  
  
}

proc biophys() {
  forsec all {
    Ra = 150
    cm = 0.75
    insert pasnts
      g_pasnts = 1e-05
      e_pasnts = -50
  }
  forsec all_biophys {
    insert CAV13
      gbar_CAV13 = 1.25
      iLCa_CAV13 = 0
    insert Ih
      gbar_Ih = 3
    insert kaDa
      gbar_kaDa = 50
      taurecov_kaDa = 25
    insert kdrDA
      gbar_kdrDA = 150
    insert Na12
      gbar_Na12 = 75
    insert cad
    insert kca
      gbar_kca = 0.1
        
  }
  soma {
    insert CAV13
      gbar_CAV13 = 1.25
      iLCa_CAV13 = 0
    insert Ih
      gbar_Ih = 3
    insert kaDasoma
      gbar_kaDasoma = 150
      taurecov_kaDasoma = 25
    insert kdrDA
      gbar_kdrDA = 150
    insert Na12
      gbar_Na12 = 75
    insert cad
    insert kca
      gbar_kca = 0.1
        
  }
  AIS {
    insert kdrDA
      gbar_kdrDA = 4000
    insert Na12
      gbar_Na12 = 4000
  }
  axon {
    insert kdrDA
      gbar_kdrDA = 400
    insert Na12
      gbar_Na12 = 400
  }
    forsec all { ena=60
ek=-90	}
}

access soma

celldef()