wormsim 0.0.1__py3-none-any.whl

wormsim/components/model/DA01.hoc

@@ -0,0 +1,177 @@
+begintemplate DA01
+
+public init, topol, basic_shape, subsets, geom, memb
+public x, y, z, position
+
+
+//  Some methods for referencing the cells
+
+public toString, netInfo, set_initial_v, set_initial_ion_properties, synlist
+
+
+// Section: Soma, id: Soma, parent: $s.parent
+create Soma
+public Soma
+// Section: Axon, id: Axon, parent: Soma
+create Axon
+public Axon
+// Section: Dendrite2, id: Dendrite2, parent: Soma
+create Dendrite2
+public Dendrite2
+// Section: Neurite3, id: Neurite3, parent: Axon
+create Neurite3
+public Neurite3
+// Section: Neurite4, id: Neurite4, parent: Axon
+create Neurite4
+public Neurite4
+
+// Group: {name=soma_group, groups=[], sections=[Soma]}
+objref soma_group
+// Group: {name=axon_group, groups=[], sections=[Axon]}
+objref axon_group
+// Group: {name=dendrite_group, groups=[], sections=[Dendrite2, Neurite3, Neurite4]}
+objref dendrite_group
+// Group: {name=all, sections=[Soma, Axon, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite4, Neurite4]}
+objref all
+
+objref synlist
+
+proc init() {
+    topol()
+    geom_nseg()
+    subsets()
+    subsets_inhomogeneous()
+    biophys()
+    biophys_inhomogeneous()
+    synlist = new List()
+    x = y = z = 0
+
+}
+
+
+
+
+
+proc topol() {
+    basic_shape()
+    connect Axon(0), Soma(1.0)
+    connect Dendrite2(0), Soma(1.0)
+    connect Neurite3(0), Axon(1.0)
+    connect Neurite4(0), Axon(1.0)
+
+}
+
+
+proc basic_shape() {
+
+    // Section: Soma, id: Soma, parent: $s.parent (entry count 0/100)
+    Soma { pt3dclear() }
+    Soma { pt3dadd( -0.75, -227.07501, 3.425, 3.8910155 ) }
+    Soma { pt3dadd( -0.75, -223.18399449999998, 3.425, 3.8910155 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -0.75, -227.07501, 3.425, 0.67082036 ) }
+    Axon { pt3dadd( -0.75, -228.20001, 4.2, 0.67082036 ) }
+    Axon { pt3dadd( -0.8, -231.65, 6.4, 0.5744563 ) }
+    Axon { pt3dadd( -0.8, -238.00002, 10.9, 0.6 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 6/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -0.75, -227.07501, 3.425, 0.76811457 ) }
+    Dendrite2 { pt3dadd( -0.75, -225.95, 2.6499999, 0.76811457 ) }
+    Dendrite2 { pt3dadd( -0.75, -223.55, 1.0, 0.70710677 ) }
+    Dendrite2 { pt3dadd( -0.75, -221.05, -0.8, 0.70710677 ) }
+    // Section: Neurite3, id: Neurite3, parent: Axon (entry count 10/100)
+    Neurite3 { pt3dclear() }
+    Neurite3 { pt3dadd( -0.8, -238.00002, 10.9, 0.6 ) }
+    Neurite3 { pt3dadd( -0.6, -238.25, 11.025001, 0.71589106 ) }
+    Neurite3 { pt3dadd( -0.2, -238.25, 11.05, 0.50990194 ) }
+    Neurite3 { pt3dadd( 3.1, -238.35, 10.95, 0.42426404 ) }
+    Neurite3 { pt3dadd( 7.3250003, -238.2, 11.325, 0.6363961 ) }
+    Neurite3 { pt3dadd( 14.900001, -236.8, 15.5, 0.6 ) }
+    Neurite3 { pt3dadd( 18.775, -234.55, 22.2, 0.5937171 ) }
+    Neurite3 { pt3dadd( 20.4, -232.22499, 29.225, 0.6041523 ) }
+    Neurite3 { pt3dadd( 18.775, -229.92499, 36.225, 0.6062178 ) }
+    Neurite3 { pt3dadd( 14.900001, -227.675, 42.95, 0.6576473 ) }
+    Neurite3 { pt3dadd( 7.3250003, -226.3, 47.15, 0.7697402 ) }
+    Neurite3 { pt3dadd( 3.1, -226.3, 47.525, 0.60207975 ) }
+    Neurite3 { pt3dadd( 0.4, -227.04999, 47.525, 0.4387482 ) }
+    Neurite3 { pt3dadd( -0.75, -228.6, 47.7, 0.64031243 ) }
+    Neurite3 { pt3dadd( -0.70000005, -240.9, 52.499996, 0.56568545 ) }
+    Neurite3 { pt3dadd( -1.0, -272.19998, 61.5, 0.56568545 ) }
+    Neurite3 { pt3dadd( -1.0, -275.7, 62.5, 0.56568545 ) }
+    Neurite3 { pt3dadd( -1.75, -290.30002, 64.700005, 0.64031243 ) }
+    Neurite3 { pt3dadd( -1.8, -293.5, 65.100006, 0.56568545 ) }
+    // Section: Neurite4, id: Neurite4, parent: Axon (entry count 29/100)
+    Neurite4 { pt3dclear() }
+    Neurite4 { pt3dadd( -0.8, -238.00002, 10.9, 0.6 ) }
+    Neurite4 { pt3dadd( -0.8, -238.5, 11.150001, 0.53851646 ) }
+    Neurite4 { pt3dadd( -0.8, -242.8, 14.0, 0.6 ) }
+
+}
+
+
+proc subsets() { local i
+
+    // Group: {name=soma_group, groups=[], sections=[Soma]}
+    soma_group = new SectionList()
+    Soma soma_group.append()
+
+    // Group: {name=axon_group, groups=[], sections=[Axon]}
+    axon_group = new SectionList()
+    Axon axon_group.append()
+
+    // Group: {name=dendrite_group, groups=[], sections=[Dendrite2, Neurite3, Neurite4]}
+    dendrite_group = new SectionList()
+    Dendrite2 dendrite_group.append()
+    Neurite3 dendrite_group.append()
+    Neurite4 dendrite_group.append()
+
+    // Group: {name=all, sections=[Soma, Axon, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite4, Neurite4]}
+	all = new SectionList()
+	Soma all.append()
+	Axon all.append()
+	Dendrite2 all.append()
+	Neurite3 all.append()
+	Neurite4 all.append()
+}
+
+
+proc subsets_inhomogeneous() {
+}
+
+proc biophys() {
+
+}
+
+func H() { // Heaviside function
+    if ($1>=0) return 1
+    if ($1==0) return 0.5
+    return 0
+}
+
+proc biophys_inhomogeneous() {
+}
+
+proc geom_nseg() {
+    // All sections not mentioned here have nseg = 1
+	Soma nseg = 2
+	Axon nseg = 4
+	Dendrite2 nseg = 4
+	Neurite3 nseg = 19
+	Neurite4 nseg = 3
+}
+
+
+proc position() { local i
+    forsec all {
+        for i = 0, n3d()-1 {
+            pt3dchange(i, $1+x3d(i), $2+y3d(i), $3+z3d(i), diam3d(i))
+        }
+    }
+    x = $1  y = $2  z = $3
+}
+
+
+endtemplate DA01
+
+

wormsim/components/model/DA02.hoc

@@ -0,0 +1,180 @@
+begintemplate DA02
+
+public init, topol, basic_shape, subsets, geom, memb
+public x, y, z, position
+
+
+//  Some methods for referencing the cells
+
+public toString, netInfo, set_initial_v, set_initial_ion_properties, synlist
+
+
+// Section: Soma, id: Soma, parent: $s.parent
+create Soma
+public Soma
+// Section: Axon, id: Axon, parent: Soma
+create Axon
+public Axon
+// Section: Dendrite2, id: Dendrite2, parent: Soma
+create Dendrite2
+public Dendrite2
+// Section: Neurite3, id: Neurite3, parent: Axon
+create Neurite3
+public Neurite3
+// Section: Neurite4, id: Neurite4, parent: Axon
+create Neurite4
+public Neurite4
+
+// Group: {name=soma_group, groups=[], sections=[Soma]}
+objref soma_group
+// Group: {name=axon_group, groups=[], sections=[Axon]}
+objref axon_group
+// Group: {name=dendrite_group, groups=[], sections=[Dendrite2, Neurite3, Neurite4]}
+objref dendrite_group
+// Group: {name=all, sections=[Soma, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite4, Neurite4, Neurite4, Neurite4, Neurite4, Neurite4]}
+objref all
+
+objref synlist
+
+proc init() {
+    topol()
+    geom_nseg()
+    subsets()
+    subsets_inhomogeneous()
+    biophys()
+    biophys_inhomogeneous()
+    synlist = new List()
+    x = y = z = 0
+
+}
+
+
+
+
+
+proc topol() {
+    basic_shape()
+    connect Axon(0), Soma(1.0)
+    connect Dendrite2(0), Soma(1.0)
+    connect Neurite3(0), Axon(1.0)
+    connect Neurite4(0), Axon(1.0)
+
+}
+
+
+proc basic_shape() {
+
+    // Section: Soma, id: Soma, parent: $s.parent (entry count 0/100)
+    Soma { pt3dclear() }
+    Soma { pt3dadd( -1.9, -190.75, -21.675, 3.9610605 ) }
+    Soma { pt3dadd( -1.9, -186.7889395, -21.675, 3.9610605 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -1.9, -190.75, -21.675, 0.6 ) }
+    Axon { pt3dadd( -1.9, -191.90001, -20.900002, 0.6 ) }
+    Axon { pt3dadd( -1.6, -195.65001, -18.4, 0.64031243 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 5/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -1.9, -190.75, -21.675, 0.53851646 ) }
+    Dendrite2 { pt3dadd( -1.9, -189.6, -22.45, 0.53851646 ) }
+    Dendrite2 { pt3dadd( -1.9, -187.05, -24.2, 0.64031243 ) }
+    Dendrite2 { pt3dadd( -1.85, -185.15001, -25.5, 0.37416574 ) }
+    // Section: Neurite3, id: Neurite3, parent: Axon (entry count 9/100)
+    Neurite3 { pt3dclear() }
+    Neurite3 { pt3dadd( -1.6, -195.65001, -18.4, 0.64031243 ) }
+    Neurite3 { pt3dadd( -1.8, -195.9, -18.199999, 0.82462114 ) }
+    Neurite3 { pt3dadd( -2.0, -195.9, -18.199999, 0.4472136 ) }
+    Neurite3 { pt3dadd( -4.9, -196.0, -18.4, 0.56568545 ) }
+    Neurite3 { pt3dadd( -11.325, -195.75, -17.95, 0.63442886 ) }
+    Neurite3 { pt3dadd( -19.575, -193.3, -13.824999, 0.73824114 ) }
+    Neurite3 { pt3dadd( -23.800001, -189.34999, -7.225, 0.6576473 ) }
+    Neurite3 { pt3dadd( -25.625, -185.22499, -0.32500002, 0.5722762 ) }
+    Neurite3 { pt3dadd( -23.800001, -181.05, 6.5750003, 0.559017 ) }
+    Neurite3 { pt3dadd( -19.575, -177.125, 13.2, 0.6041523 ) }
+    Neurite3 { pt3dadd( -11.325, -174.65, 17.35, 0.63442886 ) }
+    Neurite3 { pt3dadd( -4.9, -174.4, 17.800001, 0.56568545 ) }
+    Neurite3 { pt3dadd( -1.6, -175.525, 17.85, 0.6576473 ) }
+    Neurite3 { pt3dadd( -0.70000005, -177.40001, 19.25, 0.53851646 ) }
+    Neurite3 { pt3dadd( -0.70000005, -205.95, 37.7, 0.5744563 ) }
+    Neurite3 { pt3dadd( -0.70000005, -210.75, 40.7, 0.5744563 ) }
+    Neurite3 { pt3dadd( -0.70000005, -240.9, 52.499996, 0.56568545 ) }
+    Neurite3 { pt3dadd( -0.9, -269.85, 60.8, 0.5744563 ) }
+    Neurite3 { pt3dadd( -1.0, -272.19998, 61.5, 0.56568545 ) }
+    // Section: Neurite4, id: Neurite4, parent: Axon (entry count 28/100)
+    Neurite4 { pt3dclear() }
+    Neurite4 { pt3dadd( -1.6, -195.65001, -18.4, 0.64031243 ) }
+    Neurite4 { pt3dadd( -1.6, -196.15001, -18.0, 0.64031243 ) }
+    Neurite4 { pt3dadd( -1.5, -199.05, -16.050001, 0.50990194 ) }
+    Neurite4 { pt3dadd( -1.4499999, -210.2, -8.4, 0.53851646 ) }
+    Neurite4 { pt3dadd( -1.4499999, -214.94998, -5.25, 0.4358899 ) }
+    Neurite4 { pt3dadd( -1.4499999, -241.5, 13.3, 0.5 ) }
+    Neurite4 { pt3dadd( -1.4499999, -243.35, 14.55, 0.4358899 ) }
+
+}
+
+
+proc subsets() { local i
+
+    // Group: {name=soma_group, groups=[], sections=[Soma]}
+    soma_group = new SectionList()
+    Soma soma_group.append()
+
+    // Group: {name=axon_group, groups=[], sections=[Axon]}
+    axon_group = new SectionList()
+    Axon axon_group.append()
+
+    // Group: {name=dendrite_group, groups=[], sections=[Dendrite2, Neurite3, Neurite4]}
+    dendrite_group = new SectionList()
+    Dendrite2 dendrite_group.append()
+    Neurite3 dendrite_group.append()
+    Neurite4 dendrite_group.append()
+
+    // Group: {name=all, sections=[Soma, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite4, Neurite4, Neurite4, Neurite4, Neurite4, Neurite4]}
+	all = new SectionList()
+	Soma all.append()
+	Axon all.append()
+	Dendrite2 all.append()
+	Neurite3 all.append()
+	Neurite4 all.append()
+}
+
+
+proc subsets_inhomogeneous() {
+}
+
+proc biophys() {
+
+}
+
+func H() { // Heaviside function
+    if ($1>=0) return 1
+    if ($1==0) return 0.5
+    return 0
+}
+
+proc biophys_inhomogeneous() {
+}
+
+proc geom_nseg() {
+    // All sections not mentioned here have nseg = 1
+	Soma nseg = 2
+	Axon nseg = 3
+	Dendrite2 nseg = 4
+	Neurite3 nseg = 19
+	Neurite4 nseg = 7
+}
+
+
+proc position() { local i
+    forsec all {
+        for i = 0, n3d()-1 {
+            pt3dchange(i, $1+x3d(i), $2+y3d(i), $3+z3d(i), diam3d(i))
+        }
+    }
+    x = $1  y = $2  z = $3
+}
+
+
+endtemplate DA02
+
+

wormsim/components/model/DA03.hoc

@@ -0,0 +1,160 @@
+begintemplate DA03
+
+public init, topol, basic_shape, subsets, geom, memb
+public x, y, z, position
+
+
+//  Some methods for referencing the cells
+
+public toString, netInfo, set_initial_v, set_initial_ion_properties, synlist
+
+
+// Section: Soma, id: Soma, parent: $s.parent
+create Soma
+public Soma
+// Section: Axon, id: Axon, parent: Soma
+create Axon
+public Axon
+// Section: Dendrite2, id: Dendrite2, parent: Soma
+create Dendrite2
+public Dendrite2
+
+// Group: {name=soma_group, groups=[], sections=[Soma]}
+objref soma_group
+// Group: {name=axon_group, groups=[], sections=[Axon]}
+objref axon_group
+// Group: {name=dendrite_group, groups=[], sections=[Dendrite2]}
+objref dendrite_group
+// Group: {name=all, sections=[Soma, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2]}
+objref all
+
+objref synlist
+
+proc init() {
+    topol()
+    geom_nseg()
+    subsets()
+    subsets_inhomogeneous()
+    biophys()
+    biophys_inhomogeneous()
+    synlist = new List()
+    x = y = z = 0
+
+}
+
+
+
+
+
+proc topol() {
+    basic_shape()
+    connect Axon(0), Soma(1.0)
+    connect Dendrite2(0), Soma(1.0)
+
+}
+
+
+proc basic_shape() {
+
+    // Section: Soma, id: Soma, parent: $s.parent (entry count 0/100)
+    Soma { pt3dclear() }
+    Soma { pt3dadd( -1.65, -123.65, -58.350002, 4.0632496 ) }
+    Soma { pt3dadd( -1.65, -119.5867504, -58.350002, 4.0632496 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -1.65, -123.65, -58.350002, 0.67082036 ) }
+    Axon { pt3dadd( -1.65, -122.3, -58.8, 0.67082036 ) }
+    Axon { pt3dadd( -1.65, -120.00001, -59.525, 0.5408327 ) }
+    Axon { pt3dadd( -0.70000005, -118.675, -60.625, 0.6670832 ) }
+    Axon { pt3dadd( 2.6000001, -118.6, -60.625, 0.53150725 ) }
+    Axon { pt3dadd( 8.825, -118.425, -60.100002, 0.6964194 ) }
+    Axon { pt3dadd( 17.675001, -116.9, -55.075, 0.80311894 ) }
+    Axon { pt3dadd( 22.175001, -114.450005, -47.0, 0.78262377 ) }
+    Axon { pt3dadd( 24.125, -111.899994, -38.5, 0.65000004 ) }
+    Axon { pt3dadd( 22.175001, -109.325005, -30.1, 0.79056937 ) }
+    Axon { pt3dadd( 17.675001, -106.850006, -22.0, 0.6873864 ) }
+    Axon { pt3dadd( 8.8, -105.350006, -16.949999, 1.0295631 ) }
+    Axon { pt3dadd( 2.6000001, -105.200005, -16.45, 0.64031243 ) }
+    Axon { pt3dadd( 0.05, -106.05, -16.65, 0.65574384 ) }
+    Axon { pt3dadd( -0.70000005, -107.9, -16.699999, 0.56568545 ) }
+    Axon { pt3dadd( -0.70000005, -114.450005, -14.599999, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -130.35, -8.4, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -162.75, 9.700001, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -205.95, 37.7, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -210.75, 40.7, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -240.9, 52.499996, 0.56568545 ) }
+    Axon { pt3dadd( -1.0, -267.4, 59.7, 0.56568545 ) }
+    Axon { pt3dadd( -1.0, -270.84998, 60.7, 0.5744563 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 25/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -1.65, -123.65, -58.350002, 0.67082036 ) }
+    Dendrite2 { pt3dadd( -1.65, -125.0, -57.9, 0.67082036 ) }
+    Dendrite2 { pt3dadd( -1.7, -128.15, -56.85, 0.50990194 ) }
+    Dendrite2 { pt3dadd( -1.5, -135.45001, -54.000004, 0.5744563 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -167.6, -37.6, 0.5 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -211.8, -7.4500003, 0.42426404 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -216.54999, -4.25, 0.4358899 ) }
+
+}
+
+
+proc subsets() { local i
+
+    // Group: {name=soma_group, groups=[], sections=[Soma]}
+    soma_group = new SectionList()
+    Soma soma_group.append()
+
+    // Group: {name=axon_group, groups=[], sections=[Axon]}
+    axon_group = new SectionList()
+    Axon axon_group.append()
+
+    // Group: {name=dendrite_group, groups=[], sections=[Dendrite2]}
+    dendrite_group = new SectionList()
+    Dendrite2 dendrite_group.append()
+
+    // Group: {name=all, sections=[Soma, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2]}
+	all = new SectionList()
+	Soma all.append()
+	Axon all.append()
+	Dendrite2 all.append()
+}
+
+
+proc subsets_inhomogeneous() {
+}
+
+proc biophys() {
+
+}
+
+func H() { // Heaviside function
+    if ($1>=0) return 1
+    if ($1==0) return 0.5
+    return 0
+}
+
+proc biophys_inhomogeneous() {
+}
+
+proc geom_nseg() {
+    // All sections not mentioned here have nseg = 1
+	Soma nseg = 2
+	Axon nseg = 23
+	Dendrite2 nseg = 8
+}
+
+
+proc position() { local i
+    forsec all {
+        for i = 0, n3d()-1 {
+            pt3dchange(i, $1+x3d(i), $2+y3d(i), $3+z3d(i), diam3d(i))
+        }
+    }
+    x = $1  y = $2  z = $3
+}
+
+
+endtemplate DA03
+
+

wormsim/components/model/DA04.hoc

@@ -0,0 +1,167 @@
+begintemplate DA04
+
+public init, topol, basic_shape, subsets, geom, memb
+public x, y, z, position
+
+
+//  Some methods for referencing the cells
+
+public toString, netInfo, set_initial_v, set_initial_ion_properties, synlist
+
+
+// Section: Soma, id: Soma, parent: $s.parent
+create Soma
+public Soma
+// Section: Axon, id: Axon, parent: Soma
+create Axon
+public Axon
+// Section: Dendrite2, id: Dendrite2, parent: Soma
+create Dendrite2
+public Dendrite2
+
+// Group: {name=soma_group, groups=[], sections=[Soma]}
+objref soma_group
+// Group: {name=axon_group, groups=[], sections=[Axon]}
+objref axon_group
+// Group: {name=dendrite_group, groups=[], sections=[Dendrite2]}
+objref dendrite_group
+// Group: {name=all, sections=[Soma, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2]}
+objref all
+
+objref synlist
+
+proc init() {
+    topol()
+    geom_nseg()
+    subsets()
+    subsets_inhomogeneous()
+    biophys()
+    biophys_inhomogeneous()
+    synlist = new List()
+    x = y = z = 0
+
+}
+
+
+
+
+
+proc topol() {
+    basic_shape()
+    connect Axon(0), Soma(1.0)
+    connect Dendrite2(0), Soma(1.0)
+
+}
+
+
+proc basic_shape() {
+
+    // Section: Soma, id: Soma, parent: $s.parent (entry count 0/100)
+    Soma { pt3dclear() }
+    Soma { pt3dadd( -1.7, -32.4, -61.75, 3.2908964 ) }
+    Soma { pt3dadd( -1.7, -29.109103599999997, -61.75, 3.2908964 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -1.7, -32.4, -61.75, 0.5744563 ) }
+    Axon { pt3dadd( -1.7, -31.25, -61.5, 0.5744563 ) }
+    Axon { pt3dadd( -1.65, -28.400002, -60.85, 0.42426404 ) }
+    Axon { pt3dadd( -1.2, -26.499998, -60.45, 0.41231057 ) }
+    Axon { pt3dadd( 1.4000001, -25.350002, -60.725, 0.39051247 ) }
+    Axon { pt3dadd( 9.675, -25.325, -60.2, 0.7106335 ) }
+    Axon { pt3dadd( 19.275002, -27.050001, -54.725, 0.717635 ) }
+    Axon { pt3dadd( 24.125, -29.750002, -46.0, 0.6873864 ) }
+    Axon { pt3dadd( 26.300001, -32.625, -36.8, 0.80156094 ) }
+    Axon { pt3dadd( 24.125, -35.5, -27.7, 0.68007356 ) }
+    Axon { pt3dadd( 19.275002, -38.225002, -18.975, 0.75332594 ) }
+    Axon { pt3dadd( 9.700001, -39.925, -13.474999, 1.1510864 ) }
+    Axon { pt3dadd( 1.8, -40.1, -12.974999, 0.60207975 ) }
+    Axon { pt3dadd( -0.70000005, -41.9, -14.300001, 0.56568545 ) }
+    Axon { pt3dadd( -0.70000005, -47.850002, -17.0, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -77.450005, -22.2, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -81.3, -22.9, 0.56568545 ) }
+    Axon { pt3dadd( -0.70000005, -98.1, -19.5, 0.56568545 ) }
+    Axon { pt3dadd( -0.70000005, -114.450005, -14.599999, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -130.35, -8.4, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -162.75, 9.700001, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -205.95, 37.7, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -210.75, 40.7, 0.5744563 ) }
+    Axon { pt3dadd( -0.70000005, -240.9, 52.499996, 0.56568545 ) }
+    Axon { pt3dadd( -0.70000005, -251.09999, 55.4, 0.56568545 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 27/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -1.7, -32.4, -61.75, 0.5744563 ) }
+    Dendrite2 { pt3dadd( -1.7, -33.55, -62.0, 0.5744563 ) }
+    Dendrite2 { pt3dadd( -1.7, -36.149998, -62.699997, 0.5744563 ) }
+    Dendrite2 { pt3dadd( -1.5, -47.15, -65.85, 0.50990194 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -53.3, -67.049995, 0.42426404 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -84.15, -66.649994, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -102.35, -64.0, 0.50990194 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -118.49999, -60.2, 0.5 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -135.45001, -53.95, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -167.6, -37.6, 0.5 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -185.85, -25.25, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -188.25, -23.65, 0.4358899 ) }
+
+}
+
+
+proc subsets() { local i
+
+    // Group: {name=soma_group, groups=[], sections=[Soma]}
+    soma_group = new SectionList()
+    Soma soma_group.append()
+
+    // Group: {name=axon_group, groups=[], sections=[Axon]}
+    axon_group = new SectionList()
+    Axon axon_group.append()
+
+    // Group: {name=dendrite_group, groups=[], sections=[Dendrite2]}
+    dendrite_group = new SectionList()
+    Dendrite2 dendrite_group.append()
+
+    // Group: {name=all, sections=[Soma, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Dendrite2]}
+	all = new SectionList()
+	Soma all.append()
+	Axon all.append()
+	Dendrite2 all.append()
+}
+
+
+proc subsets_inhomogeneous() {
+}
+
+proc biophys() {
+
+}
+
+func H() { // Heaviside function
+    if ($1>=0) return 1
+    if ($1==0) return 0.5
+    return 0
+}
+
+proc biophys_inhomogeneous() {
+}
+
+proc geom_nseg() {
+    // All sections not mentioned here have nseg = 1
+	Soma nseg = 2
+	Axon nseg = 25
+	Dendrite2 nseg = 13
+}
+
+
+proc position() { local i
+    forsec all {
+        for i = 0, n3d()-1 {
+            pt3dchange(i, $1+x3d(i), $2+y3d(i), $3+z3d(i), diam3d(i))
+        }
+    }
+    x = $1  y = $2  z = $3
+}
+
+
+endtemplate DA04
+
+