wormsim 0.0.1__py3-none-any.whl

wormsim/components/model/DD06.hoc

@@ -0,0 +1,211 @@
+begintemplate DD06
+
+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: Neurite3
+create Neurite4
+public Neurite4
+// Section: Neurite5, id: Neurite5, parent: Neurite3
+create Neurite5
+public Neurite5
+// Section: Neurite6, id: Neurite6, parent: Axon
+create Neurite6
+public Neurite6
+
+// 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, Neurite5, Neurite6]}
+objref dendrite_group
+// Group: {name=all, sections=[Soma, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite4, Neurite4, Neurite4, Neurite4, Neurite5, Neurite5, Neurite5, Neurite5, Neurite5, Neurite5, Neurite5, Neurite5, Neurite6, Neurite6, Neurite6, Neurite6]}
+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), Neurite3(1.0)
+    connect Neurite5(0), Neurite3(1.0)
+    connect Neurite6(0), Axon(1.0)
+
+}
+
+
+proc basic_shape() {
+
+    // Section: Soma, id: Soma, parent: $s.parent (entry count 0/100)
+    Soma { pt3dclear() }
+    Soma { pt3dadd( -1.9, 365.775, -16.475, 3.717526 ) }
+    Soma { pt3dadd( -1.9, 369.492526, -16.475, 3.717526 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -1.9, 365.775, -16.475, 0.6480741 ) }
+    Axon { pt3dadd( -1.9, 364.55, -16.949999, 0.6480741 ) }
+    Axon { pt3dadd( -1.9, 361.45, -18.55, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, 355.35, -21.449999, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 350.75, -23.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, 322.8, -26.050001, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 317.6, -26.499998, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 288.94998, -25.5, 0.50990194 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 10/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -1.9, 365.775, -16.475, 0.8717798 ) }
+    Dendrite2 { pt3dadd( -1.9, 367.0, -16.0, 0.8717798 ) }
+    Dendrite2 { pt3dadd( -1.85, 370.0, -14.95, 0.73484695 ) }
+    Dendrite2 { pt3dadd( -1.5, 392.45, -4.9, 0.5744563 ) }
+    Dendrite2 { pt3dadd( -1.4499999, 393.85, -4.4, 0.50990194 ) }
+    // Section: Neurite3, id: Neurite3, parent: Axon (entry count 15/100)
+    Neurite3 { pt3dclear() }
+    Neurite3 { pt3dadd( -1.4499999, 288.94998, -25.5, 0.50990194 ) }
+    Neurite3 { pt3dadd( -1.6, 288.725, -25.475002, 0.5700877 ) }
+    Neurite3 { pt3dadd( -1.9, 288.75, -25.475002, 0.39051247 ) }
+    Neurite3 { pt3dadd( -3.5, 288.65, -25.350002, 0.42426404 ) }
+    Neurite3 { pt3dadd( -9.3, 288.7, -24.9, 0.6324555 ) }
+    Neurite3 { pt3dadd( -15.800001, 289.15, -20.4, 0.5744563 ) }
+    Neurite3 { pt3dadd( -19.2, 289.9, -13.224999, 0.61846584 ) }
+    Neurite3 { pt3dadd( -20.675001, 290.675, -5.725, 0.4769696 ) }
+    Neurite3 { pt3dadd( -19.2, 291.45, 1.7750001, 0.52201533 ) }
+    Neurite3 { pt3dadd( -15.800001, 292.19998, 8.925, 0.60207975 ) }
+    Neurite3 { pt3dadd( -9.3, 292.65, 13.400001, 0.64031243 ) }
+    Neurite3 { pt3dadd( -2.2, 292.7, 13.474999, 0.42720017 ) }
+    Neurite3 { pt3dadd( -1.1, 292.65, 12.775, 0.39051247 ) }
+    Neurite3 { pt3dadd( -0.9, 292.65, 12.75, 0.5830952 ) }
+    // Section: Neurite4, id: Neurite4, parent: Neurite3 (entry count 29/100)
+    Neurite4 { pt3dclear() }
+    Neurite4 { pt3dadd( -0.9, 292.65, 12.75, 0.5830952 ) }
+    Neurite4 { pt3dadd( -0.70000005, 292.4, 12.8, 0.56568545 ) }
+    Neurite4 { pt3dadd( -0.70000005, 288.2, 13.400001, 0.56568545 ) }
+    Neurite4 { pt3dadd( -0.70000005, 266.85, 19.6, 0.5744563 ) }
+    Neurite4 { pt3dadd( -0.70000005, 263.15, 20.6, 0.5744563 ) }
+    // Section: Neurite5, id: Neurite5, parent: Neurite3 (entry count 34/100)
+    Neurite5 { pt3dclear() }
+    Neurite5 { pt3dadd( -0.9, 292.65, 12.75, 0.5830952 ) }
+    Neurite5 { pt3dadd( -0.70000005, 292.9, 12.700001, 0.56568545 ) }
+    Neurite5 { pt3dadd( -0.70000005, 321.65, 8.1, 0.5744563 ) }
+    Neurite5 { pt3dadd( -0.70000005, 326.2, 8.1, 0.56568545 ) }
+    Neurite5 { pt3dadd( -0.70000005, 354.45, 8.299999, 0.5744563 ) }
+    Neurite5 { pt3dadd( -0.70000005, 358.75, 8.8, 0.5744563 ) }
+    Neurite5 { pt3dadd( -0.70000005, 388.85, 12.3, 0.5744563 ) }
+    Neurite5 { pt3dadd( -0.70000005, 394.5, 13.7, 0.56568545 ) }
+    Neurite5 { pt3dadd( -0.70000005, 398.25, 14.1, 0.5744563 ) }
+    // Section: Neurite6, id: Neurite6, parent: Axon (entry count 43/100)
+    Neurite6 { pt3dclear() }
+    Neurite6 { pt3dadd( -1.4499999, 288.94998, -25.5, 0.50990194 ) }
+    Neurite6 { pt3dadd( -1.4499999, 288.5, -25.45, 0.42426404 ) }
+    Neurite6 { pt3dadd( -1.4499999, 283.3, -25.0, 0.5 ) }
+    Neurite6 { pt3dadd( -1.4499999, 268.9, -23.55, 0.42426404 ) }
+    Neurite6 { pt3dadd( -1.4499999, 261.7, -22.45, 0.42426404 ) }
+
+}
+
+
+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, Neurite5, Neurite6]}
+    dendrite_group = new SectionList()
+    Dendrite2 dendrite_group.append()
+    Neurite3 dendrite_group.append()
+    Neurite4 dendrite_group.append()
+    Neurite5 dendrite_group.append()
+    Neurite6 dendrite_group.append()
+
+    // Group: {name=all, sections=[Soma, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Dendrite2, Dendrite2, Dendrite2, Dendrite2, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite3, Neurite4, Neurite4, Neurite4, Neurite4, Neurite5, Neurite5, Neurite5, Neurite5, Neurite5, Neurite5, Neurite5, Neurite5, Neurite6, Neurite6, Neurite6, Neurite6]}
+	all = new SectionList()
+	Soma all.append()
+	Axon all.append()
+	Dendrite2 all.append()
+	Neurite3 all.append()
+	Neurite4 all.append()
+	Neurite5 all.append()
+	Neurite6 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 = 8
+	Dendrite2 nseg = 5
+	Neurite3 nseg = 14
+	Neurite4 nseg = 5
+	Neurite5 nseg = 9
+	Neurite6 nseg = 5
+}
+
+
+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 DD06
+
+

wormsim/components/model/DVA.hoc

@@ -0,0 +1,178 @@
+begintemplate DVA
+
+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
+
+// Group: {name=soma_group, groups=[], sections=[Soma]}
+objref soma_group
+// Group: {name=axon_group, groups=[], sections=[Axon]}
+objref axon_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, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon]}
+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)
+
+}
+
+
+proc basic_shape() {
+
+    // Section: Soma, id: Soma, parent: $s.parent (entry count 0/100)
+    Soma { pt3dclear() }
+    Soma { pt3dadd( -2.345, 394.6, 3.678, 3.0187428 ) }
+    Soma { pt3dadd( -2.345, 397.6187428, 3.678, 3.0187428 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -2.345, 394.6, 3.678, 0.6402687 ) }
+    Axon { pt3dadd( -2.345, 394.53, 3.6509998, 0.6402687 ) }
+    Axon { pt3dadd( -2.831, 393.431, 3.112, 0.48192117 ) }
+    Axon { pt3dadd( -3.9810002, 391.071, 2.0679998, 0.481132 ) }
+    Axon { pt3dadd( -2.637, 385.346, -5.1210003, 0.47828862 ) }
+    Axon { pt3dadd( -1.2609999, 382.553, -9.573, 0.4780209 ) }
+    Axon { pt3dadd( -1.463, 355.358, -21.439, 0.47861883 ) }
+    Axon { pt3dadd( -1.463, 350.739, -22.991, 0.47721696 ) }
+    Axon { pt3dadd( -1.463, 322.783, -26.029, 0.4780209 ) }
+    Axon { pt3dadd( -1.463, 317.644, -26.503, 0.47943717 ) }
+    Axon { pt3dadd( -1.463, 289.169, -25.485, 0.4780209 ) }
+    Axon { pt3dadd( -1.463, 283.305, -25.018002, 0.4780209 ) }
+    Axon { pt3dadd( -1.463, 256.25702, -21.51, 0.4780209 ) }
+    Axon { pt3dadd( -1.463, 249.145, -20.244, 0.47807112 ) }
+    Axon { pt3dadd( -1.464, 174.688, 1.087, 0.4801833 ) }
+    Axon { pt3dadd( -1.463, 167.575, 2.271, 0.48002085 ) }
+    Axon { pt3dadd( -1.464, 125.06799, 4.474, 0.48002085 ) }
+    Axon { pt3dadd( -1.463, 116.23501, 4.46, 0.4786147 ) }
+    Axon { pt3dadd( -1.464, 89.319, -0.487, 0.4800333 ) }
+    Axon { pt3dadd( -1.464, 84.752, -1.9959999, 0.47880685 ) }
+    Axon { pt3dadd( -1.8750001, 77.804, -6.3529997, 0.4725886 ) }
+    Axon { pt3dadd( -2.211, 69.501, -11.827001, 0.46855524 ) }
+    Axon { pt3dadd( -5.843, 65.517006, -10.744, 0.4165093 ) }
+    Axon { pt3dadd( -10.378, 61.816, -12.658999, 0.46703747 ) }
+    Axon { pt3dadd( -13.425, 56.226997, -14.43, 0.4281355 ) }
+    Axon { pt3dadd( -13.309, 47.605, -19.862001, 0.4382876 ) }
+    Axon { pt3dadd( -10.605, 42.071, -24.422, 0.4727029 ) }
+    Axon { pt3dadd( -4.344, 36.12, -30.537998, 0.47843912 ) }
+    Axon { pt3dadd( -1.463, 32.201, -35.333, 0.47898227 ) }
+    Axon { pt3dadd( -1.464, 3.7870002, -50.083, 0.47882357 ) }
+    Axon { pt3dadd( -1.463, -3.4490001, -53.231003, 0.47882357 ) }
+    Axon { pt3dadd( -1.463, -47.151, -65.867004, 0.47884443 ) }
+    Axon { pt3dadd( -1.464, -53.324, -67.068, 0.47851858 ) }
+    Axon { pt3dadd( -1.463, -84.147, -66.674, 0.479925 ) }
+    Axon { pt3dadd( -1.464, -102.354004, -64.013, 0.47843078 ) }
+    Axon { pt3dadd( -1.464, -118.490005, -60.203, 0.47756466 ) }
+    Axon { pt3dadd( -1.464, -135.459, -53.970997, 0.47921184 ) }
+    Axon { pt3dadd( -1.463, -162.827, -40.074, 0.47898227 ) }
+    Axon { pt3dadd( -1.464, -167.617, -37.6, 0.4792369 ) }
+    Axon { pt3dadd( -1.464, -210.193, -8.407, 0.47921184 ) }
+    Axon { pt3dadd( -1.463, -214.966, -5.242, 0.4803707 ) }
+    Axon { pt3dadd( -1.464, -243.343, 14.582001, 0.48062462 ) }
+    Axon { pt3dadd( -1.463, -247.91, 17.366999, 0.47968322 ) }
+    Axon { pt3dadd( -1.9640001, -268.733, 27.205, 0.48282915 ) }
+    Axon { pt3dadd( -2.45, -271.404, 33.438, 0.48254743 ) }
+    Axon { pt3dadd( -3.577, -272.72, 36.007, 0.48088256 ) }
+    Axon { pt3dadd( -4.802, -273.156, 38.11, 0.39507467 ) }
+    Axon { pt3dadd( -7.119, -273.407, 39.839, 0.4022636 ) }
+    Axon { pt3dadd( -8.688, -273.783, 42.467003, 0.4014424 ) }
+    Axon { pt3dadd( -9.201, -274.205, 45.482002, 0.40333113 ) }
+    Axon { pt3dadd( -8.655, -274.66, 48.519, 0.40116832 ) }
+    Axon { pt3dadd( -7.121, -274.998, 51.095997, 0.43534353 ) }
+    Axon { pt3dadd( -4.8129997, -275.3, 52.814, 0.4349207 ) }
+    Axon { pt3dadd( -2.108, -275.368, 53.405, 0.4497822 ) }
+    Axon { pt3dadd( 0.596, -275.3, 52.814, 0.4349207 ) }
+    Axon { pt3dadd( 2.904, -274.998, 51.095997, 0.4330958 ) }
+    Axon { pt3dadd( 4.438, -274.66, 48.519, 0.40190047 ) }
+    Axon { pt3dadd( 4.9839997, -274.20398, 45.482002, 0.40232325 ) }
+    Axon { pt3dadd( 4.4709997, -273.783, 42.467003, 0.4006295 ) }
+    Axon { pt3dadd( 2.903, -273.407, 39.839, 0.4022636 ) }
+    Axon { pt3dadd( 0.63299996, -273.155, 38.111, 0.40208954 ) }
+    Axon { pt3dadd( -0.0019999999, -273.088, 36.629, 0.40106857 ) }
+    Axon { pt3dadd( -0.306, -273.088, 34.036, 0.4006944 ) }
+
+}
+
+
+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=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, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon]}
+	all = new SectionList()
+	Soma all.append()
+	Axon 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 = 63
+}
+
+
+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 DVA
+
+

wormsim/components/model/DVB.hoc

@@ -0,0 +1,137 @@
+begintemplate DVB
+
+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
+
+// Group: {name=soma_group, groups=[], sections=[Soma]}
+objref soma_group
+// Group: {name=axon_group, groups=[], sections=[Axon]}
+objref axon_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]}
+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)
+
+}
+
+
+proc basic_shape() {
+
+    // Section: Soma, id: Soma, parent: $s.parent (entry count 0/100)
+    Soma { pt3dclear() }
+    Soma { pt3dadd( -0.75, 394.5, 4.0, 3.1128764 ) }
+    Soma { pt3dadd( -0.75, 397.6128764, 4.0, 3.1128764 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -0.75, 394.5, 4.0, 0.53851646 ) }
+    Axon { pt3dadd( -0.85, 394.5, 4.0, 0.53851646 ) }
+    Axon { pt3dadd( -0.475, 394.1, 3.7500002, 0.5408327 ) }
+    Axon { pt3dadd( 2.325, 391.45, 2.2250001, 0.5244044 ) }
+    Axon { pt3dadd( 3.075, 390.5, 1.35, 0.5024938 ) }
+    Axon { pt3dadd( 3.325, 388.625, -0.975, 0.4974937 ) }
+    Axon { pt3dadd( 1.8249999, 385.325, -5.175, 0.4555217 ) }
+    Axon { pt3dadd( -0.85, 382.65, -9.650001, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 355.35, -21.449999, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 350.75, -23.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, 322.8, -26.050001, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 317.6, -26.499998, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 289.19998, -25.5, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 283.3, -25.0, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 256.3, -21.5, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 249.09999, -20.25, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 174.65, 1.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 167.6, 2.25, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 125.100006, 4.4500003, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 116.2, 4.4500003, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 98.4, 1.4000001, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 94.2, 0.85, 0.42426404 ) }
+
+}
+
+
+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=all, sections=[Soma, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon]}
+	all = new SectionList()
+	Soma all.append()
+	Axon 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 = 22
+}
+
+
+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 DVB
+
+

wormsim/components/model/DVC.hoc

@@ -0,0 +1,178 @@
+begintemplate DVC
+
+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
+
+// Group: {name=soma_group, groups=[], sections=[Soma]}
+objref soma_group
+// Group: {name=axon_group, groups=[], sections=[Axon]}
+objref axon_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, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon]}
+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)
+
+}
+
+
+proc basic_shape() {
+
+    // Section: Soma, id: Soma, parent: $s.parent (entry count 0/100)
+    Soma { pt3dclear() }
+    Soma { pt3dadd( -0.116, 395.43298, 5.992, 2.5611413 ) }
+    Soma { pt3dadd( -0.116, 397.99412129999996, 5.992, 2.5611413 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -0.116, 395.43298, 5.992, 0.8499435 ) }
+    Axon { pt3dadd( -0.036000002, 394.95398, 5.992, 0.8499435 ) }
+    Axon { pt3dadd( 0.603, 393.889, 4.98, 0.56603885 ) }
+    Axon { pt3dadd( 3.119, 390.978, 2.105, 0.5657314 ) }
+    Axon { pt3dadd( 3.153, 388.345, -1.206, 0.5663215 ) }
+    Axon { pt3dadd( 1.8270001, 385.54202, -5.095, 0.51613176 ) }
+    Axon { pt3dadd( 0.639, 384.08798, -7.664, 0.47828862 ) }
+    Axon { pt3dadd( -0.479, 382.716, -9.896, 0.477841 ) }
+    Axon { pt3dadd( -1.463, 355.358, -21.439, 0.47861883 ) }
+    Axon { pt3dadd( -1.464, 350.739, -22.991, 0.47863555 ) }
+    Axon { pt3dadd( -1.464, 322.783, -26.029, 0.4780209 ) }
+    Axon { pt3dadd( -1.464, 317.644, -26.503, 0.47943717 ) }
+    Axon { pt3dadd( -1.463, 289.169, -25.484, 0.48084924 ) }
+    Axon { pt3dadd( -1.464, 283.305, -25.018002, 0.47943717 ) }
+    Axon { pt3dadd( -1.464, 256.25702, -21.51, 0.4780209 ) }
+    Axon { pt3dadd( -1.463, 249.145, -20.244, 0.47948724 ) }
+    Axon { pt3dadd( -1.463, 174.688, 1.087, 0.47876924 ) }
+    Axon { pt3dadd( -1.464, 167.575, 2.271, 0.48002085 ) }
+    Axon { pt3dadd( -1.463, 125.06799, 4.474, 0.48002085 ) }
+    Axon { pt3dadd( -1.463, 116.23501, 4.461, 0.47860628 ) }
+    Axon { pt3dadd( -1.463, 89.319, -0.48600003, 0.47721696 ) }
+    Axon { pt3dadd( -1.463, 84.752, -1.9959999, 0.47880685 ) }
+    Axon { pt3dadd( -1.8750001, 77.804, -6.3529997, 0.4725886 ) }
+    Axon { pt3dadd( -2.211, 69.501, -11.827001, 0.46855524 ) }
+    Axon { pt3dadd( -5.843, 65.517006, -10.744, 0.4165093 ) }
+    Axon { pt3dadd( -10.378, 61.816, -12.658999, 0.46703747 ) }
+    Axon { pt3dadd( -13.425, 56.228, -14.43, 0.4279346 ) }
+    Axon { pt3dadd( -13.309, 47.605, -19.862001, 0.4382876 ) }
+    Axon { pt3dadd( -10.605, 42.071, -24.422, 0.4727029 ) }
+    Axon { pt3dadd( -4.344, 36.12, -30.537998, 0.47843912 ) }
+    Axon { pt3dadd( -1.464, 32.201, -35.333, 0.47756466 ) }
+    Axon { pt3dadd( -1.463, 3.7870002, -50.083, 0.47882357 ) }
+    Axon { pt3dadd( -1.463, -3.4490001, -53.232002, 0.47877342 ) }
+    Axon { pt3dadd( -1.464, -47.151, -65.867004, 0.4802583 ) }
+    Axon { pt3dadd( -1.463, -53.324, -67.068, 0.47851858 ) }
+    Axon { pt3dadd( -1.464, -84.147, -66.674, 0.479925 ) }
+    Axon { pt3dadd( -1.464, -102.354004, -64.013, 0.47701156 ) }
+    Axon { pt3dadd( -1.463, -118.490005, -60.203, 0.47898227 ) }
+    Axon { pt3dadd( -1.463, -135.459, -53.970997, 0.47921184 ) }
+    Axon { pt3dadd( -1.464, -162.826, -40.074, 0.4792369 ) }
+    Axon { pt3dadd( -1.464, -167.617, -37.599, 0.47921184 ) }
+    Axon { pt3dadd( -1.464, -210.193, -8.407, 0.47782004 ) }
+    Axon { pt3dadd( -1.463, -214.966, -5.242, 0.4803707 ) }
+    Axon { pt3dadd( -1.464, -243.343, 14.582001, 0.48062462 ) }
+    Axon { pt3dadd( -1.463, -247.91, 17.366999, 0.47968322 ) }
+    Axon { pt3dadd( -1.9640001, -269.86002, 28.431002, 0.48344183 ) }
+    Axon { pt3dadd( -2.339, -271.03702, 33.142002, 0.48344183 ) }
+    Axon { pt3dadd( -3.517, -272.911, 36.086, 0.4823028 ) }
+    Axon { pt3dadd( -4.8069997, -273.147, 38.088, 0.3996999 ) }
+    Axon { pt3dadd( -7.119, -273.407, 39.839, 0.4022636 ) }
+    Axon { pt3dadd( -8.688, -273.783, 42.467003, 0.4014424 ) }
+    Axon { pt3dadd( -9.201, -274.205, 45.482002, 0.40333113 ) }
+    Axon { pt3dadd( -8.655, -274.66, 48.519, 0.40116832 ) }
+    Axon { pt3dadd( -7.121, -274.998, 51.095997, 0.43534353 ) }
+    Axon { pt3dadd( -4.8129997, -275.3, 52.814, 0.4349207 ) }
+    Axon { pt3dadd( -2.108, -275.368, 53.405, 0.4497822 ) }
+    Axon { pt3dadd( 0.596, -275.3, 52.814, 0.4349207 ) }
+    Axon { pt3dadd( 2.904, -274.998, 51.095997, 0.4330958 ) }
+    Axon { pt3dadd( 4.438, -274.66, 48.519, 0.40190047 ) }
+    Axon { pt3dadd( 4.9839997, -274.20398, 45.482002, 0.40231827 ) }
+    Axon { pt3dadd( 4.4709997, -273.783, 42.467003, 0.4006295 ) }
+    Axon { pt3dadd( 2.903, -273.407, 39.839, 0.4022636 ) }
+    Axon { pt3dadd( 2.588, -273.37, 39.521, 0.40152213 ) }
+
+}
+
+
+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=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, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon, Axon]}
+	all = new SectionList()
+	Soma all.append()
+	Axon 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 = 63
+}
+
+
+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 DVC
+
+