wormsim 0.0.1__py3-none-any.whl

wormsim/components/model/AVEL.hoc

@@ -0,0 +1,149 @@
+begintemplate AVEL
+
+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]}
+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( 2.75, -269.35, 40.65, 1.6093478 ) }
+    Soma { pt3dadd( 2.75, -267.7406522, 40.65, 1.6093478 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( 2.75, -269.35, 40.65, 0.37416574 ) }
+    Axon { pt3dadd( 2.75, -269.35, 40.7, 0.37416574 ) }
+    Axon { pt3dadd( 2.85, -269.65, 41.25, 0.4358899 ) }
+    Axon { pt3dadd( 3.525, -270.19998, 45.55, 0.33541018 ) }
+    Axon { pt3dadd( 2.75, -270.8, 50.075, 0.39051247 ) }
+    Axon { pt3dadd( -1.65, -272.075, 52.55, 0.40311286 ) }
+    Axon { pt3dadd( -1.925, -272.525, 52.55, 0.39370042 ) }
+    Axon { pt3dadd( -1.925, -274.9, 53.375, 0.43011624 ) }
+    Axon { pt3dadd( -2.5, -275.35, 53.399998, 0.36055514 ) }
+    Axon { pt3dadd( -4.8500004, -275.3, 52.824997, 0.33541018 ) }
+    Axon { pt3dadd( -7.1000004, -275.0, 51.1, 0.34641016 ) }
+    Axon { pt3dadd( -8.65, -274.65, 48.525, 0.42720017 ) }
+    Axon { pt3dadd( -9.2, -274.2, 45.5, 0.4472136 ) }
+    Axon { pt3dadd( -8.7, -273.775, 42.449997, 0.33541018 ) }
+    Axon { pt3dadd( -7.125, -273.42502, 39.825, 0.4330127 ) }
+    Axon { pt3dadd( -4.8500004, -272.32498, 37.575, 0.44158804 ) }
+    Axon { pt3dadd( -2.2749999, -271.35, 35.8, 0.4387482 ) }
+    Axon { pt3dadd( -1.95, -266.8, 24.95, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -247.90001, 17.35, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -243.35, 14.55, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -214.94998, -5.25, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -210.2, -8.4, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -167.6, -37.6, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -135.45001, -53.95, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -118.49999, -60.2, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -102.35, -64.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, -84.15, -66.649994, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -53.3, -67.049995, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -47.15, -65.85, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -3.4499998, -53.250004, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 3.7500002, -50.050003, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 28.55, -36.649998, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 29.699999, -35.9, 0.41231057 ) }
+
+}
+
+
+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]}
+	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 = 34
+}
+
+
+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 AVEL
+
+

wormsim/components/model/AVER.hoc

@@ -0,0 +1,149 @@
+begintemplate AVER
+
+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]}
+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( -8.4, -269.35, 40.65, 1.5297059 ) }
+    Soma { pt3dadd( -8.4, -267.8202941, 40.65, 1.5297059 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -8.4, -269.35, 40.65, 0.37416574 ) }
+    Axon { pt3dadd( -8.349999, -269.35, 40.7, 0.37416574 ) }
+    Axon { pt3dadd( -8.45, -269.65, 41.25, 0.4358899 ) }
+    Axon { pt3dadd( -9.15, -270.19998, 45.55, 0.37416574 ) }
+    Axon { pt3dadd( -8.349999, -270.8, 50.075, 0.39051247 ) }
+    Axon { pt3dadd( -3.9500003, -272.075, 52.55, 0.40311286 ) }
+    Axon { pt3dadd( -3.675, -272.525, 52.55, 0.39370042 ) }
+    Axon { pt3dadd( -3.675, -274.9, 53.375, 0.43011624 ) }
+    Axon { pt3dadd( -3.1, -275.35, 53.399998, 0.36055514 ) }
+    Axon { pt3dadd( -0.8, -275.3, 52.824997, 0.3774917 ) }
+    Axon { pt3dadd( 1.5, -275.0, 51.1, 0.34641016 ) }
+    Axon { pt3dadd( 3.05, -274.65, 48.525, 0.42720017 ) }
+    Axon { pt3dadd( 3.6, -274.2, 45.5, 0.4472136 ) }
+    Axon { pt3dadd( 3.075, -273.775, 42.449997, 0.44158804 ) }
+    Axon { pt3dadd( 1.525, -273.42502, 39.825, 0.4330127 ) }
+    Axon { pt3dadd( -0.75, -272.32498, 37.575, 0.44158804 ) }
+    Axon { pt3dadd( -3.3500001, -271.35, 35.8, 0.46904156 ) }
+    Axon { pt3dadd( -3.6499999, -266.8, 24.95, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -247.90001, 17.35, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -243.35, 14.55, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -214.94998, -5.25, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -210.2, -8.4, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -167.6, -37.6, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -135.45001, -53.95, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -118.49999, -60.2, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -102.35, -64.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, -84.15, -66.649994, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -53.3, -67.049995, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -47.15, -65.85, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -3.4499998, -53.250004, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 3.7500002, -50.050003, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 28.25, -36.85, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 29.499998, -36.05, 0.46904156 ) }
+
+}
+
+
+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]}
+	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 = 34
+}
+
+
+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 AVER
+
+

wormsim/components/model/AVFL.hoc

@@ -0,0 +1,195 @@
+begintemplate AVFL
+
+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, 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, 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( 2.1, -246.4, 18.6, 3.6945906 ) }
+    Soma { pt3dadd( 2.1, -242.7054094, 18.6, 3.6945906 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( 2.1, -246.4, 18.6, 0.8717798 ) }
+    Axon { pt3dadd( 2.1, -245.09999, 18.099998, 0.8717798 ) }
+    Axon { pt3dadd( 1.65, -244.37498, 16.8, 0.41533118 ) }
+    Axon { pt3dadd( -1.35, -241.15, 14.55, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -214.94998, -5.25, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -210.2, -8.4, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -167.6, -37.6, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -135.45001, -53.95, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -118.49999, -60.2, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -102.35, -64.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, -84.15, -66.649994, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -53.3, -67.049995, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -47.15, -65.85, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -3.4499998, -53.250004, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 3.7500002, -50.050003, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 32.2, -35.350002, 0.42426404 ) }
+    Axon { pt3dadd( -4.35, 36.1, -30.55, 0.46904156 ) }
+    Axon { pt3dadd( -10.625, 42.05, -24.449999, 0.55 ) }
+    Axon { pt3dadd( -13.349999, 47.600002, -19.875, 0.4387482 ) }
+    Axon { pt3dadd( -13.45, 56.199997, -14.45, 0.42426404 ) }
+    Axon { pt3dadd( -10.375, 61.85, -12.65, 0.45 ) }
+    Axon { pt3dadd( -5.85, 65.525, -10.75, 0.45 ) }
+    Axon { pt3dadd( -2.2, 69.5, -11.85, 0.41231057 ) }
+    Axon { pt3dadd( -1.85, 77.8, -6.3500004, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 84.75, -2.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, 89.3, -0.5, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 116.2, 4.4500003, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 125.100006, 4.4500003, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 167.6, 2.25, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 174.65, 1.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 249.09999, -20.25, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 256.3, -21.5, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 283.3, -25.0, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 289.19998, -25.5, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 317.6, -26.499998, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 322.8, -26.050001, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 350.75, -23.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, 355.35, -21.449999, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 386.1, -8.2, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 396.95, -2.6000001, 0.50990194 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 43/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( 2.1, -246.4, 18.6, 0.8717798 ) }
+    Dendrite2 { pt3dadd( 2.1, -247.7, 19.1, 0.8717798 ) }
+    Dendrite2 { pt3dadd( 2.1, -249.05, 19.050001, 0.6480741 ) }
+    Dendrite2 { pt3dadd( 2.1, -253.55, 19.55, 0.50990194 ) }
+    Dendrite2 { pt3dadd( 2.1, -266.5, 25.25, 0.53851646 ) }
+    Dendrite2 { pt3dadd( 0.55, -271.75, 33.75, 0.4358899 ) }
+    Dendrite2 { pt3dadd( 0.1, -272.55002, 36.55, 0.50990194 ) }
+    Dendrite2 { pt3dadd( 0.525, -273.15, 38.05, 0.55 ) }
+    Dendrite2 { pt3dadd( 2.8999999, -273.42502, 39.825, 0.43011624 ) }
+    Dendrite2 { pt3dadd( 4.475, -273.775, 42.449997, 0.44158804 ) }
+    Dendrite2 { pt3dadd( 4.975, -274.2, 45.5, 0.42720017 ) }
+    Dendrite2 { pt3dadd( 4.4500003, -274.65, 48.525, 0.4924429 ) }
+    Dendrite2 { pt3dadd( 2.8999999, -275.0, 51.1, 0.48989794 ) }
+    Dendrite2 { pt3dadd( 0.6, -275.3, 52.824997, 0.5123476 ) }
+    Dendrite2 { pt3dadd( -2.1, -275.35, 53.399998, 0.5 ) }
+    Dendrite2 { pt3dadd( -4.8500004, -275.3, 52.824997, 0.33541018 ) }
+    Dendrite2 { pt3dadd( -7.1000004, -275.0, 51.1, 0.34641016 ) }
+    Dendrite2 { pt3dadd( -8.65, -274.65, 48.525, 0.42720017 ) }
+    Dendrite2 { pt3dadd( -9.2, -274.2, 45.5, 0.4472136 ) }
+    Dendrite2 { pt3dadd( -8.7, -273.775, 42.449997, 0.33541018 ) }
+    Dendrite2 { pt3dadd( -7.125, -273.42502, 39.825, 0.4330127 ) }
+    Dendrite2 { pt3dadd( -5.2999997, -272.925, 37.2, 0.32015622 ) }
+    Dendrite2 { pt3dadd( -4.1499996, -271.7, 33.7, 0.41231057 ) }
+    Dendrite2 { pt3dadd( -3.975, -257.9, 25.625, 0.40620193 ) }
+    Dendrite2 { pt3dadd( -3.975, -257.45, 25.325, 0.39370042 ) }
+
+}
+
+
+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, 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, 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 = 41
+	Dendrite2 nseg = 25
+}
+
+
+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 AVFL
+
+

wormsim/components/model/AVFR.hoc

@@ -0,0 +1,196 @@
+begintemplate AVFR
+
+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, 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, 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( -6.5, -246.4, 18.6, 3.6945906 ) }
+    Soma { pt3dadd( -6.5, -242.7054094, 18.6, 3.6945906 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -6.5, -246.4, 18.6, 0.8717798 ) }
+    Axon { pt3dadd( -6.5, -245.09999, 18.099998, 0.8717798 ) }
+    Axon { pt3dadd( -6.025, -244.37498, 16.8, 0.43011624 ) }
+    Axon { pt3dadd( -3.05, -241.15, 14.55, 0.4358899 ) }
+    Axon { pt3dadd( -2.45, -239.94998, 13.75, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -214.94998, -5.25, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -210.2, -8.4, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -167.6, -37.6, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -135.45001, -53.95, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -118.49999, -60.2, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -102.35, -64.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, -84.15, -66.649994, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -53.3, -67.049995, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -47.15, -65.85, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -3.4499998, -53.250004, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 3.7500002, -50.050003, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 32.2, -35.350002, 0.42426404 ) }
+    Axon { pt3dadd( -4.35, 36.1, -30.55, 0.46904156 ) }
+    Axon { pt3dadd( -10.625, 42.05, -24.449999, 0.55 ) }
+    Axon { pt3dadd( -13.349999, 47.600002, -19.875, 0.4387482 ) }
+    Axon { pt3dadd( -13.45, 56.199997, -14.45, 0.42426404 ) }
+    Axon { pt3dadd( -10.375, 61.85, -12.65, 0.45 ) }
+    Axon { pt3dadd( -5.85, 65.525, -10.75, 0.45 ) }
+    Axon { pt3dadd( -2.2, 69.5, -11.85, 0.41231057 ) }
+    Axon { pt3dadd( -1.85, 77.8, -6.3500004, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 84.75, -2.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, 89.3, -0.5, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 116.2, 4.4500003, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 125.100006, 4.4500003, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 167.6, 2.25, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 174.65, 1.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 249.09999, -20.25, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 256.3, -21.5, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 283.3, -25.0, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 289.19998, -25.5, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 317.6, -26.499998, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 322.8, -26.050001, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, 350.75, -23.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, 355.35, -21.449999, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, 386.1, -8.2, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, 396.95, -2.6000001, 0.50990194 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 44/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -6.5, -246.4, 18.6, 0.8717798 ) }
+    Dendrite2 { pt3dadd( -6.5, -247.7, 19.1, 0.8717798 ) }
+    Dendrite2 { pt3dadd( -6.5, -249.05, 19.050001, 0.6480741 ) }
+    Dendrite2 { pt3dadd( -6.5, -253.55, 19.55, 0.50990194 ) }
+    Dendrite2 { pt3dadd( -6.5, -266.5, 25.25, 0.53851646 ) }
+    Dendrite2 { pt3dadd( -4.9, -271.75, 33.75, 0.50990194 ) }
+    Dendrite2 { pt3dadd( -4.5, -272.55002, 36.55, 0.50990194 ) }
+    Dendrite2 { pt3dadd( -4.9249997, -273.15, 38.05, 0.55 ) }
+    Dendrite2 { pt3dadd( -7.2999997, -273.42502, 39.825, 0.43011624 ) }
+    Dendrite2 { pt3dadd( -8.875, -273.775, 42.449997, 0.44158804 ) }
+    Dendrite2 { pt3dadd( -9.375, -274.2, 45.5, 0.42720017 ) }
+    Dendrite2 { pt3dadd( -8.825, -274.65, 48.525, 0.46368092 ) }
+    Dendrite2 { pt3dadd( -7.2999997, -275.0, 51.1, 0.48989794 ) }
+    Dendrite2 { pt3dadd( -5.0, -275.3, 52.824997, 0.5123476 ) }
+    Dendrite2 { pt3dadd( -2.3, -275.35, 53.399998, 0.5 ) }
+    Dendrite2 { pt3dadd( 0.45, -275.3, 52.824997, 0.33541018 ) }
+    Dendrite2 { pt3dadd( 2.7, -275.0, 51.1, 0.34641016 ) }
+    Dendrite2 { pt3dadd( 4.25, -274.65, 48.525, 0.42720017 ) }
+    Dendrite2 { pt3dadd( 4.8250003, -274.2, 45.5, 0.32015622 ) }
+    Dendrite2 { pt3dadd( 4.3, -273.775, 42.449997, 0.33541018 ) }
+    Dendrite2 { pt3dadd( 2.725, -273.42502, 39.825, 0.4330127 ) }
+    Dendrite2 { pt3dadd( 0.9, -272.925, 37.2, 0.32015622 ) }
+    Dendrite2 { pt3dadd( -0.25, -271.7, 33.7, 0.41231057 ) }
+    Dendrite2 { pt3dadd( -0.375, -257.9, 25.625, 0.35355338 ) }
+    Dendrite2 { pt3dadd( -0.425, -257.45, 25.325, 0.39370042 ) }
+
+}
+
+
+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, 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, 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 = 42
+	Dendrite2 nseg = 25
+}
+
+
+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 AVFR
+
+