wormsim 0.0.1__py3-none-any.whl

wormsim/components/model/VA02.hoc

@@ -0,0 +1,144 @@
+begintemplate VA02
+
+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, 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( -1.85, -217.1, -3.9500003, 4.0730824 ) }
+    Soma { pt3dadd( -1.85, -213.0269176, -3.9500003, 4.0730824 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -1.85, -217.1, -3.9500003, 0.70710677 ) }
+    Axon { pt3dadd( -1.85, -218.24998, -3.1, 0.70710677 ) }
+    Axon { pt3dadd( -1.85, -221.0, -1.05, 0.46904156 ) }
+    Axon { pt3dadd( -1.4499999, -227.15001, 3.25, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -243.35, 14.55, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -247.90001, 17.35, 0.42426404 ) }
+    Axon { pt3dadd( -1.95, -270.7, 26.550001, 0.42426404 ) }
+    Axon { pt3dadd( -1.95, -315.15, 42.85, 0.4358899 ) }
+    Axon { pt3dadd( -1.95, -316.45, 43.3, 0.50990194 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 11/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -1.85, -217.1, -3.9500003, 0.70710677 ) }
+    Dendrite2 { pt3dadd( -1.85, -215.94998, -4.8, 0.70710677 ) }
+    Dendrite2 { pt3dadd( -1.8, -213.8, -6.3500004, 0.53851646 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -210.2, -8.5, 0.53851646 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -190.0, -22.400002, 0.53851646 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -185.75, -25.650002, 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, 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 = 9
+	Dendrite2 nseg = 6
+}
+
+
+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 VA02
+
+

wormsim/components/model/VA03.hoc

@@ -0,0 +1,147 @@
+begintemplate VA03
+
+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, 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( -1.475, -184.09999, -26.374998, 4.0199504 ) }
+    Soma { pt3dadd( -1.475, -180.0800396, -26.374998, 4.0199504 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -1.475, -184.09999, -26.374998, 1.0049876 ) }
+    Axon { pt3dadd( -1.4499999, -185.3, -25.6, 1.0049876 ) }
+    Axon { pt3dadd( -1.4499999, -189.95, -22.6, 0.70710677 ) }
+    Axon { pt3dadd( -1.5, -210.1, -8.45, 0.64031243 ) }
+    Axon { pt3dadd( -1.4499999, -214.94998, -5.25, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -243.35, 14.55, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -247.90001, 17.35, 0.42426404 ) }
+    Axon { pt3dadd( -1.95, -270.7, 26.550001, 0.42426404 ) }
+    Axon { pt3dadd( -1.95, -314.65002, 42.55, 0.4358899 ) }
+    Axon { pt3dadd( -1.95, -315.94998, 43.0, 0.50990194 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 12/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -1.475, -184.09999, -26.374998, 0.8774964 ) }
+    Dendrite2 { pt3dadd( -1.5, -182.9, -27.15, 0.8774964 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -179.34999, -29.499998, 0.70710677 ) }
+    Dendrite2 { pt3dadd( -1.5, -167.70001, -37.6, 0.56568545 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -135.45001, -53.95, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -123.09999, -57.9, 0.5 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -120.200005, -58.850002, 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]}
+    dendrite_group = new SectionList()
+    Dendrite2 dendrite_group.append()
+
+    // Group: {name=all, sections=[Soma, 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 = 10
+	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 VA03
+
+

wormsim/components/model/VA04.hoc

@@ -0,0 +1,148 @@
+begintemplate VA04
+
+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, 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( -1.85, -119.50001, -58.7, 4.1097445 ) }
+    Soma { pt3dadd( -1.85, -115.3902655, -58.7, 4.1097445 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -1.85, -119.50001, -58.7, 0.9433981 ) }
+    Axon { pt3dadd( -1.85, -120.9, -58.3, 0.9433981 ) }
+    Axon { pt3dadd( -1.85, -126.2, -56.800003, 0.9433981 ) }
+    Axon { pt3dadd( -1.5, -135.35, -54.000004, 0.5744563 ) }
+    Axon { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -167.6, -37.6, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -210.2, -8.4, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -214.94998, -5.25, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -243.35, 14.55, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -247.90001, 17.35, 0.42426404 ) }
+    Axon { pt3dadd( -1.95, -271.30002, 27.7, 0.5 ) }
+    Axon { pt3dadd( -1.95, -273.2, 28.7, 0.5 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 14/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -1.85, -119.50001, -58.7, 0.9433981 ) }
+    Dendrite2 { pt3dadd( -1.85, -118.1, -59.100002, 0.9433981 ) }
+    Dendrite2 { pt3dadd( -1.85, -113.8, -60.7, 0.9433981 ) }
+    Dendrite2 { pt3dadd( -1.5, -102.450005, -63.9, 0.5744563 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -84.15, -66.649994, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -62.050003, -67.25, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -55.75, -67.2, 0.50990194 ) }
+
+}
+
+
+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, 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 = 12
+	Dendrite2 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 VA04
+
+

wormsim/components/model/VA05.hoc

@@ -0,0 +1,147 @@
+begintemplate VA05
+
+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, 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( -1.85, -54.3, -66.049995, 3.8897302 ) }
+    Soma { pt3dadd( -1.85, -50.410269799999995, -66.049995, 3.8897302 ) }
+    // Section: Axon, id: Axon, parent: Soma (entry count 2/100)
+    Axon { pt3dclear() }
+    Axon { pt3dadd( -1.85, -54.3, -66.049995, 0.70710677 ) }
+    Axon { pt3dadd( -1.85, -55.699997, -66.049995, 0.70710677 ) }
+    Axon { pt3dadd( -1.8, -58.600002, -66.1, 0.56568545 ) }
+    Axon { pt3dadd( -1.4499999, -84.1, -66.649994, 0.42426404 ) }
+    Axon { pt3dadd( -1.4499999, -102.35, -64.0, 0.50990194 ) }
+    Axon { pt3dadd( -1.4499999, -118.49999, -60.2, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -135.45001, -53.95, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -162.85, -40.05, 0.4358899 ) }
+    Axon { pt3dadd( -1.4499999, -167.6, -37.6, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -212.29999, -7.2, 0.5 ) }
+    Axon { pt3dadd( -1.4499999, -214.94998, -5.25, 0.4358899 ) }
+    // Section: Dendrite2, id: Dendrite2, parent: Soma (entry count 13/100)
+    Dendrite2 { pt3dclear() }
+    Dendrite2 { pt3dadd( -1.85, -54.3, -66.049995, 0.9899495 ) }
+    Dendrite2 { pt3dadd( -1.85, -52.899998, -66.049995, 0.9899495 ) }
+    Dendrite2 { pt3dadd( -1.85, -48.8, -66.049995, 0.70710677 ) }
+    Dendrite2 { pt3dadd( -1.5, -33.8, -62.0, 0.56568545 ) }
+    Dendrite2 { pt3dadd( -1.4499999, -3.4499998, -53.250004, 0.4358899 ) }
+    Dendrite2 { pt3dadd( -1.4499999, 18.05, -42.8, 0.50990194 ) }
+    Dendrite2 { pt3dadd( -1.4499999, 20.25, -41.4, 0.50990194 ) }
+
+}
+
+
+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, 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 = 11
+	Dendrite2 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 VA05
+
+