Initial version gate parsing

openworm · Apr 19, 2024 · 6358caf · 6358caf
1 parent d1034b0
commit 6358caf
Show file tree

Hide file tree

Showing 3 changed files with 115 additions and 3 deletions.
diff --git a/NeuroML2/AWCon_kir.channel.nml b/NeuroML2/AWCon_kir.channel.nml
@@ -2,5 +2,35 @@
     <notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
     <ionChannelHH id="AWCon_kir" conductance="10pS">
         <notes>AWCon_kir channel from Nicoletti et al. 2019</notes>
+        <gateHHtauInf id="m" instances="1">
+            <timeCourse type="kir_m_tau"/>
+            <steadyState type="kir_m_inf"/>
+        </gateHHtauInf>
     </ionChannelHH>
+    <ComponentType name="kir_m_inf" extends="baseVoltageDepVariable">
+        <Constant name="va_kir" dimension="none" value="-52.0"/>
+        <Constant name="ka_kir" dimension="none" value="13.0"/>
+        <Constant name="p1tmkir" dimension="none" value="17.0752"/>
+        <Constant name="p2tmkir" dimension="none" value="-17.8258"/>
+        <Constant name="p3tmkir" dimension="none" value="20.3154"/>
+        <Constant name="p4tmkir" dimension="none" value="-43.4414"/>
+        <Constant name="p5tmkir" dimension="none" value="11.1691"/>
+        <Constant name="p6tmkir" dimension="none" value="3.8329"/>
+        <Dynamics>
+            <DerivedVariable name="x" dimension="none" exposure="x" value="1/(1+exp((v-va_kir+30)/ka_kir))"/>
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="kir_m_tau" extends="baseVoltageDepTime">
+        <Constant name="va_kir" dimension="none" value="-52.0"/>
+        <Constant name="ka_kir" dimension="none" value="13.0"/>
+        <Constant name="p1tmkir" dimension="none" value="17.0752"/>
+        <Constant name="p2tmkir" dimension="none" value="-17.8258"/>
+        <Constant name="p3tmkir" dimension="none" value="20.3154"/>
+        <Constant name="p4tmkir" dimension="none" value="-43.4414"/>
+        <Constant name="p5tmkir" dimension="none" value="11.1691"/>
+        <Constant name="p6tmkir" dimension="none" value="3.8329"/>
+        <Dynamics>
+            <DerivedVariable name="t" dimension="time" exposure="t" value="p1tmkir/(exp(-(v-p2tmkir)/p3tmkir)+exp((v-p4tmkir)/p5tmkir))+p6tmkir"/>
+        </Dynamics>
+    </ComponentType>
 </neuroml>
diff --git a/NeuroML2/GenerateNeuroML.py b/NeuroML2/GenerateNeuroML.py
@@ -4,6 +4,8 @@
 from pyneuroml import pynml
 from pyneuroml.xppaut import parse_script
 
+from neuroml import GateHHRates
+
 
 xpps = {"RMD": parse_script("../RMD.ode"), "AWCon": parse_script("../AWC.ode")}
 
@@ -13,7 +15,7 @@
 colors = {"AWCon": "0 0 0.8", "RMD": "0 0.8 0", "GenericMuscleCell": "0.8 0 0"}
 
 
-def create_channel_file(chan_id_in_cell, cell_id, xpp):
+def create_channel_file(chan_id_in_cell, cell_id, xpp, gates={}, parameters={}):
     chan_id = "%s_%s" % (cell_id, chan_id_in_cell)
     chan_doc = NeuroMLDocument(
         id=chan_id,
@@ -29,8 +31,42 @@ def create_channel_file(chan_id_in_cell, cell_id, xpp):
         notes="%s channel from Nicoletti et al. 2019" % chan_id,
     )
 
+    for g in gates:
+
+        ss = component_factory("HHVariable", type="%s_%s_inf"%(chan_id_in_cell,g)) 
+        tc = component_factory("HHTime", type="%s_%s_tau"%(chan_id_in_cell,g)) 
+
+        gc = component_factory("GateHHTauInf", id=g, instances=gates[g][0], steady_state=ss, time_course=tc, validate=True) 
+        channel.add(gc)
+
+        ssct = component_factory("ComponentType", name=ss.type, extends="baseVoltageDepVariable")
+        tcct = component_factory("ComponentType", name=tc.type, extends="baseVoltageDepTime")
+        chan_doc.add(ssct)
+        chan_doc.add(tcct)
+
+        for p in parameters:
+            const = component_factory(
+                "Constant", name=p, dimension="none", value=str(xpp["parameters"][p])
+            )
+            ssct.add(const)
+            tcct.add(const)
+
+
+        d = component_factory("Dynamics")
+        ssct.add(d)
+        dv = component_factory("DerivedVariable", name="x", exposure="x", dimension="none", value=xpp["derived_variables"][gates[g][1]])
+        d.add(dv)
+
+        d = component_factory("Dynamics")
+        tcct.add(d)
+        dv = component_factory("DerivedVariable", name="t", exposure="t", dimension="time", value=xpp["derived_variables"][gates[g][2]])
+        d.add(dv)
+
+
+
+
     chan_doc.add(channel)
-    chan_doc.validate(recursive=True)
+    #chan_doc.validate(recursive=True)
 
     pynml.write_neuroml2_file(nml2_doc=chan_doc, nml2_file_name=chan_fn, validate=True)
 
@@ -134,7 +170,23 @@ def create_cells():
             erev="%smV" % xpps[cell_id]["parameters"]["ek"],
             ion="k",
             ion_channel="%s_kir" % cell_id,
-            ion_chan_def_file=create_channel_file("kir", cell_id, xpps[cell_id]),
+            ion_chan_def_file=create_channel_file(
+                "kir",
+                cell_id,
+                xpps[cell_id],
+                gates={'m':[1,'minf_kir','tm_kir']},
+                parameters=[
+                    "va_kir",
+                    "ka_kir",
+                    "p1tmkir",
+                    "p2tmkir",
+                    "p3tmkir",
+                    "p4tmkir",
+                    "p5tmkir",
+                    "p6tmkir",
+                ],
+
+            ),
         )
 
         cell.set_specific_capacitance("%s uF_per_cm2" % c)

diff --git a/NeuroML2/RMD_kir.channel.nml b/NeuroML2/RMD_kir.channel.nml
@@ -2,5 +2,35 @@
     <notes>An ion channel from cell RMD from Nicoletti et al. 2019</notes>
     <ionChannelHH id="RMD_kir" conductance="10pS">
         <notes>RMD_kir channel from Nicoletti et al. 2019</notes>
+        <gateHHtauInf id="m" instances="1">
+            <timeCourse type="kir_m_tau"/>
+            <steadyState type="kir_m_inf"/>
+        </gateHHtauInf>
     </ionChannelHH>
+    <ComponentType name="kir_m_inf" extends="baseVoltageDepVariable">
+        <Constant name="va_kir" dimension="none" value="-52.0"/>
+        <Constant name="ka_kir" dimension="none" value="13.0"/>
+        <Constant name="p1tmkir" dimension="none" value="17.0752"/>
+        <Constant name="p2tmkir" dimension="none" value="-17.8258"/>
+        <Constant name="p3tmkir" dimension="none" value="20.3154"/>
+        <Constant name="p4tmkir" dimension="none" value="-43.4414"/>
+        <Constant name="p5tmkir" dimension="none" value="11.1691"/>
+        <Constant name="p6tmkir" dimension="none" value="3.8329"/>
+        <Dynamics>
+            <DerivedVariable name="x" dimension="none" exposure="x" value="1/(1+exp((v-va_kir+30)/ka_kir))"/>
+        </Dynamics>
+    </ComponentType>
+    <ComponentType name="kir_m_tau" extends="baseVoltageDepTime">
+        <Constant name="va_kir" dimension="none" value="-52.0"/>
+        <Constant name="ka_kir" dimension="none" value="13.0"/>
+        <Constant name="p1tmkir" dimension="none" value="17.0752"/>
+        <Constant name="p2tmkir" dimension="none" value="-17.8258"/>
+        <Constant name="p3tmkir" dimension="none" value="20.3154"/>
+        <Constant name="p4tmkir" dimension="none" value="-43.4414"/>
+        <Constant name="p5tmkir" dimension="none" value="11.1691"/>
+        <Constant name="p6tmkir" dimension="none" value="3.8329"/>
+        <Dynamics>
+            <DerivedVariable name="t" dimension="time" exposure="t" value="p1tmkir/(exp(-(v-p2tmkir)/p3tmkir)+exp((v-p4tmkir)/p5tmkir))+p6tmkir"/>
+        </Dynamics>
+    </ComponentType>
 </neuroml>