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Python object model does not load gates into correct attributes when type= is used #205
Description
Here's an example channel file:
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="shal">
<notes>An ion channel from Nicoletti et al. 2024</notes>
<ionChannelHH id="shl1" species="k" conductance="10pS">
<gateHHtauInf id="m" instances="3">
<timeCourse type="shal_m_tau"/>
<steadyState type="shal_m_inf"/>
</gateHHtauInf>
<gateFractional id="h" instances="1">
<subGate id="hf" fractionalConductance="0.7">
<steadyState type="shal_h_hf_inf"/>
<timeCourse type="shal_h_hf_tau"/>
</subGate>
<subGate id="hs" fractionalConductance="0.3">
<steadyState type="shal_h_hs_inf"/>
<timeCourse type="shal_h_hs_tau"/>
</subGate>
</gateFractional>
</ionChannelHH>
<ComponentType name="shal_m_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="shalsfhit" dimension="none" value="18.0"/>
<Constant name="vashal" dimension="none" value="11.2"/>
<Constant name="kashal" dimension="none" value="14.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((-V - shalsfhit + vashal)/kashal) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_m_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="ptmshal1" dimension="none" value="13.8"/>
<Constant name="ptmshal2" dimension="none" value="-17.5165"/>
<Constant name="ptmshal3" dimension="none" value="12.9213"/>
<Constant name="ptmshal4" dimension="none" value="-3.7082"/>
<Constant name="ptmshal5" dimension="none" value="6.4876"/>
<Constant name="ptmshal6" dimension="none" value="1.8849"/>
<Constant name="cshal" dimension="none" value="0.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(cshal*(ptmshal1/(exp((-V + ptmshal2)/ptmshal3) + exp((V - ptmshal4)/ptmshal5)) + ptmshal6))* TIME_SCALE"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_h_hf_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="shalsfhit" dimension="none" value="18.0"/>
<Constant name="kishal" dimension="none" value="8.3"/>
<Constant name="vishal" dimension="none" value="-33.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((V + shalsfhit - vishal)/kishal) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_h_hf_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="pthfshal1" dimension="none" value="539.1584"/>
<Constant name="pthfshal2" dimension="none" value="-28.199"/>
<Constant name="pthfshal3" dimension="none" value="4.9199"/>
<Constant name="pthfshal4" dimension="none" value="27.2811"/>
<Constant name="cshal" dimension="none" value="0.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(cshal*(pthfshal1/(exp((V - pthfshal2)/pthfshal3) + 1) + pthfshal4))* TIME_SCALE"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_h_hs_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="shalsfhit" dimension="none" value="18.0"/>
<Constant name="kishal" dimension="none" value="8.3"/>
<Constant name="vishal" dimension="none" value="-33.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((V + shalsfhit - vishal)/kishal) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_h_hs_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="pthsshal1" dimension="none" value="8422.0"/>
<Constant name="pthsshal2" dimension="none" value="-37.7391"/>
<Constant name="pthsshal3" dimension="none" value="6.3785"/>
<Constant name="pthsshal4" dimension="none" value="118.8983"/>
<Constant name="cshal" dimension="none" value="0.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(cshal*(pthsshal1/(exp((V - pthsshal2)/pthsshal3) + 1) + pthsshal4))* TIME_SCALE"/>
</Dynamics>
</ComponentType>
</neuroml>
This will load correctly and channel.gate_fractionals and channel.gates_hh_tau_infs will include the objects for the two gates. However, if these gates are specified using the type= attribute rather than the tag itself, they are loaded in the gates attribute as GateHHUndetermined objects:
<gate id="m" instances="3" type="gateHHtauInf">
<timeCourse type="shal_m_tau"/>
<steadyState type="shal_m_inf"/>
</gate>
<gate id="h" instances="1" type="gateFractional">
<subGate id="hf" fractionalConductance="0.7">
<steadyState type="shal_h_hf_inf"/>
<timeCourse type="shal_h_hf_tau"/>
</subGate>
<subGate id="hs" fractionalConductance="0.3">
<steadyState type="shal_h_hs_inf"/>
<timeCourse type="shal_h_hs_tau"/>
</subGate>
</gate>
Activity
sanjayankur31 commentedon Jan 14, 2025
My initial thought is that the generateds generated parser cannot (does not?) make use of the
typeattribute. This needs to be confirmed, and if this is the case, we need to:This is important because both ways of writing are valid NeuroML, so it's unexpected when one works and the other doesn't.
feat(utils): replace undetermined gates with standard ones