diff --git a/doc/component-list.json b/doc/component-list.json new file mode 100644 index 0000000..4c48983 --- /dev/null +++ b/doc/component-list.json @@ -0,0 +1 @@ +{"Cells": ["baseCell", "baseSpikingCell", "baseCellMembPot", "baseCellMembPotDL", "baseChannelPopulation", "channelPopulation", "channelPopulationNernst", "baseChannelDensity", "baseChannelDensityCond", "variableParameter", "inhomogeneousValue", "channelDensityNonUniform", "channelDensityNonUniformNernst", "channelDensityNonUniformGHK", "channelDensity", "channelDensityVShift", "channelDensityNernst", "channelDensityNernstCa2", "channelDensityGHK", "channelDensityGHK2", "pointCellCondBased", "pointCellCondBasedCa", "distal", "proximal", "parent", "segment", "segmentGroup", "member", "from", "to", "include", "path", "subTree", "inhomogeneousParameter", "proximalDetails", "distalDetails", "morphology", "specificCapacitance", "initMembPotential", "spikeThresh", "membraneProperties", "membraneProperties2CaPools", "biophysicalProperties", "biophysicalProperties2CaPools", "intracellularProperties", "intracellularProperties2CaPools", "resistivity", "concentrationModel", "decayingPoolConcentrationModel", "fixedFactorConcentrationModel", "fixedFactorConcentrationModelTraub", "species", "cell", "cell2CaPools", "baseCellMembPotCap", "baseIaf", "iafTauCell", "iafTauRefCell", "baseIafCapCell", "iafCell", "iafRefCell", "izhikevichCell", "izhikevich2007Cell", "adExIaFCell", "fitzHughNagumoCell", "pinskyRinzelCA3Cell", "hindmarshRose1984Cell"], "Synapses": ["baseSynapse", "baseVoltageDepSynapse", "baseSynapseDL", "baseCurrentBasedSynapse", "alphaCurrentSynapse", "baseConductanceBasedSynapse", "baseConductanceBasedSynapseTwo", "expOneSynapse", "alphaSynapse", "expTwoSynapse", "expThreeSynapse", "baseBlockMechanism", "voltageConcDepBlockMechanism", "basePlasticityMechanism", "tsodyksMarkramDepMechanism", "tsodyksMarkramDepFacMechanism", "blockingPlasticSynapse", "doubleSynapse", "stdpSynapse", "gapJunction", "baseGradedSynapse", "silentSynapse", "linearGradedSynapse", "gradedSynapse"], "Channels": ["baseVoltageDepRate", "baseVoltageConcDepRate", "baseHHRate", "HHExpRate", "HHSigmoidRate", "HHExpLinearRate", "baseVoltageDepVariable", "baseVoltageConcDepVariable", "baseHHVariable", "HHExpVariable", "HHSigmoidVariable", "HHExpLinearVariable", "baseVoltageDepTime", "baseVoltageConcDepTime", "fixedTimeCourse", "baseQ10Settings", "q10Fixed", "q10ExpTemp", "baseConductanceScaling", "q10ConductanceScaling", "baseConductanceScalingCaDependent", "baseGate", "gate", "gateHHrates", "gateHHtauInf", "gateHHInstantaneous", "gateHHratesTau", "gateHHratesInf", "gateHHratesTauInf", "gateFractional", "subGate", "baseIonChannel", "ionChannelPassive", "ionChannelHH", "ionChannel", "ionChannelVShift", "KSState", "closedState", "openState", "ionChannelKS", "KSTransition", "forwardTransition", "reverseTransition", "vHalfTransition", "tauInfTransition", "gateKS"], "Inputs": ["basePointCurrent", "baseVoltageDepPointCurrent", "baseVoltageDepPointCurrentSpiking", "basePointCurrentDL", "baseVoltageDepPointCurrentDL", "baseSpikeSource", "spikeGenerator", "spikeGeneratorRandom", "spikeGeneratorPoisson", "spikeGeneratorRefPoisson", "poissonFiringSynapse", "transientPoissonFiringSynapse", "timedSynapticInput", "spikeArray", "spike", "pulseGenerator", "compoundInput", "compoundInputDL", "pulseGeneratorDL", "sineGenerator", "sineGeneratorDL", "rampGenerator", "rampGeneratorDL", "voltageClamp", "voltageClampTriple"], "Networks": ["network", "networkWithTemperature", "basePopulation", "population", "populationList", "instance", "location", "region", "rectangularExtent", "projection", "explicitConnection", "connection", "synapticConnection", "synapticConnectionWD", "connectionWD", "electricalConnection", "electricalConnectionInstance", "electricalConnectionInstanceW", "electricalProjection", "continuousConnection", "continuousConnectionInstance", "continuousConnectionInstanceW", "continuousProjection", "explicitInput", "inputList", "input", "inputW"], "PyNN": ["basePyNNCell", "basePyNNIaFCell", "basePyNNIaFCondCell", "IF_curr_alpha", "IF_curr_exp", "IF_cond_alpha", "IF_cond_exp", "EIF_cond_exp_isfa_ista", "EIF_cond_alpha_isfa_ista", "HH_cond_exp", "basePynnSynapse", "expCondSynapse", "expCurrSynapse", "alphaCondSynapse", "alphaCurrSynapse", "SpikeSourcePoisson"], "NeuroMLCoreDimensions": [], "NeuroMLCoreCompTypes": ["notes", "annotation", "property", "baseStandalone", "rdf_RDF", "rdf_Description", "baseBqbiol", "bqbiol_encodes", "bqbiol_hasPart", "bqbiol_hasProperty", "bqbiol_hasVersion", "bqbiol_is", "bqbiol_isDescribedBy", "bqbiol_isEncodedBy", "bqbiol_isHomologTo", "bqbiol_isPartOf", "bqbiol_isPropertyOf", "bqbiol_isVersionOf", "bqbiol_occursIn", "bqbiol_hasTaxon", "bqmodel_is", "bqmodel_isDescribedBy", "bqmodel_isDerivedFrom", "rdf_Bag", "rdf:li", "point3DWithDiam"], "Simulation": ["Simulation", "Display", "Line", "OutputFile", "OutputColumn", "EventOutputFile", "EventSelection", "Meta"]} diff --git a/doc/helpers/nml-core-docs.py b/doc/helpers/nml-core-docs.py index 71dfc58..4de678b 100644 --- a/doc/helpers/nml-core-docs.py +++ b/doc/helpers/nml-core-docs.py @@ -7,10 +7,42 @@ Copyright 2023 NeuroML authors """ +import json import textwrap print("Generating list of nml classes") +component_type_list = None +with open("../component-list.json", "r") as f: + component_type_list = json.load(f) + +component_type_list["Other"] = [] + +output_files = {} +comp_num_dict = {} + +for ctype in component_type_list.keys(): + fwrite = open(f"../userdocs/{ctype}_list.rst", "w") + output_files[ctype] = fwrite + print(ctype, file=fwrite) + print("#" * len(ctype), file=fwrite) + print("\n", file=fwrite) + print("\n", file=fwrite) + print( + f"This documentation is auto-generated from the `NeuroML schema `__.", + file=fwrite, + ) + print("\n", file=fwrite) + print("\n", file=fwrite) + print(".. Generated using nml-core-docs.py", file=fwrite) + + comp_num_dict[ctype] = 0 + +comp_to_file_map = {} +for file, ctypes in component_type_list.items(): + for ctype in ctypes: + comp_to_file_map[ctype[0].capitalize() + ctype[1:]] = file + classes = {} files = { "generatedssupersuper.py": [], @@ -24,10 +56,6 @@ "PlasticityTypes", "ZeroOrOne", "allowedSpaces", - "channelTypes", - "gateTypes", - "networkTypes", - "populationTypes", "_FixedOffsetTZ", "GdsCollector_", "GeneratedsSuperSuper", @@ -52,47 +80,62 @@ classlist.sort() classes[f] = classlist -with open("../userdocs/coreclasses_list.txt", "w") as fwrite: - print(".. Generated using nml-core-docs.py", file=fwrite) - for module, clist in classes.items(): - f = module.split(".")[0] - for aclass in clist: - # do not print all the internal methods in GeneratedsSuper - if aclass == "GeneratedsSuper": - towrite = textwrap.dedent( - """ - {} - {} - - .. autoclass:: neuroml.nml.{}.{} - :show-inheritance: - - """.format( - aclass, - "#" * len(aclass), - f, - aclass, - ) + +for module, clist in classes.items(): + f = module.split(".")[0] + for aclass in clist: + # do not print all the internal methods in GeneratedsSuper + if aclass == "GeneratedsSuper": + towrite = textwrap.dedent( + """ + {} + {} + + .. autoclass:: neuroml.nml.{}.{} + :show-inheritance: + + """.format( + aclass, + "^" * len(aclass), + f, + aclass, ) - else: - towrite = textwrap.dedent( - """ - {} - {} - - .. autoclass:: neuroml.nml.{}.{} - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - """.format( - aclass, - "#" * len(aclass), - f, - aclass, - ) + ) + else: + towrite = textwrap.dedent( + """ + {} + {} + + .. autoclass:: neuroml.nml.{}.{} + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + """.format( + aclass, + "^" * len(aclass), + f, + aclass, ) + ) + try: + category = comp_to_file_map[aclass] + except KeyError: + if "cell" in aclass.lower(): + category = "Cells" + elif "gate" in aclass.lower(): + category = "Channels" + else: + category = "Other" + else: + comp_num_dict[category] += 1 + fwrite = output_files[category] print(towrite, file=fwrite) -print("Saved to userdocs/coreclasses_list.txt") +print("Done") +print(comp_num_dict) + +for comp, num in comp_num_dict.items(): + output_files[comp].close() diff --git a/doc/userdocs/Cells_list.rst b/doc/userdocs/Cells_list.rst new file mode 100644 index 0000000..85437ed --- /dev/null +++ b/doc/userdocs/Cells_list.rst @@ -0,0 +1,549 @@ +Cells +##### + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py + +AdExIaFCell +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.AdExIaFCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BaseCell +^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BaseCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BaseCellMembPotCap +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BaseCellMembPotCap + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BiophysicalProperties +^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BiophysicalProperties + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BiophysicalProperties2CaPools +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BiophysicalProperties2CaPools + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Cell +^^^^ + +.. autoclass:: neuroml.nml.nml.Cell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Cell2CaPools +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Cell2CaPools + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensity +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensity + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensityGHK +^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensityGHK + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensityGHK2 +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensityGHK2 + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensityNernst +^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensityNernst + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensityNernstCa2 +^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensityNernstCa2 + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensityNonUniform +^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensityNonUniform + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensityNonUniformGHK +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensityNonUniformGHK + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensityNonUniformNernst +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensityNonUniformNernst + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelDensityVShift +^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelDensityVShift + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ChannelPopulation +^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ChannelPopulation + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +DecayingPoolConcentrationModel +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.DecayingPoolConcentrationModel + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +DistalDetails +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.DistalDetails + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +FitzHughNagumoCell +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.FitzHughNagumoCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +FixedFactorConcentrationModel +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.FixedFactorConcentrationModel + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +HindmarshRose1984Cell +^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.HindmarshRose1984Cell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IafCell +^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IafCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IafRefCell +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IafRefCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IafTauCell +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IafTauCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IafTauRefCell +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IafTauRefCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Include +^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Include + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +InhomogeneousParameter +^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.InhomogeneousParameter + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +InhomogeneousValue +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.InhomogeneousValue + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +InitMembPotential +^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.InitMembPotential + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IntracellularProperties +^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IntracellularProperties + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IntracellularProperties2CaPools +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IntracellularProperties2CaPools + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Izhikevich2007Cell +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Izhikevich2007Cell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IzhikevichCell +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IzhikevichCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Member +^^^^^^ + +.. autoclass:: neuroml.nml.nml.Member + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +MembraneProperties +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.MembraneProperties + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +MembraneProperties2CaPools +^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.MembraneProperties2CaPools + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Morphology +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Morphology + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Path +^^^^ + +.. autoclass:: neuroml.nml.nml.Path + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +PinskyRinzelCA3Cell +^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.PinskyRinzelCA3Cell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ProximalDetails +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ProximalDetails + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Resistivity +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Resistivity + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Segment +^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Segment + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SegmentGroup +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SegmentGroup + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Species +^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Species + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SpecificCapacitance +^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SpecificCapacitance + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SpikeThresh +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SpikeThresh + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SubTree +^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SubTree + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +VariableParameter +^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.VariableParameter + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/Channels_list.rst b/doc/userdocs/Channels_list.rst new file mode 100644 index 0000000..2f5cdcf --- /dev/null +++ b/doc/userdocs/Channels_list.rst @@ -0,0 +1,153 @@ +Channels +######## + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py + +ClosedState +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ClosedState + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ForwardTransition +^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ForwardTransition + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GateFractional +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateFractional + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GateHHInstantaneous +^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateHHInstantaneous + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GateKS +^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateKS + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IonChannel +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IonChannel + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IonChannelHH +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IonChannelHH + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IonChannelKS +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IonChannelKS + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IonChannelVShift +^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IonChannelVShift + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +OpenState +^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.OpenState + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Q10ConductanceScaling +^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Q10ConductanceScaling + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ReverseTransition +^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ReverseTransition + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +TauInfTransition +^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.TauInfTransition + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/Inputs_list.rst b/doc/userdocs/Inputs_list.rst new file mode 100644 index 0000000..f03a0ea --- /dev/null +++ b/doc/userdocs/Inputs_list.rst @@ -0,0 +1,219 @@ +Inputs +###### + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py + +CompoundInput +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.CompoundInput + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +CompoundInputDL +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.CompoundInputDL + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +PoissonFiringSynapse +^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.PoissonFiringSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +PulseGenerator +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.PulseGenerator + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +PulseGeneratorDL +^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.PulseGeneratorDL + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +RampGenerator +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.RampGenerator + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +RampGeneratorDL +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.RampGeneratorDL + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SineGenerator +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SineGenerator + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SineGeneratorDL +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SineGeneratorDL + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Spike +^^^^^ + +.. autoclass:: neuroml.nml.nml.Spike + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SpikeArray +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SpikeArray + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SpikeGenerator +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SpikeGenerator + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SpikeGeneratorPoisson +^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SpikeGeneratorPoisson + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SpikeGeneratorRandom +^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SpikeGeneratorRandom + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SpikeGeneratorRefPoisson +^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SpikeGeneratorRefPoisson + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +TimedSynapticInput +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.TimedSynapticInput + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +TransientPoissonFiringSynapse +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.TransientPoissonFiringSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +VoltageClamp +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.VoltageClamp + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +VoltageClampTriple +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.VoltageClampTriple + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/Networks_list.rst b/doc/userdocs/Networks_list.rst new file mode 100644 index 0000000..a188dd0 --- /dev/null +++ b/doc/userdocs/Networks_list.rst @@ -0,0 +1,241 @@ +Networks +######## + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py + +Connection +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Connection + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ConnectionWD +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ConnectionWD + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ContinuousConnection +^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ContinuousConnection + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ContinuousConnectionInstance +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ContinuousConnectionInstance + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ContinuousConnectionInstanceW +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ContinuousConnectionInstanceW + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ContinuousProjection +^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ContinuousProjection + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ElectricalConnection +^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ElectricalConnection + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ElectricalConnectionInstance +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ElectricalConnectionInstance + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ElectricalConnectionInstanceW +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ElectricalConnectionInstanceW + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ElectricalProjection +^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ElectricalProjection + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ExplicitInput +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ExplicitInput + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Input +^^^^^ + +.. autoclass:: neuroml.nml.nml.Input + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +InputList +^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.InputList + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +InputW +^^^^^^ + +.. autoclass:: neuroml.nml.nml.InputW + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Instance +^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Instance + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Location +^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Location + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Network +^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Network + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Population +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Population + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Projection +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Projection + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Region +^^^^^^ + +.. autoclass:: neuroml.nml.nml.Region + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SynapticConnection +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SynapticConnection + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/NeuroMLCoreCompTypes_list.rst b/doc/userdocs/NeuroMLCoreCompTypes_list.rst new file mode 100644 index 0000000..a6ca859 --- /dev/null +++ b/doc/userdocs/NeuroMLCoreCompTypes_list.rst @@ -0,0 +1,43 @@ +NeuroMLCoreCompTypes +#################### + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py + +Annotation +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Annotation + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Point3DWithDiam +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Point3DWithDiam + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +Property +^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Property + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/NeuroMLCoreDimensions_list.rst b/doc/userdocs/NeuroMLCoreDimensions_list.rst new file mode 100644 index 0000000..a33bb2c --- /dev/null +++ b/doc/userdocs/NeuroMLCoreDimensions_list.rst @@ -0,0 +1,12 @@ +NeuroMLCoreDimensions +##################### + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py diff --git a/doc/userdocs/Other_list.rst b/doc/userdocs/Other_list.rst new file mode 100644 index 0000000..5496c29 --- /dev/null +++ b/doc/userdocs/Other_list.rst @@ -0,0 +1,12 @@ +Other +##### + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py diff --git a/doc/userdocs/PyNN_list.rst b/doc/userdocs/PyNN_list.rst new file mode 100644 index 0000000..cf7cfc8 --- /dev/null +++ b/doc/userdocs/PyNN_list.rst @@ -0,0 +1,153 @@ +PyNN +#### + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py + +AlphaCondSynapse +^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.AlphaCondSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +AlphaCurrSynapse +^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.AlphaCurrSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BasePynnSynapse +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BasePynnSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +EIF_cond_alpha_isfa_ista +^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.EIF_cond_alpha_isfa_ista + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +EIF_cond_exp_isfa_ista +^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.EIF_cond_exp_isfa_ista + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ExpCondSynapse +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ExpCondSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ExpCurrSynapse +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ExpCurrSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +HH_cond_exp +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.HH_cond_exp + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IF_cond_alpha +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IF_cond_alpha + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IF_cond_exp +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IF_cond_exp + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IF_curr_alpha +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IF_curr_alpha + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +IF_curr_exp +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IF_curr_exp + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SpikeSourcePoisson +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SpikeSourcePoisson + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/Simulation_list.rst b/doc/userdocs/Simulation_list.rst new file mode 100644 index 0000000..79bd500 --- /dev/null +++ b/doc/userdocs/Simulation_list.rst @@ -0,0 +1,12 @@ +Simulation +########## + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py diff --git a/doc/userdocs/Synapses_list.rst b/doc/userdocs/Synapses_list.rst new file mode 100644 index 0000000..9533a47 --- /dev/null +++ b/doc/userdocs/Synapses_list.rst @@ -0,0 +1,186 @@ +Synapses +######## + + + + +This documentation is auto-generated from the `NeuroML schema `__. + + + + +.. Generated using nml-core-docs.py + +AlphaCurrentSynapse +^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.AlphaCurrentSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +AlphaSynapse +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.AlphaSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BaseConductanceBasedSynapse +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BaseConductanceBasedSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BaseConductanceBasedSynapseTwo +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BaseConductanceBasedSynapseTwo + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BaseCurrentBasedSynapse +^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BaseCurrentBasedSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BaseSynapse +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BaseSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BaseVoltageDepSynapse +^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BaseVoltageDepSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +BlockingPlasticSynapse +^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.BlockingPlasticSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +DoubleSynapse +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.DoubleSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ExpOneSynapse +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ExpOneSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ExpThreeSynapse +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ExpThreeSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ExpTwoSynapse +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ExpTwoSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GapJunction +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GapJunction + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GradedSynapse +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GradedSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +LinearGradedSynapse +^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.LinearGradedSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +SilentSynapse +^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.SilentSynapse + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/coreclasses.rst b/doc/userdocs/coreclasses.rst index 275208f..2eed868 100644 --- a/doc/userdocs/coreclasses.rst +++ b/doc/userdocs/coreclasses.rst @@ -42,4 +42,13 @@ This documentation is auto-generated from the `NeuroML schema `__. -.. include:: coreclasses_list.txt +.. toctree:: + :maxdepth: 1 + + Cells_list + Synapses_list + Channels_list + Inputs_list + Networks_list + PyNN_list + NeuroMLCoreCompTypes_list diff --git a/doc/userdocs/coreclasses_list.txt b/doc/userdocs/coreclasses_list.txt deleted file mode 100644 index af542cf..0000000 --- a/doc/userdocs/coreclasses_list.txt +++ /dev/null @@ -1,2218 +0,0 @@ -.. Generated using nml-core-docs.py - -GeneratedsSuperSuper -#################### - -.. autoclass:: neuroml.nml.generatedssupersuper.GeneratedsSuperSuper - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GdsCollector -############ - -.. autoclass:: neuroml.nml.generatedscollector.GdsCollector - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -AdExIaFCell -########### - -.. autoclass:: neuroml.nml.nml.AdExIaFCell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -AlphaCondSynapse -################ - -.. autoclass:: neuroml.nml.nml.AlphaCondSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -AlphaCurrSynapse -################ - -.. autoclass:: neuroml.nml.nml.AlphaCurrSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -AlphaCurrentSynapse -################### - -.. autoclass:: neuroml.nml.nml.AlphaCurrentSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -AlphaSynapse -############ - -.. autoclass:: neuroml.nml.nml.AlphaSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Annotation -########## - -.. autoclass:: neuroml.nml.nml.Annotation - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Base -#### - -.. autoclass:: neuroml.nml.nml.Base - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseCell -######## - -.. autoclass:: neuroml.nml.nml.BaseCell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseCellMembPotCap -################## - -.. autoclass:: neuroml.nml.nml.BaseCellMembPotCap - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseConductanceBasedSynapse -########################### - -.. autoclass:: neuroml.nml.nml.BaseConductanceBasedSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseConductanceBasedSynapseTwo -############################## - -.. autoclass:: neuroml.nml.nml.BaseConductanceBasedSynapseTwo - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseConnection -############## - -.. autoclass:: neuroml.nml.nml.BaseConnection - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseConnectionNewFormat -####################### - -.. autoclass:: neuroml.nml.nml.BaseConnectionNewFormat - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseConnectionOldFormat -####################### - -.. autoclass:: neuroml.nml.nml.BaseConnectionOldFormat - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseCurrentBasedSynapse -####################### - -.. autoclass:: neuroml.nml.nml.BaseCurrentBasedSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseNonNegativeIntegerId -######################## - -.. autoclass:: neuroml.nml.nml.BaseNonNegativeIntegerId - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseProjection -############## - -.. autoclass:: neuroml.nml.nml.BaseProjection - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BasePynnSynapse -############### - -.. autoclass:: neuroml.nml.nml.BasePynnSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseSynapse -########### - -.. autoclass:: neuroml.nml.nml.BaseSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseVoltageDepSynapse -##################### - -.. autoclass:: neuroml.nml.nml.BaseVoltageDepSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BaseWithoutId -############# - -.. autoclass:: neuroml.nml.nml.BaseWithoutId - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BiophysicalProperties -##################### - -.. autoclass:: neuroml.nml.nml.BiophysicalProperties - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BiophysicalProperties2CaPools -############################# - -.. autoclass:: neuroml.nml.nml.BiophysicalProperties2CaPools - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BlockMechanism -############## - -.. autoclass:: neuroml.nml.nml.BlockMechanism - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -BlockingPlasticSynapse -###################### - -.. autoclass:: neuroml.nml.nml.BlockingPlasticSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Case -#### - -.. autoclass:: neuroml.nml.nml.Case - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Cell -#### - -.. autoclass:: neuroml.nml.nml.Cell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Cell2CaPools -############ - -.. autoclass:: neuroml.nml.nml.Cell2CaPools - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -CellSet -####### - -.. autoclass:: neuroml.nml.nml.CellSet - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensity -############## - -.. autoclass:: neuroml.nml.nml.ChannelDensity - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensityGHK -################# - -.. autoclass:: neuroml.nml.nml.ChannelDensityGHK - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensityGHK2 -################## - -.. autoclass:: neuroml.nml.nml.ChannelDensityGHK2 - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensityNernst -#################### - -.. autoclass:: neuroml.nml.nml.ChannelDensityNernst - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensityNernstCa2 -####################### - -.. autoclass:: neuroml.nml.nml.ChannelDensityNernstCa2 - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensityNonUniform -######################## - -.. autoclass:: neuroml.nml.nml.ChannelDensityNonUniform - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensityNonUniformGHK -########################### - -.. autoclass:: neuroml.nml.nml.ChannelDensityNonUniformGHK - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensityNonUniformNernst -############################## - -.. autoclass:: neuroml.nml.nml.ChannelDensityNonUniformNernst - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelDensityVShift -#################### - -.. autoclass:: neuroml.nml.nml.ChannelDensityVShift - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ChannelPopulation -################# - -.. autoclass:: neuroml.nml.nml.ChannelPopulation - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ClosedState -########### - -.. autoclass:: neuroml.nml.nml.ClosedState - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ComponentType -############# - -.. autoclass:: neuroml.nml.nml.ComponentType - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -CompoundInput -############# - -.. autoclass:: neuroml.nml.nml.CompoundInput - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -CompoundInputDL -############### - -.. autoclass:: neuroml.nml.nml.CompoundInputDL - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ConcentrationModel_D -#################### - -.. autoclass:: neuroml.nml.nml.ConcentrationModel_D - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ConditionalDerivedVariable -########################## - -.. autoclass:: neuroml.nml.nml.ConditionalDerivedVariable - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Connection -########## - -.. autoclass:: neuroml.nml.nml.Connection - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ConnectionWD -############ - -.. autoclass:: neuroml.nml.nml.ConnectionWD - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Constant -######## - -.. autoclass:: neuroml.nml.nml.Constant - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ContinuousConnection -#################### - -.. autoclass:: neuroml.nml.nml.ContinuousConnection - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ContinuousConnectionInstance -############################ - -.. autoclass:: neuroml.nml.nml.ContinuousConnectionInstance - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ContinuousConnectionInstanceW -############################# - -.. autoclass:: neuroml.nml.nml.ContinuousConnectionInstanceW - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ContinuousProjection -#################### - -.. autoclass:: neuroml.nml.nml.ContinuousProjection - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -DecayingPoolConcentrationModel -############################## - -.. autoclass:: neuroml.nml.nml.DecayingPoolConcentrationModel - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -DerivedParameter -################ - -.. autoclass:: neuroml.nml.nml.DerivedParameter - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -DerivedVariable -############### - -.. autoclass:: neuroml.nml.nml.DerivedVariable - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -DistalDetails -############# - -.. autoclass:: neuroml.nml.nml.DistalDetails - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -DoubleSynapse -############# - -.. autoclass:: neuroml.nml.nml.DoubleSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Dynamics -######## - -.. autoclass:: neuroml.nml.nml.Dynamics - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -EIF_cond_alpha_isfa_ista -######################## - -.. autoclass:: neuroml.nml.nml.EIF_cond_alpha_isfa_ista - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -EIF_cond_exp_isfa_ista -###################### - -.. autoclass:: neuroml.nml.nml.EIF_cond_exp_isfa_ista - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ElectricalConnection -#################### - -.. autoclass:: neuroml.nml.nml.ElectricalConnection - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ElectricalConnectionInstance -############################ - -.. autoclass:: neuroml.nml.nml.ElectricalConnectionInstance - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ElectricalConnectionInstanceW -############################# - -.. autoclass:: neuroml.nml.nml.ElectricalConnectionInstanceW - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ElectricalProjection -#################### - -.. autoclass:: neuroml.nml.nml.ElectricalProjection - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -EventOut -######## - -.. autoclass:: neuroml.nml.nml.EventOut - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ExpCondSynapse -############## - -.. autoclass:: neuroml.nml.nml.ExpCondSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ExpCurrSynapse -############## - -.. autoclass:: neuroml.nml.nml.ExpCurrSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ExpOneSynapse -############# - -.. autoclass:: neuroml.nml.nml.ExpOneSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ExpThreeSynapse -############### - -.. autoclass:: neuroml.nml.nml.ExpThreeSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ExpTwoSynapse -############# - -.. autoclass:: neuroml.nml.nml.ExpTwoSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ExplicitInput -############# - -.. autoclass:: neuroml.nml.nml.ExplicitInput - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Exposure -######## - -.. autoclass:: neuroml.nml.nml.Exposure - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ExtracellularProperties -####################### - -.. autoclass:: neuroml.nml.nml.ExtracellularProperties - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ExtracellularPropertiesLocal -############################ - -.. autoclass:: neuroml.nml.nml.ExtracellularPropertiesLocal - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -FitzHughNagumo1969Cell -###################### - -.. autoclass:: neuroml.nml.nml.FitzHughNagumo1969Cell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -FitzHughNagumoCell -################## - -.. autoclass:: neuroml.nml.nml.FitzHughNagumoCell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -FixedFactorConcentrationModel -############################# - -.. autoclass:: neuroml.nml.nml.FixedFactorConcentrationModel - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ForwardTransition -################# - -.. autoclass:: neuroml.nml.nml.ForwardTransition - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GapJunction -########### - -.. autoclass:: neuroml.nml.nml.GapJunction - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateFractional -############## - -.. autoclass:: neuroml.nml.nml.GateFractional - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateFractionalSubgate -##################### - -.. autoclass:: neuroml.nml.nml.GateFractionalSubgate - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateHHInstantaneous -################### - -.. autoclass:: neuroml.nml.nml.GateHHInstantaneous - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateHHRates -########### - -.. autoclass:: neuroml.nml.nml.GateHHRates - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateHHRatesInf -############## - -.. autoclass:: neuroml.nml.nml.GateHHRatesInf - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateHHRatesTau -############## - -.. autoclass:: neuroml.nml.nml.GateHHRatesTau - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateHHRatesTauInf -################# - -.. autoclass:: neuroml.nml.nml.GateHHRatesTauInf - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateHHTauInf -############ - -.. autoclass:: neuroml.nml.nml.GateHHTauInf - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateHHUndetermined -################## - -.. autoclass:: neuroml.nml.nml.GateHHUndetermined - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GateKS -###### - -.. autoclass:: neuroml.nml.nml.GateKS - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GeneratedsSuper -############### - -.. autoclass:: neuroml.nml.nml.GeneratedsSuper - :show-inheritance: - - - -GradedSynapse -############# - -.. autoclass:: neuroml.nml.nml.GradedSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -GridLayout -########## - -.. autoclass:: neuroml.nml.nml.GridLayout - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -HHRate -###### - -.. autoclass:: neuroml.nml.nml.HHRate - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -HHTime -###### - -.. autoclass:: neuroml.nml.nml.HHTime - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -HHVariable -########## - -.. autoclass:: neuroml.nml.nml.HHVariable - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -HH_cond_exp -########### - -.. autoclass:: neuroml.nml.nml.HH_cond_exp - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IF_cond_alpha -############# - -.. autoclass:: neuroml.nml.nml.IF_cond_alpha - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IF_cond_exp -########### - -.. autoclass:: neuroml.nml.nml.IF_cond_exp - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IF_curr_alpha -############# - -.. autoclass:: neuroml.nml.nml.IF_curr_alpha - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IF_curr_exp -########### - -.. autoclass:: neuroml.nml.nml.IF_curr_exp - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IafCell -####### - -.. autoclass:: neuroml.nml.nml.IafCell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IafRefCell -########## - -.. autoclass:: neuroml.nml.nml.IafRefCell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IafTauCell -########## - -.. autoclass:: neuroml.nml.nml.IafTauCell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IafTauRefCell -############# - -.. autoclass:: neuroml.nml.nml.IafTauRefCell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Include -####### - -.. autoclass:: neuroml.nml.nml.Include - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IncludeType -########### - -.. autoclass:: neuroml.nml.nml.IncludeType - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -InhomogeneousParameter -###################### - -.. autoclass:: neuroml.nml.nml.InhomogeneousParameter - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -InhomogeneousValue -################## - -.. autoclass:: neuroml.nml.nml.InhomogeneousValue - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -InitMembPotential -################# - -.. autoclass:: neuroml.nml.nml.InitMembPotential - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Input -##### - -.. autoclass:: neuroml.nml.nml.Input - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -InputList -######### - -.. autoclass:: neuroml.nml.nml.InputList - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -InputW -###### - -.. autoclass:: neuroml.nml.nml.InputW - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Instance -######## - -.. autoclass:: neuroml.nml.nml.Instance - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -InstanceRequirement -################### - -.. autoclass:: neuroml.nml.nml.InstanceRequirement - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IntracellularProperties -####################### - -.. autoclass:: neuroml.nml.nml.IntracellularProperties - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IntracellularProperties2CaPools -############################### - -.. autoclass:: neuroml.nml.nml.IntracellularProperties2CaPools - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IonChannel -########## - -.. autoclass:: neuroml.nml.nml.IonChannel - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IonChannelHH -############ - -.. autoclass:: neuroml.nml.nml.IonChannelHH - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IonChannelKS -############ - -.. autoclass:: neuroml.nml.nml.IonChannelKS - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IonChannelScalable -################## - -.. autoclass:: neuroml.nml.nml.IonChannelScalable - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IonChannelVShift -################ - -.. autoclass:: neuroml.nml.nml.IonChannelVShift - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Izhikevich2007Cell -################## - -.. autoclass:: neuroml.nml.nml.Izhikevich2007Cell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -IzhikevichCell -############## - -.. autoclass:: neuroml.nml.nml.IzhikevichCell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -LEMS_Property -############# - -.. autoclass:: neuroml.nml.nml.LEMS_Property - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Layout -###### - -.. autoclass:: neuroml.nml.nml.Layout - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -LinearGradedSynapse -################### - -.. autoclass:: neuroml.nml.nml.LinearGradedSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Location -######## - -.. autoclass:: neuroml.nml.nml.Location - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Member -###### - -.. autoclass:: neuroml.nml.nml.Member - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -MembraneProperties -################## - -.. autoclass:: neuroml.nml.nml.MembraneProperties - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -MembraneProperties2CaPools -########################## - -.. autoclass:: neuroml.nml.nml.MembraneProperties2CaPools - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Morphology -########## - -.. autoclass:: neuroml.nml.nml.Morphology - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -NamedDimensionalType -#################### - -.. autoclass:: neuroml.nml.nml.NamedDimensionalType - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -NamedDimensionalVariable -######################## - -.. autoclass:: neuroml.nml.nml.NamedDimensionalVariable - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Network -####### - -.. autoclass:: neuroml.nml.nml.Network - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -NeuroMLDocument -############### - -.. autoclass:: neuroml.nml.nml.NeuroMLDocument - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -OnCondition -########### - -.. autoclass:: neuroml.nml.nml.OnCondition - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -OnEntry -####### - -.. autoclass:: neuroml.nml.nml.OnEntry - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -OnEvent -####### - -.. autoclass:: neuroml.nml.nml.OnEvent - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -OnStart -####### - -.. autoclass:: neuroml.nml.nml.OnStart - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -OpenState -######### - -.. autoclass:: neuroml.nml.nml.OpenState - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Parameter -######### - -.. autoclass:: neuroml.nml.nml.Parameter - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Path -#### - -.. autoclass:: neuroml.nml.nml.Path - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -PinskyRinzelCA3Cell -################### - -.. autoclass:: neuroml.nml.nml.PinskyRinzelCA3Cell - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -PlasticityMechanism -################### - -.. autoclass:: neuroml.nml.nml.PlasticityMechanism - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Point3DWithDiam -############### - -.. autoclass:: neuroml.nml.nml.Point3DWithDiam - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -PoissonFiringSynapse -#################### - -.. autoclass:: neuroml.nml.nml.PoissonFiringSynapse - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Population -########## - -.. autoclass:: neuroml.nml.nml.Population - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Projection -########## - -.. autoclass:: neuroml.nml.nml.Projection - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Property -######## - -.. autoclass:: neuroml.nml.nml.Property - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ProximalDetails -############### - -.. autoclass:: neuroml.nml.nml.ProximalDetails - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -PulseGenerator -############## - -.. autoclass:: neuroml.nml.nml.PulseGenerator - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -PulseGeneratorDL -################ - -.. autoclass:: neuroml.nml.nml.PulseGeneratorDL - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Q10ConductanceScaling -##################### - -.. autoclass:: neuroml.nml.nml.Q10ConductanceScaling - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Q10Settings -########### - -.. autoclass:: neuroml.nml.nml.Q10Settings - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -RampGenerator -############# - -.. autoclass:: neuroml.nml.nml.RampGenerator - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -RampGeneratorDL -############### - -.. autoclass:: neuroml.nml.nml.RampGeneratorDL - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -RandomLayout -############ - -.. autoclass:: neuroml.nml.nml.RandomLayout - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ReactionScheme -############## - -.. autoclass:: neuroml.nml.nml.ReactionScheme - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Regime -###### - -.. autoclass:: neuroml.nml.nml.Regime - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Region -###### - -.. autoclass:: neuroml.nml.nml.Region - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Requirement -########### - -.. autoclass:: neuroml.nml.nml.Requirement - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Resistivity -########### - -.. autoclass:: neuroml.nml.nml.Resistivity - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -ReverseTransition -################# - -.. autoclass:: neuroml.nml.nml.ReverseTransition - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -Segment -####### - -.. autoclass:: neuroml.nml.nml.Segment - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -SegmentEndPoint -############### - -.. autoclass:: neuroml.nml.nml.SegmentEndPoint - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - - - -SegmentGroup -############ - -.. autoclass:: neuroml.nml.nml.SegmentGroup - :members: - :undoc-members: - :show-inheritance: - :inherited-members: - 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