emodelrunner.factsheets.ion_channel_mechanisms¶
To extract ion channel mechanisms information from static parameter files.
Functions
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Append equation to location map dict. |
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Remove empty locations. |
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Edit function expression to be latex and plot readable. |
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Returns the channel and a dictionary containing equation type (uniform or exp) and value. |
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Return a dictionary containing channel mechanisms for each section. |
- emodelrunner.factsheets.ion_channel_mechanisms.append_equation(location_map, section, channel, biophys, equation_dict)[source]¶
Append equation to location map dict.
- Parameters:
location_map (dict) – contains the equations for each channel at each location. To be filled by this function
section (str) – the section(s) to which the equations should be appended Can be “alldend”, “somadend”, “somaxon”, “allact”, “apical”, “basal”, “axonal” or “somatic”
channel (str) – name of the channel (ex: “Ca_HVA2”)
biophys (str) – parameter name (ex: “gCa_HVAbar”)
equation_dict (dict) – dictionary containing equation values (for plotting and latex display) and type (uniform or exponential)
- emodelrunner.factsheets.ion_channel_mechanisms.clean_location_map(location_map)[source]¶
Remove empty locations.
- Parameters:
location_map (dict) – contains the equations for each channel at each location
- emodelrunner.factsheets.ion_channel_mechanisms.edit_dist_func(value)[source]¶
Edit function expression to be latex and plot readable.
- Parameters:
value (str) – the distribution function expressed as a string. ex: “(-0.8696 + 2.087*math.exp((x)*0.0031))*3.1236056887012746e-06”
- Returns:
a tuple containing
latex (str): a latex-compatible version of the distrib. function ex: “(-0.8696 + 2.087*e^{x*0.0031})*3.1236056887012746e-06”
value (str): a plottable version of the distrib. function ex: “(-0.8696 + 2.087exp(x*0.0031))*3.1236056887012746e-06”
- emodelrunner.factsheets.ion_channel_mechanisms.get_channel_and_equations(name, param_config, full_name, exp_fun, decay_fun, release_params)[source]¶
Returns the channel and a dictionary containing equation type (uniform or exp) and value.
- Parameters:
name (str) – the name of the ion channel and its parameter. should have the form parameter_channel (ex: “gCa_HVAbar_Ca_HVA2”)
param_config (dict) – parameter dictionary taken from parameter data file. should have a “dist” key if the distribution is exponential.
full_name (str) – should have the form name.section
exp_fun (str) – the distribution function expressed as a string. ex: “(-0.8696 + 2.087*math.exp((x)*0.0031))*3.1236056887012746e-06”
decay_fun (str) – the decay function expressed as a string.
release_params (dict) – final parameters of the optimised cell.
- Returns:
a tuple containing
channel (str): name of the channel (ex: “Ca_HVA2”)
biophys (str): parameter name (ex: “gCa_HVAbar”)
equation_dict (dict): contains equation values and equation type (uniform or exp)
- emodelrunner.factsheets.ion_channel_mechanisms.get_mechanisms_data(emodel, optimized_params_dict, unoptimized_params_dict)[source]¶
Return a dictionary containing channel mechanisms for each section.
- Parameters:
emodel (str) – name of the emodel
optimized_params_dict (dict) – contains the optimized parameters
unoptimized_params_dict (dict) – contains the unoptimized parameters, and also contains the decay and exponential equations
- Returns:
containing the channel mechanisms
- Return type:
dict