biophysics Package

biophysics Package

class CellBiophysics(cell)[source]

Bases: object

__init__(cell)[source]
add_channel(channel, targetter, applicator)[source]
add_passive(passiveproperty, targetter, value)[source]
apply_channel(channel, where=None, parameter_overrides=None, parameter_multipliers=None)[source]

A simplified interface to applying channels.

get_all_channels_applied_to_cell()[source]
get_applied_mtas()[source]
get_applied_passives()[source]
get_channel(name)[source]
get_passive_property_for_section(section, passive)[source]
get_passives_for_section(section)[source]
get_resolved_mtas_for_section(section)[source]
set_passive(passiveproperty, value, where=None)[source]
class Channel(**kwargs)[source]

Bases: morphforge.simulation.base.base_classes.NamedSimulationObject

__init__(**kwargs)[source]
get_default(key)[source]
get_defaults()[source]
get_variables()[source]
class PassiveProperty[source]

Bases: object

AxialResistance = 'AxialResistance'
SpecificCapacitance = 'SpecificCapacitance'
all = ['SpecificCapacitance', 'AxialResistance']
defaults = {'SpecificCapacitance': <Mock object at 0x7f0a90086890>, 'AxialResistance': <Mock object at 0x7f0a90086810>}
class ChannelApplicator[source]

Bases: object

__init__()[source]
get_description()[source]
get_variable_value_for_section(variablename, section)[source]
get_variables_overriden()[source]
set_target_channel(target_channel)[source]
class ChannelApplicatorUniform(parameter_multipliers=None, parameter_overrides=None)[source]

Bases: morphforge.simulation.base.biophysics.channelapplicators.ChannelApplicator

__init__(parameter_multipliers=None, parameter_overrides=None)[source]
get_description()[source]
get_variable_value_for_section(variable_name, section)[source]
get_variables_overriden()[source]
class Targeter(priority, **kwargs)[source]

Bases: object

__init__(priority, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
get_priority()[source]
class PassiveTargetterEverywhereDefault(priority=0, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=0, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class PassiveTargetterEverywhere(priority=5, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=5, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class PassiveTargetterRegion(region, priority=10, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(region, priority=10, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterEverywhere(priority=10, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=10, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterRegion(region, priority=20, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(region, priority=20, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterSection(section, priority=40, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(section, priority=40, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterSectionPath(priority, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

does_target_section(section)[source]
get_description()[source]

cellbiophysics Module

class CellBiophysics(cell)[source]

Bases: object

__init__(cell)[source]
add_channel(channel, targetter, applicator)[source]
add_passive(passiveproperty, targetter, value)[source]
apply_channel(channel, where=None, parameter_overrides=None, parameter_multipliers=None)[source]

A simplified interface to applying channels.

get_all_channels_applied_to_cell()[source]
get_applied_mtas()[source]
get_applied_passives()[source]
get_channel(name)[source]
get_passive_property_for_section(section, passive)[source]
get_passives_for_section(section)[source]
get_resolved_mtas_for_section(section)[source]
set_passive(passiveproperty, value, where=None)[source]
class _MechanismTargetApplicator(channel, targetter, applicator)[source]

Bases: object

__init__(channel, targetter, applicator)[source]
class _PassiveTargetApplicator(passiveproperty, targetter, value)[source]

Bases: object

__init__(passiveproperty, targetter, value)[source]

channel Module

class Channel(**kwargs)[source]

Bases: morphforge.simulation.base.base_classes.NamedSimulationObject

__init__(**kwargs)[source]
get_default(key)[source]
get_defaults()[source]
get_variables()[source]

channelapplicators Module

class ChannelApplicator[source]

Bases: object

__init__()[source]
get_description()[source]
get_variable_value_for_section(variablename, section)[source]
get_variables_overriden()[source]
set_target_channel(target_channel)[source]
class ChannelApplicatorUniform(parameter_multipliers=None, parameter_overrides=None)[source]

Bases: morphforge.simulation.base.biophysics.channelapplicators.ChannelApplicator

__init__(parameter_multipliers=None, parameter_overrides=None)[source]
get_description()[source]
get_variable_value_for_section(variable_name, section)[source]
get_variables_overriden()[source]

channeltargetters Module

class ChannelTargeterEverywhere(priority=10, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=10, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterRegion(region, priority=20, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(region, priority=20, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterSection(section, priority=40, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(section, priority=40, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterSectionPath(priority, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

does_target_section(section)[source]
get_description()[source]
class PassiveTargetterEverywhere(priority=5, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=5, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class PassiveTargetterEverywhereDefault(priority=0, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=0, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class PassiveTargetterRegion(region, priority=10, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(region, priority=10, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class Targeter(priority, **kwargs)[source]

Bases: object

__init__(priority, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
get_priority()[source]

passiveproperties Module

class PassiveProperty[source]

Bases: object

AxialResistance = 'AxialResistance'
SpecificCapacitance = 'SpecificCapacitance'
all = ['SpecificCapacitance', 'AxialResistance']
defaults = {'SpecificCapacitance': <Mock object at 0x7f0a90086890>, 'AxialResistance': <Mock object at 0x7f0a90086810>}