Modigliani  2.0
A stochastic simulator for axons, neurons, and networks
Public Member Functions | List of all members
modigliani_core::Spherical_compartment Class Reference

This class simulates a spherical Hodgkin-Huxley neuron. More...

+ Inheritance diagram for modigliani_core::Spherical_compartment:

Public Member Functions

 Spherical_compartment (modigliani_base::Real radius, modigliani_base::Real cM)
 Constructs a new spherical compartment. More...
 
 Spherical_compartment (boost::property_tree::ptree compartment_parameters)
 Constructs a new spherical compartment using parameters given in a ptree. More...
 
modigliani_base::Real radius () const
 Returns the radius. More...
 
- Public Member Functions inherited from modigliani_core::Membrane_compartment
 Membrane_compartment (const modigliani_base::Real newArea, const modigliani_base::Real newTemperature, const modigliani_base::Real newCm, const modigliani_base::Real newRa)
 Constructor. More...
 
virtual modigliani_base::ReturnEnum AttachCurrent (Membrane_current *currentPtr, CurrentType type=IONIC)
 Adds a new current to the compartment. More...
 
virtual modigliani_base::ReturnEnum Step (const modigliani_base::Real newVM)
 Sets the membrane potential to the specified value and runs of step of simulation. More...
 
virtual modigliani_base::ReturnEnum Step ()
 Sets the membrane potential according to membrane current and runs of step of simulation. More...
 
modigliani_base::ReturnEnum InjectCurrent (modigliani_base::Real current)
 Injects current into the compartment. More...
 
modigliani_base::Real AttachedConductance (modigliani_base::Size currentIndex)
 Returns the current conductance of the attached conductance source. More...
 
modigliani_base::Real AttachedReversalPotential (modigliani_base::Size currentIndex)
 Returns the reversal potential of the attached conductance source. More...
 
virtual modigliani_base::ReturnEnum SetupOutput (std::string output_file_name)
 Opens an output file and writes the header. More...
 
virtual modigliani_base::ReturnEnum WriteOutput () const
 Writes the current flwoing through all attached Membrane_current instances to a binary file. More...
 
modigliani_base::Real TimeConstant () const
 Membrane time constant at instaneous membrane conductivity. More...
 
const Membrane_currentCurrent (modigliani_base::Size currentIndex) const
 Returns the current object at the given index. More...
 
modigliani_base::Real area () const
 Returns the membrane surface area. More...
 
modigliani_base::Real vm () const
 Returns the membrane potential. More...
 
void set_vm (modigliani_base::Real newVoltage)
 Sets the membrane potential. More...
 
modigliani_base::Real cm () const
 Sets the membrane capacitance per surface area. More...
 
modigliani_base::Real ra () const
 Sets the axial resistance. More...
 
virtual modigliani_base::ReturnEnum set_temperature (modigliani_base::Real newTemp)
 Set temperature in compartment and for all currents within the compartments. More...
 
modigliani_base::Real temperature () const
 Returns temperature in compartment. More...
 
modigliani_base::Real CompartmentMembraneCapacitance () const
 Returns total compartment capacitance. More...
 
modigliani_base::Real CompartmentMembraneNetCurrent () const
 Returns net membrane current. More...
 
modigliani_base::Real CompartmentChannelStateTimeConstant () const
 Sum of escape rates from current state. More...
 
bool GillespieStep ()
 Perform one step of the Gillespie algorithm. More...
 
modigliani_base::Size NumberCurrents () const
 Returns the number of currents attached to the compartment. More...
 
modigliani_base::Real WeightedConductance () const
 Returns the sum of attached conductance weighted by the difference between the membrane potential and the reversal potential. More...
 
const std::vector
< Membrane_current * > 
current_vec () const
 Returns the vector of attached currents. More...
 
- Public Member Functions inherited from modigliani_core::Object
modigliani_base::Real timestep () const
 Returns simulation timestep. More...
 
void set_timestep (modigliani_base::Real newTimeStep)
 Sets simulation timestep. More...
 

Detailed Description

This class simulates a spherical Hodgkin-Huxley neuron.

Constructor & Destructor Documentation

modigliani_core::Spherical_compartment::Spherical_compartment ( modigliani_base::Real  radius,
modigliani_base::Real  cM 
)

Constructs a new spherical compartment.

Parameters
radiusRadius in [ $\si{\micro\meter}$]
cMMembrane capacitance in [ $\si{\micro\farad\per\centi\meter\squared}$]
modigliani_core::Spherical_compartment::Spherical_compartment ( boost::property_tree::ptree  compartment_parameters)
explicit

Constructs a new spherical compartment using parameters given in a ptree.

Parameters
compartment_parametersptree containing parameters necessary for the compartment. The ptree is expected to contain the following values :
  • double radius Radius in [ $\si{\micro\meter}$]
  • double Cm Membrane capacitance in [ $\si{\micro\farad\per\centi\meter\squared}$]
  • double Ra Axoplasmic resistance in [ $\si{\ohm\centi\meter}$]

Member Function Documentation

modigliani_base::Real modigliani_core::Spherical_compartment::radius ( ) const
inline

Returns the radius.

Returns
Radius in [ $\si{\micro\meter}$]

The documentation for this class was generated from the following files: