PulseSubstances Class Reference

Manages and initializes all systems with substances needed by Pulse. More...

#include <Substances.h>

Inherits SESubstanceManager.

Public Member Functions
	PulseSubstances (PulseData &data)
virtual	~PulseSubstances ()=default
virtual void	Clear ()
virtual bool	LoadSubstanceDirectory (const std::string &data_dir=".")
virtual bool	Setup ()
virtual void	InitializeSubstances ()
virtual void	AddActiveSubstance (const SESubstance &substance)
virtual bool	IsActive (const SESubstance &sub) const
SESubstance &	GetO2 ()
SESubstance &	GetCO ()
SESubstance &	GetCO2 ()
SESubstance &	GetN2 ()
SESubstance &	GetHb ()
SESubstance &	GetHbO2 ()
SESubstance &	GetHbCO2 ()
SESubstance &	GetHbCO ()
SESubstance &	GetHbO2CO2 ()
SESubstance &	GetHCO3 ()
SESubstance &	GetEpi ()
SESubstance &	GetAcetoacetate ()
SESubstance &	GetAlbumin ()
SESubstance &	GetBicarbonate ()
SESubstance &	GetCalcium ()
SESubstance &	GetChloride ()
SESubstance &	GetCreatinine ()
SESubstance &	GetGlobulin ()
SESubstance &	GetGlucose ()
SESubstance &	GetInsulin ()
SESubstance &	GetLactate ()
SESubstance &	GetPotassium ()
SESubstance &	GetTristearin ()
SESubstance &	GetSodium ()
SESubstance &	GetUrea ()
void	CalculateGenericClearance (double volumeCleared_mL, SELiquidCompartment &cmpt, SESubstance &sub, SEScalarMass *cleared=nullptr)
	Calculates the substance mass cleared for a node. More...
void	CalculateGenericClearance (double volumeCleared_mL, SETissueCompartment &cmpt, SESubstance &sub, SEScalarMass *cleared=nullptr)
	Calculates the substance mass cleared for a tissue compartment based on a volume. More...
void	CalculateGenericExcretion (double VascularFlow_mL_Per_s, SETissueCompartment &cmpt, SESubstance &sub, double FractionExcreted, double timestep_s, SEScalarMass *excreted=nullptr)
	Calculates the substance mass excreted for a compartment. More...
const SizeIndependentDepositionEfficencyCoefficient &	GetSizeIndependentDepositionEfficencyCoefficient (const SESubstance &substance)
double	GetSubstanceMass (SESubstance &, const std::vector< SELiquidCompartment *> &, const MassUnit &unit)
double	GetSubstanceMass (SESubstance &, const std::vector< SETissueCompartment *> &, const MassUnit &unit)
void	WriteBloodGases ()
void	WritePulmonaryGases ()
void	ProbeBloodGases (SELiquidCompartment &cmpt, const std::string &prefix="")
Public Member Functions inherited from SESubstanceManager
	SESubstanceManager (Logger *logger)
virtual	~SESubstanceManager ()
virtual const std::vector< SESubstance * > &	GetSubstances ()
virtual const std::vector< const SESubstance * > &	GetSubstances () const
virtual bool	HasSubstance (const std::string &name) const
virtual SESubstance *	GetSubstance (const std::string &name)
virtual const SESubstance *	GetSubstance (const std::string &name) const
virtual const std::vector< SESubstance * > &	GetActiveSubstances ()
virtual const std::vector< const SESubstance * > &	GetActiveSubstances () const
virtual void	RemoveActiveSubstance (const SESubstance &substance)
virtual void	RemoveActiveSubstances (const std::vector< SESubstance *> &substances)
virtual void	RemoveActiveSubstances ()
virtual const std::vector< SESubstance * > &	GetActiveGases ()
virtual const std::vector< const SESubstance * > &	GetActiveGases () const
virtual const std::vector< SESubstance * > &	GetActiveLiquids ()
virtual const std::vector< const SESubstance * > &	GetActiveLiquids () const
virtual const std::vector< SESubstanceCompound * > &	GetCompounds ()
virtual const std::vector< const SESubstanceCompound * > &	GetCompounds () const
virtual bool	HasCompound (const std::string &name) const
virtual SESubstanceCompound *	GetCompound (const std::string &name)
virtual const SESubstanceCompound *	GetCompound (const std::string &name) const
virtual bool	IsActive (const SESubstanceCompound &compound) const
virtual const std::vector< SESubstanceCompound * > &	GetActiveCompounds ()
virtual const std::vector< const SESubstanceCompound * > &	GetActiveCompounds () const
virtual void	AddActiveCompound (const SESubstanceCompound &compound)
virtual void	RemoveActiveCompound (const SESubstanceCompound &compound)
virtual void	RemoveActiveCompounds (const std::vector< SESubstanceCompound *> &compounds)
Public Member Functions inherited from Loggable
	Loggable (Logger *logger=nullptr)
	Loggable (std::string const &logfile)
virtual	~Loggable ()
virtual Logger *	GetLogger () const
virtual void	SetLogger (Logger &logger)
virtual void	Debug (std::string const &msg, std::string const &origin=empty) const
virtual void	Debug (std::stringstream &msg, std::string const &origin=empty) const
virtual void	Debug (std::ostream &msg, std::string const &origin=empty) const
virtual void	Info (std::string const &msg, std::string const &origin=empty) const
virtual void	Info (std::stringstream &msg, std::string const &origin=empty) const
virtual void	Info (const std::stringstream &msg, std::string const &origin=empty) const
virtual void	Info (std::ostream &msg, std::string const &origin=empty) const
virtual void	Warning (std::string const &msg, std::string const &origin=empty) const
virtual void	Warning (std::stringstream &msg, std::string const &origin=empty) const
virtual void	Warning (std::ostream &msg, std::string const &origin=empty) const
virtual void	Error (std::string const &msg, std::string const &origin=empty) const
virtual void	Error (std::stringstream &msg, std::string const &origin=empty) const
virtual void	Error (std::ostream &msg, std::string const &origin=empty) const
virtual void	Fatal (std::string const &msg, std::string const &origin=empty) const
virtual void	Fatal (std::stringstream &msg, std::string const &origin=empty) const
virtual void	Fatal (std::ostream &msg, std::string const &origin=empty) const
std::string	to_string (int i)
std::string	to_string (unsigned int i)
std::string	to_string (size_t t)
std::string	to_string (float f)
std::string	to_string (double d)

Protected Member Functions
virtual void	InitializeGasCompartments ()
virtual void	InitializeLiquidCompartmentGases ()
virtual void	InitializeLiquidCompartmentNonGases ()
virtual void	InitializeBloodGases (SETissueCompartment &tissue, SELiquidCompartment &vascular)
virtual void	InitializeBloodGases (SELiquidCompartment &cmpt, double Hb_total_mM, double O2_sat, double O2_mmol_Per_L, double CO2_sat, double CO2_mmol_Per_L, double HCO3_mmol_Per_L, double pH, bool distribute=true)
void	SetSubstanceMolarity (SESubstance &, const std::vector< SELiquidCompartment *> &, const SEScalarAmountPerVolume &molarity)
void	SetSubstanceMolarity (SESubstance &, const std::vector< SETissueCompartment *> &, const SEScalarAmountPerVolume &molarity)
void	SetSubstanceMolarity (SESubstance &, const std::vector< SETissueCompartment *> &, const SEScalarAmountPerVolume &extracellular, const SEScalarAmountPerVolume &intracellular)
void	SetSubstanceConcentration (SESubstance &, const std::vector< SELiquidCompartment *> &, const SEScalarMassPerVolume &concentration)
void	SetSubstanceConcentration (SESubstance &, const std::vector< SETissueCompartment *> &, const SEScalarMassPerVolume &concentration)
void	SetSubstanceConcentration (SESubstance &, const std::vector< SETissueCompartment *> &, const SEScalarMassPerVolume &extracellular, const SEScalarMassPerVolume &intracellular)

Protected Attributes
SESubstance *	m_O2
SESubstance *	m_CO
SESubstance *	m_CO2
SESubstance *	m_N2
SESubstance *	m_Hb
SESubstance *	m_HbO2
SESubstance *	m_HbCO2
SESubstance *	m_HbCO
SESubstance *	m_HbO2CO2
SESubstance *	m_HCO3
SESubstance *	m_epi
SESubstance *	m_acetoacetate
SESubstance *	m_albumin
SESubstance *	m_calcium
SESubstance *	m_chloride
SESubstance *	m_creatinine
SESubstance *	m_globulin
SESubstance *	m_glucose
SESubstance *	m_insulin
SESubstance *	m_lactate
SESubstance *	m_tristearin
SESubstance *	m_potassium
SESubstance *	m_sodium
SESubstance *	m_urea
bool	m_isCOActive
std::map< const SESubstance *, SizeIndependentDepositionEfficencyCoefficient * >	m_SIDECoefficients
PulseData &	m_data
Protected Attributes inherited from SESubstanceManager
std::vector< SESubstance * >	m_Substances
std::vector< const SESubstance * >	m_cSubstances
std::vector< SESubstance * >	m_ActiveSubstances
std::vector< const SESubstance * >	m_cActiveSubstances
std::vector< SESubstance * >	m_ActiveGases
std::vector< const SESubstance * >	m_cActiveGases
std::vector< SESubstance * >	m_ActiveLiquids
std::vector< const SESubstance * >	m_cActiveLiquids
std::vector< SESubstanceCompound * >	m_Compounds
std::vector< const SESubstanceCompound * >	m_cCompounds
std::vector< SESubstanceCompound * >	m_ActiveCompounds
std::vector< const SESubstanceCompound * >	m_cActiveCompounds
Protected Attributes inherited from Loggable
bool	myLogger
Logger *	m_Logger

Friends
class	PulseEngineTest

Additional Inherited Members
Static Public Attributes inherited from Loggable
static const std::string	empty

Detailed Description

Manages and initializes all systems with substances needed by Pulse.

Constructor & Destructor Documentation

PulseSubstances()

PulseSubstances::PulseSubstances

(

PulseData &

data

)

~PulseSubstances()

virtual PulseSubstances::~PulseSubstances ( )

virtualdefault

Member Function Documentation

AddActiveSubstance()

void PulseSubstances::AddActiveSubstance ( const SESubstance &  substance )

virtual

Reimplemented from SESubstanceManager.

CalculateGenericClearance() [1/2]

void PulseSubstances::CalculateGenericClearance	(	double	volumeCleared_mL,
		SELiquidCompartment &	cmpt,
		SESubstance &	sub,
		SEScalarMass *	cleared = nullptr
	)

Calculates the substance mass cleared for a node.

---

The volume cleared, the compartment, and the substance are provided to clear the mass of the substance from the node. This generic methodology can be used by other systems to calculate the mass cleared.

CalculateGenericClearance() [2/2]

void PulseSubstances::CalculateGenericClearance	(	double	VolumeCleared_mL,
		SETissueCompartment &	tissue,
		SESubstance &	sub,
		SEScalarMass *	cleared = nullptr
	)

Calculates the substance mass cleared for a tissue compartment based on a volume.

---

Parameters

VolumeCleared_mL	the volume of fluid cleared of a substance by some process
tissue	a tissue compartment
sub	a substance
cleared	mass cleared

The volume cleared, the compartment, and the substance are provided to clear the mass of the substance from the node. This generic methodology can be used by other systems to calculate the mass cleared.

CalculateGenericExcretion()

void PulseSubstances::CalculateGenericExcretion	(	double	VascularFlow_mL_Per_s,
		SETissueCompartment &	tissue,
		SESubstance &	sub,
		double	FractionExcreted,
		double	timestep_s,
		SEScalarMass *	excreted = nullptr
	)

Calculates the substance mass excreted for a compartment.

---

The volume cleared, the compartment, and the substance are provided to clear the mass of the substance from the node. This generic methodology can be used by other systems to calculate the mass excreted.

Clear()

void PulseSubstances::Clear ( )

virtual

Reimplemented from SESubstanceManager.

GetAcetoacetate()

SESubstance& PulseSubstances::GetAcetoacetate ( )

inline

GetAlbumin()

SESubstance& PulseSubstances::GetAlbumin ( )

inline

GetBicarbonate()

SESubstance& PulseSubstances::GetBicarbonate ( )

inline

GetCalcium()

SESubstance& PulseSubstances::GetCalcium ( )

inline

GetChloride()

SESubstance& PulseSubstances::GetChloride ( )

inline

GetCO()

SESubstance& PulseSubstances::GetCO ( )

inline

GetCO2()

SESubstance& PulseSubstances::GetCO2 ( )

inline

GetCreatinine()

SESubstance& PulseSubstances::GetCreatinine ( )

inline

GetEpi()

SESubstance& PulseSubstances::GetEpi ( )

inline

GetGlobulin()

SESubstance& PulseSubstances::GetGlobulin ( )

inline

GetGlucose()

SESubstance& PulseSubstances::GetGlucose ( )

inline

GetHb()

SESubstance& PulseSubstances::GetHb ( )

inline

GetHbCO()

SESubstance& PulseSubstances::GetHbCO ( )

inline

GetHbCO2()

SESubstance& PulseSubstances::GetHbCO2 ( )

inline

GetHbO2()

SESubstance& PulseSubstances::GetHbO2 ( )

inline

GetHbO2CO2()

SESubstance& PulseSubstances::GetHbO2CO2 ( )

inline

GetHCO3()

SESubstance& PulseSubstances::GetHCO3 ( )

inline

GetInsulin()

SESubstance& PulseSubstances::GetInsulin ( )

inline

GetLactate()

SESubstance& PulseSubstances::GetLactate ( )

inline

GetN2()

SESubstance& PulseSubstances::GetN2 ( )

inline

GetO2()

SESubstance& PulseSubstances::GetO2 ( )

inline

GetPotassium()

SESubstance& PulseSubstances::GetPotassium ( )

inline

GetSizeIndependentDepositionEfficencyCoefficient()

const SizeIndependentDepositionEfficencyCoefficient & PulseSubstances::GetSizeIndependentDepositionEfficencyCoefficient

(

const SESubstance &

substance

)

GetSodium()

SESubstance& PulseSubstances::GetSodium ( )

inline

GetSubstanceMass() [1/2]

double PulseSubstances::GetSubstanceMass	(	SESubstance &	sub,
		const std::vector< SELiquidCompartment *> &	cmpts,
		const MassUnit &	unit
	)

GetSubstanceMass() [2/2]

double PulseSubstances::GetSubstanceMass	(	SESubstance &	sub,
		const std::vector< SETissueCompartment *> &	cmpts,
		const MassUnit &	unit
	)

GetTristearin()

SESubstance& PulseSubstances::GetTristearin ( )

inline

GetUrea()

SESubstance& PulseSubstances::GetUrea ( )

inline

InitializeBloodGases() [1/2]

void PulseSubstances::InitializeBloodGases ( SETissueCompartment &  tissue, SELiquidCompartment &  vascular  )

protectedvirtual

InitializeBloodGases() [2/2]

void PulseSubstances::InitializeBloodGases ( SELiquidCompartment &  cmpt, double  Hb_total_mM, double  O2_sat, double  O2_mmol_Per_L, double  CO2_sat, double  CO2_mmol_Per_L, double  HCO3_mmol_Per_L, double  pH, bool  distribute = true  )

protectedvirtual

InitializeGasCompartments()

void PulseSubstances::InitializeGasCompartments ( )

protectedvirtual

InitializeLiquidCompartmentGases()

void PulseSubstances::InitializeLiquidCompartmentGases ( )

protectedvirtual

InitializeLiquidCompartmentNonGases()

void PulseSubstances::InitializeLiquidCompartmentNonGases ( )

protectedvirtual

Todo:

Tristearin is actually all triacylglycerols. Change name.

InitializeSubstances()

void PulseSubstances::InitializeSubstances ( )

virtual

IsActive()

bool PulseSubstances::IsActive ( const SESubstance &  sub ) const

virtual

Reimplemented from SESubstanceManager.

LoadSubstanceDirectory()

bool PulseSubstances::LoadSubstanceDirectory ( const std::string &  data_dir = "." )

virtual

Reimplemented from SESubstanceManager.

ProbeBloodGases()

void PulseSubstances::ProbeBloodGases	(	SELiquidCompartment &	cmpt,
		const std::string &	prefix = ""
	)

SetSubstanceConcentration() [1/3]

void PulseSubstances::SetSubstanceConcentration ( SESubstance &  sub, const std::vector< SELiquidCompartment *> &  cmpts, const SEScalarMassPerVolume &  concentration  )

protected

SetSubstanceConcentration() [2/3]

void PulseSubstances::SetSubstanceConcentration ( SESubstance &  sub, const std::vector< SETissueCompartment *> &  cmpts, const SEScalarMassPerVolume &  concentration  )

protected

SetSubstanceConcentration() [3/3]

void PulseSubstances::SetSubstanceConcentration ( SESubstance &  sub, const std::vector< SETissueCompartment *> &  cmpts, const SEScalarMassPerVolume &  extracellular, const SEScalarMassPerVolume &  intracellular  )

protected

SetSubstanceMolarity() [1/3]

void PulseSubstances::SetSubstanceMolarity ( SESubstance &  sub, const std::vector< SELiquidCompartment *> &  cmpts, const SEScalarAmountPerVolume &  molarity  )

protected

SetSubstanceMolarity() [2/3]

void PulseSubstances::SetSubstanceMolarity ( SESubstance &  sub, const std::vector< SETissueCompartment *> &  cmpts, const SEScalarAmountPerVolume &  molarity  )

protected

SetSubstanceMolarity() [3/3]

void PulseSubstances::SetSubstanceMolarity ( SESubstance &  sub, const std::vector< SETissueCompartment *> &  cmpts, const SEScalarAmountPerVolume &  extracellular, const SEScalarAmountPerVolume &  intracellular  )

protected

Setup()

bool PulseSubstances::Setup ( )

virtual

WriteBloodGases()

void PulseSubstances::WriteBloodGases

(

)

WritePulmonaryGases()

void PulseSubstances::WritePulmonaryGases

(

)

Friends And Related Function Documentation

PulseEngineTest

friend class PulseEngineTest

friend

Member Data Documentation

m_acetoacetate

SESubstance* PulseSubstances::m_acetoacetate

protected

m_albumin

SESubstance* PulseSubstances::m_albumin

protected

m_calcium

SESubstance* PulseSubstances::m_calcium

protected

m_chloride

SESubstance* PulseSubstances::m_chloride

protected

m_CO

SESubstance* PulseSubstances::m_CO

protected

m_CO2

SESubstance* PulseSubstances::m_CO2

protected

m_creatinine

SESubstance* PulseSubstances::m_creatinine

protected

m_data

PulseData& PulseSubstances::m_data

protected

m_epi

SESubstance* PulseSubstances::m_epi

protected

m_globulin

SESubstance* PulseSubstances::m_globulin

protected

m_glucose

SESubstance* PulseSubstances::m_glucose

protected

m_Hb

SESubstance* PulseSubstances::m_Hb

protected

m_HbCO

SESubstance* PulseSubstances::m_HbCO

protected

m_HbCO2

SESubstance* PulseSubstances::m_HbCO2

protected

m_HbO2

SESubstance* PulseSubstances::m_HbO2

protected

m_HbO2CO2

SESubstance* PulseSubstances::m_HbO2CO2

protected

m_HCO3

SESubstance* PulseSubstances::m_HCO3

protected

m_insulin

SESubstance* PulseSubstances::m_insulin

protected

m_isCOActive

bool PulseSubstances::m_isCOActive

protected

m_lactate

SESubstance* PulseSubstances::m_lactate

protected

m_N2

SESubstance* PulseSubstances::m_N2

protected

m_O2

SESubstance* PulseSubstances::m_O2

protected

m_potassium

SESubstance* PulseSubstances::m_potassium

protected

m_SIDECoefficients

std::map<const SESubstance*, SizeIndependentDepositionEfficencyCoefficient*> PulseSubstances::m_SIDECoefficients

protected

m_sodium

SESubstance* PulseSubstances::m_sodium

protected

m_tristearin

SESubstance* PulseSubstances::m_tristearin

protected

m_urea

SESubstance* PulseSubstances::m_urea

protected