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

#include <BioGearsSubstances.h>

Inheritance diagram for biogears::BioGearsSubstances:

Public Member Functions
	BioGearsSubstances (BioGears &data)

virtual	~BioGearsSubstances ()=default

virtual void	Clear ()

virtual bool	LoadSubstanceDirectory ()

virtual void	InitializeSubstances ()

virtual void	AddActiveSubstance (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 &	GetAlbumin ()

SESubstance &	GetAminoAcids ()

SESubstance &	GetBicarbonate ()

SESubstance &	GetCalcium ()

SESubstance &	GetChloride ()

SESubstance &	GetCreatinine ()

SESubstance &	GetGlobulin ()

SESubstance &	GetGlucagon ()

SESubstance &	GetGlucose ()

SESubstance &	GetInsulin ()

SESubstance &	GetKetones ()

SESubstance &	GetLactate ()

SESubstance &	GetPotassium ()

SESubstance &	GetTriacylglycerol ()

SESubstance &	GetSodium ()

SESubstance &	GetUrea ()

SESubstance &	GetPlatelets ()

SESubstance &	GetAntigen_A ()

SESubstance &	GetAntigen_B ()

SESubstance &	GetRBC ()

SESubstance &	GetWBC ()

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...

void	SetLiquidCompartmentNonGasesForStarvation (double time_h)
	Sets the status of blood concentrations to appropriate starved values. More...

const SizeIndependentDepositionEfficencyCoefficient &	GetSizeIndependentDepositionEfficencyCoefficient (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 biogears::SESubstanceManager
	SESubstanceManager (Logger *logger)

virtual	~SESubstanceManager ()

virtual void	Reset ()

virtual const std::vector< SESubstance * > &	GetSubstances () const

virtual SESubstance *	GetSubstance (const char *name) const

virtual SESubstance *	GetSubstance (const std::string &name) const

virtual void	AddSubstance (SESubstance &substance)

virtual const std::vector< 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 () const

virtual const std::vector< SESubstance * > &	GetActiveLiquids () const

virtual const std::vector< SESubstance * > &	GetActiveDrugs () const

virtual const std::vector< SESubstanceCompound * > &	GetCompounds () const

virtual SESubstanceCompound *	GetCompound (const char *name) const

virtual SESubstanceCompound *	GetCompound (const std::string &name) const

virtual void	AddCompound (SESubstanceCompound &compound)

virtual bool	IsActive (const SESubstanceCompound &compound) const

virtual const std::vector< SESubstanceCompound * > &	GetActiveCompounds () const

virtual void	AddActiveCompound (SESubstanceCompound &compound)

virtual void	RemoveActiveCompound (SESubstanceCompound &compound)

virtual void	RemoveActiveCompounds (const std::vector< SESubstanceCompound * > &compounds)

virtual SESubstance *	ReadSubstanceFile (const char *xmlFile)

virtual SESubstance *	ReadSubstanceFile (const std::string &xmlFile)

Public Member Functions inherited from biogears::Loggable
	Loggable ()

	Loggable (Logger *log)

virtual	~Loggable ()

virtual Logger *	GetLogger () const

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	SetSubstanceMolarity (SESubstance &, 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 Member Functions inherited from biogears::Loggable
virtual void	Debug (const char msg, const char origin="") const

virtual void	Debug (const std::string &msg, const std::string &origin=empty) const

virtual void	Debug (std::ostream &msg, const std::string &origin=empty) const

virtual void	Info (const char msg, const char origin="") const

virtual void	Info (const std::string &msg, const std::string &origin=empty) const

virtual void	Info (std::ostream &msg, const std::string &origin=empty) const

virtual void	Warning (const char msg, const char origin="") const

virtual void	Warning (const std::string &msg, const std::string &origin=empty) const

virtual void	Warning (std::ostream &msg, const std::string &origin=empty) const

virtual void	Error (const char msg, const char origin="") const

virtual void	Error (const std::string msg, const std::string origin=empty) const

virtual void	Error (std::ostream &msg, const std::string &origin=empty) const

virtual void	Fatal (const char msg, const char origin="") const

virtual void	Fatal (const std::string &msg, const std::string &origin=empty) const

virtual void	Fatal (std::ostream &msg, const std::string &origin=empty) const

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_albumin

SESubstance *	m_aminoAcids

SESubstance *	m_calcium

SESubstance *	m_chloride

SESubstance *	m_creatinine

SESubstance *	m_globulin

SESubstance *	m_glucagon

SESubstance *	m_glucose

SESubstance *	m_insulin

SESubstance *	m_ketones

SESubstance *	m_lactate

SESubstance *	m_triacylglycerol

SESubstance *	m_potassium

SESubstance *	m_sodium

SESubstance *	m_urea

SESubstance *	m_platelets

SESubstance *	m_AntigenA

SESubstance *	m_AntigenB

SESubstance *	m_RBC

SESubstance *	m_WBC

bool	m_isCOActive

std::map< SESubstance , SizeIndependentDepositionEfficencyCoefficient >	m_SIDECoefficients

BioGears &	m_data

Protected Attributes inherited from biogears::SESubstanceManager
std::vector< SESubstance * >	m_Substances

std::vector< SESubstance * >	m_ActiveSubstances

std::vector< SESubstance * >	m_ActiveGases

std::vector< SESubstance * >	m_ActiveLiquids

std::vector< SESubstance * >	m_ActiveDrugs

std::vector< SESubstanceCompound * >	m_Compounds

std::vector< SESubstanceCompound * >	m_ActiveCompounds

Protected Attributes inherited from biogears::Loggable
Logger *	m_Logger

Friends
class	BioGearsEngineTest

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

static const char *	empty_cStr

Detailed Description

Manages and initializes all systems with substances needed by BioGears.

Constructor & Destructor Documentation

biogears::BioGearsSubstances::BioGearsSubstances ( BioGears & data )

virtual biogears::BioGearsSubstances::~BioGearsSubstances ( )

virtualdefault

Member Function Documentation

void biogears::BioGearsSubstances::AddActiveSubstance ( SESubstance & substance )

virtual

Reimplemented from biogears::SESubstanceManager.

void biogears::BioGearsSubstances::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.

void biogears::BioGearsSubstances::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.

void biogears::BioGearsSubstances::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.

void biogears::BioGearsSubstances::Clear ( )

virtual

Reimplemented from biogears::SESubstanceManager.

SESubstance& biogears::BioGearsSubstances::GetAlbumin ( )

inline

SESubstance& biogears::BioGearsSubstances::GetAminoAcids ( )

inline

SESubstance& biogears::BioGearsSubstances::GetAntigen_A ( )

inline

SESubstance& biogears::BioGearsSubstances::GetAntigen_B ( )

inline

SESubstance& biogears::BioGearsSubstances::GetBicarbonate ( )

inline

SESubstance& biogears::BioGearsSubstances::GetCalcium ( )

inline

SESubstance& biogears::BioGearsSubstances::GetChloride ( )

inline

SESubstance& biogears::BioGearsSubstances::GetCO ( )

inline

SESubstance& biogears::BioGearsSubstances::GetCO2 ( )

inline

SESubstance& biogears::BioGearsSubstances::GetCreatinine ( )

inline

SESubstance& biogears::BioGearsSubstances::GetEpi ( )

inline

SESubstance& biogears::BioGearsSubstances::GetGlobulin ( )

inline

SESubstance& biogears::BioGearsSubstances::GetGlucagon ( )

inline

SESubstance& biogears::BioGearsSubstances::GetGlucose ( )

inline

SESubstance& biogears::BioGearsSubstances::GetHb ( )

inline

SESubstance& biogears::BioGearsSubstances::GetHbCO ( )

inline

SESubstance& biogears::BioGearsSubstances::GetHbCO2 ( )

inline

SESubstance& biogears::BioGearsSubstances::GetHbO2 ( )

inline

SESubstance& biogears::BioGearsSubstances::GetHbO2CO2 ( )

inline

SESubstance& biogears::BioGearsSubstances::GetHCO3 ( )

inline

SESubstance& biogears::BioGearsSubstances::GetInsulin ( )

inline

SESubstance& biogears::BioGearsSubstances::GetKetones ( )

inline

SESubstance& biogears::BioGearsSubstances::GetLactate ( )

inline

SESubstance& biogears::BioGearsSubstances::GetN2 ( )

inline

SESubstance& biogears::BioGearsSubstances::GetO2 ( )

inline

SESubstance& biogears::BioGearsSubstances::GetPlatelets ( )

inline

SESubstance& biogears::BioGearsSubstances::GetPotassium ( )

inline

SESubstance& biogears::BioGearsSubstances::GetRBC ( )

inline

const SizeIndependentDepositionEfficencyCoefficient & biogears::BioGearsSubstances::GetSizeIndependentDepositionEfficencyCoefficient ( SESubstance & substance )

SESubstance& biogears::BioGearsSubstances::GetSodium ( )

inline

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

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

SESubstance& biogears::BioGearsSubstances::GetTriacylglycerol ( )

inline

SESubstance& biogears::BioGearsSubstances::GetUrea ( )

inline

SESubstance& biogears::BioGearsSubstances::GetWBC ( )

inline

void biogears::BioGearsSubstances::InitializeBloodGases	(	SETissueCompartment &	tissue,
		SELiquidCompartment &	vascular
	)

protectedvirtual

void biogears::BioGearsSubstances::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

void biogears::BioGearsSubstances::InitializeGasCompartments ( )

protectedvirtual

void biogears::BioGearsSubstances::InitializeLiquidCompartmentGases ( )

protectedvirtual

void biogears::BioGearsSubstances::InitializeLiquidCompartmentNonGases ( )

protectedvirtual

void biogears::BioGearsSubstances::InitializeSubstances ( )

virtual

bool biogears::BioGearsSubstances::IsActive ( const SESubstance & sub ) const

virtual

Reimplemented from biogears::SESubstanceManager.

bool biogears::BioGearsSubstances::LoadSubstanceDirectory ( )

virtual

Reimplemented from biogears::SESubstanceManager.

void biogears::BioGearsSubstances::ProbeBloodGases	(	SELiquidCompartment &	cmpt,
		const std::string &	prefix = `""`
	)

void biogears::BioGearsSubstances::SetLiquidCompartmentNonGasesForStarvation ( double time_h )

Sets the status of blood concentrations to appropriate starved values.

The blood concentrations of glucose and ketones are set to match literature values. Insulin and glucagon are not set because they react to set glucose quickly. Other metabolites are not set, but they could be in the future if appropriate validation data is found.

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

protected

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

protected

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

protected

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

protected

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

protected

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

protected

void biogears::BioGearsSubstances::SetSubstanceMolarity	(	SESubstance &	sub,
		const SEScalarAmountPerVolume &	extracellular,
		const SEScalarAmountPerVolume &	intracellular
	)

protected

void biogears::BioGearsSubstances::WriteBloodGases ( )

void biogears::BioGearsSubstances::WritePulmonaryGases ( )

Friends And Related Function Documentation

friend class BioGearsEngineTest

friend

Member Data Documentation

SESubstance* biogears::BioGearsSubstances::m_albumin

protected

SESubstance* biogears::BioGearsSubstances::m_aminoAcids

protected

SESubstance* biogears::BioGearsSubstances::m_AntigenA

protected

SESubstance* biogears::BioGearsSubstances::m_AntigenB

protected

SESubstance* biogears::BioGearsSubstances::m_calcium

protected

SESubstance* biogears::BioGearsSubstances::m_chloride

protected

SESubstance* biogears::BioGearsSubstances::m_CO

protected

SESubstance* biogears::BioGearsSubstances::m_CO2

protected

SESubstance* biogears::BioGearsSubstances::m_creatinine

protected

BioGears& biogears::BioGearsSubstances::m_data

protected

SESubstance* biogears::BioGearsSubstances::m_epi

protected

SESubstance* biogears::BioGearsSubstances::m_globulin

protected

SESubstance* biogears::BioGearsSubstances::m_glucagon

protected

SESubstance* biogears::BioGearsSubstances::m_glucose

protected

SESubstance* biogears::BioGearsSubstances::m_Hb

protected

SESubstance* biogears::BioGearsSubstances::m_HbCO

protected

SESubstance* biogears::BioGearsSubstances::m_HbCO2

protected

SESubstance* biogears::BioGearsSubstances::m_HbO2

protected

SESubstance* biogears::BioGearsSubstances::m_HbO2CO2

protected

SESubstance* biogears::BioGearsSubstances::m_HCO3

protected

SESubstance* biogears::BioGearsSubstances::m_insulin

protected

bool biogears::BioGearsSubstances::m_isCOActive

protected

SESubstance* biogears::BioGearsSubstances::m_ketones

protected

SESubstance* biogears::BioGearsSubstances::m_lactate

protected

SESubstance* biogears::BioGearsSubstances::m_N2

protected

SESubstance* biogears::BioGearsSubstances::m_O2

protected

SESubstance* biogears::BioGearsSubstances::m_platelets

protected

SESubstance* biogears::BioGearsSubstances::m_potassium

protected

SESubstance* biogears::BioGearsSubstances::m_RBC

protected

std::map<SESubstance*, SizeIndependentDepositionEfficencyCoefficient*> biogears::BioGearsSubstances::m_SIDECoefficients

protected

SESubstance* biogears::BioGearsSubstances::m_sodium

protected

SESubstance* biogears::BioGearsSubstances::m_triacylglycerol

protected

SESubstance* biogears::BioGearsSubstances::m_urea

protected

SESubstance* biogears::BioGearsSubstances::m_WBC

protected

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation