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| PulseSubstances (PulseData &data) |
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virtual | ~PulseSubstances ()=default |
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virtual void | Clear () |
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virtual bool | LoadSubstanceDirectory (const std::string &data_dir=".") |
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virtual bool | Setup () |
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virtual void | InitializeSubstances () |
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virtual void | AddActiveSubstance (const SESubstance &substance) |
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virtual bool | IsActive (const SESubstance &sub) const |
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SESubstance & | GetO2 () |
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SESubstance & | GetCO () |
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SESubstance & | GetCO2 () |
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SESubstance & | GetN2 () |
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SESubstance & | GetHb () |
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SESubstance & | GetHbO2 () |
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SESubstance & | GetHbCO2 () |
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SESubstance & | GetHbCO () |
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SESubstance & | GetHbO2CO2 () |
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SESubstance & | GetHCO3 () |
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SESubstance & | GetEpi () |
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SESubstance & | GetAcetoacetate () |
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SESubstance & | GetAlbumin () |
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SESubstance & | GetBicarbonate () |
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SESubstance & | GetCalcium () |
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SESubstance & | GetChloride () |
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SESubstance & | GetCreatinine () |
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SESubstance & | GetGlobulin () |
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SESubstance & | GetGlucose () |
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SESubstance & | GetInsulin () |
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SESubstance & | GetLactate () |
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SESubstance & | GetPotassium () |
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SESubstance & | GetTristearin () |
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SESubstance & | GetSodium () |
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SESubstance & | GetUrea () |
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void | CalculateGenericClearance (double volumeCleared_mL, SELiquidCompartment &cmpt, SESubstance &sub, SEScalarMass *cleared=nullptr) |
| Calculates the substance mass cleared for a node. More...
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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...
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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...
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const SizeIndependentDepositionEfficencyCoefficient & | GetSizeIndependentDepositionEfficencyCoefficient (const SESubstance &substance) |
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double | GetSubstanceMass (SESubstance &, const std::vector< SELiquidCompartment *> &, const MassUnit &unit) |
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double | GetSubstanceMass (SESubstance &, const std::vector< SETissueCompartment *> &, const MassUnit &unit) |
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void | WriteBloodGases () |
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void | WritePulmonaryGases () |
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void | ProbeBloodGases (SELiquidCompartment &cmpt, const std::string &prefix="") |
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| SESubstanceManager (Logger *logger) |
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virtual | ~SESubstanceManager () |
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virtual const std::vector< SESubstance * > & | GetSubstances () |
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virtual const std::vector< const SESubstance * > & | GetSubstances () const |
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virtual bool | HasSubstance (const std::string &name) const |
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virtual SESubstance * | GetSubstance (const std::string &name) |
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virtual const SESubstance * | GetSubstance (const std::string &name) const |
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virtual const std::vector< SESubstance * > & | GetActiveSubstances () |
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virtual const std::vector< const SESubstance * > & | GetActiveSubstances () const |
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virtual void | RemoveActiveSubstance (const SESubstance &substance) |
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virtual void | RemoveActiveSubstances (const std::vector< SESubstance *> &substances) |
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virtual void | RemoveActiveSubstances () |
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virtual const std::vector< SESubstance * > & | GetActiveGases () |
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virtual const std::vector< const SESubstance * > & | GetActiveGases () const |
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virtual const std::vector< SESubstance * > & | GetActiveLiquids () |
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virtual const std::vector< const SESubstance * > & | GetActiveLiquids () const |
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virtual const std::vector< SESubstanceCompound * > & | GetCompounds () |
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virtual const std::vector< const SESubstanceCompound * > & | GetCompounds () const |
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virtual bool | HasCompound (const std::string &name) const |
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virtual SESubstanceCompound * | GetCompound (const std::string &name) |
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virtual const SESubstanceCompound * | GetCompound (const std::string &name) const |
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virtual bool | IsActive (const SESubstanceCompound &compound) const |
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virtual const std::vector< SESubstanceCompound * > & | GetActiveCompounds () |
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virtual const std::vector< const SESubstanceCompound * > & | GetActiveCompounds () const |
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virtual void | AddActiveCompound (const SESubstanceCompound &compound) |
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virtual void | RemoveActiveCompound (const SESubstanceCompound &compound) |
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virtual void | RemoveActiveCompounds (const std::vector< SESubstanceCompound *> &compounds) |
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| Loggable (Logger *logger=nullptr) |
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| Loggable (std::string const &logfile) |
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virtual | ~Loggable () |
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virtual Logger * | GetLogger () const |
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virtual void | SetLogger (Logger &logger) |
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virtual void | Debug (std::string const &msg, std::string const &origin=empty) const |
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virtual void | Debug (std::stringstream &msg, std::string const &origin=empty) const |
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virtual void | Debug (std::ostream &msg, std::string const &origin=empty) const |
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virtual void | Info (std::string const &msg, std::string const &origin=empty) const |
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virtual void | Info (std::stringstream &msg, std::string const &origin=empty) const |
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virtual void | Info (const std::stringstream &msg, std::string const &origin=empty) const |
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virtual void | Info (std::ostream &msg, std::string const &origin=empty) const |
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virtual void | Warning (std::string const &msg, std::string const &origin=empty) const |
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virtual void | Warning (std::stringstream &msg, std::string const &origin=empty) const |
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virtual void | Warning (std::ostream &msg, std::string const &origin=empty) const |
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virtual void | Error (std::string const &msg, std::string const &origin=empty) const |
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virtual void | Error (std::stringstream &msg, std::string const &origin=empty) const |
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virtual void | Error (std::ostream &msg, std::string const &origin=empty) const |
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virtual void | Fatal (std::string const &msg, std::string const &origin=empty) const |
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virtual void | Fatal (std::stringstream &msg, std::string const &origin=empty) const |
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virtual void | Fatal (std::ostream &msg, std::string const &origin=empty) const |
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std::string | to_string (int i) |
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std::string | to_string (unsigned int i) |
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std::string | to_string (size_t t) |
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std::string | to_string (float f) |
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std::string | to_string (double d) |
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virtual void | InitializeGasCompartments () |
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virtual void | InitializeLiquidCompartmentGases () |
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virtual void | InitializeLiquidCompartmentNonGases () |
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virtual void | InitializeBloodGases (SETissueCompartment &tissue, SELiquidCompartment &vascular) |
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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) |
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void | SetSubstanceMolarity (SESubstance &, const std::vector< SELiquidCompartment *> &, const SEScalarAmountPerVolume &molarity) |
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void | SetSubstanceMolarity (SESubstance &, const std::vector< SETissueCompartment *> &, const SEScalarAmountPerVolume &molarity) |
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void | SetSubstanceMolarity (SESubstance &, const std::vector< SETissueCompartment *> &, const SEScalarAmountPerVolume &extracellular, const SEScalarAmountPerVolume &intracellular) |
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void | SetSubstanceConcentration (SESubstance &, const std::vector< SELiquidCompartment *> &, const SEScalarMassPerVolume &concentration) |
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void | SetSubstanceConcentration (SESubstance &, const std::vector< SETissueCompartment *> &, const SEScalarMassPerVolume &concentration) |
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void | SetSubstanceConcentration (SESubstance &, const std::vector< SETissueCompartment *> &, const SEScalarMassPerVolume &extracellular, const SEScalarMassPerVolume &intracellular) |
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Manages and initializes all systems with substances needed by Pulse.