roadrunner
2.6.0
Fast simulator for SBML models
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An SBML species definition. More...
#include <rrSymbol.h>
Public Attributes | |
bool | rateRule |
Set if species also has a rate rule. More... | |
double | value |
set to initial concentration. More... | |
bool | constant |
std::string | compartmentName |
Used when symbol is a species. | |
bool | hasOnlySubstance |
used when symbol is a species | |
std::string | formula |
There are only two places where formula was created, in rrModelSymbols.cpp, readBoundarySpecies and readFloatingSpeciesConcentrationList In both cases, formula was formated as the exact same C language std::string of formula < <toString(dValue, ModelSymbols::mDoubleFormat)<< "/ md->c[" << nCompartmentIndex << "]";,. More... | |
std::string | keyName |
Used when storing local parameters, keyName is the reaction name. | |
std::string | name |
An SBML species definition.
TODO: should this be named something better than 'Symbol', say SpeciesDefinition or something??? TODO: Why do we even have this? Shoud'nt this just be a sbml::Species ???
std::string rr::Symbol::formula |
There are only two places where formula was created, in rrModelSymbols.cpp, readBoundarySpecies and readFloatingSpeciesConcentrationList In both cases, formula was formated as the exact same C language std::string of formula < <toString(dValue, ModelSymbols::mDoubleFormat)<< "/ md->c[" << nCompartmentIndex << "]";,.
where dValue was always the initialAmmount. So, ammount / volume = concentration.
General idea behind 'formula' was to convert initialAmmount to an initial concentration, that logic belongs in the code generator, not the symbolic processor, so we just declare what the initialAmmount and compartment volume here and leave the logic of converting to concentration in the code generators.
There is no need to keep the compartment index here, the code generators can just grab it from the compartment list using the compartment name.
bool rr::Symbol::rateRule |
Set if species also has a rate rule.
Use to prevent a floatingSpeciesAmountRates being output in the model function if there is a rate rule for it.
double rr::Symbol::value |
set to initial concentration.
If initialAmmount is given, this is converted to a concentration via initialAmmount / initialCompartmentVolume. TODO: should this be named 'initialConcentration'???