roadrunner  2.6.0
Fast simulator for SBML models
Public Member Functions | List of all members
rr::CModelGenerator Class Reference

Generate executable SBML models by generating and compiling C source code into shared libraries with an external C compiler. More...

#include <rrCModelGenerator.h>

Inheritance diagram for rr::CModelGenerator:
rr::CompiledModelGenerator

Public Member Functions

 CModelGenerator (const std::string &tempFolder, const std::string &supportCodeFolder, const std::string &compiler)
 
virtual ExecutableModelcreateModel (const std::string &sbml, uint options)
 
virtual bool setTemporaryDirectory (const std::string &path)
 
virtual std::string getTemporaryDirectory ()
 Get the location where this model generator creates source file and shared libraries.
 
virtual CompilergetCompiler ()
 Get the compiler object that the model generator is using to 'compile' sbml.
 
virtual bool setCompiler (const std::string &compiler)
 Set the name of the compiler to use. More...
 
std::string getHeaderCode ()
 These are access in the c_api, should they be??? TODO: fix this.
 
std::string getSourceCode ()
 
std::string getSourceCodeFileName ()
 

Additional Inherited Members

- Protected Member Functions inherited from rr::CompiledModelGenerator
std::string substituteTerms (const std::string &reactionName, const std::string &inputEquation, bool bFixAmounts)
 
std::string substituteTerms (const int &numReactions, const std::string &reactionName, const std::string &equation)
 
virtual void writeComputeAllRatesOfChange (CodeBuilder &sb, const int &numIndependentSpecies, const int &numDependentSpecies, ls::DoubleMatrix &L0)=0
 
virtual void writeUpdateDependentSpecies (CodeBuilder &sb, const int &numIndependentSpecies, const int &numDependentSpecies, ls::DoubleMatrix &L0)=0
 
void reset ()
 
int numAdditionalRates ()
 
virtual std::string getInfo ()
 get various information about the model in a user displayable format.
 
ls::DoubleMatrix * initializeL0 (int &nrRows, int &nrCols)
 
bool expressionContainsSymbol (ASTNode *ast, const std::string &symbol)
 
bool expressionContainsSymbol (const std::string &expression, const std::string &symbol)
 
const SymbolgetSpecies (const std::string &id)
 
int readGlobalParameters ()
 
void readLocalParameters (const int &numReactions, std::vector< int > &localParameterDimensions, int &totalLocalParmeters)
 
int readCompartments ()
 
std::string writeDouble (const double &value, const std::string &format="%G")
 
- Static Protected Member Functions inherited from rr::CompiledModelGenerator
static ASTNode * cleanEquation (ASTNode *ast)
 creates a new AST node
 
static std::string cleanEquation (const std::string &equation)
 
- Protected Attributes inherited from rr::CompiledModelGenerator
ls::LibStructural * mLibStruct
 Refernce to libstruct library this are set by createModel, and for the time being remain after createModel completes.
 
NOMSupportmNOM
 Object that provide some wrappers and new "NOM" functions. More...
 
bool mComputeAndAssignConsevationLaws
 
const std::string mFixAmountCompartments
 
StringList mWarnings
 
ModelSymbols ms
 hold all the symbolic (AKA metadata) information in the model The idea is that all the memebers of this class will be const, and the entire thing will be created anew each time createModel is called. More...
 

Detailed Description

Generate executable SBML models by generating and compiling C source code into shared libraries with an external C compiler.

Member Function Documentation

◆ setCompiler()

bool rr::CModelGenerator::setCompiler ( const std::string &  compiler)
virtual

Set the name of the compiler to use.

As this is a C source code compiler, this is the name of the external C compiler, which would typically be 'gcc', 'cc', 'icc', etc...


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