roadrunner
2.6.0
Fast simulator for SBML models
|
Generate executable SBML models by generating and compiling C source code into shared libraries with an external C compiler. More...
#include <rrCModelGenerator.h>
Public Member Functions | |
CModelGenerator (const std::string &tempFolder, const std::string &supportCodeFolder, const std::string &compiler) | |
virtual ExecutableModel * | createModel (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 Compiler * | getCompiler () |
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 | |
![]() | |
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 Symbol * | getSpecies (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 ASTNode * | cleanEquation (ASTNode *ast) |
creates a new AST node | |
static std::string | cleanEquation (const std::string &equation) |
![]() | |
ls::LibStructural * | mLibStruct |
Refernce to libstruct library this are set by createModel, and for the time being remain after createModel completes. | |
NOMSupport * | mNOM |
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... | |
Generate executable SBML models by generating and compiling C source code into shared libraries with an external C 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...