rrc_api.cpp File Reference

roadRunner C API 2012 More...

#include <string>
#include <iostream>
#include <sstream>
#include <fstream>
#include "rrRoadRunner.h"
#include "c/rrCModelGenerator.h"
#include "rrLogger.h"
#include "rrException.h"
#include "rrVersionInfo.h"
#include "rrUtils.h"
#include "rrc_api.h"
#include "rrc_utilities.h"
#include "rrc_cpp_support.h"
#include <unistd.h>
#include <limits.h>

Macros
#define	RR_MAX_PATH   PATH_MAX
	macro for MAX_PATH

Functions
RRHandle	createRRInstance ()
	Initialize a new roadRunner instance and return a handle to it. More...
RRHandle	createRRInstanceEx (const char *tempFolder, const char *compiler_cstr)
	Initialize a new roadRunner instance and return a handle to it. More...
char *	getInstallFolder ()
	Returns the folder in which the RoadRunner API is installed. More...
bool	setInstallFolder (const char *folder)
	Set the internal string containing the folder in where the RoadRunner C API is installed. More...
char *	getAPIVersion ()
	Retrieve the current version number of the C API library. More...
char *	getCPPAPIVersion (RRHandle handle)
	Retrieve the current version number of the C++ API (Core RoadRunner API) library. More...
int	getVersion ()
char *	getVersionStr ()
char *	getVersionEx ()
char *	getRRCAPILocation ()
	Retrieve the directory path of the shared rrCApi library. More...
char *	getCopyright ()
	Retrieve the current copyright notice for the library. More...
char *	getInfo (RRHandle handle)
	Retrieve info about current state of roadrunner, e.g. loaded model, conservationAnalysis etc. More...
char *	getExtendedAPIInfo ()
	Retrieve extended API info. More...
char *	getlibSBMLVersion (RRHandle handle)
	Retrieve the current version number of the libSBML library. More...
char *	getCurrentSBML (RRHandle handle)
	Retrieve the current state of the model in the form of an SBML string. More...
bool	setComputeAndAssignConservationLaws (RRHandle handle, const bool OnOrOff)
	Enable or disable conservation analysis. More...
bool	setTempFolder (RRHandle handle, const char *folder)
	Set the path to the temporary folder where the C code will be stored. More...
char *	getTempFolder (RRHandle handle)
	Retrieve the current temporary folder path. More...
bool	setCompiler (RRHandle handle, const char *fName)
	Set the path and filename to the compiler to be used by roadrunner. More...
char *	getCompiler (RRHandle handle)
	Get the name of the compiler currently being used by roadrunner.
bool	setCompilerLocation (RRHandle handle, const char *folder)
	Set the path to a folder containing the compiler to be used. More...
char *	getCompilerLocation (RRHandle handle)
	Get the path to a folder containing the compiler being used. More...
bool	setSupportCodeFolder (RRHandle handle, const char *folder)
	Set the path to a folder containing support code for model generation. More...
char *	getSupportCodeFolder (RRHandle handle)
	Get the path to a folder containing support code. More...
char *	getWorkingDirectory ()
	Retrieve the current working directory path. More...
bool	loadSBMLFromFile (RRHandle _handle, const char *fileName)
	Load a model from a SBML file. More...
bool	loadSBMLFromFileE (RRHandle _handle, const char *fileName, bool forceRecompile)
	Load a model from a SBML file, force recompilation. More...
bool	loadSBML (RRHandle handle, const char *sbml)
	Load a model from an SBML string. More...
bool	loadSBMLEx (RRHandle handle, const char *sbml, bool forceRecompile)
	Load a model from an SBML string. More...
bool	loadSimulationSettings (RRHandle handle, const char *fileName)
	Load simulation settings from a file. More...
char *	getSBML (RRHandle handle)
	Retrieve the SBML model that was last loaded into roadRunner. More...
bool	isModelLoaded (RRHandle handle)
	check if a model is loaded More...
bool	unLoadModel (RRHandle handle)
	Unload current model. More...
bool	setTimeStart (RRHandle handle, const double timeStart)
	Set the time start for a time course simulation. More...
bool	setTimeEnd (RRHandle handle, const double timeEnd)
	Set the time end for a time course simulation. More...
bool	setNumPoints (RRHandle handle, const int nrPoints)
	Set the number of points to generate in a time course simulation. More...
bool	getTimeStart (RRHandle handle, double *timeStart)
	Get the value of the current time start. More...
bool	getTimeEnd (RRHandle handle, double *timeEnd)
	Get the value of the current time end. More...
bool	getNumPoints (RRHandle handle, int *numPoints)
	Get the value of the current number of points. More...
bool	setTimeCourseSelectionList (RRHandle handle, const char *list)
	Set the selection list for output from simulate(void) or simulateEx(void) More...
RRStringArrayPtr	getTimeCourseSelectionList (RRHandle handle)
	Get the current selection list for simulate(void) or simulateEx(void) More...
RRDataHandle	simulate (RRHandle handle)
	Carry out a time-course simulation, use setTimeStart, setTimeEnd and setNumPoints etc to set the simulation characteristics. More...
RRDataHandle	simulateEx (RRHandle handle, const double timeStart, const double timeEnd, const int numberOfPoints)
	Carry out a time-course simulation based on the given arguments, time start, time end and number of points. More...
RRCDataPtr	getSimulationResult (RRHandle handle)
	Retrieve the result of the last simulation. More...
RRDataHandle	getRoadRunnerData (RRHandle handle)
	Retrieve a handle to RoadRunners internal data. More...
RRStringArrayPtr	getReactionIds (RRHandle handle)
	Obtain the list of reaction Ids. More...
RRVectorPtr	getRatesOfChange (RRHandle handle)
	Retrieve the vector of rates of change as determined by the current state of the model. More...
RRStringArrayPtr	getRatesOfChangeIds (RRHandle handle)
	Retrieve the string list of rates of change Ids. More...
RRDoubleMatrixPtr	getUnscaledElasticityMatrix (RRHandle handle)
	Retrieve the unscaled elasticity matrix for the current model. More...
RRDoubleMatrixPtr	getScaledElasticityMatrix (RRHandle handle)
	Retrieve the scaled elasticity matrix for the current model. More...
bool	getValue (RRHandle handle, const char *symbolId, double *value)
	Get the value for a given symbol, use getAvailableTimeCourseSymbols(void) for a list of symbols. More...
bool	setValue (RRHandle handle, const char *symbolId, const double value)
	Set the value for a given symbol, use getAvailableTimeCourseSymbols(void) for a list of symbols. More...
RRDoubleMatrixPtr	getStoichiometryMatrix (RRHandle handle)
	Retrieve the stoichiometry matrix for the current model. More...
RRDoubleMatrixPtr	getConservationMatrix (RRHandle handle)
	Retrieve the conservation matrix for the current model. More...
RRDoubleMatrixPtr	getLinkMatrix (RRHandle handle)
	Retrieve the Link matrix for the current model. More...
RRDoubleMatrixPtr	getNrMatrix (RRHandle handle)
	Retrieve the reduced stoichiometry matrix for the current model. More...
bool	hasError ()
	Check if there is an error string to retrieve. More...
char *	getLastError ()
	Retrieve the current error string. More...
bool	reset (RRHandle handle)
	Reset all floating species concentrations to their intial conditions. More...
int	getNumberOfReactions (RRHandle handle)
	Obtain the number of reactions in the loaded model. More...
bool	getReactionRate (RRHandle handle, const int rateNr, double *value)
	Retrieve a give reaction rate as indicated by the index parameter. More...
RRVectorPtr	getReactionRates (RRHandle handle)
	Retrieve a vector of reaction rates as determined by the current state of the model. More...
int	getNumberOfBoundarySpecies (RRHandle handle)
	Returns the number of boundary species in the model. More...
RRStringArrayPtr	getBoundarySpeciesIds (RRHandle handle)
	Obtain the list of boundary species Ids. More...
int	getNumberOfFloatingSpecies (RRHandle handle)
	Returns the number of floating species in the model. More...
RRStringArrayPtr	getFloatingSpeciesIds (RRHandle handle)
	Obtain the list of floating species Id. More...
int	getNumberOfGlobalParameters (RRHandle handle)
	Returns the number of global parameters in the model. More...
RRStringArrayPtr	getGlobalParameterIds (RRHandle handle)
	Obtain the list of global parameter Ids. More...
bool	getFloatingSpeciesInitialConcentrationByIndex (RRHandle handle, int index, double *value)
	Get the initial concentration for a particular floating species. More...
RRVectorPtr	getFloatingSpeciesConcentrations (RRHandle handle)
	Retrieve in a vector the concentrations for all the floating species. More...
RRVectorPtr	getBoundarySpeciesConcentrations (RRHandle handle)
	Retrieve the concentrations for all the boundary species in a vector. More...
RRVectorPtr	getFloatingSpeciesInitialConcentrations (RRHandle handle)
	Get the initial floating species concentrations. More...
bool	setFloatingSpeciesByIndex (RRHandle handle, const int index, const double value)
	Set the concentration for a particular floating species. More...
bool	setBoundarySpeciesByIndex (RRHandle handle, const int index, const double value)
	Set the concentration for a particular boundary species. More...
bool	setGlobalParameterByIndex (RRHandle handle, const int index, const double value)
	Set the value for a particular global parameter. More...
bool	setFloatingSpeciesInitialConcentrationByIndex (RRHandle handle, const int index, const double value)
	Set the initial concentration for a particular floating species. More...
bool	setFloatingSpeciesInitialConcentrations (RRHandle handle, const RRVectorPtr vec)
	Set the initial floating species concentrations. More...
bool	setFloatingSpeciesConcentrations (RRHandle handle, const RRVectorPtr vec)
	Set the floating species concentration to the vector vec. More...
bool	setBoundarySpeciesConcentrations (RRHandle handle, const RRVectorPtr vec)
	Set the boundary species concentration to the vector vec. More...
bool	oneStep (RRHandle handle, const double currentTime, const double stepSize, double *value)
	Carry out a one step integration of the model. More...
RRVectorPtr	getGlobalParameterValues (RRHandle handle)
	Retrieve the values for all the lgobal parameter values in a vector. More...
RRListPtr	getAvailableTimeCourseSymbols (RRHandle handle)
	Obtain the list of all available symbols. More...
RRListPtr	getAvailableSteadyStateSymbols (RRHandle handle)
	Obtain the list of all available steady state symbols. More...
bool	getBoundarySpeciesByIndex (RRHandle handle, const int index, double *value)
	Retrieve the concentration for a particular floating species. More...
bool	getFloatingSpeciesByIndex (RRHandle handle, const int index, double *value)
	Retrieve the concentration for a particular floating species. More...
bool	getGlobalParameterByIndex (RRHandle handle, const int index, double *value)
	Retrieve the global parameter value. More...
bool	getuCC (RRHandle handle, const char *variable, const char *parameter, double *value)
	Retrieve a single unscaled control coefficient. More...
bool	getCC (RRHandle handle, const char *variable, const char *parameter, double *value)
	Retrieve a single control coefficient. More...
bool	getuEE (RRHandle handle, const char *name, const char *species, double *value)
	Retrieve a single unscaled elasticity coefficient. More...
bool	getEE (RRHandle handle, const char *name, const char *species, double *value)
	Retrieve a single elasticity coefficient. More...
int	getNumberOfDependentSpecies (RRHandle handle)
	Returns the number of dependent species in the model. More...
int	getNumberOfIndependentSpecies (RRHandle handle)
	Returns the number of independent species in the model. More...
bool	steadyState (RRHandle handle, double *value)
	Compute the steady state of the current model. More...
bool	evalModel (RRHandle handle)
	Evaluate the current model, that it update all assignments and rates of change. Do not carry out an integration step. More...
char *	getParamPromotedSBML (RRHandle handle, const char *sArg)
	Promote any local parameters to global status. More...
RRVectorPtr	computeSteadyStateValues (RRHandle handle)
	A convenient method for returning a vector of the steady state species concentrations. More...
bool	setSteadyStateSelectionList (RRHandle handle, const char *list)
	Set the selection list of the steady state analysis. More...
RRStringArrayPtr	getSteadyStateSelectionList (RRHandle handle)
	Get the selection list for the steady state analysis. More...
RRDoubleMatrixPtr	getFullJacobian (RRHandle handle)
	Retrieve the full Jacobian for the current model. More...
RRDoubleMatrixPtr	getReducedJacobian (RRHandle handle)
	Retrieve the reduced Jacobian for the current model. More...
RRDoubleMatrixPtr	getEigenvalues (RRHandle handle)
	Retrieve the eigenvalue matrix for the current model. More...
bool	setCodeGenerationMode (RRHandle handle, int mode)
	Set the runtime generation option [Not yet implemented]. More...
bool	getScaledFloatingSpeciesElasticity (RRHandle handle, const char *reactionId, const char *speciesId, double *value)
	Retrieve the scaled elasticity matrix for the current model. More...
RRStringArrayPtr	getFloatingSpeciesInitialConditionIds (RRHandle handle)
	Get the initial floating species Ids. More...
RRVectorPtr	getRatesOfChangeEx (RRHandle handle, const RRVectorPtr vec)
	Retrieve the vector of rates of change given a vector of floating species concentrations. More...
RRVectorPtr	getReactionRatesEx (RRHandle handle, const RRVectorPtr vec)
	Retrieve a vector of reaction rates given a vector of species concentrations. More...
RRListPtr	getElasticityCoefficientIds (RRHandle handle)
	Obtain the list of elasticity coefficient Ids. More...
bool	setConfigurationXML (RRHandle handle, const char *caps)
	Set the simulator's capabilities. More...
char *	getConfigurationXML (RRHandle handle)
	Get the simulator's capabilities. More...
RRStringArrayPtr	getEigenvalueIds (RRHandle handle)
	Obtain the list of eigenvalue Ids. More...
RRListPtr	getFluxControlCoefficientIds (RRHandle handle)
	Obtain the list of flux control coefficient Ids. More...
RRDoubleMatrixPtr	getUnscaledConcentrationControlCoefficientMatrix (RRHandle handle)
	Retrieve the matrix of unscaled concentration control coefficients for the current model. More...
RRDoubleMatrixPtr	getScaledConcentrationControlCoefficientMatrix (RRHandle handle)
	Retrieve the matrix of scaled concentration control coefficients for the current model. More...
RRDoubleMatrixPtr	getUnscaledFluxControlCoefficientMatrix (RRHandle handle)
	Retrieve the matrix of unscaled flux control coefficients for the current model. More...
RRDoubleMatrixPtr	getScaledFluxControlCoefficientMatrix (RRHandle handle)
	Retrieve the matrix of scaled flux control coefficients for the current model. More...
RRListPtr	getUnscaledFluxControlCoefficientIds (RRHandle handle)
	Obtain the list of unscaled flux control coefficient Ids. More...
RRList *	getConcentrationControlCoefficientIds (RRHandle handle)
	Obtain the list of concentration coefficient Ids. More...
RRListPtr	getUnscaledConcentrationControlCoefficientIds (RRHandle handle)
	Obtain the list of unscaled concentration control coefficient Ids. More...
int	getNumberOfCompartments (RRHandle handle)
	Returns the number of compartments in the model. More...
bool	getCompartmentByIndex (RRHandle handle, const int index, double *value)
	Retrieve the compartment volume for a particular compartment. More...
bool	setCompartmentByIndex (RRHandle handle, const int index, const double value)
	Set the volume for a particular compartment. More...
RRStringArrayPtr	getCompartmentIds (RRHandle handle)
	Obtain the list of compartment Ids. More...
bool	getRateOfChange (RRHandle handle, const int index, double *value)
	Retrieve the rate of change for a given floating species. More...
char *	getBuildDate ()
	Retrieve the current build date of the library. More...
char *	getBuildTime ()
	Retrieve the current build time (HH:MM:SS) of the library. More...
char *	getBuildDateTime ()
	Retrieve the current build date + time of the library. More...
bool	freeRRInstance (RRHandle handle)
	Free the roadRunner instance. More...

Detailed Description

roadRunner C API 2012

Author

Totte Karlsson & Herbert M Sauro

<-----------------------------------------------------------— This file is part of cRoadRunner. See http://code.google.com/p/roadrunnerlib for more details.

Copyright (C) 2012-2013 University of Washington, Seattle, WA, USA

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

In plain english this means:

You CAN freely download and use this software, in whole or in part, for personal, company internal, or commercial purposes;

You CAN use the software in packages or distributions that you create.

You SHOULD include a copy of the license in any redistribution you may make;

You are NOT required include the source of software, or of any modifications you may have made to it, in any redistribution you may assemble that includes it.

YOU CANNOT:

redistribute any piece of this software without proper attribution;