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libRoadRunner C API
1.0.0
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libRoadRunner C API
1.0.0
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libRoadRunner C API 2012-2013 More...
#include "rrc_exporter.h"#include "rrc_types.h"#include "rrc_utilities.h"#include "rrc_logging_api.h"#include "rrc_nom_api.h"#include "rrc_libstruct_api.h"Go to the source code of this file.
Functions | |
| RRHandle | createRRInstance (void) |
| Initialize a new roadRunner instance and return a handle to it. More... | |
| RRHandle | createRRInstanceEx (const char *tempFolder, const char *compiler) |
| Initialize a new roadRunner instance and return a handle to it. More... | |
| bool | freeRRInstance (RRHandle handle) |
| Free the roadRunner instance. More... | |
| char * | getInstallFolder (void) |
| 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 (void) |
| 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 * | getExtendedAPIInfo () |
| Retrieve extended API info. More... | |
| char * | getBuildDate (void) |
| Retrieve the current build date of the library. More... | |
| char * | getBuildTime (void) |
| Retrieve the current build time (HH:MM:SS) of the library. More... | |
| char * | getBuildDateTime (void) |
| Retrieve the current build date + time of the library. More... | |
| char * | getCopyright (void) |
| 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 * | getlibSBMLVersion (RRHandle handle) |
| Retrieve the current version number of the libSBML library. 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... | |
| char * | getWorkingDirectory (void) |
| Retrieve the current working directory path. More... | |
| char * | getRRCAPILocation (void) |
| Retrieve the directory path of the shared rrCApi library. More... | |
| bool | setCompiler (RRHandle handle, const char *fNameWithPath) |
| 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... | |
| bool | setCodeGenerationMode (RRHandle handle, int mode) |
| Set the runtime generation option [Not yet implemented]. More... | |
| bool | hasError (void) |
| Check if there is an error string to retrieve. More... | |
| char * | getLastError (void) |
| Retrieve the current error string. More... | |
| bool | setComputeAndAssignConservationLaws (RRHandle handle, const bool On_Or_Off) |
| Enable or disable conservation analysis. 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 | 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 | unLoadModel (RRHandle handle) |
| Unload current model. More... | |
| bool | isModelLoaded (RRHandle handle) |
| check if a model is loaded More... | |
| bool | loadSimulationSettings (RRHandle handle, const char *fileName) |
| Load simulation settings from a file. More... | |
| char * | getCurrentSBML (RRHandle handle) |
| Retrieve the current state of the model in the form of an SBML string. More... | |
| char * | getSBML (RRHandle handle) |
| Retrieve the SBML model that was last loaded into roadRunner. More... | |
| char * | getParamPromotedSBML (RRHandle handle, const char *sArg) |
| Promote any local parameters to global status. More... | |
| bool | setConfigurationXML (RRHandle handle, const char *caps) |
| Set the simulator's capabilities. More... | |
| char * | getConfigurationXML (RRHandle handle) |
| Get the simulator's capabilities. More... | |
| bool | setTimeStart (RRHandle handle, double timeStart) |
| Set the time start for a time course simulation. More... | |
| bool | setTimeEnd (RRHandle handle, double timeEnd) |
| Set the time end for a time course simulation. More... | |
| bool | setNumPoints (RRHandle handle, int numberOfPoints) |
| Set the number of points to generate in a time course simulation. 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... | |
| RRCDataPtr | getSimulationResult (RRHandle handle) |
| Retrieve the result of the last simulation. More... | |
| RRDataHandle | getRoadRunnerData (RRHandle handle) |
| Retrieve a handle to RoadRunners internal data. 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... | |
| bool | oneStep (RRHandle handle, const double currentTime, const double stepSize, double *value) |
| Carry out a one step integration of the model. 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 | steadyState (RRHandle handle, double *value) |
| Compute the steady state of the current model. 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... | |
| 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... | |
| 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 | getGlobalParameterValues (RRHandle handle) |
| Retrieve the values for all the lgobal parameter values in a vector. More... | |
| bool | setBoundarySpeciesByIndex (RRHandle handle, const int index, const double value) |
| Set the concentration for a particular boundary species. More... | |
| bool | setFloatingSpeciesInitialConcentrationByIndex (RRHandle handle, int index, double value) |
| Set the initial concentration for a particular floating species. More... | |
| bool | getFloatingSpeciesInitialConcentrationByIndex (RRHandle handle, int index, double *value) |
| Get the initial concentration for a particular floating species. More... | |
| bool | setFloatingSpeciesByIndex (RRHandle handle, const int index, const double value) |
| Set the concentration for a particular floating species. More... | |
| bool | setGlobalParameterByIndex (RRHandle handle, const int index, const double value) |
| Set the value for a particular global parameter. 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 | 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... | |
| 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... | |
| 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... | |
| RRDoubleMatrixPtr | getStoichiometryMatrix (RRHandle handle) |
| Retrieve the stoichiometry 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... | |
| RRDoubleMatrixPtr | getConservationMatrix (RRHandle handle) |
| Retrieve the conservation matrix for the current model. More... | |
| bool | reset (RRHandle handle) |
| Reset all floating species concentrations to their intial conditions. More... | |
| bool | setFloatingSpeciesInitialConcentrations (RRHandle handle, const RRVectorPtr vec) |
| Set the initial floating species concentrations. More... | |
| RRVectorPtr | getFloatingSpeciesInitialConcentrations (RRHandle handle) |
| Get the initial floating species concentrations. More... | |
| RRStringArrayPtr | getFloatingSpeciesInitialConditionIds (RRHandle handle) |
| Get the initial floating species Ids. More... | |
| int | getNumberOfReactions (RRHandle handle) |
| Obtain the number of reactions in the loaded model. More... | |
| bool | getReactionRate (RRHandle handle, const int index, double *rate) |
| 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... | |
| RRVectorPtr | getReactionRatesEx (RRHandle handle, const RRVectorPtr vec) |
| Retrieve a vector of reaction rates given a vector of species concentrations. 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... | |
| bool | getRateOfChange (RRHandle handle, const int, double *value) |
| Retrieve the rate of change for a given floating species. More... | |
| RRVectorPtr | getRatesOfChangeEx (RRHandle handle, const RRVectorPtr vec) |
| Retrieve the vector of rates of change given a vector of floating species concentrations. 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... | |
| int | getNumberOfCompartments (RRHandle handle) |
| Returns the number of compartments in the model. More... | |
| int | getNumberOfBoundarySpecies (RRHandle handle) |
| Returns the number of boundary species in the model. More... | |
| int | getNumberOfFloatingSpecies (RRHandle handle) |
| Returns the number of floating species in the model. More... | |
| int | getNumberOfGlobalParameters (RRHandle handle) |
| Returns the number of global parameters in the model. 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... | |
| RRStringArrayPtr | getReactionIds (RRHandle handle) |
| Obtain the list of reaction Ids. More... | |
| RRStringArrayPtr | getBoundarySpeciesIds (RRHandle handle) |
| Obtain the list of boundary species Ids. More... | |
| RRStringArrayPtr | getFloatingSpeciesIds (RRHandle handle) |
| Obtain the list of floating species Id. More... | |
| RRStringArrayPtr | getGlobalParameterIds (RRHandle handle) |
| Obtain the list of global parameter Ids. More... | |
| RRStringArrayPtr | getCompartmentIds (RRHandle handle) |
| Obtain the list of compartment Ids. More... | |
| RRStringArrayPtr | getEigenvalueIds (RRHandle handle) |
| Obtain the list of eigenvalue Ids. 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... | |
| RRListPtr | getElasticityCoefficientIds (RRHandle handle) |
| Obtain the list of elasticity coefficient Ids. More... | |
| RRListPtr | getUnscaledFluxControlCoefficientIds (RRHandle handle) |
| Obtain the list of unscaled flux control coefficient Ids. More... | |
| RRListPtr | getFluxControlCoefficientIds (RRHandle handle) |
| Obtain the list of flux control coefficient Ids. More... | |
| RRListPtr | getUnscaledConcentrationControlCoefficientIds (RRHandle handle) |
| Obtain the list of unscaled concentration control coefficient Ids. More... | |
| RRListPtr | getConcentrationControlCoefficientIds (RRHandle handle) |
| Obtain the list of concentration coefficient 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 | getScaledFloatingSpeciesElasticity (RRHandle handle, const char *reactionId, const char *speciesId, double *value) |
| Retrieve the scaled elasticity matrix for the current model. 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... | |
| 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 | getEE (RRHandle handle, const char *name, const char *species, double *value) |
| Retrieve a single elasticity coefficient. More... | |
| bool | getuEE (RRHandle handle, const char *name, const char *species, double *value) |
| Retrieve a single unscaled elasticity coefficient. More... | |
libRoadRunner C API 2012-2013
<-----------------------------------------------------------— This file is part of libRoadRunner. See http://code.google.com/p/roadrunnerlib/ for more details.
Copyright (C) 2012 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;
| char* getParamPromotedSBML | ( | RRHandle | handle, |
| const char * | sArg | ||
| ) |
Promote any local parameters to global status.
This routine will convert any local reaction parameters and promote them to global status. The promoted parameters are prefixed with the name of the reaction to make them unique.
| [in] | handle | Handle to a RoadRunner instance |
| [in] | sArg | points to the SBML model to promote |
| int getVersion | ( | ) |
Get the version number.
returns the individual version numbers as XXYYZZ where XX is the major version, YY the minor and ZZ the revision, eg 10000, or 10100, 20000 etc
| char* getVersionEx | ( | ) |
returns something like "1.0.0; compiled with clang "3.3 (tags/RELEASE_33/final)" on date Dec 8 2013, 17:24:57'
| char* getVersionStr | ( | ) |
returns roadrunner as a string, i.e. "1.0.0"
1.8.5