C API Documentation
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#include <rrRoadRunner.h>
Public Member Functions | |
RoadRunner (unsigned int level=3, unsigned int version=2) | |
RoadRunner (const std::string &uriOrSBML, const Dictionary *options=0) | |
RoadRunner (const std::string &compiler, const std::string &tempDir, const std::string &supportCodeDir) | |
RoadRunner (const RoadRunner &rr) | |
virtual | ~RoadRunner () |
int | getInstanceID () |
int | getInstanceCount () |
std::string | getInfo () |
class Compiler * | getCompiler () |
void | setCompiler (const std::string &compiler) |
Integrator * | getIntegrator () |
Integrator * | getIntegratorByName (const std::string &name) |
Integrator * | makeIntegrator (std::string name) |
SteadyStateSolver * | getSteadyStateSolver () |
std::vector< std::string > | getExistingIntegratorNames () |
void | setIntegrator (std::string name) |
bool | integratorExists (std::string name) |
void | setSteadyStateSolver (std::string name) |
bool | steadyStateSolverExists (std::string name) |
bool | isModelLoaded () |
std::string | getModelName () |
bool | clearModel () |
Clears the currently loaded model and all associated memory. More... | |
double | oneStep (double currentTime, double stepSize, bool reset=true) |
double | internalOneStep (double currentTime, double stepSize, bool reset=true) |
const ls::DoubleMatrix * | simulate (const Dictionary *options=0) |
void | saveState (std::string filename, char opt='b') |
void | loadState (std::string filename) |
const ls::DoubleMatrix * | getSimulationData () const |
void | setSimulateOptions (const SimulateOptions &settings) |
SimulateOptions & | getSimulateOptions () |
RoadRunnerOptions & | getOptions () |
void | setOptions (const RoadRunnerOptions &) |
std::string | getSBML (int level=0, int version=0) |
std::string | getCurrentSBML (int level=0, int version=0) |
void | reset () |
void | reset (int options) |
void | resetSelectionLists () |
void | changeInitialConditions (const std::vector< double > &ic) |
ExecutableModel * | getModel () |
void | load (const std::string &uriOrSBML, const Dictionary *options=0) |
rr::SelectionRecord | createSelection (const std::string &str) |
std::vector< rr::SelectionRecord > & | getSelections () |
double | getValue (const std::string &sel) |
double | getValue (const SelectionRecord &record) |
void | setSelections (const std::vector< std::string > &selections) |
void | setSelections (const std::vector< rr::SelectionRecord > &selections) |
std::vector< double > | getSelectedValues () |
void | getIds (int types, std::list< std::string > &ids) |
std::vector< std::string > | getIndependentFloatingSpeciesIds () |
Gets the ids for all independent floating species. More... | |
std::vector< std::string > | getDependentFloatingSpeciesIds () |
Gets the ids for all dependent floating species. More... | |
std::vector< std::string > | getFloatingSpeciesConcentrationIds () |
Gets the ids for all floating species concentrations. More... | |
std::vector< std::string > | getFloatingSpeciesInitialConcentrationIds () |
Gets the ids for all initial floating species concentrations. More... | |
int | getSupportedIdTypes () |
void | setValue (const std::string &id, double value) |
ls::DoubleMatrix | getFloatingSpeciesAmountsNamedArray () |
Returns the floating species amounts as a named array. More... | |
ls::DoubleMatrix | getFloatingSpeciesConcentrationsNamedArray () |
Returns the floating species concentrations as a named array. More... | |
ls::DoubleMatrix | getBoundarySpeciesAmountsNamedArray () |
Returns the boundary species amounts as a named array. More... | |
ls::DoubleMatrix | getBoundarySpeciesConcentrationsNamedArray () |
Returns the boundary species concentrations as a named array. More... | |
std::vector< double > | getRatesOfChange () |
Returns the rate of change of the floating species as an array. More... | |
ls::DoubleMatrix | getRatesOfChangeNamedArray () |
Returns the rate of change of the floating species as a named array. More... | |
std::vector< double > | getIndependentRatesOfChange () |
Returns the rate of change of the independent floating species as an array. More... | |
ls::DoubleMatrix | getIndependentRatesOfChangeNamedArray () |
Returns the rate of change of the independent floating species as a named array. More... | |
std::vector< double > | getDependentRatesOfChange () |
Returns the rate of change of the dependent floating species as an array. More... | |
ls::DoubleMatrix | getDependentRatesOfChangeNamedArray () |
Returns the rate of change of the dependent floating species as a named array. More... | |
ls::DoubleMatrix | getFullJacobian () |
ls::DoubleMatrix | getFullReorderedJacobian () |
ls::DoubleMatrix | getReducedJacobian (double h=-1.0) |
std::vector< ls::Complex > | getFullEigenValues () |
std::vector< ls::Complex > | getReducedEigenValues () |
ls::DoubleMatrix | getLinkMatrix () |
ls::DoubleMatrix | getNrMatrix () |
ls::DoubleMatrix | getKMatrix () |
ls::DoubleMatrix | getReducedStoichiometryMatrix () |
ls::DoubleMatrix | getFullStoichiometryMatrix () |
ls::DoubleMatrix | getExtendedStoichiometryMatrix () |
ls::DoubleMatrix | getL0Matrix () |
ls::DoubleMatrix | getConservationMatrix () |
ls::DoubleMatrix | getUnscaledConcentrationControlCoefficientMatrix () |
ls::DoubleMatrix | getScaledConcentrationControlCoefficientMatrix () |
ls::DoubleMatrix | getUnscaledFluxControlCoefficientMatrix () |
ls::DoubleMatrix | getScaledFluxControlCoefficientMatrix () |
std::vector< std::string > | getEigenValueIds () |
double | getUnscaledParameterElasticity (const string &reactionName, const string ¶meterName) |
ls::DoubleMatrix | getFrequencyResponse (double startFrequency, int numberOfDecades, int numberOfPoints, const std::string ¶meterName, const std::string &variableName, bool useDB, bool useHz) |
void | setConservedMoietyAnalysis (bool value) |
bool | getConservedMoietyAnalysis () |
double | getDiffStepSize () const |
Set the differential step size used in MCA routines like getCC. More... | |
void | setDiffStepSize (double val) |
Set the differential step size used in MCA routines like getCC. More... | |
double | getSteadyStateThreshold () const |
Get the steady state threshold used in getCC. More... | |
void | setSteadyStateThreshold (double val) |
Set the steady state threshold used in getCC. More... | |
double | getuCC (const std::string &variableName, const std::string ¶meterName) |
double | getCC (const std::string &variableName, const std::string ¶meterName) |
double | getuEE (const std::string &reactionName, const std::string ¶meterName) |
double | getuEE (const std::string &reactionName, const std::string ¶meterName, bool computeSteadystate) |
double | getEE (const std::string &reactionName, const std::string ¶meterName) |
double | getEE (const std::string &reactionName, const std::string ¶meterName, bool computeSteadyState) |
ls::DoubleMatrix | getUnscaledElasticityMatrix () |
ls::DoubleMatrix | getScaledElasticityMatrix () |
double | getScaledFloatingSpeciesElasticity (const std::string &reactionName, const std::string &speciesName) |
double | getUnscaledSpeciesElasticity (int reactionId, int speciesIndex) |
void | addSpecies (const std::string &sid, const std::string &compartment, double initAmount=0, bool hasOnlySubstanceUnits=false, bool boundaryCondition=false, const std::string &substanceUnits="", bool forceRegenerate=true) |
void | removeSpecies (const std::string &sid, bool forceRegenerate=true) |
void | setBoundary (const std::string &sid, bool boundaryCondition, bool forceRegenerate=true) |
void | setHasOnlySubstanceUnits (const std::string &sid, bool hasOnlySubstanceUnits, bool forceRegenerate=true) |
void | setInitAmount (const std::string &sid, double initAmount, bool forceRegenerate=true) |
void | setInitConcentration (const std::string &sid, double initConcentration, bool forceRegenerate=true) |
void | setConstant (const std::string &sid, bool constant, bool forceRegenerate=true) |
void | addReaction (const std::string &sbmlRep, bool forceRegenerate=true) |
void | addReaction (const std::string &rid, std::vector< string > reactants, std::vector< string > products, const std::string &kineticLaw, bool forceRegenerate=true) |
void | removeReaction (const std::string &rid, bool deleteUnusedParameters=false, bool forceRegenerate=true) |
void | setReversible (const std::string &rid, bool reversible, bool forceRegenerate=true) |
void | setKineticLaw (const std::string &rid, const std::string &kineticLaw, bool forceRegenerate=true) |
std::string | getKineticLaw (const std::string &rid) |
void | addParameter (const std::string &pid, double value, bool forceRegenerate=true) |
void | removeParameter (const std::string &pid, bool forceRegenerate=true) |
void | addCompartment (const std::string &cid, double initVolume, bool forceRegenerate=true) |
void | removeCompartment (const std::string &cid, bool forceRegenerate=true) |
void | addAssignmentRule (const std::string &vid, const std::string &formula, bool forceRegenerate=true) |
void | addRateRule (const std::string &vid, const std::string &formula, bool forceRegenerate=true) |
void | removeRules (const std::string &vid, bool useInitialValue=false, bool forceRegenerate=true) |
void | addInitialAssignment (const std::string &vid, const std::string &formula, bool forceRegenerate=true) |
void | removeInitialAssignment (const std::string &vid, bool forceRegenerate=true) |
void | addEvent (const std::string &eid, bool useValuesFromTriggerTime, const std::string &trigger, bool forceRegenerate=true) |
void | addTrigger (const std::string &eid, const std::string &trigger, bool forceRegenerate=true) |
void | setPersistent (const std::string &eid, bool persistent, bool forceRegenerate=true) |
void | setTriggerInitialValue (const std::string &eid, bool initValue, bool forceRegenerate=true) |
void | addPriority (const std::string &eid, const std::string &priority, bool forceRegenerate=true) |
void | addDelay (const std::string &eid, const std::string &delay, bool forceRegenerate=true) |
void | addEventAssignment (const std::string &eid, const std::string &vid, const std::string &formula, bool forceRegenerate=true) |
void | removeEventAssignments (const std::string &eid, const std::string &vid, bool forceRegenerate=true) |
void | removeEvent (const std::string &eid, bool forceRegenerate=true) |
void | validateCurrentSBML () |
double | mcaSteadyState () |
double | steadyState (const Dictionary *dict=0) |
double | steadyStateApproximate (const Dictionary *dict=0) |
ls::DoubleMatrix | steadyStateNamedArray (const Dictionary *dict=0) |
std::vector< rr::SelectionRecord > & | getSteadyStateSelections () |
void | setSteadyStateSelections (const std::vector< std::string > &steadyStateSelections) |
void | setSteadyStateSelections (const std::vector< rr::SelectionRecord > &steadyStateSelections) |
std::vector< double > | getSteadyStateValues () |
std::vector< std::string > | getSteadyStateSelectionStrings () const |
ls::DoubleMatrix | getSteadyStateValuesNamedArray () |
void | regenerate (bool forceRegenerate=true, bool reset=false) |
void | setBoundarySpeciesByIndex (const int &index, const double &value) |
int | getNumberOfIndependentSpecies () |
std::vector< std::string > | getGlobalParameterIds () |
std::vector< std::string > | getBoundarySpeciesIds () |
std::vector< std::string > | getBoundarySpeciesConcentrationIds () |
Gets the ids for all boundary species concentrations. More... | |
double | getBoundarySpeciesByIndex (const int &index) |
double | getGlobalParameterByIndex (const int &index) |
void | setGlobalParameterByName (const std::string ¶m, double value) |
set the parameter with id More... | |
double | getGlobalParameterByName (const std::string ¶m) |
get the More... | |
std::vector< double > | getConservedMoietyValues () |
Returns the sum of each conserved cycle. More... | |
std::vector< std::string > | getConservedMoietyIds () |
RR_DEPRECATED (int getNumberOfReactions()) | |
RR_DEPRECATED (double getReactionRate(const int &index)) | |
RR_DEPRECATED (double getRateOfChange(const int &index)) | |
RR_DEPRECATED (std::vector< std::string > getRateOfChangeIds()) | |
RR_DEPRECATED (int getNumberOfCompartments()) | |
RR_DEPRECATED (void setCompartmentByIndex(const int &index, const double &value)) | |
RR_DEPRECATED (double getCompartmentByIndex(const int &index)) | |
RR_DEPRECATED (std::vector< std::string > getCompartmentIds()) | |
RR_DEPRECATED (int getNumberOfBoundarySpecies()) | |
RR_DEPRECATED (std::vector< double > getBoundarySpeciesConcentrations()) | |
RR_DEPRECATED (void setBoundarySpeciesConcentrations(const std::vector< double > &values)) | |
RR_DEPRECATED (int getNumberOfFloatingSpecies()) | |
RR_DEPRECATED (double getFloatingSpeciesByIndex(int index)) | |
RR_DEPRECATED (void setFloatingSpeciesByIndex(int index, double value)) | |
RR_DEPRECATED (std::vector< double > getFloatingSpeciesConcentrationsV()) | |
RR_DEPRECATED (std::vector< double > getFloatingSpeciesAmountsV()) | |
RR_DEPRECATED (std::vector< double > getBoundarySpeciesConcentrationsV()) | |
RR_DEPRECATED (std::vector< double > getBoundarySpeciesAmountsV()) | |
RR_DEPRECATED (std::vector< double > getFloatingSpeciesInitialConcentrations()) | |
RR_DEPRECATED (void setFloatingSpeciesConcentrations(const std::vector< double > &values)) | |
RR_DEPRECATED (void setFloatingSpeciesInitialConcentrationByIndex(const int &index, const double &value)) | |
RR_DEPRECATED (void setFloatingSpeciesInitialConcentrations(const std::vector< double > &values)) | |
RR_DEPRECATED (std::vector< std::string > getFloatingSpeciesIds()) | |
RR_DEPRECATED (std::vector< std::string > getFloatingSpeciesInitialConditionIds()) | |
RR_DEPRECATED (size_t getNumberOfGlobalParameters()) | |
RR_DEPRECATED (void setGlobalParameterByIndex(const int index, const double value)) | |
RR_DEPRECATED (std::vector< double > getGlobalParameterValues()) | |
void | evalModel () |
RR_DEPRECATED (int getNumberOfDependentSpecies()) | |
RR_DEPRECATED (std::vector< double > getReactionRates()) | |
RR_DEPRECATED (std::vector< std::string > getReactionIds()) | |
void | setTempDir (const std::string &folder) |
std::string | getTempDir () |
Static Public Member Functions | |
static std::string | getParamPromotedSBML (const std::string &sArg) |
static std::vector< std::string > | getRegisteredIntegratorNames () |
static std::vector< std::string > | getRegisteredSteadyStateSolverNames () |
static void | ensureSolversRegistered () |
static std::string | getExtendedVersionInfo () |
The main RoadRunner class.
The RoadRunner class is responsible for loading and simulating SBML models.
MemoryManagment: Any pointer returned by a get... method is owned by the RoadRunner object and does NOT have to be deleted.
rr::RoadRunner::RoadRunner | ( | unsigned int | level = 3 , |
unsigned int | version = 2 |
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create an empty RoadRunner object with given SBML level and version.
rr::RoadRunner::RoadRunner | ( | const std::string & | uriOrSBML, |
const Dictionary * | options = 0 |
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load an sbml document from anywhere.
same arguments as load.
If options is not null, then the RoadRunner::computeAndAssignConservationLaws flag is set to whatever value is specified in the options struct.
uriOrSBML | a URI, local path or sbml document contents. |
options | an options struct, if null, default values are used. |
rr::RoadRunner::RoadRunner | ( | const std::string & | compiler, |
const std::string & | tempDir, | ||
const std::string & | supportCodeDir | ||
) |
All three of the RoadRunner options default to the empty string, in this case, the default values are used.
compiler | If LLVM build is enabled, the compiler defaults to LLVM. |
tempDir | If the old external C compiler is used, this is the where the C files are written to. |
supportCodeDir | If the old external C compiler is used, this is the location where roadrunner C include files are. |
rr::RoadRunner::RoadRunner | ( | const RoadRunner & | rr | ) |
RoadRunner copy constructor Explicitly defined because of Python.
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free any memory this class allocated
void rr::RoadRunner::addCompartment | ( | const std::string & | cid, |
double | initVolume, | ||
bool | forceRegenerate = true |
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) |
Add a compartment to the current model
cid | the ID of the compartment to be added |
initVolume | the initial volume of the compartment to be added |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::addParameter | ( | const std::string & | pid, |
double | value, | ||
bool | forceRegenerate = true |
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) |
Add a parameter to the current model
pid | the ID of the parameter to be added |
value | the value of the parameter to be added |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::addSpecies | ( | const std::string & | sid, |
const std::string & | compartment, | ||
double | initAmount = 0 , |
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bool | hasOnlySubstanceUnits = false , |
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bool | boundaryCondition = false , |
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const std::string & | substanceUnits = "" , |
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bool | forceRegenerate = true |
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) |
Add a species to the current model.
sid | the ID of the species to be added |
compartment | the compartment of the species to be added |
initAmount | the initial amount of the species to be added |
substanceUnits | the substance unit of the species to be added |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
bool rr::RoadRunner::clearModel | ( | ) |
Clears the currently loaded model and all associated memory.
Deletes jitted code and libStruct data
rr::SelectionRecord rr::RoadRunner::createSelection | ( | const std::string & | str | ) |
create a selection record. This record can be used to select values.
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Ensures all integrators and steady state solvers are registered
ls::DoubleMatrix rr::RoadRunner::getBoundarySpeciesAmountsNamedArray | ( | ) |
Returns the boundary species amounts as a named array.
std::vector<std::string> rr::RoadRunner::getBoundarySpeciesConcentrationIds | ( | ) |
Gets the ids for all boundary species concentrations.
ls::DoubleMatrix rr::RoadRunner::getBoundarySpeciesConcentrationsNamedArray | ( | ) |
Returns the boundary species concentrations as a named array.
double rr::RoadRunner::getCC | ( | const std::string & | variableName, |
const std::string & | parameterName | ||
) |
Get scaled control coefficient with respect to a global parameter
The variableName must be either a reaction id, or a floating species id.
The parameterName must be either a global parameter, boundary species, or conserved sum.
class Compiler* rr::RoadRunner::getCompiler | ( | ) |
The Compiler that the ModelGenerator is using to compile / interpret sbml code.
bool rr::RoadRunner::getConservedMoietyAnalysis | ( | ) |
is conservation analysis enabled. This is set
std::vector<double> rr::RoadRunner::getConservedMoietyValues | ( | ) |
Returns the sum of each conserved cycle.
std::string rr::RoadRunner::getCurrentSBML | ( | int | level = 0 , |
int | version = 0 |
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) |
Returns the SBML with the current model parameters. This is different than getSBML which returns the orginal SBML.
This may optionally up or downconvert the document to a different version, if the level and version arguments are non-zero.
If both arguments are zero, then the document is left alone and the original version is returned.
std::vector<std::string> rr::RoadRunner::getDependentFloatingSpeciesIds | ( | ) |
Gets the ids for all dependent floating species.
See getIndependentFloatingSpeciesIds for an explanation of independent vs. dependent.
std::vector<double> rr::RoadRunner::getDependentRatesOfChange | ( | ) |
Returns the rate of change of the dependent floating species as an array.
ls::DoubleMatrix rr::RoadRunner::getDependentRatesOfChangeNamedArray | ( | ) |
Returns the rate of change of the dependent floating species as a named array.
double rr::RoadRunner::getDiffStepSize | ( | ) | const |
Set the differential step size used in MCA routines like getCC.
double rr::RoadRunner::getEE | ( | const std::string & | reactionName, |
const std::string & | parameterName | ||
) |
Get scaled elasticity coefficient with respect to a global parameter or species
double rr::RoadRunner::getEE | ( | const std::string & | reactionName, |
const std::string & | parameterName, | ||
bool | computeSteadyState | ||
) |
Get scaled elasticity coefficient with respect to a global parameter or species. Optionally the model is brought to steady state after the computation.
std::vector<std::string> rr::RoadRunner::getEigenValueIds | ( | ) |
returns the list of floating species, but with a "eigen(...)" string wrapped around them.
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getVersion plus info about dependent libs versions..
ls::DoubleMatrix rr::RoadRunner::getFloatingSpeciesAmountsNamedArray | ( | ) |
Returns the floating species amounts as a named array.
std::vector<std::string> rr::RoadRunner::getFloatingSpeciesConcentrationIds | ( | ) |
Gets the ids for all floating species concentrations.
ls::DoubleMatrix rr::RoadRunner::getFloatingSpeciesConcentrationsNamedArray | ( | ) |
Returns the floating species concentrations as a named array.
std::vector<std::string> rr::RoadRunner::getFloatingSpeciesInitialConcentrationIds | ( | ) |
Gets the ids for all initial floating species concentrations.
See getIndependentFloatingSpeciesIds for an explanation of independent vs. dependent.
std::vector<ls::Complex> rr::RoadRunner::getFullEigenValues | ( | ) |
Returns the eigenvalues of the full jacobian.
If the eigenvalues are all real, this returns a N x 1 matrix, if complex, returns an N x 2 matrix where the first column is the real values and the second is the imaginary part.
ls::DoubleMatrix rr::RoadRunner::getFullJacobian | ( | ) |
compute the full Jacobian at the current operating point
ls::DoubleMatrix rr::RoadRunner::getFullStoichiometryMatrix | ( | ) |
Get the stoichiometry matrix that coresponds to the full model, even it it was converted via conservation conversion.
double rr::RoadRunner::getGlobalParameterByName | ( | const std::string & | param | ) |
get the
value | of global parameter with id |
param |
void rr::RoadRunner::getIds | ( | int | types, |
std::list< std::string > & | ids | ||
) |
populates a given list with all the ids that this class can accept.
std::vector<std::string> rr::RoadRunner::getIndependentFloatingSpeciesIds | ( | ) |
Gets the ids for all independent floating species.
Independent means (in this case) that the species is unique up to a conserved cycle, i.e. each conserved cycle counts for only one species. See Sauro, Systems Biology: Introduction to Pathway Modeling, 1st ed. pp. 60.
std::vector<double> rr::RoadRunner::getIndependentRatesOfChange | ( | ) |
Returns the rate of change of the independent floating species as an array.
ls::DoubleMatrix rr::RoadRunner::getIndependentRatesOfChangeNamedArray | ( | ) |
Returns the rate of change of the independent floating species as a named array.
std::string rr::RoadRunner::getInfo | ( | ) |
information about the current state of this object.
int rr::RoadRunner::getInstanceCount | ( | ) |
Number of currently running RoadRunner instances.
int rr::RoadRunner::getInstanceID | ( | ) |
When there are multiple instances of RoadRunner, this is the instance id.
Integrator* rr::RoadRunner::getIntegrator | ( | ) |
get a pointer to the integrator which is currently being used to time evolve the system.
Integrator* rr::RoadRunner::getIntegratorByName | ( | const std::string & | name | ) |
Get an integrator by name without switching the current integrator
std::string rr::RoadRunner::getKineticLaw | ( | const std::string & | rid | ) |
Get the kinetic law of an existing reaction in the current model.
rid | the ID of reaction to be modified |
ls::DoubleMatrix rr::RoadRunner::getKMatrix | ( | ) |
Returns the K matrix (right nullspace of Nr) The K matrix has the structure, [I K0]'
ExecutableModel* rr::RoadRunner::getModel | ( | ) |
get a pointer to the ExecutableModel owned by the RoadRunner object.
std::string rr::RoadRunner::getModelName | ( | ) |
returns the model name if a model is loaded, empty string otherwise.
ls::DoubleMatrix rr::RoadRunner::getNrMatrix | ( | ) |
get the reduced stochiometry matrix. If conservation conversion is enabled, this is the matrix that coresponds to the independent species.
A synonym for getReducedStoichiometryMatrix().
RoadRunnerOptions& rr::RoadRunner::getOptions | ( | ) |
Get a reference to the options that determine how this class should behave.
These are general options. For options specific for loading or simulationg,
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Given an sbml document or path to an sbml document, this method moves all the local parameters to global parameters.
std::vector<double> rr::RoadRunner::getRatesOfChange | ( | ) |
Returns the rate of change of the floating species as an array.
ls::DoubleMatrix rr::RoadRunner::getRatesOfChangeNamedArray | ( | ) |
Returns the rate of change of the floating species as a named array.
std::vector<ls::Complex> rr::RoadRunner::getReducedEigenValues | ( | ) |
Returns the eigenvalues of the reduced jacobian.
If the eigenvalues are all real, this returns a N x 1 matrix, if complex, returns an N x 2 matrix where the first column is the real values and the second is the imaginary part.
ls::DoubleMatrix rr::RoadRunner::getReducedJacobian | ( | double | h = -1.0 | ) |
Compute the reduced Jacobian at the current operating point.
h | The step sized used for central difference method. If negative, the default value from the config file is used. |
ls::DoubleMatrix rr::RoadRunner::getReducedStoichiometryMatrix | ( | ) |
get the reduced stochiometry matrix. If conservation conversion is enabled, this is the matrix that coresponds to the independent species.
A synonym for getNrMatrix().
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Return a vector of the names of all registered integrators
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Return a vector of the names of all registered integrators
std::string rr::RoadRunner::getSBML | ( | int | level = 0 , |
int | version = 0 |
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) |
get the originally loaded sbml document as a string.
This may optionally up or downconvert the document to a different version, if the level and version arguments are non-zero.
If both arguments are zero, then the document is left alone and the
ls::DoubleMatrix rr::RoadRunner::getScaledElasticityMatrix | ( | ) |
Compute the unscaled elasticity matrix at the current operating point
double rr::RoadRunner::getScaledFloatingSpeciesElasticity | ( | const std::string & | reactionName, |
const std::string & | speciesName | ||
) |
Compute the scaled elasticity for a given reaction and given species
std::vector<double> rr::RoadRunner::getSelectedValues | ( | ) |
returns the values selected with SimulateOptions for the current model time / timestep")
std::vector<rr::SelectionRecord>& rr::RoadRunner::getSelections | ( | ) |
Returns the currently selected columns that will be returned by calls to simulate() or simulateEx(,,).
SimulateOptions& rr::RoadRunner::getSimulateOptions | ( | ) |
get a reference to the SimulateOptions that were set either by setSimulateOptions or simulate.
const ls::DoubleMatrix* rr::RoadRunner::getSimulationData | ( | ) | const |
RoadRunner keeps a copy of the simulation data around until the next call to simulate. This matrix can be obtained here.
std::vector<rr::SelectionRecord>& rr::RoadRunner::getSteadyStateSelections | ( | ) |
returns the current set of steady state selections.
std::vector<std::string> rr::RoadRunner::getSteadyStateSelectionStrings | ( | ) | const |
Returns a vector of the steady state selection strings
SteadyStateSolver* rr::RoadRunner::getSteadyStateSolver | ( | ) |
get a pointer to the current steady state solver
double rr::RoadRunner::getSteadyStateThreshold | ( | ) | const |
Get the steady state threshold used in getCC.
In the MCA routines, RoadRunner will keep trying to converge to a steady state until this threshold is met
std::vector<double> rr::RoadRunner::getSteadyStateValues | ( | ) |
Performs a steady state calculation (evolves the system to a steady state), then calculates and returns the set of values specifed by the steady state selections.
ls::DoubleMatrix rr::RoadRunner::getSteadyStateValuesNamedArray | ( | ) |
Like getSteadyStateValues but returns a named array
int rr::RoadRunner::getSupportedIdTypes | ( | ) |
returns a bit field of the ids that this class supports.
double rr::RoadRunner::getuCC | ( | const std::string & | variableName, |
const std::string & | parameterName | ||
) |
Get unscaled control coefficient with respect to a global parameter
variableName must be either a reaction or floating species.
parameterName must be eithe a global parameter, boundary species, or conserved sum.
double rr::RoadRunner::getuEE | ( | const std::string & | reactionName, |
const std::string & | parameterName | ||
) |
Get unscaled elasticity coefficient with respect to a global parameter or species
double rr::RoadRunner::getuEE | ( | const std::string & | reactionName, |
const std::string & | parameterName, | ||
bool | computeSteadystate | ||
) |
Get unscaled elasticity coefficient with respect to a global parameter or species. Optionally the model is brought to steady state after the computation.
ls::DoubleMatrix rr::RoadRunner::getUnscaledElasticityMatrix | ( | ) |
Compute the unscaled species elasticity matrix at the current operating point
double rr::RoadRunner::getUnscaledParameterElasticity | ( | const string & | reactionName, |
const string & | parameterName | ||
) |
Returns the unscaled elasticity for a named reaction with respect to a named parameter
double rr::RoadRunner::getUnscaledSpeciesElasticity | ( | int | reactionId, |
int | speciesIndex | ||
) |
Get a single species elasticity value IMPORTANT: Assumes that the reaction rates have been precomputed at the operating point !!
double rr::RoadRunner::getValue | ( | const std::string & | sel | ) |
Creates a new selection based on the selection string, and returns the value it queries.
double rr::RoadRunner::internalOneStep | ( | double | currentTime, |
double | stepSize, | ||
bool | reset = true |
||
) |
Carry out a single internal solver integration step.
t0 | starting time |
tf | final time |
options | override current options. |
void rr::RoadRunner::load | ( | const std::string & | uriOrSBML, |
const Dictionary * | options = 0 |
||
) |
load an sbml document from anywhere.
If options is not null, then the RoadRunner::computeAndAssignConservationLaws flag is set to whatever value is specified in the options struct.
WARNING, will no longer return a value in next version.
uriOrSBML | a URI, local path or sbml document contents. |
options | an options struct, if null, default values are used. |
Integrator* rr::RoadRunner::makeIntegrator | ( | std::string | name | ) |
Make an integrator for the given name
double rr::RoadRunner::oneStep | ( | double | currentTime, |
double | stepSize, | ||
bool | reset = true |
||
) |
Carry out a single integration step using a stepsize as indicated in the method call.
t0 | starting time |
tf | final time |
options | override current options. |
void rr::RoadRunner::regenerate | ( | bool | forceRegenerate = true , |
bool | reset = false |
||
) |
Regenerate this RoadRunner instance's ExecutableModel based on the model in its SBMLDocument
void rr::RoadRunner::removeCompartment | ( | const std::string & | cid, |
bool | forceRegenerate = true |
||
) |
Remove a compartment from the current model
cid | the ID of the compartment to be removed |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::removeEvent | ( | const std::string & | eid, |
bool | forceRegenerate = true |
||
) |
Remove an event from the current model
eid | the ID of the event to be removed |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::removeEventAssignments | ( | const std::string & | eid, |
const std::string & | vid, | ||
bool | forceRegenerate = true |
||
) |
Remove event assignments for given variable from an existing event
eid | the ID of the event |
eid | the ID of the vairable of the event assignments |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::removeInitialAssignment | ( | const std::string & | vid, |
bool | forceRegenerate = true |
||
) |
Remove initial assignment for a symbol from the current model
vid | ID of the symbol |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::removeParameter | ( | const std::string & | pid, |
bool | forceRegenerate = true |
||
) |
Remove a parameter from the current model
pid | the ID of the parameter to be removed |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::removeReaction | ( | const std::string & | rid, |
bool | deleteUnusedParameters = false , |
||
bool | forceRegenerate = true |
||
) |
Remove a reaction from the current model
rid | the ID of the reaction to be removed |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::removeRules | ( | const std::string & | vid, |
bool | useInitialValue = false , |
||
bool | forceRegenerate = true |
||
) |
Remove rules related to given variable from the current model
vid | ID of variable that rules assign formula to |
useInitialValue | a boolean value to indicate whether using initial value as current value when the assignment rule of a variable is removed otherwise, it will keep the value of assignment rule as current value |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::reset | ( | ) |
Picks up default options from config.
The current default is SelectionRecord::TIME | SelectionRecord::RATE | SelectionRecord::FLOATING.
void rr::RoadRunner::reset | ( | int | options | ) |
reset the model accordign to a bitfield specified by the SelectionRecord::SelectionType values.
Note, this would make more sense as an unsigned, however SWIG has issues mapping an enum to an unsigned, but seems to map enums just fine to an int.
For example, to reset the floating species, time and rate rule values:
options | a bitmask made from the SelectionRecord::SelectionTypes values. |
void rr::RoadRunner::resetSelectionLists | ( | ) |
resets time course and steady state selection lists to defaults
void rr::RoadRunner::setBoundary | ( | const std::string & | sid, |
bool | boundaryCondition, | ||
bool | forceRegenerate = true |
||
) |
Set the boundary condition of an existing species. By default, the boundary condition for a species is false.
sid | the ID of the species |
boundaryCondition | boundary condition to be set |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::setCompiler | ( | const std::string & | compiler | ) |
Set the name of the externa compiler to use. Some ModelGenerators may have no use for this value.
An exception is raised if the string is invalid.
void rr::RoadRunner::setConservedMoietyAnalysis | ( | bool | value | ) |
This method turns on / off the computation and adherence to conservation laws.
void rr::RoadRunner::setConstant | ( | const std::string & | sid, |
bool | constant, | ||
bool | forceRegenerate = true |
||
) |
Set the constant attribute for an existing species/ parameter/ compartment By default, the constant attribute is false.
sid | the ID of a species/ parameter/ compartment |
constant | the constant attribute to be set |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::setDiffStepSize | ( | double | val | ) |
Set the differential step size used in MCA routines like getCC.
void rr::RoadRunner::setGlobalParameterByName | ( | const std::string & | param, |
double | value | ||
) |
set the parameter with id
param | to |
value |
void rr::RoadRunner::setHasOnlySubstanceUnits | ( | const std::string & | sid, |
bool | hasOnlySubstanceUnits, | ||
bool | forceRegenerate = true |
||
) |
Set the hasOnlySubstanceUnits attribute for an existing species.
sid | the ID of a species |
hasOnlySubstanceUnits | the value of hasOnlySubstanceUnits attribute to be set |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::setInitAmount | ( | const std::string & | sid, |
double | initAmount, | ||
bool | forceRegenerate = true |
||
) |
Set initial amount for an existing species. Initial amount/concentration set before will be unset.
sid | the ID of a species |
initAmount | the initial amount to be set |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::setInitConcentration | ( | const std::string & | sid, |
double | initConcentration, | ||
bool | forceRegenerate = true |
||
) |
Set initial concentration for an existing species. Initial amount/concentration set before will be unset.
sid | the ID of a species |
initConcentration | the initial concentration to be set |
forceRegenerate | a boolean value to indicate if the model is regenerated after this function call default value is true to regenerate model after each call of editing function to save time for editing for multiple times, one could set this flag to true only in the last call of editing |
void rr::RoadRunner::setSteadyStateSelections | ( | const std::vector< rr::SelectionRecord > & | steadyStateSelections | ) |
makes a copy of an existing list of selection records. These will be saved and used for selection values in getSteadyStateValues().
void rr::RoadRunner::setSteadyStateSelections | ( | const std::vector< std::string > & | steadyStateSelections | ) |
parses the given list of strings and generates selections records which will be used for the steady state selections.
void rr::RoadRunner::setSteadyStateThreshold | ( | double | val | ) |
Set the steady state threshold used in getCC.
In the MCA routines, RoadRunner will keep trying to converge to a steady state until this threshold is met
void rr::RoadRunner::setValue | ( | const std::string & | id, |
double | value | ||
) |
sets the value coresponding to the given selection string
raises an exception in the selection string is invalid.
const ls::DoubleMatrix* rr::RoadRunner::simulate | ( | const Dictionary * | options = 0 | ) |
Simulate the current SBML model.
If options is null, then the current simulation settings (start time, end time, n steps) are used. If options is not null, then the current simulation settings are set to the values specified by options and they are used.
The options Dictionary may contain a large number of options, for a complete list of all available options for each integrator type,
For example, to perform a simulation from time 0 to 10 with 1000 steps, using a stiff integtator, you would:
Similarly, if one wants to use a stochastic integrator, such as the Gillespie integrator, this is set via the "integrator" key, i.e.
Here, the "integrator" specifies the integrator to use. The "stiff" key is only used by the deterministic solvers, and it is safely ignored by the stochastic solvers. Also, the "seed" sets the random seed that the integrator uses. For more information about all of the avaialble options for each integrator,
If one wants to not store the result matrix in memory and instead write it to a file during simulation, one can set the output_file option. When output file is nonempty, simulate() will write to its path once every Config::K_ROWS_PER_WRITE rows are generated and clear the matrix. So an empty result matrix is returned, and the last simulation results are not stored.
an | std::exception if any options are invalid. |
double rr::RoadRunner::steadyState | ( | const Dictionary * | dict = 0 | ) |
Compute the steady state of the model, returns the sum of squares of the solution
The steady state solver and whatever options it needs may be specified via the given dictionary. For a list of all available steady state solvers,
dict | a pointer to a dictionary which has the steady state options. May be NULL, in this case the existing options are used. |
double rr::RoadRunner::steadyStateApproximate | ( | const Dictionary * | dict = 0 | ) |
Appoximate the steady state of the model by checking the changes in time course simulation. Returns the sum of squares of the solution
Appoximation will use CVODE with variable step sizes.
dict | a pointer to a dictionary which has the steady state options. May be NULL, in this case the existing options are used. |
ls::DoubleMatrix rr::RoadRunner::steadyStateNamedArray | ( | const Dictionary * | dict = 0 | ) |
Like steadyState but returns a named array of the steady state values
void rr::RoadRunner::validateCurrentSBML | ( | ) |
Validate the current SBML