roadrunner
2.6.0
Fast simulator for SBML models
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The main RoadRunner class. More...
#include <rrRoadRunner.h>
Public Member Functions | |
RoadRunner (unsigned int level=3, unsigned int version=2) | |
create an empty RoadRunner object with given SBML level and version. | |
RoadRunner (const std::string &uriOrSBML, const Dictionary *options=0) | |
load an sbml document from anywhere. More... | |
RoadRunner (const std::string &compiler, const std::string &tempDir, const std::string &supportCodeDir) | |
All three of the RoadRunner options default to the empty std::string, in this case, the default values are used. More... | |
RoadRunner (const RoadRunner &rr) | |
RoadRunner copy constructor. | |
void | operator= (const RoadRunner &rr) |
RoadRunner copy constructor. | |
virtual | ~RoadRunner () |
free any memory this class allocated | |
int | getInstanceID () |
When there are multiple instances of RoadRunner, this is the instance id. | |
int | getInstanceCount () |
Number of currently running RoadRunner instances. | |
std::string | getInfo () |
information about the current state of this object. | |
double | getCurrentTime () |
return the current time as a double | |
class Compiler * | getCompiler () |
The Compiler that the ModelGenerator is using to compile / interpret sbml code. | |
void | setCompiler (const std::string &compiler) |
Set the name of the externa compiler to use. More... | |
Integrator * | getIntegrator () |
get a pointer to the integrator which is currently being used to time evolve the system. | |
SteadyStateSolver * | getSteadyStateSolver () |
get a pointer to the current steady state solver | |
SensitivitySolver * | getSensitivitySolver () |
get a pointer to the current sensitivities solver | |
Integrator * | getIntegratorByName (const std::string &name) |
Get an integrator by name without switching the current integrator. | |
SteadyStateSolver * | getSteadyStateSolverByName (const std::string &name) |
Get an SteadyStateSolver by name without switching the current solver. | |
SensitivitySolver * | getSensitivitySolverByName (const std::string &name) |
Get an SensitivitySolver by name without switching the current solver. | |
Integrator * | makeIntegrator (const std::string &name) |
Make an integrator for the given name. | |
SteadyStateSolver * | makeSteadyStateSolver (const std::string &name) |
Make an SteadyStateSolver* for the given name. | |
SensitivitySolver * | makeSensitivitySolver (const std::string &name) |
Make SensitivitySolver for the given name. | |
std::vector< std::string > | getExistingIntegratorNames () |
Return a list of the names of all existing integrators. | |
std::vector< std::string > | getExistingSteadyStateSolverNames () |
Return a list of the names of all existing integrators. | |
std::vector< std::string > | getExistingSensitivitySolverNames () |
Return a list of the names of all existing sensitivity solvers. | |
void | setIntegrator (const std::string &name) |
set the current Integrator to More... | |
void | setSteadyStateSolver (const std::string &name) |
set the current SteadyStateSolver to More... | |
void | setSensitivitySolver (const std::string &name) |
set the current SensitivitySolver to More... | |
bool | integratorExists (const std::string &name) |
returns true if integrator More... | |
bool | steadyStateSolverExists (const std::string &name) |
returns true if SteadyStateSolver More... | |
bool | sensitivitySolverExists (const std::string &name) |
returns true if SensitivitySolver More... | |
bool | isModelLoaded () |
std::string | getModelName () |
returns the model name if a model is loaded, empty std::string otherwise. | |
void | setModelName (const std::string &name) |
sets the model name if a model is loaded. | |
std::string | getModelId () |
returns the model id if a model is loaded, empty std::string otherwise. | |
void | setModelId (const std::string &id) |
sets the model id if a model is loaded. | |
bool | clearModel () |
Clears the currently loaded model and all associated memory. More... | |
double | oneStep (double currentTime, double stepSize, bool reset=true) |
Carry out a single integration step using a stepsize as indicated in the method call. More... | |
double | internalOneStep (double currentTime, double stepSize, bool reset=true) |
Carry out a single internal solver integration step. More... | |
const ls::DoubleMatrix * | simulate (const SimulateOptions *options=0) |
Simulate the current SBML model. More... | |
const ls::DoubleMatrix * | simulate (double start, double stop, int points) |
simulate the model using currently set integrator More... | |
const ls::DoubleMatrix * | simulate (const std::vector< double > ×) |
simulate the model using currently set integrator More... | |
Matrix3D< double, double > | timeSeriesSensitivities (double start, double stop, int num, std::vector< std::string > params=std::vector< std::string >(), std::vector< std::string > species=std::vector< std::string >(), int k=0) |
simulate a timeseries with sensitivities from start to step with num data points. More... | |
void | saveState (std::string filename, char opt='b') |
similar to saveStateS but save data to file More... | |
std::stringstream * | saveStateS (char opt='b') |
save state as binary to a stringstream so it can be loaded again later. More... | |
void | loadState (const std::string &filename) |
Loads a roadrunner instance saved by saveState with the 'b' option. More... | |
void | loadStateS (std::stringstream *state) |
load state from a More... | |
const ls::DoubleMatrix * | getSimulationData () const |
RoadRunner keeps a copy of the simulation data around until the next call to simulate. More... | |
void | setSimulateOptions (const SimulateOptions &settings) |
SimulateOptions & | getSimulateOptions () |
get a reference to the SimulateOptions that were set either by setSimulateOptions or simulate. | |
RoadRunnerOptions & | getOptions () |
Get a reference to the options that determine how this class should behave. More... | |
void | setOptions (const RoadRunnerOptions &) |
std::string | getSBML (int level=0, int version=0) |
get the originally loaded sbml document as a std::string. More... | |
std::string | getCurrentSBML (int level=0, int version=0) |
Returns the SBML with the current model parameters. More... | |
void | reset () |
Picks up default options from config. More... | |
void | reset (int options) |
reset the model accordign to a bitfield specified by the SelectionRecord::SelectionType values. More... | |
void | resetSelectionLists () |
resets time course and steady state selection lists to defaults | |
void | changeInitialConditions (const std::vector< double > &ic) |
set the floating species initial concentrations. More... | |
ExecutableModel * | getModel () |
get a pointer to the ExecutableModel owned by the RoadRunner object. | |
void | load (const std::string &uriOrSBML, const Dictionary *options=0) |
load an sbml document from anywhere. More... | |
rr::SelectionRecord | createSelection (const std::string &str) |
create a selection record. More... | |
std::vector< rr::SelectionRecord > & | getSelections () |
Returns the currently selected columns that will be returned by calls to simulate() or simulateEx(,,). | |
double | getValue (const std::string &sel) |
Creates a new selection based on the selection std::string, and returns the value it queries. | |
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 () |
returns the values selected with SimulateOptions for the current model time / timestep") | |
void | getIds (int types, std::list< std::string > &ids) |
populates a given list with all the ids that this class can accept. More... | |
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 () |
returns a bit field of the ids that this class supports. | |
void | setValue (const std::string &id, double value) |
sets the value coresponding to the given selection std::string More... | |
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 > | getIndependentFloatingSpeciesAmountsV () |
Returns the independent floating species amounts as an array. More... | |
std::vector< double > | getDependentFloatingSpeciesAmountsV () |
Returns the dependent floating species amounts as an array. More... | |
std::vector< double > | getIndependentFloatingSpeciesConcentrationsV () |
Returns the independent floating species concentrations as an array. More... | |
std::vector< double > | getDependentFloatingSpeciesConcentrationsV () |
Returns the dependent floating species concentrations as an array. More... | |
ls::DoubleMatrix | getIndependentFloatingSpeciesAmountsNamedArray () |
Returns the independent floating species amounts as a named array. More... | |
ls::DoubleMatrix | getDependentFloatingSpeciesAmountsNamedArray () |
Returns the dependent floating species amounts as a named array. More... | |
ls::DoubleMatrix | getIndependentFloatingSpeciesConcentrationsNamedArray () |
Returns the independent floating concentrations amounts as a named array. More... | |
ls::DoubleMatrix | getDependentFloatingSpeciesConcentrationsNamedArray () |
Returns the dependent floating concentrations amounts 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 () |
compute the full Jacobian at the current operating point | |
ls::DoubleMatrix | getFullReorderedJacobian () |
ls::DoubleMatrix | getReducedJacobian (double h=-1.0) |
Compute the reduced Jacobian at the current operating point. More... | |
std::vector< std::complex< double > > | getFullEigenValues () |
Returns the eigenvalues of the full jacobian. More... | |
std::vector< std::complex< double > > | getReducedEigenValues () |
Returns the eigenvalues of the reduced jacobian. More... | |
ls::DoubleMatrix | getFullEigenValuesNamedArray () |
Returns the eigenvalues of the full jacobian as a named array. More... | |
ls::DoubleMatrix | getReducedEigenValuesNamedArray () |
Returns the eigenvalues of the reduced jacobian as a named array. More... | |
ls::DoubleMatrix | getLinkMatrix () |
ls::DoubleMatrix | getNrMatrix () |
get the reduced stochiometry matrix. More... | |
ls::DoubleMatrix | getKMatrix () |
Returns the K matrix (right nullspace of Nr) The K matrix has the structure, [I K0]'. | |
ls::DoubleMatrix | getReducedStoichiometryMatrix () |
get the reduced stochiometry matrix. More... | |
ls::DoubleMatrix | getFullStoichiometryMatrix () |
Get the stoichiometry matrix that coresponds to the full model, even it it was converted via conservation conversion. | |
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 () |
returns the list of floating species, but with a "eigen(...)" std::string wrapped around them. | |
double | getUnscaledParameterElasticity (const std::string &reactionName, const std::string ¶meterName) |
Returns the unscaled elasticity for a named reaction with respect to a named parameter. | |
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) |
This method turns on / off the computation and adherence to conservation laws. | |
bool | getConservedMoietyAnalysis () |
is conservation analysis enabled. More... | |
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 | getFluxThreshold () const |
Get the flux threshold used in getCC. More... | |
void | setFluxThreshold (double val) |
Set the flux threshold used in getCC. More... | |
double | getuCC (const std::string &variableName, const std::string ¶meterName) |
Get unscaled control coefficient with respect to a global parameter. More... | |
double | getCC (const std::string &variableName, const std::string ¶meterName) |
Get scaled control coefficient with respect to a global parameter. More... | |
double | getuEE (const std::string &reactionName, const std::string ¶meterName) |
Get unscaled elasticity coefficient with respect to a global parameter or species. | |
double | getuEE (const std::string &reactionName, const std::string ¶meterName, bool computeSteadystate) |
Get unscaled elasticity coefficient with respect to a global parameter or species. More... | |
double | getEE (const std::string &reactionName, const std::string ¶meterName) |
Get scaled elasticity coefficient with respect to a global parameter or species. | |
double | getEE (const std::string &reactionName, const std::string ¶meterName, bool computeSteadyState) |
Get scaled elasticity coefficient with respect to a global parameter or species. More... | |
ls::DoubleMatrix | getUnscaledElasticityMatrix () |
Compute the unscaled species elasticity matrix at the current operating point. | |
ls::DoubleMatrix | getScaledElasticityMatrix () |
Compute the unscaled elasticity matrix at the current operating point. | |
double | getScaledFloatingSpeciesElasticity (const std::string &reactionName, const std::string &speciesName) |
Compute the scaled elasticity for a given reaction and given species. | |
double | getUnscaledSpeciesElasticity (int reactionId, int speciesIndex) |
Get a single species elasticity value IMPORTANT: Assumes that the reaction rates have been precomputed at the operating point !! | |
void | addSpeciesConcentration (const std::string &sid, const std::string &compartment, double initConcentration, bool hasOnlySubstanceUnits=false, bool boundaryCondition=false, const std::string &substanceUnits="", bool forceRegenerate=true) |
Add a species to the current model and set its concentration. More... | |
void | addSpeciesAmount (const std::string &sid, const std::string &compartment, double initAmount=0, bool hasOnlySubstanceUnits=false, bool boundaryCondition=false, const std::string &substanceUnits="", bool forceRegenerate=true) |
Add a species to the current model. More... | |
void | removeSpecies (const std::string &sid, bool forceRegenerate=true) |
void | setBoundary (const std::string &sid, bool boundaryCondition, bool forceRegenerate=true) |
Set the boundary condition of an existing species. More... | |
void | setHasOnlySubstanceUnits (const std::string &sid, bool hasOnlySubstanceUnits, bool forceRegenerate=true) |
Set the hasOnlySubstanceUnits attribute for an existing species. More... | |
bool | getHasOnlySubstanceUnits (const std::string &sid) |
Get the hasOnlySubstanceUnits attribute for an existing species. More... | |
void | setInitAmount (const std::string &sid, double initAmount, bool forceRegenerate=true) |
Set initial amount for an existing species. More... | |
void | setInitConcentration (const std::string &sid, double initConcentration, bool forceRegenerate=true) |
Set initial concentration for an existing species. More... | |
void | 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. More... | |
void | addReaction (const std::string &sbmlRep, bool forceRegenerate=true) |
void | addReaction (const std::string &rid, std::vector< std::string > reactants, std::vector< std::string > products, const std::string &kineticLaw, bool forceRegenerate=true) |
void | removeReaction (const std::string &rid, bool deleteUnusedParameters=false, bool forceRegenerate=true) |
Remove a reaction from the current model. More... | |
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) |
Get the kinetic law of an existing reaction in the current model. More... | |
void | addParameter (const std::string &pid, double value, bool forceRegenerate=true) |
Add a parameter to the current model. More... | |
void | removeParameter (const std::string &pid, bool forceRegenerate=true) |
Remove a parameter from the current model. More... | |
void | addCompartment (const std::string &cid, double initVolume, bool forceRegenerate=true) |
Add a compartment to the current model. More... | |
void | removeCompartment (const std::string &cid, bool forceRegenerate=true) |
Remove a compartment from the current model. More... | |
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) |
Remove rules related to given variable from the current model. More... | |
void | addInitialAssignment (const std::string &vid, const std::string &formula, bool forceRegenerate=true) |
void | removeInitialAssignment (const std::string &vid, bool forceRegenerate=true, bool errIfNotExist=true) |
Remove initial assignment for a symbol from the current model. More... | |
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) |
Remove event assignments for given variable from an existing event. More... | |
void | removeEvent (const std::string &eid, bool forceRegenerate=true) |
Remove an event from the current model. More... | |
void | validateCurrentSBML () |
Validate the current SBML. | |
double | mcaSteadyState () |
double | steadyState (Dictionary *dict=0) |
Compute the steady state of the model, returns the sum of squares of the solution. More... | |
ls::DoubleMatrix | steadyStateNamedArray (const Dictionary *dict=0) |
Like steadyState but returns a named array of the steady state values. | |
std::vector< rr::SelectionRecord > & | getSteadyStateSelections () |
returns the current set of steady state selections. | |
void | 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 | setSteadyStateSelections (const std::vector< rr::SelectionRecord > &steadyStateSelections) |
makes a copy of an existing list of selection records. More... | |
std::vector< double > | 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. | |
std::vector< std::string > | getSteadyStateSelectionStrings () const |
Returns a std::vector of the steady state selection strings. | |
ls::DoubleMatrix | getSteadyStateValuesNamedArray () |
Like getSteadyStateValues but returns a named array. | |
void | regenerateModel (bool forceRegenerate=true, bool reset=false) |
regenerate a model, this recompiles the internal runtime model. More... | |
void | setBoundarySpeciesByIndex (const int &index, const double &value) |
Alias for this function on the child model object. | |
int | getNumberOfIndependentSpecies () |
Alias for this function on the child model object. | |
int | getNumberOfDependentSpecies () |
Alias for this function on the child model object. | |
std::vector< std::string > | getGlobalParameterIds () |
Alias for this function on the child model object. More... | |
std::vector< std::string > | getBoundarySpeciesIds () |
Alias for this function on the child model object. | |
std::vector< std::string > | getAssignmentRuleIds () |
Get the Ids of the elements assigned by assignment rules. | |
std::vector< std::string > | getRateRuleIds () |
Get the Ids of the elements assigned by rate rules. | |
std::vector< std::string > | getInitialAssignmentIds () |
Get the Ids of the elements with an initial assignment. | |
std::vector< std::string > | getBoundarySpeciesConcentrationIds () |
Gets the ids for all boundary species concentrations. | |
double | getBoundarySpeciesByIndex (const int &index) |
Alias for this function on the child model object. | |
double | getGlobalParameterByIndex (const int &index) |
Alias for this function on the child model object. More... | |
void | setGlobalParameterByName (const std::string ¶m, double value) |
set the parameter with id More... | |
double | getGlobalParameterByName (const std::string ¶m) |
get the value of global parameter with id More... | |
std::vector< double > | getConservedMoietyValues () |
Returns the sum of each conserved cycle. More... | |
std::vector< std::string > | getConservedMoietyIds () |
void | setSeed (long int seed, bool resetModel=true) |
Set the value of Config::RANDOM_SEED. | |
int64_t | getSeed (const std::string &integratorName="") |
Returns the value of Config::RANDOM_SEED. | |
void | resetSeed () |
Reset seed's value. More... | |
int | getNumberOfReactions () |
Alias for this function on the child model object. | |
double | getReactionRate (const int &index) |
Alias for this function on the child model object. | |
double | getRateOfChange (const int &index) |
Alias for this function on the child model object. | |
std::vector< std::string > | getRateOfChangeIds () |
Alias for this function on the child model object. | |
int | getNumberOfCompartments () |
Alias for this function on the child model object. | |
void | setCompartmentByIndex (const int &index, const double &value) |
Alias for this function on the child model object. | |
double | getCompartmentByIndex (const int &index) |
Alias for this function on the child model object. | |
std::vector< std::string > | getCompartmentIds () |
Alias for this function on the child model object. | |
int | getNumberOfBoundarySpecies () |
Alias for this function on the child model object. | |
void | setBoundarySpeciesConcentrations (const std::vector< double > &values) |
Alias for this function on the child model object. | |
void | setBoundarySpeciesAmounts (const std::vector< double > &values) |
Alias for this function on the child model object. | |
int | getNumberOfFloatingSpecies () |
Alias for this function on the child model object. | |
double | getFloatingSpeciesByIndex (int index) |
Alias for this function on the child model object. | |
void | setFloatingSpeciesByIndex (int index, double value) |
Alias for this function on the child model object. | |
std::vector< double > | getFloatingSpeciesConcentrationsV () |
Alias for this function on the child model object. | |
std::vector< double > | getFloatingSpeciesAmountsV () |
Alias for this function on the child model object. | |
std::vector< double > | getBoundarySpeciesConcentrationsV () |
Alias for this function on the child model object. | |
std::vector< double > | getBoundarySpeciesAmountsV () |
Alias for this function on the child model object. | |
std::vector< double > | getFloatingSpeciesInitialConcentrations () |
Alias for this function on the child model object. | |
void | setFloatingSpeciesConcentrations (const std::vector< double > &values) |
Alias for this function on the child model object. | |
void | setFloatingSpeciesInitialConcentrationByIndex (const int &index, const double &value) |
Alias for this function on the child model object. | |
void | setFloatingSpeciesInitialConcentrations (const std::vector< double > &values) |
Alias for this function on the child model object. | |
std::vector< std::string > | getFloatingSpeciesIds () |
Alias for this function on the child model object. | |
std::vector< std::string > | getFloatingSpeciesInitialConditionIds () |
Alias for this function on the child model object. | |
size_t | getNumberOfGlobalParameters () |
Alias for this function on the child model object. | |
void | setGlobalParameterByIndex (const int index, const double value) |
Alias for this function on the child model object. | |
std::vector< double > | getGlobalParameterValues () |
Alias for this function on the child model object. More... | |
void | evalModel () |
Updates the model based on all recent changes. | |
std::vector< double > | getReactionRates () |
Alias for this function on the child model object. More... | |
std::vector< std::string > | getReactionIds () |
Alias for this function on the child model object. More... | |
Static Public Member Functions | |
static std::string | getParamPromotedSBML (const std::string &sArg) |
Given an sbml document or path to an sbml document, this method moves all the local parameters to global parameters. | |
static std::vector< std::string > | getRegisteredIntegratorNames () |
Return a std::vector of the names of all registered integrators. | |
static std::vector< std::string > | getRegisteredSteadyStateSolverNames () |
Return a std::vector of the names of all registered SteadyStateSolver names. | |
static std::vector< std::string > | getRegisteredSensitivitySolverNames () |
Return a std::vector of the names of all registered sensitivity solvers. | |
static void | registerSolvers () |
Ensures all integrators and steady state solvers are registered. | |
static std::string | getExtendedVersionInfo () |
getVersion plus info about dependent libs versions. More... | |
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 | ( | const std::string & | uriOrSBML, |
const Dictionary * | options = 0 |
||
) |
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. |
Register solvers
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 std::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. |
void rr::RoadRunner::addCompartment | ( | const std::string & | cid, |
double | initVolume, | ||
bool | forceRegenerate = true |
||
) |
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 |
||
) |
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::addSpeciesAmount | ( | const std::string & | sid, |
const std::string & | compartment, | ||
double | initAmount = 0 , |
||
bool | hasOnlySubstanceUnits = false , |
||
bool | boundaryCondition = false , |
||
const std::string & | substanceUnits = "" , |
||
bool | forceRegenerate = true |
||
) |
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 |
hasOnlySubstanceUnits | the boolean value of the hasOnlySubstanceUnits attribute, indicating whether the species is to be used as an amount when encountered in formulas elsewhere in the model. |
boundaryCondition | the boolean value of the boundaryCondition attribute, indicating whether the species is a boundary species. |
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 |
void rr::RoadRunner::addSpeciesConcentration | ( | const std::string & | sid, |
const std::string & | compartment, | ||
double | initConcentration, | ||
bool | hasOnlySubstanceUnits = false , |
||
bool | boundaryCondition = false , |
||
const std::string & | substanceUnits = "" , |
||
bool | forceRegenerate = true |
||
) |
Add a species to the current model and set its concentration.
sid | the ID of the species to be added |
compartment | the compartment of the species to be added |
initConcentration | the initial concentration of the species to be added |
hasOnlySubstanceUnits | the boolean value of the hasOnlySubstanceUnits attribute, indicating whether the species is to be used as an amount when encountered in formulas elsewhere in the model. |
boundaryCondition | the boolean value of the boundaryCondition attribute, indicating whether the species is a boundary species. |
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 |
void rr::RoadRunner::changeInitialConditions | ( | const std::vector< double > & | ic | ) |
set the floating species initial concentrations.
equivalent to ExecutableModel::reset, then ExecutableModel::setFloatingSpeciesConcentrations
bool rr::RoadRunner::clearModel | ( | ) |
Clears the currently loaded model and all associated memory.
Deletes jitted code and libStruct data
SelectionRecord rr::RoadRunner::createSelection | ( | const std::string & | str | ) |
create a selection record.
This record can be used to select values.
ls::DoubleMatrix rr::RoadRunner::getBoundarySpeciesAmountsNamedArray | ( | ) |
Returns the boundary species amounts as a named array.
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.
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 |
||
) |
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.
ls::DoubleMatrix rr::RoadRunner::getDependentFloatingSpeciesAmountsNamedArray | ( | ) |
Returns the dependent floating species amounts as a named array.
std::vector< double > rr::RoadRunner::getDependentFloatingSpeciesAmountsV | ( | ) |
Returns the dependent floating species amounts as an array.
ls::DoubleMatrix rr::RoadRunner::getDependentFloatingSpeciesConcentrationsNamedArray | ( | ) |
Returns the dependent floating concentrations amounts as a named array.
std::vector< double > rr::RoadRunner::getDependentFloatingSpeciesConcentrationsV | ( | ) |
Returns the dependent floating species concentrations as an array.
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, | ||
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.
|
static |
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.
double rr::RoadRunner::getFluxThreshold | ( | ) | const |
Get the flux 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< std::complex< double > > rr::RoadRunner::getFullEigenValues | ( | ) |
Returns the eigenvalues of the full jacobian.
This returns a vector of Complex numbers. In the python bindings, the values are complex only if there are non-zero imaginary parts of the values.
DoubleMatrix rr::RoadRunner::getFullEigenValuesNamedArray | ( | ) |
Returns the eigenvalues of the full jacobian as a named array.
This returns an N x 2 matrix where the first column is the real values and the second is the imaginary part. The rows are labeled with the corresponding species ids, and the columns are labeled 'real' and 'imaginary'.
double rr::RoadRunner::getGlobalParameterByIndex | ( | const int & | index | ) |
Alias for this function on the child model object.
double rr::RoadRunner::getGlobalParameterByName | ( | const std::string & | param | ) |
get the value of global parameter with id
param |
std::vector< std::string > rr::RoadRunner::getGlobalParameterIds | ( | ) |
Alias for this function on the child model object.
use ExecutableModel::getGlobalParameterIds
std::vector< double > rr::RoadRunner::getGlobalParameterValues | ( | ) |
Alias for this function on the child model object.
bool rr::RoadRunner::getHasOnlySubstanceUnits | ( | const std::string & | sid | ) |
Get the hasOnlySubstanceUnits attribute for an existing species.
sid | the ID of a species |
void rr::RoadRunner::getIds | ( | int | types, |
std::list< std::string > & | ids | ||
) |
populates a given list with all the ids that this class can accept.
types is -1 when SelectionRecord is set to ALL.
ls::DoubleMatrix rr::RoadRunner::getIndependentFloatingSpeciesAmountsNamedArray | ( | ) |
Returns the independent floating species amounts as a named array.
std::vector< double > rr::RoadRunner::getIndependentFloatingSpeciesAmountsV | ( | ) |
Returns the independent floating species amounts as an array.
ls::DoubleMatrix rr::RoadRunner::getIndependentFloatingSpeciesConcentrationsNamedArray | ( | ) |
Returns the independent floating concentrations amounts as a named array.
std::vector< double > rr::RoadRunner::getIndependentFloatingSpeciesConcentrationsV | ( | ) |
Returns the independent floating species concentrations as an array.
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::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::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,
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< std::string > rr::RoadRunner::getReactionIds | ( | ) |
Alias for this function on the child model object.
returns a list of reaction ids obtained from ExecutableModel::getReactionId
std::vector< double > rr::RoadRunner::getReactionRates | ( | ) |
Alias for this function on the child model object.
std::vector< std::complex< double > > rr::RoadRunner::getReducedEigenValues | ( | ) |
Returns the eigenvalues of the reduced jacobian.
This returns a vector of Complex numbers. In the python bindings, the values are complex only if there are non-zero imaginary parts of the values.
DoubleMatrix rr::RoadRunner::getReducedEigenValuesNamedArray | ( | ) |
Returns the eigenvalues of the reduced jacobian as a named array.
This returns an N x 2 matrix where the first column is the real values and the second is the imaginary part. The rows are labeled with the corresponding species ids, and the columns are labeled 'real' and 'imaginary'.
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().
std::string rr::RoadRunner::getSBML | ( | int | level = 0 , |
int | version = 0 |
||
) |
get the originally loaded sbml document as a std::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
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.
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
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, | ||
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.
bool rr::RoadRunner::integratorExists | ( | const std::string & | name | ) |
returns true if integrator
name | exists. |
Use getRegisteredIntegratorNames to get a list of available integrator solver names.
double rr::RoadRunner::internalOneStep | ( | double | currentTime, |
double | stepSize, | ||
bool | reset = true |
||
) |
Carry out a single internal solver integration step.
currentTime | current time |
stepSize | the step size |
reset | whether to reset the model (defaults to true). |
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. |
void rr::RoadRunner::loadState | ( | const std::string & | filename | ) |
Loads a roadrunner instance saved by saveState with the 'b' option.
void rr::RoadRunner::loadStateS | ( | std::stringstream * | state | ) |
load state from a
state | stringstream that was produced by RoadRunner::saveStateS. |
The stingstream pointer should be heap allocated and generated from RoadRunner::saveStateS. It is an error to use a stringstream that was generated in any other way. The memory associated with the stringstream is automatically cleaned up after loading the state.
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.
currentTime | current time |
stepSize | the step size |
reset | whether to reset the model (defaults to true). |
void rr::RoadRunner::regenerateModel | ( | bool | forceRegenerate = true , |
bool | reset = false |
||
) |
regenerate a model, this recompiles the internal runtime model.
This would be used after a series of addSpecies, addReaction calls and the model is then ready to be compiled into executable form.
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 |
vid | 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 , |
||
bool | errIfNotExist = 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 |
deleteUnusedParameters; | a boolean value to indicate whether to remove unused parameters from the model as well. |
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 std::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::resetSeed | ( | ) |
Reset seed's value.
Set the value of Config::RANDOM_SEED to -1
void rr::RoadRunner::saveState | ( | std::string | filename, |
char | opt = 'b' |
||
) |
similar to saveStateS but save data to file
filename | the filename to save the data to. |
opt | either 'b' (default) or 'r'. The latter is used for debugging. |
std::stringstream * rr::RoadRunner::saveStateS | ( | char | opt = 'b' | ) |
save state as binary to a stringstream so it can be loaded again later.
opt | either 'b' (default) or 'r'. The latter is used for debugging. |
bool rr::RoadRunner::sensitivitySolverExists | ( | const std::string & | name | ) |
returns true if SensitivitySolver
name | exists. |
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 std::string is invalid.
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::setFluxThreshold | ( | double | val | ) |
Set the flux threshold used in getCC.
In getCC, RoadRunner will return 0.0 for flux control coefficients if the
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::setIntegrator | ( | const std::string & | name | ) |
set the current Integrator to
name; |
void rr::RoadRunner::setSensitivitySolver | ( | const std::string & | name | ) |
set the current SensitivitySolver to
name; |
use getRegisteredSensitivitySolverNames to get a list of available sensitivity solver names
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::setSteadyStateSolver | ( | const std::string & | name | ) |
set the current SteadyStateSolver to
name; |
use getRegisteredSteadyStateSolverNames to get a list of available names
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 std::string
raises an exception in the selection std::string is invalid.
const ls::DoubleMatrix * rr::RoadRunner::simulate | ( | const SimulateOptions * | 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, options specific to a particular integrator, such as the 'seed' option with the Gillespie integrator, this is set via the 'setIntegrator' "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 available 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. |
const ls::DoubleMatrix * rr::RoadRunner::simulate | ( | const std::vector< double > & | times | ) |
simulate the model using currently set integrator
times | a vector of all the time outputs desired. |
const ls::DoubleMatrix * rr::RoadRunner::simulate | ( | double | start, |
double | stop, | ||
int | points | ||
) |
simulate the model using currently set integrator
start | starting time to simulate |
stop | what time point does the simulation end? |
points | how many points to output (one greater than the number of steps to take). |
double rr::RoadRunner::steadyState | ( | 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. |
bool rr::RoadRunner::steadyStateSolverExists | ( | const std::string & | name | ) |
returns true if SteadyStateSolver
name | exists. |
Matrix3D< double, double > rr::RoadRunner::timeSeriesSensitivities | ( | double | start, |
double | stop, | ||
int | num, | ||
std::vector< std::string > | params = std::vector<std::string>() , |
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std::vector< std::string > | species = std::vector<std::string>() , |
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int | k = 0 |
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) |
simulate a timeseries with sensitivities from start to step with num data points.
Matrix3D indexed by time. Each element of the 3D matrix is a Matrix<double> with rows and columns parameters and model variables respectively. The parameter k determines the kth order derivative of the sensitivity information that will be returned
start | starting time for time series simulation |
stop | last time point for time series simulation |
num | number of data points to simulate. Determines Z of Matrix3D. |
params | vector of parameters that you want sensitivity for. When empty (default), compute sensitivities for all parameters vs all variables. |
species | vector of species to include in the results Default is empty, in which case all species will be included. All species are selected during solving and slicing only occurs at the end. |
k | (default 0) return the kth other derivative of the sensitivity data. |