roadrunner
2.6.0
Fast simulator for SBML models
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generic interface for sensitivity solvers that integrate the model and compute sensitivities at each time point More...
#include <SensitivitySolver.h>
Public Member Functions | |
virtual double | integrate (double t0, double hstep)=0 |
integrate the model from t0 to t0 + hstep. More... | |
virtual Matrix3D< double, double > | solveSensitivities (double start, double stop, int num, std::vector< std::string > params, std::vector< std::string > species, int k)=0 |
simulate a timeseries with sensitivities from start to step with num data points. More... | |
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virtual rr::Matrix< double > | getSensitivityMatrix (int k=0)=0 |
get current values of sensitivities of model variables to parameters. More... | |
Solver ()=default | |
Solver (ExecutableModel *model) | |
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Solver (ExecutableModel *model) | |
void | updateSettings (Dictionary *inputSettings) |
Update settings values. More... | |
std::vector< std::string > | getSettings () const |
Get a list of all settings for this solver. More... | |
std::unordered_map< std::string, Setting > & | getSettingsMap () |
get settings for this solver More... | |
virtual void | resetSettings () |
Reset all settings to their respective default values. | |
virtual Setting | getValue (const std::string &key) const |
Get the value of an integrator setting. More... | |
virtual Setting | hasValue (const std::string &key) const |
Return true if this setting is supported by the integrator. More... | |
virtual size_t | getNumParams () const |
Get the number of parameters. More... | |
virtual std::string | getParamName (size_t n) const |
Get the name of the parameter at index n. More... | |
virtual std::string | getParamDisplayName (int n) const |
Get the display name of the parameter at index n. More... | |
virtual std::string | getParamHint (int n) const |
Get the hint of the parameter at index n. More... | |
virtual std::string | getParamDesc (int n) const |
Get the description of the parameter at index n. More... | |
virtual std::string | getValueAsString (const std::string &key) |
Wrapper for getValue which converts output to a specific type. More... | |
virtual void | setValue (const std::string &key, Setting value) |
virtual std::string | getSettingsRepr () const |
Get the solver settings as a std::string. More... | |
virtual std::string | settingsPyDictRepr () const |
Python dictionary-style std::string representation of settings. More... | |
virtual std::string | toString () const |
Return a std::string representation of the solver. More... | |
virtual std::string | toRepr () const |
Return std::string representation a la Python repr method. More... | |
const std::string & | getDisplayName (const std::string &key) const |
Gets the hint associated with a given key. More... | |
const std::string & | getHint (const std::string &key) const |
Gets the hint associated with a given key. More... | |
const std::string & | getDescription (const std::string &key) const |
Gets the description associated with a given key. More... | |
Setting::TypeId | getType (const std::string &key) const |
Gets the type associated with a given key. More... | |
virtual void | syncWithModel (ExecutableModel *m)=0 |
Called whenever a new model is loaded to allow integrator to reset internal state. More... | |
virtual ExecutableModel * | getModel () const |
returns the pointer to the ExecutableModel | |
virtual std::string | getName () const=0 |
Gets the name associated with this Solver type. More... | |
virtual std::string | getHint () const=0 |
Gets the hint associated with this Solver type. More... | |
virtual std::string | getDescription () const=0 |
Gets the description associated with this Solver type. More... | |
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virtual std::string | getName () const =0 |
Gets the name associated with this Solver type. More... | |
virtual std::string | getDescription () const =0 |
Gets the description associated with this Solver type. More... | |
virtual std::string | getHint () const =0 |
Gets the hint associated with this Solver type. More... | |
virtual Solver * | construct (ExecutableModel *model) const =0 |
Constructs a new Solver of a given type. More... | |
Additional Inherited Members | |
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using | SettingsList = std::vector< std::string > |
using | SettingsMap = std::unordered_map< std::string, Setting > |
using | DisplayNameMap = std::unordered_map< std::string, std::string > |
using | HintMap = std::unordered_map< std::string, std::string > |
using | DescriptionMap = std::unordered_map< std::string, std::string > |
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SettingsList | sorted_settings |
SettingsMap | settings |
DisplayNameMap | display_names_ |
HintMap | hints |
DescriptionMap | descriptions |
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void | addSetting (const std::string &name, const Setting &val, const std::string &display_name, const std::string &hint, const std::string &description) |
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ExecutableModel * | mModel = nullptr |
non-owning pointer to model | |
generic interface for sensitivity solvers that integrate the model and compute sensitivities at each time point
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pure virtual |
integrate the model from t0 to t0 + hstep.
integrating the model should update the sensitivities, which are available from getSensitivities()
Implemented in rr::ForwardSensitivitySolver.
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pure virtual |
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. Note that unlike for params, reducing the number of species does not solve faster because the matrix slicing only occurs at the end. When empty (default) all species are returned. |
k | (default 0) return the kth other derivative of the sensitivity data. |
Implemented in rr::ForwardSensitivitySolver.