roadrunner  2.6.0
Fast simulator for SBML models
Public Member Functions | Public Attributes | List of all members
rr::SimulateOptions Class Reference

This class is frozen, no new features RoadRunner simulation options. More...

#include <rrRoadRunnerOptions.h>

Public Member Functions

 SimulateOptions ()
 init with default options.
 
std::string toString () const
 get a description of this object, compatable with python str
 
std::string toRepr () const
 get a short descriptions of this object, compatable with python repr.
 
void loadSBMLSettings (const std::string &filename)
 
virtual void initialize ()
 
virtual double getNext (size_t step)
 
virtual void reset ()
 Reset all values to defaults.
 

Public Attributes

bool reset_model
 reset the model to the initial state.
 
bool structured_result
 Simulate should return a raw result matrix without adding any column names.
 
bool copy_result
 Make a copy of the simulation result in Python. More...
 
int steps
 The number of steps at which the output is sampled. More...
 
double start
 The start time of the simulation time-series data. More...
 
double duration
 The duration of the simulation run, in the model's units of time.
 
std::string output_file
 The ouptut file for simulation results. More...
 
std::vector< std::string > variables
 The variables (in addition to time) whose values will be saved in the result. More...
 
std::vector< std::string > amounts
 A list of the variable whose output in the results file is in amount (not concentration) units. More...
 
std::vector< std::string > concentrations
 A list of the variable whose output in the results file is in concentration (not amount) units. More...
 
std::vector< double > times
 

Detailed Description

This class is frozen, no new features RoadRunner simulation options.

This is the full set of options that determines how RoadRunner performs a simulation of an sbml model.

This is a superset of the values stored in a sbml test suite settings file, the documentation of the fields which correspond to an sbml test suite settings was taken from http://sbml.org

Member Function Documentation

◆ initialize()

void rr::SimulateOptions::initialize ( )
virtual

hasKey("times"))

Member Data Documentation

◆ amounts

std::vector<std::string> rr::SimulateOptions::amounts

A list of the variable whose output in the results file is in amount (not concentration) units.

This list of variables must be a subset of the names listed in variables.

◆ concentrations

std::vector<std::string> rr::SimulateOptions::concentrations

A list of the variable whose output in the results file is in concentration (not amount) units.

This list of variables must be a subset of the names listed in variables.

◆ copy_result

bool rr::SimulateOptions::copy_result

Make a copy of the simulation result in Python.

Large simulations should have this disabled.

◆ output_file

std::string rr::SimulateOptions::output_file

The ouptut file for simulation results.

If non-empty, then the simulation results are batch-written to output_file every Config::K_ROWS_PER_WRITE rows, and an empty result matrix is returned.

◆ start

double rr::SimulateOptions::start

The start time of the simulation time-series data.

Often this is 0, but not necessarily.

◆ steps

int rr::SimulateOptions::steps

The number of steps at which the output is sampled.

The samples are evenly spaced. When a simulation system calculates the data points to record, it will typically divide the duration by the number of time steps. Thus, for X steps, the output will have X+1 data rows.

◆ variables

std::vector<std::string> rr::SimulateOptions::variables

The variables (in addition to time) whose values will be saved in the result.

These are SBML model id's. Order is significant, as this determines the order of the columns in the result matrix.

Important: if a symbol in this list refers to a species in the model, then that symbol will also be listed in either the amount or concentration lists below.

NOTE:If a listed variable has two underscores in it ('__'), that variable is actually present only in a submodel of the main model, from the Hierarchical Model Composition package, in the format submodelID__variableID. If the model is flattened, the variable will appear automatically.


The documentation for this class was generated from the following files: