libRoadRunner C++ API  1.3
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rr::SimulateOptions Class Reference

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

#include <rrRoadRunnerOptions.h>

Inheritance diagram for rr::SimulateOptions:
rr::BasicDictionary rr::Dictionary

Public Member Functions

 SimulateOptions ()
 
std::string toString () const
 
std::string toRepr () const
 
virtual void setItem (const std::string &key, const rr::Variant &value)
 
- Public Member Functions inherited from rr::BasicDictionary
virtual Variant getItem (const std::string &key) const
 
virtual bool hasKey (const std::string &key) const
 
virtual int deleteItem (const std::string &key)
 
virtual std::vector< std::string > getKeys () const
 
virtual ~BasicDictionary ()
 
- Public Member Functions inherited from rr::Dictionary
virtual ~Dictionary ()
 

Public Attributes

bool reset_model
 
bool structured_result
 
bool copy_result
 
int steps
 
double start
 
double duration
 
std::vector< std::string > variables
 
std::vector< std::string > amounts
 
std::vector< std::string > concentrations
 

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

Constructor & Destructor Documentation

rr::SimulateOptions::SimulateOptions ( )

init with default options.

Member Function Documentation

void rr::SimulateOptions::setItem ( const std::string &  key,
const rr::Variant value 
)
virtual

sets an item in the internal unordered map.

Reimplemented from rr::BasicDictionary.

std::string rr::SimulateOptions::toRepr ( ) const

get a short descriptions of this object, compatable with python repr.

std::string rr::SimulateOptions::toString ( ) const

get a description of this object, compatable with python str

Member Data Documentation

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.

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.

bool rr::SimulateOptions::copy_result

Make a copy of the simulation result in Python. Large simulations should have this disabled.

double rr::SimulateOptions::duration

The duration of the simulation run, in the model's units of time.

bool rr::SimulateOptions::reset_model

reset the model to the initial state.

double rr::SimulateOptions::start

The start time of the simulation time-series data. Often this is 0, but not necessarily.

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.

bool rr::SimulateOptions::structured_result

Simulate should return a raw result matrix without adding any column names.

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: