roadrunner
2.6.0
Fast simulator for SBML models
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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 |
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
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virtual |
hasKey("times"))
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.
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.
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.
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.