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

a way to find sbml model elements using the RoadRunner syntax. More...

#include <rrSelectionRecord.h>

Public Types

enum  SelectionType {
  TIME = (0x1 << 0) , CONCENTRATION = (0x1 << 1) , AMOUNT = (0x1 << 2) , RATE = (0x1 << 3) ,
  BOUNDARY = (0x1 << 4) , FLOATING = (0x1 << 5) , _COMPARTMENT = (0x1 << 6) , _GLOBAL_PARAMETER = (0x1 << 7) ,
  REACTION = (0x1 << 8) , INITIAL = (0x1 << 9) , CURRENT = (0x1 << 10) , UNSCALED = (0x1 << 11) ,
  ELASTICITY = (0x1 << 12) , CONTROL = (0x1 << 13) , EIGENVALUE_REAL = (0x1 << 14) , ELEMENT = (0x1 << 15) ,
  STOICHIOMETRY = (0x1 << 16) , UNKNOWN = (0x1 << 17) , DEPENDENT = (0x1 << 18) , INDEPENDENT = (0x1 << 19) ,
  CONSERVED_MOIETY = (0x1 << 20) , STATE_VECTOR = (0x1 << 21) , EVENT = (0x1 << 22) , EIGENVALUE_IMAG = (0x1 << 23) ,
  ALL = (0xffffffff) , EIGENVALUE_COMPLEX = EIGENVALUE_REAL | EIGENVALUE_IMAG , UNKNOWN_CONCENTRATION = UNKNOWN | CONCENTRATION , COMPARTMENT = _COMPARTMENT | INDEPENDENT | DEPENDENT | CURRENT ,
  GLOBAL_PARAMETER = _GLOBAL_PARAMETER | INDEPENDENT | DEPENDENT | CURRENT , FLOATING_AMOUNT = FLOATING | AMOUNT | INDEPENDENT | DEPENDENT | CURRENT , INDEPENDENT_FLOATING_AMOUNT = FLOATING | AMOUNT | INDEPENDENT | CURRENT , DEPENDENT_FLOATING_AMOUNT = FLOATING | AMOUNT | DEPENDENT | CURRENT ,
  FLOATING_CONCENTRATION = FLOATING | CONCENTRATION | INDEPENDENT | DEPENDENT | CURRENT , FLOATING_AMOUNT_RATE = FLOATING | RATE | DEPENDENT , FLOATING_CONCENTRATION_RATE = FLOATING | CONCENTRATION | RATE | DEPENDENT , BOUNDARY_AMOUNT = BOUNDARY | AMOUNT | INDEPENDENT | DEPENDENT | CURRENT ,
  INDEPENDENT_BOUNDARY_AMOUNT = BOUNDARY | AMOUNT | INDEPENDENT | CURRENT , DEPENDENT_BOUNDARY_AMOUNT = BOUNDARY | AMOUNT | DEPENDENT | CURRENT , BOUNDARY_CONCENTRATION = BOUNDARY | CONCENTRATION | INDEPENDENT | DEPENDENT | CURRENT , BOUNDARY_AMOUNT_RATE = BOUNDARY | RATE | DEPENDENT ,
  BOUNDARY_CONCENTRATION_RATE = BOUNDARY | CONCENTRATION | RATE | DEPENDENT , GLOBAL_PARAMETER_RATE = _GLOBAL_PARAMETER | RATE , REACTION_RATE = REACTION | RATE | DEPENDENT , COMPARTMENT_RATE = COMPARTMENT | RATE | DEPENDENT ,
  INITIAL_AMOUNT = INITIAL | AMOUNT | INDEPENDENT | DEPENDENT , INITIAL_FLOATING_AMOUNT = INITIAL | FLOATING | AMOUNT | INDEPENDENT | DEPENDENT , INITIAL_BOUNDARY_AMOUNT = INITIAL | BOUNDARY | AMOUNT | INDEPENDENT | DEPENDENT , INITIAL_CONCENTRATION = INITIAL | CONCENTRATION | INDEPENDENT | DEPENDENT ,
  INITIAL_FLOATING_CONCENTRATION = INITIAL | FLOATING | CONCENTRATION | INDEPENDENT | DEPENDENT , INITIAL_BOUNDARY_CONCENTRATION = INITIAL | BOUNDARY | CONCENTRATION | INDEPENDENT | DEPENDENT , INITIAL_COMPARTMENT = INITIAL | _COMPARTMENT | INDEPENDENT | DEPENDENT , INITIAL_GLOBAL_PARAMETER = INITIAL | _GLOBAL_PARAMETER | INDEPENDENT | DEPENDENT ,
  DEPENDENT_INITIAL_GLOBAL_PARAMETER = INITIAL | _GLOBAL_PARAMETER | DEPENDENT , UNSCALED_ELASTICITY = UNSCALED | ELASTICITY , UNSCALED_CONTROL = UNSCALED | CONTROL , UNKNOWN_ELEMENT = UNKNOWN | ELEMENT ,
  ALL_INDEPENDENT = ~DEPENDENT , ALL_DEPENDENT = ~INDEPENDENT , ALL_INDEPENDENT_AMOUNT = ~DEPENDENT & ~CONCENTRATION , ALL_DEPENDENT_AMOUNT = ~INDEPENDENT & ~CONCENTRATION ,
  ALL_INDEPENDENT_CONCENTRATION = ~DEPENDENT & ~AMOUNT , ALL_DEPENDENT_CONCENTRATION = ~INDEPENDENT & ~AMOUNT , MODEL_STATE = ALL_INDEPENDENT_AMOUNT & ~INITIAL , SBML_INITIALIZE = STATE_VECTOR
}
 

Public Member Functions

 SelectionRecord (const int &index=0, const SelectionType type=UNKNOWN, const std::string &p1="", const std::string &p2="")
 Selections really should be constructed by the RoadRunner::createSelection method. More...
 
 SelectionRecord (const std::string str)
 creates a empty selection.
 
std::string to_string () const
 get a short description of this selection, this returns a std::string compatable with RoadRunner::createSelection.
 
std::string to_repr () const
 gets a longer description of this selection, this is intended to called as a python repr
 

Public Attributes

int index
 After the selection record is created by the roadrunner object, this is an index into the variables list that the ExecutableModel has.
 
std::string p1
 For single argument selections, i.e. More...
 
std::string p2
 the second argument of two arg selections.
 
SelectionType selectionType
 the type of selection.
 

Detailed Description

a way to find sbml model elements using the RoadRunner syntax.

Member Enumeration Documentation

◆ SelectionType

Enumerator
TIME 

SelectionType for time.

CONCENTRATION 

SelectionType for concentrations.

Species must have either a CONCENTRATION or AMOUNT modifer to distinguish it.

AMOUNT 

SelectionType for amounts.

Species must have either a CONCENTRATION or AMOUNT modifer to distinguish it.

RATE 

SelectionType for rates.

BOUNDARY 

SelectionType for bounary species.

Species must have either a BOUNDARY or FLOATING modifiers.

FLOATING 

SelectionType for floating species.

Species must have either a BOUNDARY or FLOATING modifiers.

_COMPARTMENT 

SelectionType for comparments.

Compartments and parameters can be either current or initial values. These values with and underscore, '_' are intended to be used with either an CURRENT or INITIAL value modifier.

_GLOBAL_PARAMETER 

SelectionType for global parameters.

Compartments and parameters can be either current or initial values. These values with and underscore, '_' are intended to be used with either an CURRENT or INITIAL value modifier.

REACTION 

SelectionType for reactions.

INITIAL 

SelectionType for initial values.

SBML elements can be accessed as either a initial value, or a current value, they must have one or the other.

CURRENT 

SelectionType for current values.

SBML elements can be accessed as either a initial value, or a current value, they must have one or the other.

UNSCALED 

SelectionType for unscaled values.

ELASTICITY 

SelectionType for elasticities.

CONTROL 

SelectionType for control coefficients.

EIGENVALUE_REAL 

SelectionType for eigenvalues.

Eigenvalue without complex is real part of eigenvalue.

ELEMENT 

SelectionType for elements.

(Unused)

STOICHIOMETRY 

SelectionType for stoichiometries.

UNKNOWN 

SelectionType for unknown values.

DEPENDENT 

SelectionType for dependent species.

INDEPENDENT 

SelectionType for independent species.

CONSERVED_MOIETY 

SelectionType for conserved moieties.

STATE_VECTOR 

SelectionType for state vectors.

EVENT 

SelectionType for events.

EIGENVALUE_IMAG 

SelectionType for complex values.

The complex bit, off to get real values, on to get imaginary parts.

Only used with EIGENVALUE currently.

ALL 

SelectionType for everything.

EIGENVALUE_COMPLEX 

SelectionType for complex eigenvalues.

UNKNOWN_CONCENTRATION 

SelectionType for unknown concentrations.

COMPARTMENT 

SelectionType for the current compartment value.

GLOBAL_PARAMETER 

SelectionType for the current global parameter value.

FLOATING_AMOUNT 

SelectionType for current floating species amounts.

INDEPENDENT_FLOATING_AMOUNT 

SelectionType for independent floating species amounts.

DEPENDENT_FLOATING_AMOUNT 

SelectionType for dependent floating species amounts.

(Unused)

FLOATING_CONCENTRATION 

SelectionType for current floating species concentrations.

FLOATING_AMOUNT_RATE 

SelectionType for floating species amount rates (value, not reaction rates), these are always current.

FLOATING_CONCENTRATION_RATE 

SelectionType for floating species concentration rates (value, not reaction rates), these are always current.

(Unused)

BOUNDARY_AMOUNT 

SelectionType for boundary species amounts.

INDEPENDENT_BOUNDARY_AMOUNT 

SelectionType for independent boundary species amounts.

DEPENDENT_BOUNDARY_AMOUNT 

SelectionType for dependent boundary species amounts.

(Unused)

BOUNDARY_CONCENTRATION 

SelectionType for current boundary species concentrations.

BOUNDARY_AMOUNT_RATE 

SelectionType for boundary species amount rates (value, not reaction rates), these are always current.

BOUNDARY_CONCENTRATION_RATE 

SelectionType for boundary species concentration rates (value, not reaction rates), these are always current.

(Unused)

GLOBAL_PARAMETER_RATE 

SelectionType for global parameter rates.

REACTION_RATE 

SelectionType for reaction rate, always current.

COMPARTMENT_RATE 

SelectionType for compartment rate, always current.

INITIAL_AMOUNT 

SelectionType for initial species amounts.

INITIAL_FLOATING_AMOUNT 

SelectionType for initial floating species amounts.

INITIAL_BOUNDARY_AMOUNT 

SelectionType for initial boundary species amounts.

INITIAL_CONCENTRATION 

SelectionType for initial species concentrations.

INITIAL_FLOATING_CONCENTRATION 

SelectionType for initial floating species concentrations.

INITIAL_BOUNDARY_CONCENTRATION 

SelectionType for initial floating species concentrations.

INITIAL_COMPARTMENT 

SelectionType for initial compartment values.

INITIAL_GLOBAL_PARAMETER 

SelectionType for initial global parameter values.

DEPENDENT_INITIAL_GLOBAL_PARAMETER 

SelectionType for global parameters that have initial assignment rules.

UNSCALED_ELASTICITY 

SelectionType for unscaled elasticity.

UNSCALED_CONTROL 

SelectionType for unscaled control coefficient.

UNKNOWN_ELEMENT 

SelectionType for unscaled control coefficient.

ALL_INDEPENDENT 

SelectionType for all values related to independent species.

(Unused)

ALL_DEPENDENT 

SelectionType for all values related to dependent species.

(Unused)

ALL_INDEPENDENT_AMOUNT 

SelectionType for all independent species amount.

(Unused)

ALL_DEPENDENT_AMOUNT 

SelectionType for all dependent species amount.

(Unused)

ALL_INDEPENDENT_CONCENTRATION 

SelectionType for all independent species concentration.

(Unused)

ALL_DEPENDENT_CONCENTRATION 

SelectionType for all dependent species concentration.

(Unused)

MODEL_STATE 

The combination of values that uniquely define the current state of the sbml model.

Note, any sbml variable can be defined by a rule, the model state is defined as the set of variabls that define the current state of the model. These do not include the initial values as the initial values can not be changed by advancing the model with the integrator. (Unused)

SBML_INITIALIZE 

If this bit is set, then the reset function evaluates all of the SBML model init conditions (init values and all init assignment rules), and assigns them to the model state variable.

This setting brings the model back the originally loaded state.

Constructor & Destructor Documentation

◆ SelectionRecord()

rr::SelectionRecord::SelectionRecord ( const int &  index = 0,
const SelectionType  type = UNKNOWN,
const std::string &  p1 = "",
const std::string &  p2 = "" 
)

Selections really should be constructed by the RoadRunner::createSelection method.

This just creates a new ebmpy selection.

Member Data Documentation

◆ p1

std::string rr::SelectionRecord::p1

For single argument selections, i.e.

ec( S1 ), this is the argument, for two arg selections, this is the first arg.


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