rrSelectionRecord

class SelectionRecord

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

Public Types

enum SelectionType

Values:

enumerator TIME

SelectionType for time.

enumerator CONCENTRATION

SelectionType for concentrations.

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

enumerator AMOUNT

SelectionType for amounts.

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

enumerator RATE

SelectionType for rates.

enumerator BOUNDARY

SelectionType for bounary species.

Species must have either a BOUNDARY or FLOATING modifiers.

enumerator FLOATING

SelectionType for floating species.

Species must have either a BOUNDARY or FLOATING modifiers.

enumerator _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.

enumerator _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.

enumerator REACTION

SelectionType for reactions.

enumerator 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.

enumerator 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.

enumerator UNSCALED

SelectionType for unscaled values.

enumerator ELASTICITY

SelectionType for elasticities.

enumerator CONTROL

SelectionType for control coefficients.

enumerator EIGENVALUE_REAL

SelectionType for eigenvalues.

Eigenvalue without complex is real part of eigenvalue.

enumerator ELEMENT

SelectionType for elements.

(Unused)

enumerator STOICHIOMETRY

SelectionType for stoichiometries.

enumerator UNKNOWN

SelectionType for unknown values.

enumerator DEPENDENT

SelectionType for dependent species.

enumerator INDEPENDENT

SelectionType for independent species.

enumerator CONSERVED_MOIETY

SelectionType for conserved moieties.

enumerator STATE_VECTOR

SelectionType for state vectors.

enumerator EVENT

SelectionType for events.

enumerator EIGENVALUE_IMAG

SelectionType for complex values.

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

Only used with EIGENVALUE currently.

enumerator ALL

SelectionType for everything.

enumerator EIGENVALUE_COMPLEX

SelectionType for complex eigenvalues.

enumerator UNKNOWN_CONCENTRATION

SelectionType for unknown concentrations.

enumerator COMPARTMENT

SelectionType for the current compartment value.

enumerator GLOBAL_PARAMETER

SelectionType for the current global parameter value.

enumerator FLOATING_AMOUNT

SelectionType for current floating species amounts.

enumerator INDEPENDENT_FLOATING_AMOUNT

SelectionType for independent floating species amounts.

enumerator DEPENDENT_FLOATING_AMOUNT

SelectionType for dependent floating species amounts.

(Unused)

enumerator FLOATING_CONCENTRATION

SelectionType for current floating species concentrations.

enumerator FLOATING_AMOUNT_RATE

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

enumerator FLOATING_CONCENTRATION_RATE

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

(Unused)

enumerator BOUNDARY_AMOUNT

SelectionType for boundary species amounts.

enumerator INDEPENDENT_BOUNDARY_AMOUNT

SelectionType for independent boundary species amounts.

enumerator DEPENDENT_BOUNDARY_AMOUNT

SelectionType for dependent boundary species amounts.

(Unused)

enumerator BOUNDARY_CONCENTRATION

SelectionType for current boundary species concentrations.

enumerator BOUNDARY_AMOUNT_RATE

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

enumerator BOUNDARY_CONCENTRATION_RATE

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

(Unused)

enumerator GLOBAL_PARAMETER_RATE

SelectionType for global parameter rates.

enumerator REACTION_RATE

SelectionType for reaction rate, always current.

enumerator COMPARTMENT_RATE

SelectionType for compartment rate, always current.

enumerator INITIAL_AMOUNT

SelectionType for initial species amounts.

enumerator INITIAL_FLOATING_AMOUNT

SelectionType for initial floating species amounts.

enumerator INITIAL_BOUNDARY_AMOUNT

SelectionType for initial boundary species amounts.

enumerator INITIAL_CONCENTRATION

SelectionType for initial species concentrations.

enumerator INITIAL_FLOATING_CONCENTRATION

SelectionType for initial floating species concentrations.

enumerator INITIAL_BOUNDARY_CONCENTRATION

SelectionType for initial floating species concentrations.

enumerator INITIAL_COMPARTMENT

SelectionType for initial compartment values.

enumerator INITIAL_GLOBAL_PARAMETER

SelectionType for initial global parameter values.

enumerator DEPENDENT_INITIAL_GLOBAL_PARAMETER

SelectionType for global parameters that have initial assignment rules.

enumerator UNSCALED_ELASTICITY

SelectionType for unscaled elasticity.

enumerator UNSCALED_CONTROL

SelectionType for unscaled control coefficient.

enumerator UNKNOWN_ELEMENT

SelectionType for unscaled control coefficient.

enumerator ALL_INDEPENDENT

SelectionType for all values related to independent species.

(Unused)

enumerator ALL_DEPENDENT

SelectionType for all values related to dependent species.

(Unused)

enumerator ALL_INDEPENDENT_AMOUNT

SelectionType for all independent species amount.

(Unused)

enumerator ALL_DEPENDENT_AMOUNT

SelectionType for all dependent species amount.

(Unused)

enumerator ALL_INDEPENDENT_CONCENTRATION

SelectionType for all independent species concentration.

(Unused)

enumerator ALL_DEPENDENT_CONCENTRATION

SelectionType for all dependent species concentration.

(Unused)

enumerator 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)

enumerator 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.

Public 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.

This just creates a new ebmpy selection.

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 Members

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.

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

std::string p2

the second argument of two arg selections.

SelectionType selectionType

the type of selection.