Index

A

addelements() (brn.brn.Brn method)

B

Brn (class in brn.brn) brn.brn (module) brn.brncomp (module) brn.brneval (module) brn.conserv (module)

brn.mathutils (module) brn.sbmlimport (module) brn.simulation (module) brn.steadystate (module) BrnEvaluator (class in brn.brneval)

C

compile() (brn.brneval.CythonBrnEvaluator method) (brn.simulation.SundialsSimulator method) compile_model() (in module brn.simulation) compute() (brn.steadystate.SteadyState method) compute_outputs() (brn.simulation.GillespieSimulator method) (brn.simulation.Simulator method) Conservation (class in brn.conserv)

conservation_analysis() (brn.brn.Brn method) convert_points() (brn.brneval.BrnEvaluator method) convert_trajectory() (brn.simulation.Simulator method) CythonBrnEvaluator (class in brn.brneval)

D

do_compilation() (brn.simulation.SundialsSimulator method)

E

eval() (brn.brn.Brn method) evalexpression() (brn.brneval.ExpressionEvaluator method)

evalparam() (brn.brn.Brn method) ExpressionEvaluator (class in brn.brneval)

F

fromSBML() (in module brn.sbmlimport) fromSBMLString() (in module brn.sbmlimport)

full2reduced_fun() (brn.conserv.Conservation method) FunctionHelper (class in brn.sbmlimport)

G

GillespieSimulator (class in brn.simulation)

H

has_conservation (brn.brn.Brn attribute)

has_scale (brn.brn.Brn attribute)

I

initialize() (brn.simulation.Simulator method) (brn.simulation.SundialsSimulator method)

J

jacobian() (brn.brn.Brn method) (in module brn.brncomp)

L

linearapproximation() (brn.brn.Brn method) (in module brn.brncomp)

M

make_massaction_network() (in module brn.brn)

O

ode_jac() (brn.brneval.BrnEvaluator method) (brn.brneval.CythonBrnEvaluator method) (brn.brneval.PythonBrnEvaluator method)

ode_rhs() (brn.brneval.BrnEvaluator method) (brn.brneval.CythonBrnEvaluator method) (brn.brneval.PythonBrnEvaluator method)

P

process() (brn.sbmlimport.FunctionHelper method)

PythonBrnEvaluator (class in brn.brneval)

R

rank() (in module brn.mathutils) rate_fun() (brn.brn.Brn method) readSBML() (in module brn.sbmlimport)

reduced2full_fun() (brn.conserv.Conservation method) run() (brn.simulation.GillespieSimulator method) (brn.simulation.Simulator method) (brn.simulation.SundialsSimulator method) (brn.simulation.VodeSimulator method) (brn.simulation.VodeSimulatorStop method)

S

scale_fun() (brn.brn.Brn method) set() (brn.brn.Brn method) (brn.brneval.BrnEvaluator method) (brn.brneval.CythonBrnEvaluator method) (brn.brneval.ExpressionEvaluator method) showreact() (brn.brn.Brn method) simulate() (brn.brn.Brn method) Simulator (class in brn.simulation)

SteadyState (class in brn.steadystate) steadystate() (brn.brn.Brn method) steadystate_branch() (brn.brn.Brn method) (in module brn.steadystate) SundialsSimulator (class in brn.simulation) symbolic_stopcondition() (brn.simulation.VodeSimulatorStop method)

V

variable_substitution() (in module brn.brncomp) VodeSimulator (class in brn.simulation)

VodeSimulatorStop (class in brn.simulation)