Index

B

build() (x3cflux.NonStationaryCumomerSystemBuilder method) (x3cflux.NonStationaryEMUSystemBuilder method) (x3cflux.StationaryCumomerSystemBuilder method) (x3cflux.StationaryEMUSystemBuilder method)

C

CNMRMeasurement (class in x3cflux) compute_closest_interior_point (class in x3cflux) compute_ed_criteria (class in x3cflux) compute_free_parameter_covariance (class in x3cflux) compute_full_parameter_covariance (class in x3cflux) compute_mix_and_costs() (x3cflux.TracerMixtureSpace method) compute_mixture_samples (class in x3cflux) compute_parameters() (x3cflux.NonStationaryParameterSpace method) (x3cflux.StationaryParameterSpace method) compute_perturbed_measurements (class in x3cflux) compute_stoichiometry_error() (x3cflux.NonStationaryParameterSpace method) (x3cflux.StationaryParameterSpace method) ConstantSubstrate (class in x3cflux) contains() (x3cflux.NonStationaryParameterSpace method) (x3cflux.StationaryParameterSpace method)

copy() (x3cflux.MatrixLESSolver method) (x3cflux.MatrixLinearCVODESolver method) (x3cflux.MatrixLinearIVPSolver method) (x3cflux.MatrixLinearSDIRK43Solver method) (x3cflux.MatrixLUSolver method) (x3cflux.VectorLESSolver method) (x3cflux.VectorLinearCVODESolver method) (x3cflux.VectorLinearIVPSolver method) (x3cflux.VectorLinearSDIRK43Solver method) (x3cflux.VectorLUSolver method) create_simulator_from_data (class in x3cflux) create_simulator_from_fml (class in x3cflux) create_simulator_from_inputs (class in x3cflux) create_simulator_from_measurements (class in x3cflux) CumomerMeasurement (class in x3cflux) CumomerSpecification (class in x3cflux)

D

DefinitionConstraint (class in x3cflux)

E

evaluate_inhomogeneity() (x3cflux.MatrixLinearIVP method) (x3cflux.NonStationaryCumomerLevelSystem method) (x3cflux.NonStationaryEMULevelSystem method) (x3cflux.VectorLinearIVP method)

F

FluxMeasurement (class in x3cflux) FluxMLData (class in x3cflux)

FluxMLParser (class in x3cflux) FluxSpecification (class in x3cflux)

G

GenericMeasurement (class in x3cflux) get_inequalities_from_bounds (class in x3cflux) get_level_system() (x3cflux.NonStationaryCumomerSystem method) (x3cflux.NonStationaryEMUSystem method) (x3cflux.StationaryCumomerSystem method) (x3cflux.StationaryEMUSystem method)

get_non_constant_names (class in x3cflux) get_parameters (class in x3cflux)

H

HNMRMeasurement (class in x3cflux)

HNMRSpecification (class in x3cflux) HopsyModel (class in x3cflux)

I

InequalitySystem (class in x3cflux) IpoptError (class in x3cflux)

is_feasible() (x3cflux.NonStationaryParameterSpace method) (x3cflux.StationaryParameterSpace method)

K

kernel_basis() (x3cflux.SolutionSpace method)

L

LabelingMeasurement (class in x3cflux) LinearConstraint (class in x3cflux)

log_curvature() (x3cflux.HopsyModel method) log_density() (x3cflux.HopsyModel method) log_gradient() (x3cflux.HopsyModel method)

M

MatrixCubicHermiteSpline (class in x3cflux) MatrixLESSolver (class in x3cflux) MatrixLinearCVODESolver (class in x3cflux) MatrixLinearEquationSystem (class in x3cflux) MatrixLinearIVP (class in x3cflux) MatrixLinearIVPSolver (class in x3cflux) MatrixLinearSDIRK43Solver (class in x3cflux) MatrixLUSolver (class in x3cflux)

Measurement (class in x3cflux) MeasurementConfiguration (class in x3cflux) MIMSMeasurement (class in x3cflux) MIMSSpecification (class in x3cflux) MSMeasurement (class in x3cflux) MSMSMeasurement (class in x3cflux) MSMSSpecification (class in x3cflux) MSSpecification (class in x3cflux)

N

NetworkData (class in x3cflux) NonStationaryCumomerLevelSystem (class in x3cflux) NonStationaryCumomerSystem (class in x3cflux) NonStationaryCumomerSystemBuilder (class in x3cflux)

NonStationaryEMULevelSystem (class in x3cflux) NonStationaryEMUSystem (class in x3cflux) NonStationaryEMUSystemBuilder (class in x3cflux) NonStationaryParameterSpace (class in x3cflux)

P

ParameterClassification (class in x3cflux) ParameterConstraints (class in x3cflux) ParameterEntry (class in x3cflux) ParameterMeasurement (class in x3cflux) ParameterType (class in x3cflux)

parse() (x3cflux.FluxMLParser method) parse_tracer_mixtures (class in x3cflux) particular_solution() (x3cflux.SolutionSpace method) permutation() (x3cflux.SolutionSpace method) PoolSizeMeasurement (class in x3cflux) PoolSizeSpecification (class in x3cflux)

R

run_multi_optimization (class in x3cflux) run_non_uniform_sampling (class in x3cflux)

run_optimization (class in x3cflux) run_profile_likelihood_cis (class in x3cflux) run_uniform_sampling (class in x3cflux)

S

set_derivative_solver() (x3cflux.NonStationaryCumomerSystemBuilder method) (x3cflux.NonStationaryEMUSystemBuilder method) set_solver() (x3cflux.NonStationaryCumomerSystemBuilder method) (x3cflux.NonStationaryEMUSystemBuilder method) (x3cflux.StationaryCumomerSystemBuilder method) (x3cflux.StationaryEMUSystemBuilder method) SolutionSpace (class in x3cflux) solve() (x3cflux.MatrixLESSolver method) (x3cflux.MatrixLinearCVODESolver method) (x3cflux.MatrixLinearIVPSolver method) (x3cflux.MatrixLinearSDIRK43Solver method) (x3cflux.MatrixLUSolver method) (x3cflux.NonStationaryCumomerSystem method) (x3cflux.NonStationaryEMUSystem method) (x3cflux.StationaryCumomerSystem method) (x3cflux.StationaryEMUSystem method) (x3cflux.VectorLESSolver method) (x3cflux.VectorLinearCVODESolver method) (x3cflux.VectorLinearIVPSolver method) (x3cflux.VectorLinearSDIRK43Solver method) (x3cflux.VectorLUSolver method)

StationaryCumomerLevelSystem (class in x3cflux) StationaryCumomerSystem (class in x3cflux) StationaryCumomerSystemBuilder (class in x3cflux) StationaryEMULevelSystem (class in x3cflux) StationaryEMUSystem (class in x3cflux) StationaryEMUSystemBuilder (class in x3cflux) StationaryParameterSpace (class in x3cflux) Stoichiometry (class in x3cflux) Substrate (class in x3cflux)

T

TracerMixtureSpace (class in x3cflux)

V

VariateSubstrate (class in x3cflux) VectorCubicHermiteSpline (class in x3cflux) VectorLESSolver (class in x3cflux) VectorLinearCVODESolver (class in x3cflux)

VectorLinearEquationSystem (class in x3cflux) VectorLinearIVP (class in x3cflux) VectorLinearIVPSolver (class in x3cflux) VectorLinearSDIRK43Solver (class in x3cflux) VectorLUSolver (class in x3cflux)