Index

A

atom_positions (x3cflux.HNMRSpecification property)

auto_scalable (x3cflux.Measurement property)

B

bound (x3cflux.InequalitySystem property) build() (x3cflux.NonStationaryCumomerSystemBuilder method), [1] (x3cflux.NonStationaryEMUSystemBuilder method), [1] (x3cflux.StationaryCumomerSystemBuilder method), [1] (x3cflux.StationaryEMUSystemBuilder method), [1]

C

CNMRMeasurement (class in x3cflux) comment (x3cflux.FluxMLData property) (x3cflux.MeasurementConfiguration property) 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), [1] compute_mixture_samples (class in x3cflux) compute_parameters() (x3cflux.NonStationaryParameterSpace method), [1] (x3cflux.StationaryParameterSpace method), [1] compute_perturbed_measurements (class in x3cflux) compute_stoichiometry_error() (x3cflux.NonStationaryParameterSpace method), [1] (x3cflux.StationaryParameterSpace method), [1] configurations (x3cflux.FluxMLData property) constant (x3cflux.LinearConstraint property) ConstantSubstrate (class in x3cflux) constraint (x3cflux.ParameterClassification property)

contains() (x3cflux.NonStationaryParameterSpace method), [1] (x3cflux.StationaryParameterSpace method), [1] copy() (x3cflux.MatrixLESSolver method), [1] (x3cflux.MatrixLinearCVODESolver method) (x3cflux.MatrixLinearIVPSolver method), [1] (x3cflux.MatrixLinearSDIRK43Solver method) (x3cflux.MatrixLUSolver method) (x3cflux.VectorLESSolver method), [1] (x3cflux.VectorLinearCVODESolver method) (x3cflux.VectorLinearIVPSolver method), [1] (x3cflux.VectorLinearSDIRK43Solver method) (x3cflux.VectorLUSolver method) costs (x3cflux.Substrate property) 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

data (x3cflux.GenericMeasurement property) (x3cflux.LabelingMeasurement property) date (x3cflux.FluxMLData property) definition_constraints (x3cflux.ParameterConstraints property) DefinitionConstraint (class in x3cflux)

dependent (x3cflux.ParameterClassification property) derivative_values (x3cflux.MatrixCubicHermiteSpline property) (x3cflux.VectorCubicHermiteSpline property) domain (x3cflux.MatrixCubicHermiteSpline property) (x3cflux.VectorCubicHermiteSpline property)

E

equality_constraints (x3cflux.ParameterConstraints property) error_model (x3cflux.ParameterMeasurement property) evaluate_inhomogeneity() (x3cflux.MatrixLinearIVP method), [1] (x3cflux.NonStationaryCumomerLevelSystem method) (x3cflux.NonStationaryEMULevelSystem method) (x3cflux.VectorLinearIVP method), [1]

exchange_flux_classification (x3cflux.NonStationaryParameterSpace property) (x3cflux.StationaryParameterSpace property) exchange_flux_constraints (x3cflux.MeasurementConfiguration property) exchange_flux_solution_space (x3cflux.NonStationaryParameterSpace property) (x3cflux.StationaryParameterSpace property)

F

first_mask (x3cflux.MSMSSpecification property) first_weights (x3cflux.MSMSSpecification property) flux_names (x3cflux.FluxSpecification property) FluxMeasurement (class in x3cflux) FluxMLData (class in x3cflux)

FluxMLParser (class in x3cflux) FluxSpecification (class in x3cflux) formula (x3cflux.GenericMeasurement.SubMeasurement property) free (x3cflux.ParameterClassification property) function_values (x3cflux.MatrixCubicHermiteSpline property) (x3cflux.VectorCubicHermiteSpline property)

G

GenericMeasurement (class in x3cflux) GenericMeasurement.SubMeasurement (class in x3cflux) get_inequalities_from_bounds (class in x3cflux) get_level_system() (x3cflux.NonStationaryCumomerSystem method), [1] (x3cflux.NonStationaryEMUSystem method), [1] (x3cflux.StationaryCumomerSystem method), [1] (x3cflux.StationaryEMUSystem method), [1]

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

inequality_constraints (x3cflux.ParameterConstraints property) inequality_system (x3cflux.NonStationaryParameterSpace property) (x3cflux.StationaryParameterSpace property) InequalitySystem (class in x3cflux)

initial_value (x3cflux.MatrixLinearIVP property) (x3cflux.VectorLinearIVP property) IpoptError (class in x3cflux) is_feasible() (x3cflux.NonStationaryParameterSpace method), [1] (x3cflux.StationaryParameterSpace method), [1]

J

jacobian (x3cflux.MatrixLinearIVP property) (x3cflux.VectorLinearIVP property)

K

kernel_basis() (x3cflux.SolutionSpace method), [1]

L

labeled_mask (x3cflux.CumomerSpecification property) LabelingMeasurement (class in x3cflux) LinearConstraint (class in x3cflux)

log_curvature() (x3cflux.HopsyModel method), [1] log_density() (x3cflux.HopsyModel method), [1] log_gradient() (x3cflux.HopsyModel method), [1]

M

mask (x3cflux.MIMSSpecification property) (x3cflux.MSSpecification property) matrix (x3cflux.InequalitySystem property) (x3cflux.MatrixLinearEquationSystem property) (x3cflux.Stoichiometry property) (x3cflux.VectorLinearEquationSystem property) 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)

measurement_formula (x3cflux.ParameterMeasurement property) MeasurementConfiguration (class in x3cflux) measurements (x3cflux.GenericMeasurement.SubMeasurement property) (x3cflux.MeasurementConfiguration property) metabolite_name (x3cflux.LabelingMeasurement property) (x3cflux.Substrate property) metabolite_names (x3cflux.Stoichiometry property) metabolites (x3cflux.NetworkData property) MIMSMeasurement (class in x3cflux) MIMSSpecification (class in x3cflux) modeler_name (x3cflux.FluxMLData property) MSMeasurement (class in x3cflux) MSMSMeasurement (class in x3cflux) MSMSSpecification (class in x3cflux) MSSpecification (class in x3cflux)

N

name (x3cflux.DefinitionConstraint property) (x3cflux.FluxMLData property) (x3cflux.LinearConstraint property) (x3cflux.Measurement property) (x3cflux.MeasurementConfiguration property) (x3cflux.ParameterEntry property) (x3cflux.ParameterType property) (x3cflux.Substrate property) names (x3cflux.ParameterClassification property) net (x3cflux.FluxSpecification property) net_flux_classification (x3cflux.NonStationaryParameterSpace property) (x3cflux.StationaryParameterSpace property)

net_flux_constraints (x3cflux.MeasurementConfiguration property) net_flux_solution_space (x3cflux.NonStationaryParameterSpace property) (x3cflux.StationaryParameterSpace property) network_data (x3cflux.FluxMLData property) 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) num_atoms (x3cflux.LabelingMeasurement property)

P

parameter_coefficients (x3cflux.LinearConstraint property) parameter_entries (x3cflux.MeasurementConfiguration property) parameter_name (x3cflux.DefinitionConstraint property) parameter_names (x3cflux.LinearConstraint property) parameter_value (x3cflux.DefinitionConstraint property) ParameterClassification (class in x3cflux) ParameterConstraints (class in x3cflux) ParameterEntry (class in x3cflux) ParameterMeasurement (class in x3cflux) ParameterType (class in x3cflux) parse() (x3cflux.FluxMLParser method), [1] parse_tracer_mixtures (class in x3cflux)

particular_solution() (x3cflux.SolutionSpace method), [1] permutation() (x3cflux.SolutionSpace method), [1] places (x3cflux.MatrixCubicHermiteSpline property) (x3cflux.VectorCubicHermiteSpline property) pool_names (x3cflux.PoolSizeSpecification property) pool_size_classification (x3cflux.NonStationaryParameterSpace property) pool_size_constraints (x3cflux.MeasurementConfiguration property) pool_size_solution_space (x3cflux.NonStationaryParameterSpace property) PoolSizeMeasurement (class in x3cflux) PoolSizeSpecification (class in x3cflux) profiles (x3cflux.ConstantSubstrate property) (x3cflux.VariateSubstrate property)

Q

quasi_constraint (x3cflux.ParameterClassification property)

R

reaction_names (x3cflux.Stoichiometry property) reactions (x3cflux.NetworkData property) rhs (x3cflux.MatrixLinearEquationSystem property) (x3cflux.VectorLinearEquationSystem property)

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

second_mask (x3cflux.MSMSSpecification property) second_weights (x3cflux.MSMSSpecification property) set_derivative_solver() (x3cflux.NonStationaryCumomerSystemBuilder method), [1] (x3cflux.NonStationaryEMUSystemBuilder method), [1] set_solver() (x3cflux.NonStationaryCumomerSystemBuilder method), [1] (x3cflux.NonStationaryEMUSystemBuilder method), [1] (x3cflux.StationaryCumomerSystemBuilder method), [1] (x3cflux.StationaryEMUSystemBuilder method), [1] SolutionSpace (class in x3cflux) solve() (x3cflux.MatrixLESSolver method), [1] (x3cflux.MatrixLinearCVODESolver method), [1] (x3cflux.MatrixLinearIVPSolver method), [1] (x3cflux.MatrixLinearSDIRK43Solver method), [1] (x3cflux.MatrixLUSolver method), [1] (x3cflux.NonStationaryCumomerSystem method), [1] (x3cflux.NonStationaryEMUSystem method), [1] (x3cflux.StationaryCumomerSystem method), [1] (x3cflux.StationaryEMUSystem method), [1] (x3cflux.VectorLESSolver method), [1] (x3cflux.VectorLinearCVODESolver method), [1] (x3cflux.VectorLinearIVPSolver method), [1] (x3cflux.VectorLinearSDIRK43Solver method), [1] (x3cflux.VectorLUSolver method), [1]

specification (x3cflux.CNMRMeasurement property) (x3cflux.CumomerMeasurement property) (x3cflux.FluxMeasurement property) (x3cflux.HNMRMeasurement property) (x3cflux.MIMSMeasurement property) (x3cflux.MSMeasurement property) (x3cflux.MSMSMeasurement property) (x3cflux.PoolSizeMeasurement property) standard_deviation (x3cflux.ParameterMeasurement property) stationary (x3cflux.MeasurementConfiguration property) 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) stoichiometry (x3cflux.NonStationaryParameterSpace property) (x3cflux.StationaryParameterSpace property) sub_measurements (x3cflux.GenericMeasurement property) Substrate (class in x3cflux) substrates (x3cflux.MeasurementConfiguration property)

T

TracerMixtureSpace (class in x3cflux)

type (x3cflux.ParameterEntry property)

V

value (x3cflux.ParameterEntry property) (x3cflux.ParameterMeasurement property) variable_names (x3cflux.GenericMeasurement.SubMeasurement property) 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) version (x3cflux.FluxMLData property)

W

weights (x3cflux.MIMSSpecification property) (x3cflux.MSSpecification property)

wildcard_mask (x3cflux.CumomerSpecification property)