Index

A

align_expdata_to_function_names() (in module rxnfit.expdata_reader)

B

build_evaluator() (in module rxnfit.rate_const_ft_eval) build_lsoda_parameter_vector_p() (in module rxnfit.lsoda_p_vector)

build_t_eval_when_none_for_lsoda() (in module rxnfit.solver_backend) builder (rxnfit.solv_ode.RxnODEsolver attribute)

C

compile_numbalsoda_rhs_for_builder() (in module rxnfit.numbalsoda_rhs) COMPUTE_RSS (rxnfit.solver_backend.LsodaImplicitTEvalMode attribute) config (rxnfit.solv_ode.RxnODEsolver attribute)

create_ode_system() (rxnfit.build_ode.RxnODEbuild method) (rxnfit.rxn_reader.RxnToODE method) create_ode_system_with_rate_consts() (rxnfit.build_ode.RxnODEbuild method) create_system_rhs() (in module rxnfit.build_ode)

D

debug_ode_system() (rxnfit.build_ode.RxnODEbuild method)

E

eval_fit_metrics() (rxnfit.solv_ode.RxnODEsolver method) EVAL_ODE_FIT (rxnfit.solver_backend.LsodaImplicitTEvalMode attribute)

expdata_df_to_datasets() (in module rxnfit.fit_metrics) expdata_read() (in module rxnfit.expdata_reader) ExpDataFit (class in rxnfit.expdata_fit)

F

file_path (rxnfit.rxn_reader.RxnToODE attribute) fit_metrics() (in module rxnfit.fit_metrics)

function_names (rxnfit.rxn_reader.RxnToODE attribute) functions_dict (rxnfit.rxn_reader.RxnToODE attribute)

G

generate_ode() (in module rxnfit.rxn_reader) generate_sys_ode() (in module rxnfit.rxn_reader) get_equations() (rxnfit.rxn_reader.RxnToODE method) get_fitted_rate_const_dict() (rxnfit.expdata_fit.ExpDataFit method) get_numbalsoda_sympy_spec() (rxnfit.build_ode.RxnODEbuild method) get_ode_info() (rxnfit.build_ode.RxnODEbuild method) get_ode_system() (rxnfit.build_ode.RxnODEbuild method)

get_reactions() (in module rxnfit.rxn_reader) get_solver_config_args() (rxnfit.expdata_fit.ExpDataFit method) get_symbolic_rate_const_keys() (rxnfit.build_ode.RxnODEbuild method) get_t0_from_expdata() (in module rxnfit.expdata_reader) get_time_unit_from_expdata() (in module rxnfit.expdata_reader) get_unique_species() (in module rxnfit.rxn_reader) get_y0_from_expdata() (in module rxnfit.expdata_reader)

H

has_time_dependent_rates() (in module rxnfit.rate_const_ft_eval)

I

INTEGRATE_DATASETS (rxnfit.solver_backend.LsodaImplicitTEvalMode attribute)

L

LsodaImplicitTEvalMode (class in rxnfit.solver_backend)

M

method (rxnfit.solv_ode.SolverConfig attribute), [1] module rxnfit rxnfit.build_ode rxnfit.expdata_fit rxnfit.expdata_reader rxnfit.fit_metrics rxnfit.lsoda_p_vector rxnfit.numbalsoda_rhs rxnfit.p0_opt_fit rxnfit.plot_results rxnfit.rate_const_ft_eval rxnfit.rxn_reader rxnfit.solv_ode rxnfit.solver_backend

O

ode_construct (rxnfit.solv_ode.RxnODEsolver attribute)

optimize() (rxnfit.p0_opt_fit.P0OptFit method) optuna_log() (rxnfit.p0_opt_fit.P0OptFit method)

P

P0OptFit (class in rxnfit.p0_opt_fit)

plot_fitted_solution() (rxnfit.expdata_fit.ExpDataFit method) plot_time_course_solutions() (in module rxnfit.plot_results)

R

rate_const_values (rxnfit.solv_ode.SolverConfig attribute), [1] rate_constants() (in module rxnfit.rxn_reader) rate_consts_dict (rxnfit.rxn_reader.RxnToODE attribute) reactant_consumption() (in module rxnfit.rxn_reader) reactant_eq (rxnfit.rxn_reader.RxnToODE attribute) rtol (rxnfit.solv_ode.SolverConfig attribute), [1] run_fit() (rxnfit.expdata_fit.ExpDataFit method) run_fit_multi() (in module rxnfit.expdata_fit) rxnfit module rxnfit.build_ode module rxnfit.expdata_fit module rxnfit.expdata_reader module rxnfit.fit_metrics module

rxnfit.lsoda_p_vector module rxnfit.numbalsoda_rhs module rxnfit.p0_opt_fit module rxnfit.plot_results module rxnfit.rate_const_ft_eval module rxnfit.rxn_reader module rxnfit.solv_ode module rxnfit.solver_backend module RxnODEbuild (class in rxnfit.build_ode) RxnODEsolver (class in rxnfit.solv_ode) RxnToODE (class in rxnfit.rxn_reader)

S

solution (rxnfit.solv_ode.RxnODEsolver attribute) solution_plot() (rxnfit.solv_ode.RxnODEsolver method) solve_fit_model() (in module rxnfit.expdata_fit) solve_fit_model_multi() (in module rxnfit.expdata_fit) solve_ode() (in module rxnfit.solver_backend)

SOLVE_SYSTEM (rxnfit.solver_backend.LsodaImplicitTEvalMode attribute) solve_system() (rxnfit.solv_ode.RxnODEsolver method) SolverConfig (class in rxnfit.solv_ode) symbolic_rate_const_keys (rxnfit.solv_ode.SolverConfig attribute), [1] sympy_symbol_dict (rxnfit.rxn_reader.RxnToODE attribute) sys_odes_dict (rxnfit.rxn_reader.RxnToODE attribute)

T

t (rxnfit.rxn_reader.RxnToODE attribute) t_eval (rxnfit.solv_ode.SolverConfig attribute), [1] t_span (rxnfit.solv_ode.SolverConfig attribute), [1]

time_course() (in module rxnfit.expdata_reader) to_chempy_style() (in module rxnfit.rxn_reader) to_dataframe_list() (rxnfit.expdata_fit.ExpDataFit method) (rxnfit.solv_ode.RxnODEsolver method)

Y

y0 (rxnfit.solv_ode.SolverConfig attribute), [1]