rxnfit package

Submodules

• rxnfit.build_ode module
  • RxnODEbuild
    • RxnODEbuild.create_ode_system()
    • RxnODEbuild.create_ode_system_with_rate_consts()
    • RxnODEbuild.debug_ode_system()
    • RxnODEbuild.get_numbalsoda_sympy_spec()
    • RxnODEbuild.get_ode_info()
    • RxnODEbuild.get_ode_system()
    • RxnODEbuild.get_symbolic_rate_const_keys()
  • create_system_rhs()
• rxnfit.expdata_fit module
  • ExpDataFit
    • ExpDataFit.get_fitted_rate_const_dict()
    • ExpDataFit.get_solver_config_args()
    • ExpDataFit.plot_fitted_solution()
    • ExpDataFit.run_fit()
    • ExpDataFit.to_dataframe_list()
  • run_fit_multi()
  • solve_fit_model()
  • solve_fit_model_multi()
• rxnfit.expdata_reader module
  • align_expdata_to_function_names()
  • expdata_read()
  • get_t0_from_expdata()
  • get_time_unit_from_expdata()
  • get_y0_from_expdata()
  • time_course()
• rxnfit.fit_metrics module
  • expdata_df_to_datasets()
  • fit_metrics()
• rxnfit.lsoda_p_vector module
  • build_lsoda_parameter_vector_p()
• rxnfit.numbalsoda_rhs module
  • compile_numbalsoda_rhs_for_builder()
• rxnfit.p0_opt_fit module
  • P0OptFit
    • P0OptFit.optimize()
    • P0OptFit.optuna_log()
• rxnfit.plot_results module
  • plot_time_course_solutions()
• rxnfit.rate_const_ft_eval module
  • build_evaluator()
  • has_time_dependent_rates()
• rxnfit.rxn_reader module
  • RxnToODE
    • RxnToODE.file_path
    • RxnToODE.reactant_eq
    • RxnToODE.t
    • RxnToODE.function_names
    • RxnToODE.functions_dict
    • RxnToODE.rate_consts_dict
    • RxnToODE.sympy_symbol_dict
    • RxnToODE.sys_odes_dict
    • RxnToODE.create_ode_system()
    • RxnToODE.get_equations()
  • generate_ode()
  • generate_sys_ode()
  • get_reactions()
  • get_unique_species()
  • rate_constants()
  • reactant_consumption()
  • to_chempy_style()
• rxnfit.solv_ode module
  • RxnODEsolver
    • RxnODEsolver.builder
    • RxnODEsolver.config
    • RxnODEsolver.ode_construct
    • RxnODEsolver.solution
    • RxnODEsolver.eval_fit_metrics()
    • RxnODEsolver.solution_plot()
    • RxnODEsolver.solve_system()
    • RxnODEsolver.to_dataframe_list()
  • SolverConfig
    • SolverConfig.y0
    • SolverConfig.t_span
    • SolverConfig.t_eval
    • SolverConfig.method
    • SolverConfig.rtol
    • SolverConfig.rate_const_values
    • SolverConfig.symbolic_rate_const_keys
    • SolverConfig.method
    • SolverConfig.rate_const_values
    • SolverConfig.rtol
    • SolverConfig.symbolic_rate_const_keys
    • SolverConfig.t_eval
    • SolverConfig.t_span
    • SolverConfig.y0
• rxnfit.solver_backend module
  • LsodaImplicitTEvalMode
    • LsodaImplicitTEvalMode.COMPUTE_RSS
    • LsodaImplicitTEvalMode.EVAL_ODE_FIT
    • LsodaImplicitTEvalMode.INTEGRATE_DATASETS
    • LsodaImplicitTEvalMode.SOLVE_SYSTEM
  • build_t_eval_when_none_for_lsoda()
  • solve_ode()

Module contents

Reaction-kinetics ODE construction, integration, and fitting.

This package builds ordinary differential equation (ODE) models from elementary reaction CSVs and integrates or fits them numerically. rxnfit.solv_ode.SolverConfig and rxnfit.solv_ode.RxnODEsolver are imported explicitly below; symbols from rxnfit.rxn_reader and rxnfit.build_ode populate the default namespace via star imports.