rxnfit.build_ode module

class rxnfit.build_ode.RxnODEbuild(file_path, encoding=None, rate_const_overrides=None, rate_const_overrides_encoding=None)

Bases: RxnToODE

Build ODE systems and numerical RHS functions from reaction definitions.

Extends RxnToODE to produce callable ODE right-hand sides (e.g. for scipy.solve_ivp) and supports rate constants as expressions (e.g. k2=k1*2). Expression-defined constants are resolved to numbers when building create_ode_system(); for fitting, only free symbolic parameters appear in create_ode_system_with_rate_consts().

Inherits all attributes from RxnToODE.
create_ode_system()

Numerical ODE functions (t, y) with rate constants resolved or embedded.

create_ode_system_with_rate_consts()

ODE functions with rate constants as extra arguments (for fitting).

get_ode_system()

Full ODE construction tuple for solvers.

debug_ode_system()

Detailed debug info.

get_ode_info(debug_info=False)

Print summary and optional debug.

create_ode_system()

Build numerical ODE right-hand side functions for integration.

Rate constants that are expressions (e.g. k2=k1*2) are resolved to numbers via _resolve_rate_consts when all referenced symbols have numeric values; otherwise the expression or Symbol is left in place. Functions take (t, y) with y in function_names order.

Returns:

Species name -> callable(t, *y) returning d(species)/dt.

Return type:

dict

Raises:

RuntimeError – If lambdify fails for any species (fail fast).

create_ode_system_with_rate_consts()

Build ODE functions with rate constants as explicit arguments.

Used for fitting: rate constants are passed in at call time instead of being embedded. Only “free” parameters appear: keys that are Symbol or that appear inside expression-defined constants (e.g. k1 in k2=2*k1). Keys defined only by expressions (e.g. k2) do not appear in symbolic_rate_const_keys.

Returns:

(ode_functions, symbolic_rate_const_keys)

  • ode_functions: Species name -> callable(t, *y, *rate_consts).

  • symbolic_rate_const_keys: List of free rate constant names in order (e.g. [‘k1’, ‘k3’] when k2=k1*2).

Return type:

tuple

Raises:

RuntimeError – If lambdify fails for any species (fail fast).

debug_ode_system()

Collect debug information for the ODE system.

Returns:

function_names, rate_constants, ode_expressions,

lambdify_args, ode_functions_info (and test results).

Return type:

dict

get_ode_info(debug_info: bool = False)

Print a short summary of the ODE system (and optionally debug).

Parameters:

debug_info (bool, optional) – If True, also print detailed debug (e.g. lambdify args, ODE expressions). Defaults to False.

get_ode_system()

Return the full ODE construction for scipy.solve_ivp.

Returns:

(system_of_equations, sympy_symbol_dict, ode_system,

function_names, rate_consts_dict). ode_system is from create_ode_system() (rate constants resolved or embedded).

Return type:

tuple

get_symbolic_rate_const_keys()

Return the list of free parameter names (p0 order) for fitting.

Names are t-excluding symbols from rate_consts_dict (Symbol or free_symbols of expressions), in sorted order. Same order as create_ode_system_with_rate_consts and run_fit(p0=…) expect.

Returns:

Parameter names in order, e.g. [‘a’, ‘km’].

Return type:

list[str]

rxnfit.build_ode.create_system_rhs(ode_functions_dict, function_names, rate_const_values=None, symbolic_rate_const_keys=None)

Build the RHS function (t, y) for scipy.solve_ivp.

Creates a closure over the ODE functions and optional rate constant values. When rate_const_values and symbolic_rate_const_keys are given, the ODE functions are called with (t, y, *rate_consts) in the order of symbolic_rate_const_keys.

Parameters:

  • ode_functions_dict (dict) – Species name -> ODE function (as from create_ode_system or create_ode_system_with_rate_consts).

  • function_names (list) – Species names in the same order as y.

  • rate_const_values (dict or callable, optional) – Rate constant key -> numeric value, or a callable (t) -> dict of rate constant values for time-dependent rates. Used when ODE functions expect rate constants as args. When callable, it is called with the current time t to get the dict.

  • symbolic_rate_const_keys (list, optional) – Order of rate constant keys matching the ODE functions. Required if rate_const_values is provided.

Returns:

system_rhs(t, y) returning a list of d(species)/dt in

function_names order.

Return type:

callable

Raises:

RuntimeError – If any ODE function is None or if evaluation fails during integration (fail fast).