amici.conserved_quantities_demartino

Functions

compute_moiety_conservation_laws(...[, ...])

Compute moiety conservation laws.

amici.conserved_quantities_demartino.compute_moiety_conservation_laws(stoichiometric_list, num_species, num_reactions, max_num_monte_carlo=20, rng_seed=False, species_names=None)[source]

Compute moiety conservation laws.

According to the algorithm proposed by De Martino et al. (2014) https://doi.org/10.1371/journal.pone.0100750

Parameters:
  • stoichiometric_list (collections.abc.Sequence[float]) – the stoichiometric matrix as a list (species x reactions, column-major ordering)

  • num_species (int) – total number of species in the reaction network

  • num_reactions (int) – total number of reactions in the reaction network

  • max_num_monte_carlo (int) – maximum number of MonteCarlo steps before changing to relaxation

  • rng_seed (typing.Union[None, bool, int]) – Seed for the random number generator. If False, the RNG will not be re-initialized. Other values will be passed to random.seed().

  • species_names (typing.Optional[collections.abc.Sequence[str]]) – Species names. Optional and only used for logging.

Return type:

tuple[list[list[int]], list[list[float]]]

Returns:

Integer MCLs as list of lists of indices of involved species and list of lists of corresponding coefficients.