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)

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

Return type

typing.Tuple[typing.List[typing.List[int]], typing.List[typing.List[float]]]


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