amici.conserved_quantities_demartino
Functions
|
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 networknum_reactions (
int
) – total number of reactions in the reaction networkmax_num_monte_carlo (
int
) – maximum number of MonteCarlo steps before changing to relaxationrng_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 torandom.seed()
.species_names (
typing.Optional
[collections.abc.Sequence
[str
]]) – Species names. Optional and only used for logging.
- Return type:
- Returns:
Integer MCLs as list of lists of indices of involved species and list of lists of corresponding coefficients.