7.1.2.3. `pta.constants`

Constants used in tha PTA package.

7.1.2.3.1. Module Contents

pta.constants.default_min_eigenvalue_tds_basis = 0.001[source]: Default minimum eigenvalue for vector of the basis of the thermodynamic space.

pta.constants.default_log_conc[source]: Default distribution of metabolite concentrations.

pta.constants.default_flux_bound = 1000[source]: Default magnitude of lower/upper bounds of fluxes.

pta.constants.default_confidence_level = 0.95[source]: Default confidence level for PMO problems and TFS

pta.constants.default_min_drg = 0.1[source]: Default minimum DrG magnitude for PMO problems and TFS

pta.constants.default_max_drg = 1000[source]: Default maximum DrG magnitude for PMO problems and TFS

pta.constants.non_intracellular_compartment_ids = ['e', 'p'][source]: Identifiers of non-intracellular compartments.

pta.constants.default_theta_z = 1.0[source]: Default threshold on the z-score to consider a predicted value an anomaly.

pta.constants.default_theta_s = 0.1[source]: Default threshold on the shadow price to consider a reaction a strong thermodynamic constrain.

pta.constants.default_max_non_intracellular_conc_mM = 10[source]: Default threshold on the concentration to consider a predicted concentration an anomaly.

pta.constants.default_min_chains = 4[source]: Minimum number of chains to use by default.

pta.constants.default_num_samples = 1000[source]: Default number of samples to store.

pta.constants.us_steps_multiplier = 64[source]: Coefficient for the number of steps sampling a flux space.

pta.constants.tfs_steps_multiplier = 100[source]: Coefficient for the number of steps sampling a thermodynamic space.

pta.constants.tfs_default_feasibility_cache_size = 10000[source]: Size of the cache storing whether encountered orthants are feasible or not.

pta.constants.tfs_default_min_rel_region_length = 1e-06[source]: Minimum relative size for an orthant to be considered during Hit-and-Run.

pta.constants.default_max_psrf = 1.1[source]: Default treshold on the Potential Scale Reduction Factors (PSRFs).

pta.constants.default_max_threads[source]

pta.constants.min_samples_per_chain = 100[source]: Minimum number of samples that must be drawn from each chain in order to obtain a meaningful PSRF score.