Index

A

add() (pta.concentrations_prior.ConcentrationsPrior method) any_compartment (in module pta.compartment_parameters) apply_to_chains() (in module pta.sampling.commons)

apply_transform() (in module pta.utils) ASSUME_CYTOSOL (pta.metabolite_interpreter.CompartmentConvention attribute) autoresolve() (pta.model_assessment.StructuralAssessment method)

B

B (pta.pmo.PmoProblem property) (pta.sampling.tfs.TFSModel property)

basis_samples (pta.sampling.commons.SamplingResult property) BIGG (pta.metabolite_interpreter.Namespace attribute)

C

ceil() (in module pta.utils) chains (pta.sampling.commons.SamplingResult property) check_convergence() (pta.sampling.commons.SamplingResult method) close() (pta.pmo.PmoProblemPool method) compartment (pta.metabolite.Metabolite property) compartment_convention (pta.metabolite_interpreter.MetaboliteInterpreter property) compartment_distributions (pta.concentrations_prior.ConcentrationsPrior property) CompartmentConvention (class in pta.metabolite_interpreter) CompartmentParameters (class in pta.compartment_parameters) compute_psrf() (pta.sampling.commons.SamplerInterface method) (pta.sampling.tfs.TFSModel method) (pta.sampling.uniform.UniformSamplingModel method)

ConcentrationsPrior (class in pta.concentrations_prior) confidence_constraint (pta.pmo.PmoProblem property) confidence_level (pta.pmo.PmoProblem property) confidence_radius (pta.sampling.tfs.TFSModel property) ConvergenceManager (class in pta.sampling.convergence_manager) copy() (pta.distributions.LogNormalDistribution method) (pta.distributions.LogUniformDistribution method) (pta.distributions.NormalDistribution method) (pta.distributions.UniformDistribution method) (pta.flux_space.FluxSpace method) covariance_square_root() (in module pta.utils)

D

d (pta.pmo.PmoProblem property) default_confidence_level (in module pta.constants) default_distribution (pta.concentrations_prior.ConcentrationsPrior property) default_flux_bound (in module pta.constants) default_I (in module pta.constants) default_log_conc (in module pta.constants) default_max_drg (in module pta.constants) default_max_non_intracellular_conc_mM (in module pta.constants) default_max_psrf (in module pta.constants) default_max_threads (in module pta.constants) default_min_chains (in module pta.constants) default_min_drg (in module pta.constants) default_min_eigenvalue_tds_basis (in module pta.constants) default_num_samples (in module pta.constants) default_pH (in module pta.constants) default_phi (in module pta.constants) default_pMg (in module pta.constants) default_rmse (in module pta.constants) default_T (in module pta.constants) default_theta_s (in module pta.constants)

default_theta_z (in module pta.constants) dfg0_prime_cov (pta.thermodynamic_space.ThermodynamicSpace property) dfg0_prime_cov_sqrt (pta.thermodynamic_space.ThermodynamicSpace property) dfg0_prime_mean (pta.thermodynamic_space.ThermodynamicSpace property) dfg_prime_cov (pta.thermodynamic_space.ThermodynamicSpace property) dfg_prime_mean (pta.thermodynamic_space.ThermodynamicSpace property) dimensionality (pta.flux_space.FluxSpaceBasis property) (pta.sampling.commons.SamplerInterface property) (pta.sampling.primitives.FluxSpaceSamplingModel property) (pta.sampling.tfs.TFSModel property) (pta.thermodynamic_space.ThermodynamicSpaceBasis property) distribution_from_string() (in module pta.distributions) distribution_to_string() (in module pta.distributions) drg (pta.pmo.PmoProblem property) drg0 (pta.pmo.PmoProblem property) drg0_prime_cov (pta.thermodynamic_space.ThermodynamicSpace property) drg0_prime_cov_sqrt (pta.thermodynamic_space.ThermodynamicSpace property) drg0_prime_mean (pta.thermodynamic_space.ThermodynamicSpace property) drg_epsilon (pta.sampling.tfs.TFSModel property) drg_prime_cov (pta.thermodynamic_space.ThermodynamicSpace property) drg_prime_mean (pta.thermodynamic_space.ThermodynamicSpace property)

E

enable_all_logging() (in module pta.utils)

eq_api (pta.gibbs_estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator property) EquilibratorGibbsEstimator (class in pta.gibbs_estimators.equilibrator_gibbs_estimator)

F

F (in module pta.constants) (pta.pmo.PmoProblem property) (pta.sampling.tfs.TFSModel property) fill_common_sampling_settings() (in module pta.sampling.commons) find_blocked_reactions_from_fva_solution() (in module pta.utils) find_rotation_matrix() (in module pta.utils) floor() (in module pta.utils) flux_lb_constraint (pta.pmo.PmoProblem property) flux_scale (pta.pmo.PmoProblem property)

flux_ub_constraint (pta.pmo.PmoProblem property) FluxSpace (class in pta.flux_space) FluxSpaceBasis (class in pta.flux_space) FluxSpaceSamplingModel (class in pta.sampling.primitives) forced_internal_cycles (pta.model_assessment.StructuralAssessment property) FreeEnergiesSamplingResult (class in pta.sampling.tfs) from_cobrapy_model() (pta.flux_space.FluxSpace static method) (pta.sampling.uniform.UniformSamplingModel class method) (pta.thermodynamic_space.ThermodynamicSpace static method)

G

G (pta.flux_space.FluxSpaceBasis property) (pta.sampling.primitives.FluxSpaceSamplingModel property) get() (pta.concentrations_prior.ConcentrationsPrior method) get_candidate_thermodynamic_constraints() (in module pta.utils) get_chains() (pta.sampling.commons.SamplerInterface method) (pta.sampling.tfs.TFSModel method) (pta.sampling.uniform.UniformSamplingModel method) get_dfg0_prime() (pta.gibbs_estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator method) (pta.gibbs_estimators.gibbs_estimator_interface.GibbsEstimatorInterface method)

get_initial_points() (pta.sampling.primitives.FluxSpaceSamplingModel method) (pta.sampling.tfs.TFSModel method) get_internal_cycles() (in module pta.utils) get_internal_reactions() (in module pta.utils) get_path() (in module pta.utils) get_reactions_in_internal_cycles() (in module pta.utils) GibbsEstimatorInterface (class in pta.gibbs_estimators.gibbs_estimator_interface)

H

h (pta.flux_space.FluxSpaceBasis property) (pta.sampling.primitives.FluxSpaceSamplingModel property)

I

I() (pta.compartment_parameters.CompartmentParameters method)

id (pta.metabolite.Metabolite property) incorrect_metabolites (pta.gibbs_estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator property)

K

key (pta.metabolite.Metabolite property)

L

lb (pta.distributions.LogUniformDistribution property) (pta.distributions.UniformDistribution property) (pta.flux_space.FluxSpace property) load() (pta.compartment_parameters.CompartmentParameters static method) (pta.concentrations_prior.ConcentrationsPrior static method) load_example_model() (in module pta.utils) LOG10 (in module pta.constants)

log_c (pta.pmo.PmoProblem property) log_conc_cov (pta.thermodynamic_space.ThermodynamicSpace property) log_conc_mean (pta.thermodynamic_space.ThermodynamicSpace property) log_mean (pta.distributions.LogNormalDistribution property) log_std (pta.distributions.LogNormalDistribution property) LogNormalDistribution (class in pta.distributions) LogUniformDistribution (class in pta.distributions)

M

m (pta.pmo.PmoProblem property) map() (pta.pmo.PmoProblemPool method) max_drg (pta.pmo.PmoProblem property) max_ex_concentration (pta.model_assessment.QuantitativeAssessment property) mean (pta.distributions.NormalDistribution property) Metabolite (class in pta.metabolite) metabolite_distributions (pta.concentrations_prior.ConcentrationsPrior property) metabolite_ids (pta.flux_space.FluxSpace property) (pta.thermodynamic_space.ThermodynamicSpace property) MetaboliteInterpreter (class in pta.metabolite_interpreter) metabolites (pta.thermodynamic_space.ThermodynamicSpace property) metabolites_df (pta.model_assessment.QuantitativeAssessment property) min_drg (pta.pmo.PmoProblem property) min_samples_per_chain (in module pta.constants) module pta pta.commons pta.compartment_parameters pta.concentrations_prior pta.constants pta.data pta.data.compartment_parameters pta.data.concentration_priors pta.data.models pta.distributions pta.flux_space pta.gibbs_estimators pta.gibbs_estimators.equilibrator_gibbs_estimator pta.gibbs_estimators.gibbs_estimator_interface pta.metabolite pta.metabolite_interpreter pta.model_assessment pta.pmo pta.sampling pta.sampling.commons pta.sampling.convergence_manager pta.sampling.primitives pta.sampling.tfs pta.sampling.uniform pta.thermodynamic_space pta.utils

N

n_metabolites (pta.flux_space.FluxSpace property) n_reactions (pta.flux_space.FluxSpace property) n_reversible_reactions (pta.flux_space.FluxSpace property) Namespace (class in pta.metabolite_interpreter)

namespace (pta.metabolite_interpreter.MetaboliteInterpreter property) nH (pta.metabolite.Metabolite property) non_intracellular_compartment_ids (in module pta.constants) NONE (pta.metabolite_interpreter.Namespace attribute) NormalDistribution (class in pta.distributions)

O

objective (pta.pmo.PmoProblem property)

observables_ranges (pta.thermodynamic_space.ThermodynamicSpaceBasis property) orthants (pta.sampling.tfs.FreeEnergiesSamplingResult property)

P

parameters (pta.thermodynamic_space.ThermodynamicSpace property) pH() (pta.compartment_parameters.CompartmentParameters method) phi() (pta.compartment_parameters.CompartmentParameters method) pMg() (pta.compartment_parameters.CompartmentParameters method) pmo_args (pta.sampling.tfs.TFSModel property) PmoProblem (class in pta.pmo) PmoProblemPool (class in pta.pmo) prepare_for_pta() (in module pta.model_assessment) psrf (pta.sampling.commons.SamplingResult property) pta module pta.commons module pta.compartment_parameters module pta.concentrations_prior module pta.constants module pta.data module pta.data.compartment_parameters module pta.data.concentration_priors module pta.data.models module pta.distributions module pta.flux_space module

pta.gibbs_estimators module pta.gibbs_estimators.equilibrator_gibbs_estimator module pta.gibbs_estimators.gibbs_estimator_interface module pta.metabolite module pta.metabolite_interpreter module pta.model_assessment module pta.pmo module pta.sampling module pta.sampling.commons module pta.sampling.convergence_manager module pta.sampling.primitives module pta.sampling.tfs module pta.sampling.uniform module pta.thermodynamic_space module pta.utils module

Q

Q (in module pta.commons) qrvector() (in module pta.utils)

QuantitativeAssessment (class in pta.model_assessment) qvector() (in module pta.utils)

R

R (in module pta.constants) reaction_ids (pta.flux_space.FluxSpace property) (pta.sampling.primitives.FluxSpaceSamplingModel property) (pta.thermodynamic_space.ThermodynamicSpace property) reactions_df (pta.model_assessment.QuantitativeAssessment property)

read() (pta.metabolite_interpreter.MetaboliteInterpreter method) rebuild_for_directions() (pta.pmo.PmoProblem method) reversible_rxn_ids (pta.sampling.tfs.TFSModel property) rmse_inf (pta.gibbs_estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator property) run() (pta.sampling.convergence_manager.ConvergenceManager method)

S

S (pta.flux_space.FluxSpace property) S_constraints (pta.thermodynamic_space.ThermodynamicSpace property) sample_drg() (in module pta.sampling.tfs) sample_drg0_from_drg() (in module pta.sampling.tfs) sample_flux_space_uniform() (in module pta.sampling.uniform) sample_fluxes_from_drg() (in module pta.sampling.tfs) sample_from_chains() (in module pta.sampling.commons) sample_log_conc_from_drg() (in module pta.sampling.tfs) SamplerInterface (class in pta.sampling.commons) samples (pta.sampling.commons.SamplingResult property) SamplingException SamplingResult (class in pta.sampling.commons) save() (pta.concentrations_prior.ConcentrationsPrior method) sigmas (pta.thermodynamic_space.ThermodynamicSpaceBasis property)

sign_constraints (pta.pmo.PmoProblem property) simulate() (pta.sampling.commons.SamplerInterface method) (pta.sampling.tfs.TFSModel method) (pta.sampling.uniform.UniformSamplingModel method) solve() (pta.pmo.PmoProblem method) solver (pta.pmo.PmoProblem property) solver_options (pta.pmo.PmoProblem property) split_chains() (in module pta.sampling.commons) split_R() (in module pta.sampling.commons) std (pta.distributions.NormalDistribution property) steady_state_constraint (pta.pmo.PmoProblem property) StructuralAssessment (class in pta.model_assessment) summary() (pta.model_assessment.QuantitativeAssessment method) (pta.model_assessment.StructuralAssessment method)

T

T (pta.pmo.PmoProblem property) (pta.sampling.tfs.TFSModel property) T() (pta.compartment_parameters.CompartmentParameters method) tfs_default_feasibility_cache_size (in module pta.constants) tfs_default_min_rel_region_length (in module pta.constants) tfs_steps_multiplier (in module pta.constants) TFSModel (class in pta.sampling.tfs) ThermodynamicSpace (class in pta.thermodynamic_space) ThermodynamicSpaceBasis (class in pta.thermodynamic_space) theta_s (pta.model_assessment.QuantitativeAssessment property) theta_z (pta.model_assessment.QuantitativeAssessment property) tighten_model_bounds() (in module pta.utils)

to_drg() (pta.sampling.tfs.TFSModel method) (pta.thermodynamic_space.ThermodynamicSpaceBasis method) to_drg0() (pta.thermodynamic_space.ThermodynamicSpaceBasis method) to_drg0_transform (pta.thermodynamic_space.ThermodynamicSpaceBasis property) to_drg_transform (pta.thermodynamic_space.ThermodynamicSpaceBasis property) to_fluxes() (pta.sampling.primitives.FluxSpaceSamplingModel method) to_fluxes_transform (pta.flux_space.FluxSpaceBasis property) (pta.sampling.primitives.FluxSpaceSamplingModel property) to_log_conc() (pta.thermodynamic_space.ThermodynamicSpaceBasis method) to_log_conc_transform (pta.thermodynamic_space.ThermodynamicSpaceBasis property) to_observables_transform (pta.thermodynamic_space.ThermodynamicSpaceBasis property) to_reactions_ids() (in module pta.utils) to_reactions_idxs() (in module pta.utils)

U

ub (pta.distributions.LogUniformDistribution property) (pta.distributions.UniformDistribution property) (pta.flux_space.FluxSpace property) UNDERSCORE (pta.metabolite_interpreter.CompartmentConvention attribute)

UniformDistribution (class in pta.distributions) UniformSamplingModel (class in pta.sampling.uniform) UNSPECIFIED (pta.metabolite_interpreter.Namespace attribute) update_identifiers() (pta.concentrations_prior.ConcentrationsPrior method) us_steps_multiplier (in module pta.constants)

V

v (pta.pmo.PmoProblem property)

vs (pta.pmo.PmoProblem property)

Z

z (pta.metabolite.Metabolite property)