PTA
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PTA Overview
1. Getting started
2. Model preprocessing
3. The thermodynamic space
4. Optimizing thermodynamics
5. Model assessment
6. Sampling thermodynamics and fluxes
7. API Reference
PTA
Index
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Index
A
|
B
|
C
|
D
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E
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F
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G
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H
|
L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
add() (pta.concentrations_prior.ConcentrationsPrior method)
apply_to_chains() (in module pta.sampling.commons)
apply_transform() (in module pta.utils)
autoresolve() (pta.model_assessment.StructuralAssessment method)
B
B (pta.pmo.PmoProblem property)
(pta.sampling.tfs.TFSModel property)
basis_samples (pta.sampling.commons.SamplingResult property)
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_distributions (pta.concentrations_prior.ConcentrationsPrior property)
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.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_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_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)
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)
F
F (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_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)
get_reversible_reactions_ids_T() (pta.sampling.tfs.TFSModel method)
H
h (pta.flux_space.FluxSpaceBasis property)
(pta.sampling.primitives.FluxSpaceSamplingModel property)
L
lb (pta.flux_space.FluxSpace property)
load() (pta.concentrations_prior.ConcentrationsPrior static method)
load_example_model() (in module pta.utils)
log_c (pta.pmo.PmoProblem property)
log_conc_cov (pta.thermodynamic_space.ThermodynamicSpace property)
log_conc_mean (pta.thermodynamic_space.ThermodynamicSpace property)
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)
metabolite_distributions (pta.concentrations_prior.ConcentrationsPrior property)
metabolite_ids (pta.flux_space.FluxSpace property)
(pta.thermodynamic_space.ThermodynamicSpace property)
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.concentrations_prior
pta.constants
pta.data
pta.data.concentration_priors
pta.data.models
pta.flux_space
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)
non_intracellular_compartment_ids (in module pta.constants)
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)
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.concentrations_prior
module
pta.constants
module
pta.data
module
pta.data.concentration_priors
module
pta.data.models
module
pta.flux_space
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)
QuantitativeAssessment (class in pta.model_assessment)
R
reaction_ids (pta.flux_space.FluxSpace property)
(pta.sampling.primitives.FluxSpaceSamplingModel property)
(pta.thermodynamic_space.ThermodynamicSpace property)
reactions_df (pta.model_assessment.QuantitativeAssessment property)
rebuild_for_directions() (pta.pmo.PmoProblem method)
reversible_rxn_ids (pta.sampling.tfs.TFSModel 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)
steady_state_constraint (pta.pmo.PmoProblem property)
StructuralAssessment (class in pta.model_assessment)
subspace() (pta.thermodynamic_space.ThermodynamicSpace method)
summary() (pta.model_assessment.QuantitativeAssessment method)
(pta.model_assessment.StructuralAssessment method)
T
T (pta.pmo.PmoProblem property)
(pta.sampling.tfs.TFSModel property)
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.flux_space.FluxSpace property)
UniformSamplingModel (class in pta.sampling.uniform)
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)
W
WATER_OR_PROTON_IDS (in module pta.utils)
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